2012 05-20 --harmony_lib_sedml

LibSedML h*p://libsedml.sf.net Frank T. Bergmann HARMONY 2012, Maastricht, NL

Repeatable simulaHon experiments SimulaHon Model Task Reports Data Generators 2

LibSedML SED-‐ML Script Editor libSedMLScript libSedML libSedMLRunner SimulaHon Tool iBioSim RoadRunner h*p://libsedml.sf.net 3

LibSedML script AddTimeCourseSimulation(simulation1, KiSAO:0000071, 0, 50, 1000, 1000) AddModel(model1, urn:miriam:biomodels.db:BIOMD0000000021) AddModel(model2, model1) AddParameterChange(model2, V_mT, 0.28) AddParameterChange(model2, V_dT, 4.8) AddTask(task1, simulation1, model1) AddTask(task2, simulation1, model2) AddColumn(time, [[time, task1, time]]) AddColumn(Mt_original, [[v1, task1, Mt]]) AddColumn(Mt_chaotic, [[v2, task2, Mt]]) AddColumn(Mt_combined, [[v1, task1, Mt], [v2, task2, Mt], v1 -‐ v2 + 20]) AddPlot(plot1, tim mRNA with Oscillation and Chaos, [[time, Mt_original], [time, Mt_chaotic], [time, Mt_combined]]); h*p://libsedml.sf.net 4

libSedML h*p://libsedml.sf.net 5

Features •  LibSedML –  Read, Create, Write, Manipulate –  Validate, Archive –  Resolve models from FS, Web + Miriam URN –  Applies changes to models •  Supported Model DescripHon languages: –  SBML + CellML 6

SED-‐ML script editor h*p://libsedml.sf.net 7

SED-‐ML script editor h*p://libsedml.sf.net 8

SBW SimulaHon Tool h*p://sourceforge.net/projects/sbw/ﬁles/sbw/2.9.0/ 9

SED-‐ML Web Tools h*p://sysbioapps.dyndns.org/SED-‐ML_Web_Tools 10

HARMONY 2012 •  Tuesday 11am: –  TroubleshooHng session: ROOM 123 •  Wednesday 11am: –  Nested SimulaHons, ROOM 147 11

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2012 05-20 --harmony_lib_sedml

by Frank Bergmann

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