General updates about SBML and SBML Team activities

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Mike Hucka

Slides from presentation given at COMBINE 2011, in Heidelberg, Germany, on September 4, 2011.

Technology

General updates about SBML
and SBML Team activities

Michael Hucka and the rest of the SBML Team
Control and Dynamical Systems
Division of Engineering and Applied Science
California Institute of Technology
Pasadena, CA, USA

2

1. SBML.org Updates
Outline

2. SBML Development
3. SBML Team Software

3

New version of the SBML software survey

6

Forthcoming in the SBML Software Guide
More data about SBML software in the world
More accurate data about SBML software in the world
Statistics about SBML software in the world

• Examples: data on 81 software tools reported between May–July

MIRIAM 16
SBO 14
Supports SBGN 13
SBML Level 3 BioPAX 6
36% Does not yet CellML 3
support Level 3 SED-ML 3
64% MFAML 1
PNML 1
SBOL 1
0 5 10 15 20
Percentage supporting
Total # tools supporting other standards
SBML Level 3
7

Updated SBML Level 3 package activity table

http://sbml.org/Community/Wiki
8

SBML Development Process Progress

http://sbml.org/Documents/SBML_Development_Process
10

Elaboration of process for Level 3 packages

11

Further elaboration of package voting criteria
12

Writing L3 package specs
Proper draft spec. for Hierarchical Model Composition almost ready
New LaTeX templates for SBML package speciﬁcations

13

SBML Editor vote coming up

Chris Jim Lucian

Sarah Frank Yours truly
One new editor being replaced
• Nominations & voting open to anyone on sbml-discuss mailing list

14

libSBML 5.0.0: over 3400 downloads since April
800

700
188
600 195 158

500 64
201
93 122
400 147
52 103
126
300 103
119
Source 200
52
40 331
Mac OS X 268 298
Linux 100 215
155
Windows
0
April May June July August

Downloads of all libSBML 5.0.0 distributions since April
16

Other software news
LibSBML, JSBML, SBMLToolbox, Online SBML Validator, others....
... Listen to Sarah, Frank, Nico & Andreas

17

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General updates about SBML and SBML Team activities

1. General updates about SBML and SBML Team activities Michael Hucka and the rest of the SBML Team Control and Dynamical Systems Division of Engineering and Applied Science California Institute of Technology Pasadena, CA, USA 2

2. 1. SBML.org Updates Outline 2. SBML Development 3. SBML Team Software 3

3. SBML.org updates 4

4. SBML Software Guide changes 5

5. New version of the SBML software survey 6

6. Forthcoming in the SBML Software Guide More data about SBML software in the world More accurate data about SBML software in the world Statistics about SBML software in the world • Examples: data on 81 software tools reported between May–July MIRIAM 16 SBO 14 Supports SBGN 13 SBML Level 3 BioPAX 6 36% Does not yet CellML 3 support Level 3 SED-ML 3 64% MFAML 1 PNML 1 SBOL 1 0 5 10 15 20 Percentage supporting Total # tools supporting other standards SBML Level 3 7

7. Updated SBML Level 3 package activity table http://sbml.org/Community/Wiki 8

8. SBML Development 9

9. SBML Development Process Progress http://sbml.org/Documents/SBML_Development_Process 10

10. Elaboration of process for Level 3 packages 11

11. Further elaboration of package voting criteria 12

12. Writing L3 package specs Proper draft spec. for Hierarchical Model Composition almost ready New LaTeX templates for SBML package speciﬁcations 13

13. SBML Editor vote coming up Chris Jim Lucian Sarah Frank Yours truly One new editor being replaced • Nominations & voting open to anyone on sbml-discuss mailing list 14

14. SBML Editor vote coming up Chris Jim Lucian Sarah ? Frank Yours truly One new editor being replaced • Nominations & voting open to anyone on sbml-discuss mailing list 14

15. SBML Team Software 15

16. libSBML 5.0.0: over 3400 downloads since April 800 700 188 600 195 158 500 64 201 93 122 400 147 52 103 126 300 103 119 Source 200 52 40 331 Mac OS X 268 298 Linux 100 215 155 Windows 0 April May June July August Downloads of all libSBML 5.0.0 distributions since April 16

17. Other software news LibSBML, JSBML, SBMLToolbox, Online SBML Validator, others.... ... Listen to Sarah, Frank, Nico & Andreas 17

General updates about SBML and SBML Team activities

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