Download to read offline
Uploaded byMike Hucka
Some SBML-related resources at SBML.org
The document provides an overview of SBML (Systems Biology Markup Language), its specifications, tools like the online validator and libsbml/jsbml libraries, and the SBML test suite for conformance testing. It outlines the evolution of SBML specifications, including core and package features, and details resources for developers and users to ensure compliance and performance. The document also encourages community engagement through discussion groups and provides information on how to keep updated with SBML developments.
![Devoxx 2014 [incomplete] summary](https://cdn.slidesharecdn.com/ss_thumbnails/devoxx-2014-summary-140614152155-phpapp02-thumbnail.jpg?width=640&height=640&fit=bounds)
Some SBML-related resources at SBML.org
- 1. Some SBML-related resourcesat SBML.org Michael Hucka (on behalf of the SBML and JSBML Teams) Department of Computing and Mathematical Sciences California Institute of Technology Pasadena, CA, USA Email: mhucka@caltech.edu Twitter: @mhucka COMBINE/ERASysApp tutorial, Melbourne, Australia, September 2014
- 2. The SBML specifications The Online SBML Validator LibSBML and JSBML The SBML Test Suite How to keep in touch with SBML happenings Outline
- 3.
- 4. SBML specifications continueto evolve and improve The SBML specification documents define what SBML is • Data objects, permitted contents, syntax, etc. • Usage rules • Expected interpretation Developers need to know the specifications in detail • Library API or other software may not give the full story
- 5.
- 6.
- 7.
- 8.
- 9. http://sbml.org/Documents/Specifications 2 mainregions for SBML Level 3 • Core • Packages (Recall structure of SBML Level 3)
- 10. Important to knowfor Core: list of know issues Specification document Known issues page
- 11. Important to knowfor Core: list of know issues Specification document Known issues page
- 12. Important to knowfor Core: list of know issues Specification document Known issues page Known issues in SBML specifications are eventually incorporated into new Releases of a Version, or whole new Versions, of a specification
- 13. SBML Level 3packages have separate status pages
- 14. Example package statuspage: ‘comp’
- 15. Example package statuspage: ‘comp’ Discussion list address
- 16. Example package statuspage: ‘comp’ Discussion list address Link to latest spec.
- 17. Example package statuspage: ‘comp’ Discussion list address Link to latest spec. List of known issues
- 18. The Online SBMLValidator
- 19. A tool forchecking SBML files The Online SBML Validator tests files for compliance to the SBML spec. • Reports errors & warnings, with line numbers - Also indicates relevant section(s) in the SBML specifications • Only tests syntax! - Cannot tell you if the model is valid … Multiple interfaces available • Interactive user interface • Programmatic REST interface Implementation detail: validation engine is libSBML ⇒ You can incorporate the same validation engine in other software
- 20.
- 21.
- 22.
- 23. http://sbml.org/Facilities/Validator Find it here Click here
- 24. Using the validator’sinteractive user interface 3 ways to input SBML: • Upload file • Input a URL • Paste SBML content 2 ways to validate: • Immediate - “Short” files • Scheduled - “Big” files
- 25.
- 26. What are thosecheckboxes?
- 27. What are thosecheckboxes?
- 28. What are thosecheckboxes? Options affecting validator behavior
- 29.
- 30. Where to findthem
- 31. Where to findthem Go to “Downloads”
- 32. Where to findthem libSBML JSBML
- 33. libSBML – http://sbml.org/Software/libSBML Powerful API library for SBML: • Read • Create • Manipulate • Convert bet. SBML Levels/Versions • Check & convert units • Write • Validate Open-source (LGPL) Written in portable C++ APIs via SWIG for C, C++, C#, Java, Octave, Perl, Python, R, Ruby, MATLAB Runs on Linux, Mac, Windows
- 34. Additional notable featuresof libSBML Plug-in architecture • Supports SBML Level 3 packages via plug-in extensions Multiple types of distributions: • Stable: includes support for accepted SBML Level 3 packages • Experimental: supports draft SBML Level 3 packages Multiple installation options: • Python: via PyPI, or via Linux apt-get/yum, or via direct download • R: package installer for use with R CMD INSTALL • Binary installers for Windows, Linux, Mac • Source builds
- 35. Documentation is availableboth online and for downloading
- 36. Documentation is availableboth online and for downloading Links to docs online
- 37. JSBML – http://sbml.org/Software/JSBML Pure-Java alternative to libSBML • Unlike libSBML, no native binary API is compatible with libSBML but more Java-like Functionality is subset of libSBML • E.g., does not do full validation Open source (LGPL) Main developers: Nicolas Rodriguez and Andreas Dräger, with contributions from many people
- 38. Some features ofJSBML More unified type hierarchy, with abstract classes and Java interfaces • Permits Java change listeners, TreeNode adapters, use of JTree Uses Java exceptions, Java lists, log4j logging Uses BioJava for reading SBO ontology Provides Interface modules for CellDesigner, libSBML
- 39. Other JSBML notes Release 1.0 RC 1 forthcoming very soon • Current stable release is 0.8 Provides APIs for most SBML Level 3 packages SBML validation over the net to SBML.org validation service Maven support coming in 1.0
- 40. The SBML TestSuite
- 41. A conformance-testing systemfor SBML software Part 1: corpus of test models & expected numerical results • 1200 cases, all tagged by features tested Part 2: software facilities • Standalone test runner • Online test result assessment system (alternative) • Online database of results for different software systems
- 42.
- 43.
- 44.
- 45. http://sbml.org/Software/SBML_Test_Suite Click here Find it here
- 46. http://sbml.org/Software/SBML_Test_Suite Different optionsavailable – find them in the table of contents
- 47. http://sbml.org/Software/SBML_Test_Suite Different optionsavailable – find them in the table of contents Standalone test runner Online test system Just the test cases
- 48. Standalone SBML TestSuite Runner Runs an SBML-compatible application through the test suite cases Written in Java + SWT — installers available for Mac OS, Windows, Linux
- 49. Installers available forMac OS X, Windows, Linux Includes test case archive – no need to download separately (Runner also checks for latest version over the net) What it doesn’t provide: wrapper to control the application to test • User or developer must create or provide that
- 50. Each case hasits own directory containing • Simulator settings file • SBML model in multiple Levels/Versions • Results in CSV format • Process definition in SED-ML format Wrapper should generate CSV file Runner invokes wrapper on each case dir & compares CSV file produced to expected one Test case definitions + expected output SBML Test Runner Application wrapper Test case settings + SBML files The general scheme behind the test runner
- 51.
- 52. Database of SBMLTest Suite results Developed by Frank Bergmann
- 53. Database of SBMLTest Suite results Developed by Frank Bergmann
- 54. Database of SBMLTest Suite results Developed by Frank Bergmann
- 55. How to keepin touch with SBML happenings
- 56. Discussion groups, Twitterfeed, G+, RSS – see SBML.org All SBML mailing lists are now Google Groups
- 57. Discussion groups, Twitterfeed, G+, RSS – see SBML.org All SBML mailing lists are now Google Groups Click here
- 58. Discussion groups, Twitterfeed, G+, RSS – see SBML.org All SBML mailing lists are now Google Groups
- 59. Discussion groups, Twitterfeed, G+, RSS – see SBML.org All SBML mailing lists are now Google Groups
- 60.
- 61. SBML & JSBMLTeams today Sarah Keating Frank Bergmann Lucian Smith Andreas Dräger Nicolas Rodriguez Alex Thomas Past members: Andrew Finney, Herbert Sauro, Hamid Bolouri, Ben Bornstein, Maria Schilstra, Jo Matthews, Bruce Shapiro, Akira Funahashi, Akiya Juraku, Ben Kovitz, Kimberley Begley Not pictured: Linda Taddeo John C. Doyle Hiroaki Kitano Original PI’s:
- 62. National Institute ofGeneral Medical Sciences (USA) Air Force Office of Scientific Research (USA) BBSRC (UK) Beckman Institute, Caltech (USA) DARPA IPTO Bio-SPICE Bio-Computation Program (USA) Drug Disease Model Resources (EU-EFPIA Innovative Medicine Initiate) ELIXIR (UK) European Molecular Biology Laboratory (EMBL) Google Summer of Code International Joint Research Program of NEDO (Japan) Japanese Ministry of Agriculture Japanese Ministry of Education, Culture, Sports, Science and Technology JST ERATO Kitano Symbiotic Systems Project (Japan) (to 2003) JST ERATO-SORST Program (Japan) Keio University (Japan) Molecular Sciences Institute (USA) National Science Foundation (USA) STRI, University of Hertfordshire (UK) SBML funding sources over the past 14 years
- 63. I’d like yourfeedback! You can use this anonymous form: http://tinyurl.com/mhuckafeedback
- 64. Where to findsoftware applications compatible with SBML
- 65. Where to findsoftware applications compatible with SBML Find SBML software
- 66. SBML Software Guide– http://sbml.org/SBML_Software_Guide Information about known SBML compatible software New questionnaire – please fill it out if you’re a developer! New version of the guide is coming!