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Modeling of Oxygen and Carbon Dioxide Transport and Exchange in

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					                                      WG10: Part A.
                   Physiol/Biophys/Biochem/MolecBiol Models

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?
                        http://www.physiome.org/Models/Standards

                                                                                       www.physiome.org 1
                  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

       To establish:
       •   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, erdemira@ccf.org   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

             hypotheses?
          n What were the failed experiments, rejected ideas, ineffective

             analyses?
n   Can we develop databases for a wide range of model types?


                                                                          www.physiome.org 3

				
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posted:7/25/2013
language:English
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