Modeling Standards

Standards for Publication and Distribution of Biophysical Models

A. Background:

The purpose of this document is to provide a beginning for a group effort centered on defining standards for modeling. The particular approach outlined below as “Standards for Class 4 biophysical models” is better suited to cell and organ models than to large scale, computationally complexly structured anatomic and physiological models.

Hunter21jul07

Dear Dan, James, Jim, Maciek, et al,

Here are my views on the email discussion below on behalf of the CellML team - I'll use 'reply' then later add them to the wiki. I've added Poul Nielsen & Matt Halstead to the CC list in case they want to correct me or add anything (Poul is the primary architect of CellML and Matt is leading the Auckland effort on linking CellML models to the biology via the metadata).

Garfinkel1969 

Garfinkel. FEBS Letters, 2:S9-S13, 1969.

"Attempts are being made to establish a standard form of what a model should be like, how it should be described and documented, as well as to find out how efficient different computers are in computing its behavior. this is intended in part to facilitate communication of information about models, which may be difficult owing to their complexity. In building a model one has to keep track of why one made the decisions one did, what mistakes were made, what was learned along the way, etc.

Software and Standards

The following are summaries of some discussions that were brought during the recent Multiscale Modeling (MSM) PI Consortium Meeting (2007). The topics relate to sharing models, driving standards in multiscale modeling and the development of reliable and reusable software.

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