libSEDML (Harmony 2012)

•

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Frank Bergmann

LibSED-ML introduction at HARMONY 2012 in Maastricht, NL. For more details see me in the next three days

Technology Business

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

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

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libSEDML (Harmony 2012)

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

2. Repeatable simulaHon experiments SimulaHon Model Task Reports Data Generators 2

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

4. 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

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

6. 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

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

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

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

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

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

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