WG10: Part A.
n This Past Year accomplished:
n Defined standards for continuous systems models
n Initiated defining relationships between existent standards and actual reproducibility
n Created a website for open source, operational models running on-line that complements the
CellML/SBML archives of published preserved models.(300+ models)
n Through JSim’s usability stimulated CellML and SBML to incorporate PDEs
n Linking of JSim and SBML through SBW (System Biology Workbench)
n Next Year plan to:
n Develop standards for modules and multiscale models and for stochastic models
n Develop standards for data sets in line with those for PhysioNet (www.physionet.org)
n Develop standards for Verification and Validation
n Explore platform conflicts and collaborations for ODE/PDE models and FE models. Are there
common platforms to designate for the community?
n Publish White Papers.
n Work with journal editors re standards for reviewing and publishing. Require operational source
code for reviewers deliberations?
WG10: Part B: Standards for Models in FEA
Standards are needed for:
• Development: e.g. NAFEMS (computer aided engineering)
• Verification, validation: e.g. ASME Codes & Standards for Biomechanics J
• Storage: model markup in biological modeling: e.g. FieldML, MML
• other contexts: e.g. CFD General Notation System
• Reproducibility, reusability, accountability
But there are Problems to be solved:
• Models are tightly coupled with specific simulation platforms
• Can our community work on a few limited platforms?
• Mark-up languages and language exchange standards are needed.
• Difficult to incorporate models into multiscale modeling frameworks
. Need to store models as metadata
See White Paper #4: Finite Element Analysis Studies of Biological Structures
2010 MSM-Consortium Meeting – 10/27/2010, Ahmet Erdemir, email@example.com www.physiome.org 2
Discussion Points on:
Reproducibility and Open Sharing.
n Why don’t people share better?
n Is it the labor, cost, and time?
n Is there no suitable database?
n Not required by journals or funding agencies?
n Does sharing reduce potential for commercialization?
n Should funding agencies require sharing?
n Should all journals provide storage for supplementary materials?
n Are articles submitted to leading journals really reviewed from the point of
view of reproducibility?
n Do research articles tell their whole story?
n What is the fundamental hypothesis?
n Were the experiments designed to distinguish between competing
n What were the failed experiments, rejected ideas, ineffective
n Can we develop databases for a wide range of model types?