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<body xmlns="http://www.w3.org/1999/xhtml">Analyzing the long-term behaviors (attractors) of dynamic models of biological systems can provide valuable insight into biological phenotypes and their stability. In this paper we identify the allowed long-term behaviors of a multi-level, 70-node dynamic model of the stomatal opening process in plants. We start by reducing the model’s huge state space. We first reduce unregulated nodes and simple mediator nodes, then simplify the regulatory functions of selected nodes while keeping the model consistent with experimental observations. We perform attractor analysis on the resulting 32-node reduced model by two methods: 1. converting it into a Boolean model, then applying two attractor-finding algorithms; 2. theoretical analysis of the regulatory functions. We further demonstrate the robustness of signal propagation by showing that a large percentage of single-node knockouts does not affect the stomatal opening level. Combining both methods with analysis of perturbation scenarios, we conclude that all nodes except two in the reduced model have a single attractor; and only two nodes can admit oscillations. The multistability or oscillations of these four nodes do not affect the stomatal opening level in any situation. This conclusion applies to the original model as well in all the biologically meaningful cases. In addition, the stomatal opening level is resilient against single-node knockouts. Thus, we conclude that the complex structure of this signal transduction network provides multiple information propagation pathways while not allowing extensive multistability or oscillations, resulting in robust signal propagation. Our innovative combination of methods offers a promising way to analyze multi-level models.</body>
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<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T10:42:32Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="f8f1eccf-d0e7-460a-a904-8234ea4627fe" qual:compartment="cytosol" qual:constant="false" qual:id="S_4" qual:initialLevel="0" qual:maxLevel="1" qual:name="AnionCh_high">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Higher levels of anion efflux channels at the plasma membrane</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#f8f1eccf-d0e7-460a-a904-8234ea4627fe">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T10:04:25Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_4757c9b1-17c7-4260-90ae-487a5efa8448" qual:compartment="cytosol" qual:constant="false" qual:id="S_5" qual:initialLevel="0" qual:maxLevel="1" qual:name="PLD_high">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Higher levels of phospholipase D</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_4757c9b1-17c7-4260-90ae-487a5efa8448">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-28T17:04:05Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_8fad37fd-f109-41a7-8862-ebab0287bde9" qual:compartment="cytosol" qual:constant="false" qual:id="S_6" qual:initialLevel="0" qual:maxLevel="1" qual:name="HATPase_3">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>14-3-3 protein bound H+-ATPase</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_8fad37fd-f109-41a7-8862-ebab0287bde9">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:19:05Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_22cfabd4-cc04-4107-aead-8fdac4f3a586" qual:compartment="cytosol" qual:constant="false" qual:id="S_8" qual:initialLevel="0" qual:maxLevel="1" qual:name="PLD">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phospholipase D</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_22cfabd4-cc04-4107-aead-8fdac4f3a586">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-16T13:22:23Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_6b38ee3c-5733-4594-a698-9f1c1756a0cf" qual:compartment="cytosol" qual:constant="false" qual:id="S_9" qual:initialLevel="0" qual:maxLevel="1" qual:name="PP1cc_3">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The catalytic subunit of type 1 phosphatase located in the cytosol</p><p>To denote node levels in this model, similar to a multi-level model, the number represents the level of the node, in this case PP1cc.</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_6b38ee3c-5733-4594-a698-9f1c1756a0cf">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-28T16:55:44Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="ed887473-88b0-45aa-939e-d9083fd0bbf2" qual:compartment="cytosol" qual:constant="false" qual:id="S_10" qual:initialLevel="0" qual:maxLevel="1" qual:name="phot1_complex">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Protein: 14-3-3-like protein GF14 lambda</p><p>14-3-3 protein bound phototropin 1</p><p>Gene ID: P48349</p><p>Gene: GRF6</p><p>Protein: Phototropin-1</p><p>Gene: PHOT1</p><p>Gene ID: 823721</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#ed887473-88b0-45aa-939e-d9083fd0bbf2">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:53:57Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_97eecba0-a5b0-4245-b10d-6baa82ea3276" qual:compartment="cytosol" qual:constant="false" qual:id="S_11" qual:initialLevel="0" qual:maxLevel="1" qual:name="phph_high">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Higher levels of light-dependent reactions of photosynthesis</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_97eecba0-a5b0-4245-b10d-6baa82ea3276">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T11:52:22Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_5a9cb436-3cb0-438c-a08f-3225c3feb26d" qual:compartment="cytosol" qual:constant="false" qual:id="S_12" qual:initialLevel="0" qual:maxLevel="1" qual:name="MCPS">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Mesophyll cell photosynthesis</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_5a9cb436-3cb0-438c-a08f-3225c3feb26d">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-15T14:36:21Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="c15f5cd9-1a00-40b7-b8a8-c70aa4f77404" qual:compartment="cytosol" qual:constant="false" qual:id="S_13" qual:initialLevel="0" qual:maxLevel="1" qual:name="PLC">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phospholipase C</p><p>Gene: PLC1/ PLC2</p><p>UniProt ID: Q39032/ Q39033</p><p>Gene ID: 835981/ 819999</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#c15f5cd9-1a00-40b7-b8a8-c70aa4f77404">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2016-10-01T16:53:50Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_11b57151-2ca7-4b2b-ba6a-a10bce99f988" qual:compartment="cytosol" qual:constant="false" qual:id="S_14" qual:initialLevel="0" qual:maxLevel="1" qual:name="SO_3">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Stomatal opening</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_11b57151-2ca7-4b2b-ba6a-a10bce99f988">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2016-10-02T08:55:36Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="aadc607b-0b4c-4449-a7e2-7f7f3b60f176" qual:compartment="cytosol" qual:constant="false" qual:id="S_16" qual:initialLevel="0" qual:maxLevel="1" qual:name="HATPase_2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>14-3-3 protein bound H+-ATPase</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#aadc607b-0b4c-4449-a7e2-7f7f3b60f176">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:19:05Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_331d24d7-be27-4338-8505-ad7f58b716b5" qual:compartment="cytosol" qual:constant="false" qual:id="S_17" qual:initialLevel="0" qual:maxLevel="1" qual:name="sucrose">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Disaccharide made of glucose and fructose, produced by plants</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_331d24d7-be27-4338-8505-ad7f58b716b5">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2017-07-26T13:44:55Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_82f68d3f-0264-4a28-b0fc-eec505a1e068" qual:compartment="cytosol" qual:constant="false" qual:id="S_18" qual:initialLevel="0" qual:maxLevel="1" qual:name="CaR">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Ca2+ release from intracellular stores</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_82f68d3f-0264-4a28-b0fc-eec505a1e068">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2016-10-02T08:45:43Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="caa98cad-1805-418c-b1c3-105dcd3dc966" qual:compartment="cytosol" qual:constant="false" qual:id="S_19" qual:initialLevel="0" qual:maxLevel="1" qual:name="PLA2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phospholipase A2β</p><p>Gene: PLA2-β</p><p>UniProt ID: Q8GZB4</p><p>Gene ID: ID: 816488</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#caa98cad-1805-418c-b1c3-105dcd3dc966">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-28T13:51:42Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_6c3f8800-7426-4dfa-b67b-71a11370ef40" qual:compartment="cytosol" qual:constant="false" qual:id="S_20" qual:initialLevel="0" qual:maxLevel="1" qual:name="Ci">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular CO2 concentration</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_6c3f8800-7426-4dfa-b67b-71a11370ef40">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-15T14:36:21Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="edf998b1-b743-4593-b17a-b3b71ad456bc" qual:compartment="cytosol" qual:constant="false" qual:id="S_21" qual:initialLevel="0" qual:maxLevel="1" qual:name="Ci_sup">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular CO2 concentration</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#edf998b1-b743-4593-b17a-b3b71ad456bc">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-15T14:36:21Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_6d5d165e-05fa-46b9-bbcf-9073a420c3a1" qual:compartment="cytosol" qual:constant="false" qual:id="S_22" qual:initialLevel="0" qual:maxLevel="1" qual:name="MCPS_high">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Higher levels of mesophyll cell photosynthesis</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_6d5d165e-05fa-46b9-bbcf-9073a420c3a1">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-14T09:20:38Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="a507c578-c06c-4458-b68b-bab8b0f874a7" qual:compartment="cytosol" qual:constant="false" qual:id="S_23" qual:initialLevel="0" qual:maxLevel="1" qual:name="Kc">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>cytosolic K+ concentration</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#a507c578-c06c-4458-b68b-bab8b0f874a7">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-22T15:38:15Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="aa91eed6-7ee5-41ef-8f65-1b474ad0a562" qual:compartment="cytosol" qual:constant="false" qual:id="S_24" qual:initialLevel="0" qual:maxLevel="1" qual:name="FFA">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Free Fatty Acids</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#aa91eed6-7ee5-41ef-8f65-1b474ad0a562">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T14:27:55Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_86ef8bfb-7657-4097-981e-665f9da86097" qual:compartment="cytosol" qual:constant="false" qual:id="S_25" qual:initialLevel="0" qual:maxLevel="1" qual:name="PK_2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>a serine/threonine protein kinase that directly phosphorylates the plasma membrane H-ATPase</p><p>o denote node levels in this model, similar to a multi-level model, the number represents the level of the node, in this case PK.</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_86ef8bfb-7657-4097-981e-665f9da86097">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-28T16:21:42Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_87869dc4-0c9a-4857-ae20-ecb466c31392" qual:compartment="cytosol" qual:constant="false" qual:id="S_27" qual:initialLevel="0" qual:maxLevel="1" qual:name="KEV">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>K+ efflux from the vacuole to the cytosol</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_87869dc4-0c9a-4857-ae20-ecb466c31392">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T21:14:31Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_68516f4c-dab8-49dc-a5a2-89331120be3b" qual:compartment="cytosol" qual:constant="false" qual:id="S_28" qual:initialLevel="0" qual:maxLevel="1" qual:name="phph">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Light-dependent reactions of photosynthesis</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_68516f4c-dab8-49dc-a5a2-89331120be3b">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T14:27:55Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_1ee76dda-89cb-46db-85e1-f53527781f59" qual:compartment="cytosol" qual:constant="false" qual:id="S_29" qual:initialLevel="0" qual:maxLevel="1" qual:name="SO_2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Stomatal opening</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_1ee76dda-89cb-46db-85e1-f53527781f59">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2017-07-26T13:44:55Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="bd621ae9-3462-4ce0-9353-fcc778e85eda" qual:compartment="cytosol" qual:constant="false" qual:id="S_30" qual:initialLevel="0" qual:maxLevel="1" qual:name="SO_1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Stomatal opening</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#bd621ae9-3462-4ce0-9353-fcc778e85eda">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2016-10-02T08:53:55Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="d8c1c462-6a03-41ca-b71c-bd161228fccc" qual:compartment="cytosol" qual:constant="false" qual:id="S_31" qual:initialLevel="0" qual:maxLevel="1" qual:name="Kout">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>K+ outward channels at plasma membrane</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#d8c1c462-6a03-41ca-b71c-bd161228fccc">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-22T14:42:50Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="e39aa506-1869-4ebe-9bd1-b20b425809a3" qual:compartment="cytosol" qual:constant="false" qual:id="S_32" qual:initialLevel="0" qual:maxLevel="1" qual:name="NO">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Nitric oxide</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#e39aa506-1869-4ebe-9bd1-b20b425809a3">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-15T12:59:57Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_810f9647-56ae-4d2e-a721-c2775871d7c0" qual:compartment="cytosol" qual:constant="false" qual:id="S_33" qual:initialLevel="0" qual:maxLevel="1" qual:name="HATPase_1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>14-3-3 protein bound H+-ATPase</p><p>To denote node levels in this model, similar to a multi-level model, the number represents the level of the node, in this case HATPase.</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_810f9647-56ae-4d2e-a721-c2775871d7c0">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:19:05Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_442270f5-6ada-4e58-b578-ea5d512a3660" qual:compartment="cytosol" qual:constant="false" qual:id="S_35" qual:initialLevel="0" qual:maxLevel="1" qual:name="Kv">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>vacuolar K+ concentration</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_442270f5-6ada-4e58-b578-ea5d512a3660">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T21:14:31Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_074dfbfe-9162-4ac1-b443-5e64840370f7" qual:compartment="cytosol" qual:constant="false" qual:id="S_36" qual:initialLevel="0" qual:maxLevel="1" qual:name="carbfix">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Light-independent reactions of photosynthesis</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_074dfbfe-9162-4ac1-b443-5e64840370f7">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T11:51:34Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_3b53b9a2-3965-4f8a-b7db-aa62557e0d16" qual:compartment="cytosol" qual:constant="false" qual:id="S_38" qual:initialLevel="0" qual:maxLevel="1" qual:name="PP1cc_1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The catalytic subunit of type 1 phosphatase located in the cytosol</p><p>To denote node levels in this model, similar to a multi-level model, the number represents the level of the node, in this case PP1cc.</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_3b53b9a2-3965-4f8a-b7db-aa62557e0d16">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-28T16:44:36Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="f10d29eb-6e36-4391-b652-7d79aefe3d4d" qual:compartment="cytosol" qual:constant="false" qual:id="S_39" qual:initialLevel="0" qual:maxLevel="1" qual:name="Cac">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cytosolic Ca2+ concentration</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#f10d29eb-6e36-4391-b652-7d79aefe3d4d">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2016-10-02T08:44:54Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_7fa9bba6-2764-4e19-b6fa-c15ed5bfd6e1" qual:compartment="cytosol" qual:constant="false" qual:id="S_40" qual:initialLevel="0" qual:maxLevel="1" qual:name="PK_1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>a serine/threonine protein kinase that directly phosphorylates the plasma membrane H-ATPase</p><p>To denote node levels in this model, similar to a multi-level model, the number represents the level of the node, in this case PK.</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_7fa9bba6-2764-4e19-b6fa-c15ed5bfd6e1">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-28T16:44:36Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="ca856098-2da7-4411-a462-18df3bb91cd4" qual:compartment="cytosol" qual:constant="false" qual:id="S_41" qual:initialLevel="0" qual:maxLevel="1" qual:name="AnionCh">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Anion efflux channels at the plasma membrane</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#ca856098-2da7-4411-a462-18df3bb91cd4">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:48:08Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_68607d6b-1805-40b9-bef4-1b281d99e6e7" qual:compartment="cytosol" qual:constant="false" qual:id="S_42" qual:initialLevel="0" qual:maxLevel="1" qual:name="carbfix_high">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Higher levels of light-independent reactions of photosynthesis</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_68607d6b-1805-40b9-bef4-1b281d99e6e7">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-14T11:52:22Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="d03d630a-947c-4c4d-8c38-8722b57476de" qual:compartment="cytosol" qual:constant="false" qual:id="S_43" qual:initialLevel="0" qual:maxLevel="1" qual:name="PMV_pos ">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Positive Plasma Membrane Voltage</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#d03d630a-947c-4c4d-8c38-8722b57476de">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:17:39Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="ac39219c-929b-41ee-8b7e-0a8b122a46a9" qual:compartment="cytosol" qual:constant="false" qual:id="S_44" qual:initialLevel="0" qual:maxLevel="1" qual:name="PMV_neg">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Negative Plasma Membrane Voltage</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#ac39219c-929b-41ee-8b7e-0a8b122a46a9">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:15:40Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_661f9811-d53d-4514-9786-2c59af729eb3" qual:compartment="cytosol" qual:constant="false" qual:id="S_45" qual:initialLevel="0" qual:maxLevel="1" qual:name="ABI1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>2C-type protein phosphatase</p><p>Gene: ABI1</p><p>UniProtID: P49597</p><p>Gene ID: 828714</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_661f9811-d53d-4514-9786-2c59af729eb3">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-01T09:48:08Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="f0a09e8a-85a4-4435-afca-f4aa7ac699eb" qual:compartment="cytosol" qual:constant="false" qual:id="S_46" qual:initialLevel="0" qual:maxLevel="1" qual:name="CaIc">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Inward Ca2+ permeable channels</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#f0a09e8a-85a4-4435-afca-f4aa7ac699eb">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-19T11:35:03Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="e4e823a5-a209-4276-9da7-58a844c8b8ac" qual:compartment="cytosol" qual:constant="false" qual:id="S_47" qual:initialLevel="0" qual:maxLevel="1" qual:name="Kin">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>K+ inward channels at the plasma</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#e4e823a5-a209-4276-9da7-58a844c8b8ac">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-22T15:38:15Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="d28b594b-e83c-4547-8476-629176201255" qual:compartment="cytosol" qual:constant="false" qual:id="S_48" qual:initialLevel="0" qual:maxLevel="1" qual:name="ROS">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Reactive oxygen species</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#d28b594b-e83c-4547-8476-629176201255">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-03-15T13:00:24Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_29795aeb-76e3-4e5c-b581-4046bbde2873" qual:compartment="cytosol" qual:constant="false" qual:id="S_49" qual:initialLevel="0" qual:maxLevel="1" qual:name="PP1cc_2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The catalytic subunit of type 1 phosphatase located in the cytosol</p><p>To denote node levels in this model, similar to a multi-level model, the number represents the level of the node, in this case PP1cc.</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/">
<rdf:Description rdf:about="#_29795aeb-76e3-4e5c-b581-4046bbde2873">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2018-02-28T17:04:05Z</dcterms:W3CDTF>
</dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
</qual:listOfQualitativeSpecies>
<qual:listOfTransitions xmlns:qual="http://www.sbml.org/sbml/level3/version1/qual/version1">
<qual:transition qual:id="tr_S_1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PP1cc_1 is a positive regulators of PK_1 when specific combinations of each PP1cc are met.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_1_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular carbon dioxide (Ci) indirectly inhbits PK_3.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_49" qual:qualitativeSpecies="S_49" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular carbon dioxide (Ci) indirectly inhbits PK_3.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_38" qual:qualitativeSpecies="S_38" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_1" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CalC and CaR activate Cac_high when ABA is active. CaATPase inhibits Cac_high and is dominant to CalC and CaR.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_2_in_S_18" qual:qualitativeSpecies="S_18" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Calcium release (CaR) causes an increase in cytosolic calcium ions (Cac) (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_2_in_S_46" qual:qualitativeSpecies="S_46" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Opening of calcium-permeable channels (Calc) allows for the increase in cytosolic calcium ions (Cac) (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_2_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA indirectly activates Cac (Commelina communis L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_2_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CaATPase directly inhibits Cac. CaATPase removes calcium ions (Cac) from the cell.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_2" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_46 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_18 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_3">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cac activates CaATPase.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_3_in_S_39" qual:qualitativeSpecies="S_39" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cytosolic Ca2+ (Cac) is removed from the cell by plasma membrane Ca2+ ATPase (CaATPase). Thus activation of CaATPase is dependent on Cac.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_3" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_39 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_4">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA and Cac_high activates AnionCh_high. Ci activates AnionCh_high when Ci_sup is active. ABI1 inhibits AnionCh_high and is dominant to ABA and Cac_high.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_4_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CO2 (represented as Ci) indirectly stimulates anion channels (represented as AnionCh_high) (Vicia faba L).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CO2 (represented as Ci_sup) indirectly stimulates anion channels (represented as AnionCh_high) (Vicia faba L).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_45" qual:qualitativeSpecies="S_45" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABI1 indirectly inhibits plant response to ABA, possibly through the inactivation of MAPKKK18 (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA indirectly activates AnionCh_high (Arabidopsis thaliana, Vicia faba L).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA triggers the increase in cytosolic Ca2+ (represented as Cac_high), which activates AnionCh_high (Arabidopsis thaliana, Vicia faba L).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_4" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_5">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA activates PLD_high when NO is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_5_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD activity increases in the presence of ABA.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_5_in_S_32" qual:qualitativeSpecies="S_32" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD activity is required for NO-induced stomatal closure via the production of phosphatidic acid.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_5" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_32 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_6">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA and PLA2 are positive regulators of HATPase_3. FFA and PLA2 activate HATPase_3 when certain conditions or PK_2, PK_3, PK_1, phph and phph_high are met.</p><p>Cac_high inhibits HATPase_3 and is dominant to FFA and PLA2.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_6_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_3 activates HATPase_3 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA indirectly activates HATPase_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_19" qual:qualitativeSpecies="S_19" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLA2 indirectly activates HATPase_1 through production free fatty acids and lysophosphatidylcholine (Arabidopsis thaliana, Avena sativa L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cac_high indirectly inhibits HATPase_3 (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_40" qual:qualitativeSpecies="S_40" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_1 activates HATPase_3 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph_high yields ATP, which is converted from ATP to ADP by HATPase_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph yields ATP, which is converted from ATP to ADP by HATPase_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_25" qual:qualitativeSpecies="S_25" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_2 activates HATPase_3 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_6" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<or/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_8">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA activates PLD.</p><p>NO activates PLD.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_8_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD activity increases in the presence of ABA.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_8_in_S_32" qual:qualitativeSpecies="S_32" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD activity is required for NO-induced stomatal closure via the production of phosphatidic acid.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_8" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_32 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_9">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD_high activates PP1cc_2 when BL and photo1_complex are inactive.</p><p>BL and photo1_complex activates PP1cc_2 when PLD is active and PLD_high are inactive.</p><p>In order to correctly simulate "OR NOT" relationships (ex, Ci AND Ci_sup OR NOT Cac_high) in Cell Collective, additional positive and negative relationships have been added. The original Boolean equation reads as follows: (not (phot1_complex or BL)and not (PLD and not PLD_high)) or ((phot1_complex or BL) and PLD and not PLD_high).</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_9_in_S_8" qual:qualitativeSpecies="S_8" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD indirectly activates PP1cc through the production of phosphatidic acid.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_9_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL indirectly activates PP1cc1 through activation of type 1 protein phosphatase regulatory subunit 2-like protein1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_9_in_S_10" qual:qualitativeSpecies="S_10" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>photo1_complex indirectly activates PP1cc1 through activation of type 1 protein phosphatase regulatory subunit 2-like protein1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_9_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD indirectly activates PP1cc through the production of phosphatidic acid.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_9" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_10">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL activates phot1_complex.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_10_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phot1 is a receptor for blue light (BL). The presence of blue light activates phot1, which activates phot1_complex (Arabidopsis thaliana, Vicia faba L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_10" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_11">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Red light activates phph_high when BL is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_11_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The synergistic relationship between blue light (BL) and red light (RL) in malate formation initiates higher levels of light-dependent reactions of photosynthesis (phph_high).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_11_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The synergistic relationship between blue light (BL) and red light (RL) in malate formation initiates higher levels of light-dependent reactions of photosynthesis (phph_high).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_11" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_12">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Ci and Ci_sup activate MCPS when either BL or RL is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_12_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular CO2 (Ci) is required for mesophyll cell photosynthesis (MCPS).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_12_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Blue light (BL) induces stomata opening, which allows for CO2 uptake.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_12_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Right light (RL) induces stomata opening, which allows for CO2 uptake.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_12_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular CO2 (Ci_sup) is required for mesophyll cell photosynthesis (MCPS).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_12" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_13">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA in conjunction with Cac activates PLC.</p><p>BL activates PLC.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_13_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL indirectly activates PLC through phot2 stimulation (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_13_in_S_39" qual:qualitativeSpecies="S_39" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA in conjunction with Cac indirectly activates PLC (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_13_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA in conjunction with Cac indirectly activates PLC (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_13" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_39 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_14">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>HATPase_1 activates SO_1 when Kv is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_14_in_S_6" qual:qualitativeSpecies="S_6" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Stomatal opening (SO) requires activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_14_in_S_35" qual:qualitativeSpecies="S_35" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Membrane hyperpolarization by HATPase causes K+ to enter the vacuole (Kv).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_14" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_16">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA and PLA2 are positive regulators of HATPase_2. FFA and PLA2 activate HATPase_2 when certain conditions or PK_2, PK_3, PK_1, and phph are met.</p><p>Cac_high inhibits HATPase_2 and is dominant to FFA and PLA2.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_16_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_3 activates HATPase_2 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA indirectly activates HATPase_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_19" qual:qualitativeSpecies="S_19" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLA2 indirectly activates HATPase_1 through production free fatty acids and lysophosphatidylcholine (Arabidopsis thaliana, Avena sativa L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cac_high indirectly inhibits HATPase_2 (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_40" qual:qualitativeSpecies="S_40" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_1 activates HATPase_2 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_25" qual:qualitativeSpecies="S_25" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_2 activates HATPase_2 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph yields ATP, which is converted from ATP to ADP by HATPase_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_16_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph_high yields ATP, which is converted from ATP to ADP by HATPase_1.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_16" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_17">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD activates sucrose. ABA inhibits sucrose and is dominant to PLD.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_17_in_S_8" qual:qualitativeSpecies="S_8" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD indirectly activates sucrose.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_17_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA indirectly inhibits sucrose.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_17" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_18">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>NO activates CaR.</p><p>PLC activates CaR.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_18_in_S_13" qual:qualitativeSpecies="S_13" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLC indirectly activates CaR (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_18_in_S_32" qual:qualitativeSpecies="S_32" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>NO indirectly activates CaR.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_18" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_32 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_13 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_19">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL, RL, and phot1_complex are positive regulators of PLA2.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_19_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL indirectly activates PLA2.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_19_in_S_10" qual:qualitativeSpecies="S_10" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phot1_complex indirectly activates PLA2.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_19_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>RL indirectly activates PLA2.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_19" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_20">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CO2 activates Ci either when CO2_high is active or when carbfix_high, CO2_high, and MCPS_high is inactive.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_20_in_S_34" qual:qualitativeSpecies="S_34" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Plants are able to absorb atmospheric CO2. This happens when CO2 levels are high (CO2_high).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_20_in_S_42" qual:qualitativeSpecies="S_42" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>High levels of carbon fixation (carbfix_high) decrease intercellular CO2 concentration (Ci).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_20_in_S_37" qual:qualitativeSpecies="S_37" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Plants are able to absorb atmospheric CO2. This happens when CO2 levels are high (CO2_high).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_20_in_S_22" qual:qualitativeSpecies="S_22" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>High levels of mesophyll cell photosynthesis (MCPS_high) reduces intercellular CO2 concentration (Ci).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_20" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_37 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_34 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_34 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_42 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_22 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_21">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CO2 activates Ci_sup when carbfix_high, CO2_high, or MCPS_high is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_21_in_S_34" qual:qualitativeSpecies="S_34" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Plants are able to absorb atmospheric CO2. This happens when CO2 levels are high (CO2_high).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_21_in_S_42" qual:qualitativeSpecies="S_42" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>High levels of carbon fixation (carbfix_high) decrease intercellular CO2 concentration (Ci).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_21_in_S_37" qual:qualitativeSpecies="S_37" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Plants are able to absorb atmospheric CO2. This happens when CO2 levels are high (CO2_high).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_21_in_S_22" qual:qualitativeSpecies="S_22" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>High levels of mesophyll cell photosynthesis (MCPS_high) reduces intercellular CO2 concentration (Ci).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_21" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_37 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_34 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_42 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_22 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_22">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Ci and Ci_sup activate MCPS_high when either BL or RL is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_22_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular CO2 (Ci) is required for mesophyll cell photosynthesis (MCPS).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_22_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Blue light (BL) induces stomata opening, which allows for CO2 uptake.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_22_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Right light (RL) induces stomata opening, which allows for CO2 uptake.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_22_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular CO2 (Ci_sup) is required for mesophyll cell photosynthesis (MCPS).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_22" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_23">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>HATPase_1, HATPase_2, and HATPase_3 activate Kc when Kin or Kv and KEV are active. HATPase also activates Kc when AnionCh, HATPase_2, and KEV are active or when AnionCh and HATPase_2 and Kin is active.</p><p>Kout inhibits Kc and is dominant to HATPase_1, HATPase_2, and HATPase_3.</p><p>AnionCh_high inhibits Kc and is dominant to HATPase_2 and HATPase_3.</p><p>AnionCh can either inhibit or activate Kc depending on certain conditions.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_23_in_S_6" qual:qualitativeSpecies="S_6" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>HATPase_1 indirectly activates Kc.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_27" qual:qualitativeSpecies="S_27" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Movement of K+ from the vacuole to the cytosol (KEV) increases cytosolic K+ concentration (Kc).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_4" qual:qualitativeSpecies="S_4" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>AnionCh indirectly inhibits Kc.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_35" qual:qualitativeSpecies="S_35" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The majority of K+ released into the cytosol originates from guard cell vacuoles (Kv).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_33" qual:qualitativeSpecies="S_33" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>HATPase_1 indirectly activates Kc.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_41" qual:qualitativeSpecies="S_41" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>AnionCh indirectly inhibits Kc.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_31" qual:qualitativeSpecies="S_31" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Opening of outward K+ channels (Kout) decreases the cytosolic K+ concentration (Kc).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_47" qual:qualitativeSpecies="S_47" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Opening of inward K+ channels (Kin) increases the cytosolic K+ concentration (Kc).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_23_in_S_16" qual:qualitativeSpecies="S_16" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>HATPase_1 indirectly activates Kc.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_23" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_47 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_31 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_4 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_47 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_31 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_4 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_47 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_31 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_4 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_47 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_31 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_24">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLA2 activates FFA.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_24_in_S_19" qual:qualitativeSpecies="S_19" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA is one of the hyprolytic products of PLA2 activity.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_24" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_25">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PP1cc_1 and PP1cc_2 are positive regulators of PK_1 when specific combinations of each PP1cc are met. Ci and Ci_sup can activate PK_1 when specific conditions of PP1cc are met.</p><p>Ci and Ci_sup are negative regulators of PK_1 and are dominant to The PP1cc's.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_25_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular carbon dioxide (Ci) indirectly inhbits PK_2.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_25_in_S_49" qual:qualitativeSpecies="S_49" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_25_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_25_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular carbon dioxide (Ci) indirectly inhbits PK_2.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_25_in_S_38" qual:qualitativeSpecies="S_38" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_25" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_27">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cac_high in conjunction with Kv activates KEV.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_27_in_S_35" qual:qualitativeSpecies="S_35" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>High levels of cytosolic Ca2+ (Cac_high) trigger the release of vacuolar K+ (Kv), causing the movement of K+ from the vacuole to the cytosol (KEV).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_27_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>High levels of cytosolic Ca2+ (Cac_high) trigger the release of vacuolar K+ (Kv), causing the movement of K+ from the vacuole to the cytosol (KEV).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_27" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_28">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL and RL activate phph.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_28_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Blue light (BL) indirectly activates the light-dependent reactions of photosynthesis (phph).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_28_in_S_26" qual:qualitativeSpecies="S_26" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Red light (RL) indirectly activates the light-dependent reactions of photosynthesis (phph).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_28" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_26 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_29">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>HATPase_1 activates SO_1 when Kv is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_29_in_S_35" qual:qualitativeSpecies="S_35" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Membrane hyperpolarization by HATPase causes K+ to enter the vacuole (Kv).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_29_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Sucrose indirectly activates SO_2.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_29_in_S_16" qual:qualitativeSpecies="S_16" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Stomatal opening (SO) requires activation of HATPase.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_29" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_30">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>HATPase_1 activates SO_1 when Kv is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_30_in_S_33" qual:qualitativeSpecies="S_33" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Stomatal opening (SO) requires activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_30_in_S_35" qual:qualitativeSpecies="S_35" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Membrane hyperpolarization by HATPase causes K+ to enter the vacuole (Kv).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_30" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_35 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_31">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PMV_pos activates Kout when one of the following conditions is met: ci and Ci_sup are active, ABA is active, ROS is inactive, NO is inactive, or FFA is inactive.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_31_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Elevated intercellular CO2 (Ci) causes stomatal closure and thus indirectly activates K+ outward channels (Kout) (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_31_in_S_43" qual:qualitativeSpecies="S_43" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>A holding potential more positive than -40mV (PMV_pos) induces K+ outward flow (Kout) (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_31_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The FFA linolenic acid and arachidonic acid activates inward K+ currents, thus inhibiting K+ outward current (Kout) (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_31_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Elevated intercellular CO2 (Ci_sup) causes stomatal closure and thus indirectly activates K+ outward channels (Kout) (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_31_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA indirectly stimulates outward K+ current (Kout) (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_31_in_S_48" qual:qualitativeSpecies="S_48" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The addition of ROS, specifically H2O2, depressed K+ outward flow (Kout) (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_31_in_S_32" qual:qualitativeSpecies="S_32" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Exposure to nitric oxide (NO) reduces K+ outward flow (Kout) (Vicia faba L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_31" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_48 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_32 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_32">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph in conjunction with ROS activates NO.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_32_in_S_48" qual:qualitativeSpecies="S_48" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ROS indirectly activates NO (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_32_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Photophosphorylation (phph) indirectly activates NO through NADH.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_32" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_48 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_33">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA and PLA2 are positive regulators of HATPase_1. FFA and PLA2 activate HATPase_1 when certain conditions of PK_2, PK_3, PK_1, and phph are met.</p><p>Cac_high inhibits HATPase_1 and is dominant to FFA and PLA2.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_33_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_3 activates HATPase_1 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA indirectly activates HATPase_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cac_high indirectly inhibits HATPase_1 (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_19" qual:qualitativeSpecies="S_19" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLA2 indirectly activates HATPase_1 through aactivation of free fatty acids and lysophosphatidylcholine (Avena sativa L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_40" qual:qualitativeSpecies="S_40" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_1 activates HATPase_1 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_25" qual:qualitativeSpecies="S_25" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phosphorylation of HATPase creates a binding site for 14-3-3. Thus the PK_2 activates HATPase_1 ( Spinacia oleracea, Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_33_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph yields ATP, which is converted from ATP to ADP by HATPase_1.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_33" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_19 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_40 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_25 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_35">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Kc activates Kv.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_35_in_S_23" qual:qualitativeSpecies="S_23" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cytosolic K+ (Kc) is taken into the vacuole (Kv).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_35" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_23 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_36">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CO2 and Ci actvate carbfix when phph is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_36_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Carbon dioxide is required for carbon fixation (carbfix). This can come from the environment (CO2) or from the intercellularenvironment (Ci).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_36_in_S_37" qual:qualitativeSpecies="S_37" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Carbon dioxide is required for carbon fixation. This can come from the environment (CO2) or from the intercellularenvironment (Ci).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_36_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Photophosphorylation (phph) generates metabolites required for carbon fixation (ATP and NADPH).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_36" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_37 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_38">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL or photo1_complex activates PP1cc1.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_38_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL indirectly activates PP1cc1 through activation of type 1 protein phosphatase regulatory subunit 2-like protein1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_38_in_S_10" qual:qualitativeSpecies="S_10" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>photo1_complex indirectly activates PP1cc1 through activation of type 1 protein phosphatase regulatory subunit 2-like protein1.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_38" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_39">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA activates Cac.</p><p>CaATPase inhibits Cac and is dominant to CalC and CaR.</p><p>Calc activates Cac.</p><p>CaR activates Cac.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_39_in_S_18" qual:qualitativeSpecies="S_18" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Calcium release (CaR) causes an increase in cytosolic calcium ions (Cac) (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_39_in_S_46" qual:qualitativeSpecies="S_46" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Opening of calcium-permeable channels (Calc) allows for the increase in cytosolic calcium ions (Cac) (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_39_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA indirectly activates Cac (Commelina communis L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_39_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CaATPase directly inhibits Cac. CaATPase removes calcium ions (Cac) from the cell.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_39" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_46 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_18 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_40">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Ci and Ci_sup are negative regulators of PK_1 and are dominant to The PP1cc's.</p><p>PP1cc_1 and PP1cc_2 are positive regulators of PK_1 when specific combinations of each PP1cc are met. Ci and Ci_sup can activate PK_1 when specific conditions of PP1cc are met.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_40_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular carbon dioxide (Ci) indirectly inhbits PK_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_40_in_S_49" qual:qualitativeSpecies="S_49" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_40_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Intercellular carbon dioxide (Ci_sup) indirectly inhbits PK_1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_40_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_40_in_S_38" qual:qualitativeSpecies="S_38" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Type 1 protein phophatase (PP1cc) activates H-ATPase through PK (Vicia faba L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_40" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_49 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_38 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_41">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Cac-high, Ci, Ci_sup, and ABA are positive regulators of AnionCh. ABI1 and BL is a negative regulator of AnionCh.</p><p>In order to correctly simulate "OR NOT" relationships (ex, Ci AND Ci_sup OR NOT Cac_high) in Cell Collective, additional positive and negative relationships have been added. The original Boolean equation reads as follows: ((((Cac_high ∨ ABA) ∧ ¬ABI1) ∨ (Ci ∧ Ci_sup)) ∨ (¬(((Cac_high ∨ ABA) ∧ ¬ABI1) ∨ (Ci ∧ Ci_sup)) ∧ ¬(phot1_complex ∨ BL)))</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_41_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CO2 (represented as Ci) indirectly stimulates anion channels (represented as AnionCh) (Vicia faba L).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_41_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Blue light (BL) induces a response at the plasma membrane. The addition of blue light induces K+ inward channels.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_41_in_S_10" qual:qualitativeSpecies="S_10" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Phototropins (represented as phot1_complex) inhibit the slow anion current (AnionCh). This has been shown to happen through activation of phosphatidylinositol 4,5-bisphosphate at the plasma membrane (Arabidopsis thaliana, Commelina communis L, Vicia faba L).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_41_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CO2 (represented as Ci_sup) indirectly stimulates anion channels (represented as AnionCh) (Vicia faba L).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_41_in_S_45" qual:qualitativeSpecies="S_45" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABI1 indirectly inhibits plant response to ABA, possibly through the inactivation of MAPKKK18 (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_41_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA triggers the increase in cytosolic Ca2+ (represented as Cac_high), which activates AnionCh (Arabidopsis thaliana, Vicia faba L).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_41_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA indirectly activates AnionCh (Arabidopsis thaliana, Vicia faba L).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_41" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<or/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_42">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Ci and CO2 activate carbfix_high when phph_high is active.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_42_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Carbon dioxide is required for carbon fixation. This can come from the environment (CO2) or from the intercellularenvironment (Ci).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_42_in_S_37" qual:qualitativeSpecies="S_37" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Carbon dioxide is required for carbon fixation. This can come from the environment (CO2) or from the intercellularenvironment (Ci).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_42_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Photophosphorylation (phph_high) generates metabolites required for carbon fixation (ATP and NADPH).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_42" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_37 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_43">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>In order to correctly simulate "OR NOT" relationships (ex, PMV_neg or not PMV_pos) in Cell Collective, additional positive and negative relationships have been added. The original Boolean equation reads as follows:( not (HATPase_1 or HATPase_2 or HATPase_3) and (((AnionCh and PMV_neg) and (Cac_high or KEV)) or (not (AnionCh and PMV_neg) and not PMV_neg and PMV_pos) or (not (AnionCh and PMV_neg) and (not PMV_pos and not PMV_neg) and (Cac_high or KEV)))) or ((HATPase_1 or HATPase_2 or HATPase_3) and (not (AnionCh and PMV_neg)) and not PMV_neg and PMV_pos and (Cac_high or KEV)).</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_43_in_S_6" qual:qualitativeSpecies="S_6" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarization of the membrane is caused by the activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_43_in_S_27" qual:qualitativeSpecies="S_27" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>KEV indirectly activates PMV_pos.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_43_in_S_33" qual:qualitativeSpecies="S_33" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarization of the membrane is caused by the activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_43_in_S_43" qual:qualitativeSpecies="S_43" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PMV_pos is required for PMV_pos activation.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_43_in_S_41" qual:qualitativeSpecies="S_41" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Activation of anion channels (AnionCh) causes membrane depolarization.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_43_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Increaes in cytosolic Ca2+ levels indirectly causes membrane depolarization.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_43_in_S_16" qual:qualitativeSpecies="S_16" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarization of the membrane is caused by the activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_43_in_S_44" qual:qualitativeSpecies="S_44" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The membrane cannot be simultaneously be hyperpolarized (PMV_neg) and depolarized (PMV_pos).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_43" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_44">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>In order to correctly simulate "OR NOT" relationships (ex, PMV_neg or not PMV_pos) in Cell Collective, additional positive and negative relationships have been added. The original Boolean equation reads as follows: ((HATPase_1 or HATPase_2 or HATPase_3) and (((AnionCh and PMV_neg) and not (Cac_high or KEV)) or (not (AnionCh and PMV_neg) and ((PMV_neg) or ((not PMV_pos and not PMV_neg) and not (Cac_high or KEV)))))) or (not (HATPase_1 or HATPase_2 or HATPase_3) and (not (AnionCh and PMV_neg))and PMV_neg and not (Cac_high or KEV))</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_44_in_S_27" qual:qualitativeSpecies="S_27" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>KEV indirectly inhibits PMV_neg.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_44_in_S_6" qual:qualitativeSpecies="S_6" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarization of the membrane is caused by the activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_44_in_S_43" qual:qualitativeSpecies="S_43" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The membrane cannot be simultaneously be hyperpolarized (PMV_neg) and depolarized (PMV_pos).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_44_in_S_33" qual:qualitativeSpecies="S_33" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarization of the membrane is caused by the activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_44_in_S_41" qual:qualitativeSpecies="S_41" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Activation of anion channels (AnionCh) causes membrane depolarization.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_44_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Increaes in cytosolic Ca2+ levels indirectly causes membrane depolarization.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_44_in_S_16" qual:qualitativeSpecies="S_16" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarization of the membrane is caused by the activation of HATPase.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_44_in_S_44" qual:qualitativeSpecies="S_44" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PMV_neg is required for PMV_neg activation.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_44" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_33 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_6 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_41 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_43 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_27 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_45">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABA inhibits ABl1.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_45_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The PYL family of ABA-receptors inhibit phosphatase activity of ABI1 (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_45" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<not/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_46">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ROS activates Calc.</p><p>PMV-neg activates Calc.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_46_in_S_48" qual:qualitativeSpecies="S_48" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ROS indirectly activates CaIc.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_46_in_S_44" qual:qualitativeSpecies="S_44" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarization of the plasma membrane (PMV-neg) activates CaIc (Vicia faba L., Commelina communis L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_46" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_48 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_47">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>FFA, ABA, PMV_neg activate Kin when certain conditions with Ci, Ci_sup, Cac_high, ABA, and PMV_neg are met.</p><p>In order to correctly simulate "OR NOT" relationships (ex, FFA or not Cac_high) in Cell Collective, additional positive and negative relationships have been added. The original Boolean equation reads as follows: (FFA or not Cac_high or ABA) and (not (Ci and Ci_sup))and PMV_neg.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_47_in_S_20" qual:qualitativeSpecies="S_20" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Elevated intercellular CO2 (Ci) causes stomatal closure and thus indirectly inhibits K+ inward channels (Kin) (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_47_in_S_24" qual:qualitativeSpecies="S_24" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The FFA linolenic acid and arachidonic acid activates inward K+ currents (represented here as activating K+ inward channels [Kin]) and inhibits outward K+ currents (Arabidopsis thaliana).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_47_in_S_21" qual:qualitativeSpecies="S_21" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Elevated intercellular CO2 (Ci_sup) causes stomatal closure and thus indirectly inhibits K+ inward channels (Kin) (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_47_in_S_15" qual:qualitativeSpecies="S_15" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>K+ inward channels (Kin) are inhibited upon the addition of ABA. This inhibition is driven by the increase in Ca2+ (Cac_high) levels in guard cells (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_47_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>K+ inward channels (Kin) are inhibited upon the addition of ABA. This inhibition is driven by the increase in Ca2+ (Cac_high) levels in guard cells (Vicia faba L.).</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_47_in_S_44" qual:qualitativeSpecies="S_44" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hyperpolarized membranes (PMV_neg) activates the inward flux of K+ through K+ inward channels (Kin) (Vicia faba L.).</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_47" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_44 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_21 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_20 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_24 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_15 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_48">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph in conjunction with PDL, when ABl1 is inactive, activates ROS.</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_48_in_S_8" qual:qualitativeSpecies="S_8" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD indirectly activates ROS through production of phosphatidic acid.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_48_in_S_45" qual:qualitativeSpecies="S_45" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ABI1 inhibits OST1, an indirect activator for ROS.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_48_in_S_28" qual:qualitativeSpecies="S_28" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>phph indirectly activates ROS through the production of NADH.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_48" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_28 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_45 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_49">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL and photo1_complex activates PP1cc_2 when PLD is inactive.</p><p>PLD_high inhibits PP1cc_2 and is dominant to BL, photo1_complex, and PLD.</p><p>PLD_high activates PP1cc_2 when BL or photo1_complex are inactive.</p><p>In order to correctly simulate "OR NOT" relationships (ex, Ci AND Ci_sup OR NOT Cac_high) in Cell Collective, additional positive and negative relationships have been added. The original Boolean equation reads as follows: ((phot1_complex or BL)and not PLD and not PLD_high) or (not (phot1_complex or BL)and not PLD_high).</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_49_in_S_8" qual:qualitativeSpecies="S_8" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD indirectly activates PP1cc through the production of phosphatidic acid.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_49_in_S_7" qual:qualitativeSpecies="S_7" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>BL indirectly activates PP1cc1 through activation of type 1 protein phosphatase regulatory subunit 2-like protein1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_49_in_S_10" qual:qualitativeSpecies="S_10" qual:sign="dual" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>photo1_complex indirectly activates PP1cc1 through activation of type 1 protein phosphatase regulatory subunit 2-like protein1.</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_49_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PLD indirectly activates PP1cc through the production of phosphatidic acid.</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_49" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<not/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<or/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_7 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
</qual:listOfTransitions>
<listOfCompartments>
<compartment constant="true" id="extracellular" name="extracellular"/>
<compartment constant="true" id="cytosol" name="cytosol"/>
</listOfCompartments>
</model>
</sbml>