Breakout Report: Model and Data Sharing Working Group

Peter Hunter auckland.ac.nzHerbert Sauro uw.edu

Jim Bassingthwaighte uw.edu Roger Mark MIT.EDU

People Present:

Jacob Barhak Kevin Shelburne Thomas Radman from NIH Jessica Appler from HHS Mark Walker Brian Carlson Jim Bassingthwaite Maciej Swat Mike Hucka Jim Sluka Herbert Sauro

Reproducibility

• Poor reproducibility in infectious disease modeling and biostatistics community. Jacob Barhak

• Don’t even use electronic formats ― errors in papers, wrong units, cannot trace equations

• Probably 50 to 90% of models in our community are not reproducible.

Modularity in Models

• Various efforts underway:– Jim Bassingthwaite has a java based solution that

merged modules– SBML community has effort that uses model

composition to support modular models based on biological information. Growing list of supported software.

– CellML has the notion of components that allows modularity of model math.

Modularity in Models

What about standards for other modeling domains?

Maciej Swat (Compucell3D) et al have started to think about a virtual tissue language based on Python. It will be declarative way of defining cell behavior agent-basedaiming for a Matlab for virtual tissues

Annotation ModelsAnnotation of models allow computers to manipulate models.

Examples, name species, reactions, cellular structures and behaviors, kinetics etc.

Brian Carlson talked about their work on SemGen for annotation bring models together, attach ontological terms JB: brought up the issue of different ontologies not matching up, and synonyms Ultimate aim: Super standard to convert down to other standards like SBML, CellML, NeuroML etc.

Persistence of Data and ModelsKevin Shelburne brought up the important issue of persistence of data and models. Their current approach is to store such information on SimBios. This led to a discussion of reliability of such resources including how to manage version control of such data :

More likely to survive Least likely to survivePIs Computer Couple of years?

NIH/NSF etc Centers5 to 10 yearsCode repositories such as

(Up to 80 years?)Github, Bitbucket,Sourceforge etc.

University LibraryEg Oxford and CambridgeUni libraries have been maintained foralmost 1000 years. (Up to 1000+ years)

Centralized resources, eg EBI, MedlineUp to 40 years

New Tools

• Mike Hucka reported the release of MOCCASIN

“Model ODE Converter for Creating Awesome SBML Interoperability”

This can convert Matlab biochemical pathway models to SBML by reverse engineering the biology.

New Tools

• Herbert Sauro reported the release of libRoadRunner and Tellurium

libRoadRunner is a cross-platform library that implements a high performance ODE based simulator. Uses LLVM to generate what is effectively a machine code representation of your model. Achieves 97% if raw C compiled code. Good for real-time interactive simulation and cluster configurations for large scale optimization and simulation. You can even run it on a Raspberry Pi.

New Tools

Tellurium is Python framework that bring together a wide range of tools for modelers, including:

libRoadRunner, SBML, SEDML, Bifurcation, Antimony, Matlab export, SciPy, Matplotlib etc. Supports creation of reproducible SBML based models using community developed reproducibility standards (SEDML).

Educational Video

• There is an educational video on YouTube that describes how to create an SBML model using four different Tools:

1. Tellurium2. COPASI3. CellDesigner4. PathwayDesigner

5. See IMAG Wiki for link.

IEEE Special Issue on Reproducibly

For the Following Year

• More educational material– What are the SBML and CellML standards?– What other standards are useful– Videos on how to use specific tools– Reproducibility– Improve the mailing list– Reports from relevant workshops such as

COMBINE

And Finally…

• Satellite Meeting tomorrow!

Overview and Use of Standards and Formats Relevant to the IMAG/MSM Community

See agenda in your IMAG package.