http:\/\/ginsim.org\/ginsim-doc\/current\/format-ginml.html<\/p>\n
Chaouiya, C., Gonz\u00e1lez, A., & Thieffry, D. (n.d.). GINML: Towards a GXL Based Format for Logical Regulatory Graphs and Dynamical Graphs. Citeseer<\/i>, (i), 0\u20131. Retrieved from http:\/\/citeseerx.ist.psu.edu\/viewdoc\/download?doi=10.1.1.136.7211&rep=rep1&type=pdf<\/p>\nFunctions:<\/h2>\n
These are functions used in the rules’ semantic actions or the parts’ attributes of an attribute grammar.<\/p>\n
edge(From, To, Sign, Val)<\/strong> e.g.:\u00a0<\/em>edge(‘complex’, ‘ADE2′,’negative’,2) node(Name, MaxVal)<\/strong> e.g.:\u00a0<\/em>node(‘ADE2’,2) e.g.:\u00a0<\/em>node(‘ADE2’,1,2) e.g.:\u00a0<\/em>node(‘GEV’,0,2,1) e.g.:\u00a0<\/em>node(complex,0,2,[[1,’dCas9:complex:1′],[1,’gRNA:complex:1′],[2,’gRNA:complex:1 dCas9:complex:1′]]) e.g.:\u00a0<\/em>node(complex,0,2,0,[[1,’dCas9:complex:1′],[1,’gRNA:complex:1′],[2,’gRNA:complex:1 dCas9:complex:1′]]) Typically, a call of the compiler (SWI-Prolog) to analyze the synthetic design ‘Tokens’ (a list of parts) is:<\/p>\n where the c_start attributes are:<\/p>\n init_ginml<\/strong> end_ginml<\/strong><\/p>\n and will close the design.ginml file. process_list(S1)<\/strong> Context: http:\/\/ginsim.org\/ginsim-doc\/current\/format-ginml.html Chaouiya, C., Gonz\u00e1lez, A., & Thieffry, D. (n.d.). GINML: Towards a GXL Based Format for Logical Regulatory Graphs and Dynamical Graphs. Citeseer, (i), 0\u20131. Retrieved from http:\/\/citeseerx.ist.psu.edu\/viewdoc\/download?doi=10.1.1.136.7211&rep=rep1&type=pdf Functions: These are functions used in the rules’ semantic actions or the parts’ attributes of an attribute grammar. Edges edge(From, To, Sign, Val) gives: <edge id=”<From>_<To>” …<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":845,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"nf_dc_page":"","om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"footnotes":""},"class_list":["post-1291","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/pages\/1291","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/comments?post=1291"}],"version-history":[{"count":1,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/pages\/1291\/revisions"}],"predecessor-version":[{"id":1671,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/pages\/1291\/revisions\/1671"}],"up":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/pages\/845"}],"wp:attachment":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/media?parent=1291"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\ngives:<\/p>\n<edge id=\"<From><\/span>_<To><\/span>\" from=\"<From><\/span>\" to=\"<To><\/span>\" sign=\"<Sign><\/span>\" minvalue=\"<Val><\/span>\"\/><\/pre>\n
\n<edge id=”complex:ADE2:2″ from=”complex” to=”ADE2″ minvalue=”2″ sign=”negative”><\/em>
\n<\/edge><\/em><\/p>\nNodes<\/h3>\n
\ngives:<\/p>\n<node id=\"<Name><\/span>\" maxvalue=\"<MaxVal><\/span>\"\/><\/pre>\n
\n<node id=’ADE2′ maxvalue=’2’\/><\/em>
\nnode(Name, MinVal, MaxVal)<\/strong>
\ngives:<\/p>\n<node id=\"<Name><\/span>\" basevalue=\"<MinVal><\/span>\" maxvalue=\"<MaxVal><\/span>\"\/><\/pre>\n
\n<node id=’ADE2′ basevalue=’1′ maxvalue=’2’\/><\/em>
\nnode(Name, MinVal, MaxVal, Param)<\/strong>
\ngives:<\/p>\n<node id=\"<Name><\/span>\" basevalue=\"<MinVal><\/span>\" maxvalue=\"<MaxVal><\/span>\">\n<parameter val=\"<Param><\/span>\"\/>\n<\/node><\/pre>\n
\n<node id=”GEV” basevalue=”0″ maxvalue=”2″>
\n<parameter val=”1″\/>
\n<\/node><\/em>
\nnode(Name, MinVal, MaxVal, ListParamInteraction)<\/strong>
\ngives:<\/p>\n<node id=\"<Node>\" basevalue=\"<MinVal>\" maxvalue=\"<MaxVal>\">\n<parameter val=\"<Param>\" idActiveInteractions=\"<Interaction>\"\/>\n...\n<\/node><\/pre>\n
\n<node id=”complex” basevalue=”0″ maxvalue=”2″><\/em>
\n<parameter val=”1″ idActiveInteractions=”dCas9:complex:1″\/><\/em>
\n<parameter val=”1″ idActiveInteractions=”gRNA:complex:1″\/><\/em>
\n<parameter val=”2″ idActiveInteractions=”gRNA:complex:1 dCas9:complex:1″\/><\/em>
\n<\/node><\/em>
\nnode(Name, MinVal, MaxVal, Param, ListParamInteraction)<\/strong>
\ngives:<\/p>\n<node id=\"<Node>\" basevalue=\"<MinVal>\" maxvalue=\"<MaxVal>\">\n<parameter val=\"<Param>\"\/>\n<parameter val=\"<Param>\" idActiveInteractions=\"<Interaction>\"\/>\n...\n<\/node><\/pre>\n
\n<node id=”complex” basevalue=”0″ maxvalue=”2″><\/em>
\n<parameter val=”0″\/><\/em>
\n<parameter val=”1″ idActiveInteractions=”dCas9:complex:1″\/><\/em>
\n<parameter val=”1″ idActiveInteractions=”gRNA:complex:1″\/><\/em>
\n<parameter val=”2″ idActiveInteractions=”gRNA:complex:1 dCas9:complex:1″\/><\/em>
\n<\/node><\/em><\/p>\nUtilities:<\/h2>\n
check_grammar(Tokens) :- init_ginml,<\/strong> c_start(S1, S2, S3, Tokens, []) , write_graph(S1),process_list(S1),analyze_trans(S2,S1),end_ginml .<\/strong><\/pre>\n
\n
\nwill open a file, design.ginml and start writing:<\/p>\n<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<!DOCTYPE gxl SYSTEM \"http:\/\/gin.univ-mrs.fr\/GINsim\/GINML_2_1.dtd<\/a>\"><gxl xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink<\/a>\"><\/pre>\n
\u00a0\u00a0<\/graph>\n<\/gxl><\/pre>\n
\nwrite_graph(S1)<\/strong><\/p>\n<graph id=\"defaultID\" class=\"regulatory\" nodeorder=\"<list_of_nodes_S1><\/span>\"<\/pre>\n
\nis just going to execute all the declarations in S1 that is, it will write down all the nodes and edges found in\u00a0S1 in the ginML file.
\nNOTE: the implementation of this function has been moved to Utilities_compiler.pl. add the\u00a0consult(‘AG_API\/Utilities_compiler.pl’) in your code!
\nanalyze_trans(S2,S1)<\/strong>
\nsee trans API.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"