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:

BMES 2013 meeting, Seattle, WA

Useful documents (templates and guidelines)

  1. Modeling Standards checklists.
  2. JSim Model template (guidelines).
  3. Example Model Web page for publishing a model at www.physiome.org

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)92.34 KB

 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 exchangeAm J Physiol Heart Circ Physiol 250: H539-H545, 1986.

Submit Your Model To This Web Site

To submit a relevant model, please see contact page for more information. Please be sure to specify which category and subsequent subcategories are most suitable for your model, or suggest a new category. If submitting a model in JSim MML please follow the following guidelines in formating your model: JSim MML model template.


Model development and archiving support at https://www.imagwiki.nibib.nih.gov/physiome provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, 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.