10th Workshop on Software Platforms for Systems Biology
\n@ Harvard Medical School
\n\u3068\u3063\u3066\u3082\u9577\u3044\u306e\u3067\u3001\u8208\u5473\u306e\u3042\u308b\u65b9\u3060\u3051\u5168\u6587\u3092\u3069\u3046\u305e\u3002<\/p>\n
10th Workshop on Software Platforms for Systems Biology @ Harvard Medical School \u3068\u3063\u3066\u3082\u9577\u3044\u306e\u3067\u3001\u8208\u5473\u306e\u3042\u308b\u65b9\u3060\u3051\u5168\u6587\u3092\u3069\u3046\u305e\u3002<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":4,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":""},"categories":[10],"tags":[],"class_list":["post-750","post","type-post","status-publish","format-standard","hentry","category-conference-logs"],"_links":{"self":[{"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/posts\/750","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/comments?post=750"}],"version-history":[{"count":0,"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/posts\/750\/revisions"}],"wp:attachment":[{"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/media?parent=750"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/categories?post=750"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/yasu2.prosou.nu\/blog\/index.php\/wp-json\/wp\/v2\/tags?post=750"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\n[ libSBML update (B.Bornstein) ]
\nLevel 2 Version 2 \u3092\u30b5\u30dd\u30fc\u30c8\u3057\u305f\u5974\u304c\u3082\u3046\u66f8\u304d\u4e0a\u304c\u3063\u3066\u308b\u3089\u3057\u3044\u3002
\n\u308f\u3049\u3002
\n[ SBMLToolBox update (S.Keating) ]
\nSBML\/MATLAB import\/export
\nRelease 2.0.2
\n– schema validation \/ consistency checking
\n– with libSBML API
\n– simulation (incl. events, rules and functions)
\n[ MathSBML update (B.Shapiro) ]
\nMathematica \u3067\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3059\u308b\u3084\u3064\u3002\u304a\u4e16\u8a71\u306b\u306a\u3063\u3066\u304a\u308a\u307e\u3059\u3002
\n– Full support of events with delays
\n– Full support of L2V2 proposal
\n– More info returned by SBMLRead
\n– Enhanced plotting
\nMathematica \u306e plot \u306e\u30aa\u30d7\u30b7\u30e7\u30f3\u304c\u5168\u90e8\u4f7f\u3048\u305f\u308a\u3001\u51e1\u4f8b\u304c\u96a0\u305b\u305f\u308a\u3059\u308b\u6a21\u69d8\u3002
\n[ CellML2SBML update (M.Schilstra) ]
\nCellML \u3068 SBML \u3063\u3066\u3060\u3044\u3076\u30ce\u30ea\u304c\u9055\u3046\u306e\u306d\u3002
\nXSLT \u3067\u5909\u63db\u3057\u3066\u308b\u6a21\u69d8\u3002
\n\u304d\u3085\u3046\u3051\u3044\u3002
\n[ CD3 (A.Funahashi) ]
\nNew Feature: SBGN + Built-in SBML ODE Solver
\n[ CD Layout Annot. Converter (Y.Osana) ]
\n\u30d7\u30ed\u30b8\u30a7\u30af\u30bf\u3064\u306a\u3044\u3060\u77ac\u9593\u306b\u30de\u30b7\u30f3\u304c\u6b7b\u306b\u307e\u3057\u305f\u3002
\n\u300c\u518d\u8d77\u52d5\u3057\u3066\u304f\u3060\u3055\u3044\u300d\u3068\u3044\u3046\u30a2\u30ec\u3001\u6614\u306e Mac \u3067\u3044\u3046\u7206\u5f3e\u30de\u30fc\u30af\u3001
\nUnix \u3067\u3044\u3046\u3068\u3053\u308d\u306e kernel panic\u3001\u304c\u30d7\u30ed\u30b8\u30a7\u30af\u30bf\u306b\u6620\u3063\u3066\u3057\u307e\u3063\u305f\u3088\u3002
\n(Stack trace \u3068\u304b\u306f\u3001\u3055\u3059\u304c\u306b\u51fa\u307e\u305b\u3093\u304c)
\n\u307e\u3058\u3073\u3073\u3063\u305f\u3002\u307f\u306a\u3055\u3093\u3054\u3081\u3093\u306a\u3055\u3044\u3002
\n\u52d5\u63fa\u306e\u3042\u307e\u308a\u3072\u3069\u3044\u767a\u8868\u3067\u3057\u305f\u304c\u3001\u8cea\u7591\u5fdc\u7b54\u306f\u3061\u3083\u3093\u3068\u304b\u308f\u305b\u305f\u306e\u3067\u3001
\n\u307e\u3042\u3088\u304b\u3063\u305f\u304b\u306a\u3002
\nRender Extension \u306a\u4eba\u305f\u3061\u304b\u3089\u3001\u8272\u3068\u304b\u306e\u60c5\u5831\u3082\u5165\u308c\u3089\u308c\u306a\u3044\u304b\u3001
\n\u3068\u3044\u308f\u308c\u307e\u3057\u305f\u3002\u77e2\u5370\u3068\u304b Species \u306e\u7d20\u6027\u306e\u8a18\u8ff0\u304c\u3001Layout Extension \u3068\u304b
\nSBGN \u306e\u3042\u305f\u308a\u3067\u304b\u3063\u3061\u308a\u7d71\u4e00\u3055\u308c\u308c\u3070\u305d\u3063\u3061\u306b\u624b\u3092\u51fa\u3057\u3066\u3082\u3044\u3044\u304b\u306a\u3001
\n\u3068\u601d\u3046\u306e\u3060\u304c\u3002\u3046\u3046\u3080\u3002
\n[ ReCSiP (Y.Iwaoka) ]
\n\u5802\u3005\u3068\u3057\u3066\u3089\u3063\u3057\u3083\u3044\u307e\u3057\u305f\u3002\u308a\u3063\u3071\u306a\u3082\u3093\u3060\u3002
\n\u8cea\u554f\u591a\u3044\u305c\u3002
\n\u4efb\u610f\u306e kinetics \u3092\u52d5\u304b\u3059\u306b\u306f\u3069\u3046\u3057\u305f\u3089\u3044\u3044\u3001\u3063\u3066\u3084\u3063\u3071\u308a\u6c17\u306b\u306a\u308b\u306e\u306d\u3002
\n\u3067\u304b\u3044\u306e\u306f\u5916\u90e8\u30e1\u30e2\u30ea\u3092\u4f7f\u3046\u5fc5\u8981\u3042\u308a\u3067\u3059\u3002\u3084\u308a\u65b9\u306f\u3082\u3046\u3061\u3087\u3044\u8003\u3048\u3055\u305b\u3066\u3002
\n[ SBML Render Extension (F.Bergmann) ]
\nAdopt SBGN for default styles.
\nSBML Layout Viewer<\/a> \u3053\u308c\u3001\u3044\u3044\u3063\u3059\u306d\u3002
\nSBML Layout Extension \u3068 JDesigner Layout Annotation \u306b\u5bfe\u5fdc\u3057\u3066\u3044\u3066\u3001
\n\u308f\u3057\u306e\u3067\u5410\u3044\u305f\u5974\u3082\u898b\u3089\u308c\u307e\u3059\u3002
\nCVODE \u4f7f\u3063\u305f\u30b7\u30df\u30e5\u30ec\u30fc\u30bf\u3067\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3057\u305f\u7d50\u679c\u3092
\npathway map \u4e0a\u306b3\u6b21\u5143\u3067\u898b\u305b\u308b\u306e\u3068\u304b\u3001\u9762\u767d\u3044\u3002
\n[ More on SBML Render\/Layout Extension (S.Sahle) ]
\nLayout Extension \u5bfe\u5fdc\u306e auto layouter \u3092\u3064\u304f\u3063\u3066\u3001
\n\u307f\u3093\u306a\u3067\u5e78\u305b\u306b\u306a\u308d\u3046\u3088\u3002
\nLayout \u3092 semantic \u306a\u30ec\u30d9\u30eb\u3067\u3084\u308b\u306e\u306f\u308f\u304b\u308b\u3093\u3060\u304c\u3001
\nRendering \u306b SVG namespace \u4f7f\u3063\u3061\u3083\u3048\u3070\u3044\u3044\u3093\u3058\u3083\u306a\u3044\u306e\uff1f
\n\u2192 \u3053\u308c\u306f hot topic \u306a\u306e\u3067\u3001\u660e\u65e5\u3084\u308a\u307e\u3057\u3087\u3046
\n[ PathwayLab (M.Jirstrand) ]
\nVisio \u30d9\u30fc\u30b9\u3067\u30e2\u30c7\u30ea\u30f3\u30b0\u3068\u304b\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3068\u304b\u3002\u305d\u3093\u306a\u3093\u3067\u304d\u308b\u306e\u304b\u3002
\n\u30d3\u30c3\u30c8\u30de\u30c3\u30d7\u3068\u304b\u8cbc\u308a\u4ed8\u3051\u3066\u305d\u308c\u3092 species \u3068\u3057\u3066\u6271\u3063\u305f\u308a\u3002
\n[ SBMLmerge (W.Liebermeister) ]
\nSBML \u306e\u30e2\u30c7\u30eb\u3092\u304f\u3063\u3064\u3051\u308b\u3068\u304d\u306b\u3001ID \u304c\u3076\u3064\u304b\u3063\u305f\u308a\u3059\u308b\u308f\u3051\u3060\u304c
\n\u305d\u308c\u3092\u3046\u307e\u3044\u3053\u3068\u3084\u308b\u306e\u3092\u652f\u63f4\u3059\u308b\u305f\u3081\u306e\u30c4\u30fc\u30eb\u3002KEGG ID \u3068\u304b\u306e
\nannotation \u3082\u4f7f\u3048\u308b\u3002\u3059\u3066\u304d\u3002
\n[ DSMTS (D.Wilkinson) ]
\nDiscrete Stochastic Models in SBML.
\n\u30b7\u30df\u30e5\u30ec\u30fc\u30bf\u306e\u6319\u52d5\u3092\u30c6\u30b9\u30c8\u3059\u308b\u305f\u3081\u306e testsuite \u304c 22 \u672c\u3002
\n[ BioModels.net (M.Hucka) ]
\nSBML \u3067\u5171\u901a\u306b\u30e2\u30c7\u30eb\u304c\u66f8\u3051\u308b\u3088\u3046\u306b\u306a\u3063\u305f\u3089\u6b21\u306f\u305d\u308c\u3092\u5171\u6709\u3002
\n[ MIRIAM (N.Le Novere) ]
\nMinimum Information Requested In the Annotation of biochemical Models
\n(not SBML specific, but also for CellML, GENESIS, … )
\n[ BioModels Database (N.Le Novere) ]
\n\u30c8\u30a4\u30ec\u884c\u3063\u3066\u307e\u3057\u305f\u3002\u3042\u3046\u30fc\u3002
\n1\u6642\u9593\u307b\u3069\u30b9\u30b1\u30b8\u30e5\u30fc\u30eb\u304c\u9045\u308c\u3066\u304a\u308a\u307e\u3059\u3002
\n[ Brief Overview of SBO (M.Hucka) ]
\n[ Making SBO a Reality (N.Le Novere) ]
\nkineticLaw \u3068\u304b\u3001parameter \u3068\u304b\u3001
\ndefinitionURL=http:\/\/www.biomodels.net\/foo\/bar\/ \u3067
\n\u5b9a\u7fa9\u306e\u6240\u5728\u3092\u660e\u793a\u3057\u3066\u3084\u308b\u306e\u306f\u3069\u3046\u3060\u3002\u3075\u3080\u3002\u30e2\u30c7\u30eb\u306e\u5b9a\u7fa9\u304c\u304b\u3063\u3061\u308a\u3057\u3066\u3044\u3044\u304b\u3082\u306a\u3002
\n[ SBGN (H.Kitano) ]
\n[ SBML ODE Solver ]
\nCVODES \u3092\u4f7f\u3063\u3066 sensitivity analysis
\nDAE support with IDA
\n\u306a\u3069\u3092\u8fd1\u3005\u306e\u4e88\u5b9a\u3068\u3057\u3066\u8003\u3048\u3066\u3044\u308b\u3002
\nPrecise event determination \/ parameter determination \u306f\u9577\u671f\u7684\u4e88\u5b9a\u3002
\n[ Summary of L2V2 Draft (A.Finney) ]
\nSpeciesType \u3063\u3066\u3044\u3046\u306e\u304c\u3067\u304d\u308b\u3089\u3057\u3044\u3002
\n\u305f\u3068\u3048\u3070\u3053\u3093\u306a\u611f\u3058\u3060\u3002
\n<listOfSpeciesTypes>
\n <speciesType id=”Aspartate”>
\n<\/listOfSpeciesTypes>
\n<listOfSpecies>
\n <species id=”Aspartate_in_cytosol” speciesType=”Aspartate” compartment=”Cytosol”>
\n <species id=”Aspartate_in_Mitochondrial_Matrix” speciesType=”Aspartate” compartment=”Mitochondrial_Matrix”>
\n<\/listOfSpecies>
\n\u3053\u308a\u3083\u3044\u3044\u305c\u3002Compartment \u304c\u5c71\u307b\u3069\u3042\u308b\u5834\u5408\u306b\u3001
\n\u3069\u308c\u304c\u540c\u3058\u7269\u8cea\u306a\u306e\u304b\u304b\u3061\u3063\u3068\u66f8\u3051\u308b\u3057\u3002
\n\u3042\u3068\u306f Constraint \u3068\u304b\u3001InitialAssignment \u3068\u304b\u3002
\n\u524d\u8005\u306f\u30b7\u30b9\u30c6\u30e0\u306e\u5404\u5909\u6570\u306e\u3068\u308a\u3046\u308b\u5024\u306e\u7bc4\u56f2\u3092\u898f\u5b9a\u3057\u305f\u308a\u3068\u304b\u3067\u3001
\n\u5f8c\u8005\u306f\u521d\u671f\u5024\u3092\u307b\u304b\u306e\u521d\u671f\u5024\u304b\u3089\u8a08\u7b97\u3055\u305b\u305f\u308a\u3068\u304b\u3002
\n– Removal of predefined annotation namespaces
\n– definitionURL on SBase: \u3082\u306e\u3092\u5b9a\u7fa9\u3059\u308b\u3068\u304d\u306f\u3061\u3083\u3093\u3068 URL \u3082\u66f8\u3051
\n– nested unit definitions: minute \u306f second x60 \u3068\u304b\u3001\u305d\u3046\u3044\u3046\u5b9a\u7fa9
\n– dimensionless units
\n– substance mass derived
\n– SpeciesType
\n– constraints
\n– initial assignment structures
\n– reaction symbols
\n– use of Id attribute on SimpleSpeciesReference
\n– dependant variables semantics
\n[ Restructuring the SBML Process (M.Hucka) ]<\/p>\n","protected":false},"excerpt":{"rendered":"