1. Welcome to the NSR Physiome Project!
  2. NSR Model Database Information
  3. NSR Model Database Information

NSR Model Database Information

This page contains information relavant for (on site) internal use.

Adding new model to NSR database and website:

Below lists the steps to adding a new model to the NSR model database.
Note: Once your model has been assigned a number, DO NOT delete the modelnumber.txt from your model directory. You can change the name and any other aspect of the model but NOT the model number.

JSim project format guidlines

  • Confirm you have a JSim projext file that conforms to the following standard:

  • You can still add a model to the database if it does not follow the guidlines but it will require explicit creation of various text files.

    Note: Please add one or more of the following key words as needed to your model:
    • Tutorial: If model is used in a Physiome tutorial.
    • PDE: If model uses partial differential equations.
    • Data: If model is fitted to data contained within the project file.
    • Publication: If model reproduces a model published in a peer reviewed paper.
    • PMID##########: If published model paper has a PMID (PubMed ID) number assigned to it. Ex: PMID123456789
      To check: go to PubMed and enter in the author, date, and part of title to see if PMID exists for the paper.
      Note: PMID is different then a PMCID which means the article is available through PubMed Central. To find/convert PMID to PMCID and vice-versa go to the PMID converter

  • Log in as user webmodel and go to ~/NSR directory.

    You must be user webmodel to add models.

  • Create directory with name of the project file (Also the model name) under the ~/NSR/ sub directory.

  • Copy the model index.html template into the directory just created:

  • Example: cp -v ~/NSR/ModelTemplate/index_Model_Template.html index.html

  • Place your JSim project file into the dir.

  • Run the extractModelInfo.pl script to extract information from JSim project file.

     

  • Example usage: extractModelInfo.pl Transp3.Comp2F.proj

  • Add model information to NSR model database using addModel.pl script.

  • Example: addModel.pl

    If you see the following output, then follow instructions to add model number to project:
    Cannot open Transp3sol.Comp2F.proj, add model number manually: file error msg
    This message means the script was not able to add the model number into the JSim project file.

    For manual adding of number to project, just add: // MODEL NUMBER: #### in front of the MODEL NAME: line.
    Where #### is the four digit model number in modelnumber.txt.

  • Confirm the project file with the model number inserted compiles and runs fine.

    It is important that the JSim project file name matches the model name.

  • Confirm Model project file added to CVS.

    The JSim project file should have been added to the CVS archive under username webmodel (no other files associated with the model are archived). If you the addModel script or CVS report an error then you will have to add the project file manually. To confirm the model was added check to see if a CVS directory has been added to the model directory (ie: /webmodel/NSR/modelname/CVS). If it does not contain the directory then execute the following steps to add it to CVS:
    • cd up one directory (assume you are in the model directory), then type the following cvs command:
      cvs add modeldirname
    • cd back into the model directory (modeldirname) and add the project file to cvs:
      cvs add modelname.proj
    • Next, commit the addition to cvs:
      cvs commit -m "comments" modelname.proj
    • The project file should be added and there should now be a CVS subdirectory within the model directory.
    • More information about CVS

More information about adding the model to the website:

Files created during the above process:

  • modelname.txt
  • shortdescription.txt
  • keywords.txt
  • modelnumber.txt: created when the model added to NSR database.
  • references.txt
  • detaileddescription.txt: optional info

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.