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JSim Model Standards and NSR Physiome General Modeling Guidelines

These standards and guidelines are to be used towards making models, and the science behind them, reproducible. Please see the following slideshow that was given as an introduction to 'Reproducibilty in Modeling' at the Fall, 2013 BMES meeting:

'Reproducibilty in Modeling' (pdf) BMES 2013 meeting, Seattle, WA

Useful documents (templates and guidelines)

  1. General Model Publishing standards and guidelines (pdf).
  2. Suggested Terminology for physiological transport, exchange, and reaction (pdf)
  3. Overview of JSim and its role in reproducible modeling and data analysis (pdf)
  4. Modeling Standards checklist (pdf)
  5. JSim Model template (guidelines).
  6. Model Web page publishing guidelines for submitting a model to
  7. Example Model Web page for publishing a model at

Please see Defining standards for good modeling practice by JB Bassingthwaighte for information on the emerging model classification standards.

Suggested Terminology for physiological transport, exchange, and reaction, (Document 2). is an up-to-date (2005) expansion of Bassingthwaighte JB, Chinard FP, Crone C, Goresky CA, Lassen NA, Reneman RS, and Zierler KL. Terminology for mass transport and exchange. Am J Physiol Heart Circ Physiol 250: H539-H545, 1986.

Submit Your Model To This Web Site

Request to submit a model. Please be sure to specify which category and subsequent subcategories are most suitable for your model, or suggest a new category.
To submit a model in JSim MML please follow the following guidelines in formating your model: JSim MML model template.

For more information on how to participate in this and other physiome projects, please see the Participate page.

[This page was last modified 05Nov15, 12:59 pm.]

Model development and archiving support at provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.