1. Welcome to the NSR Physiome Project!
  2. NSR Linux User Information.
  3. NSR Software Information.

NSR Software Information.

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

Software installed on Linux system:

NSR supports LINUX only. Listed below are some commonly used applications:

Web browsers:

  • Mozilla Firefox
  • Google Chrome

Other modeling tools:

  • Matlab: Mathematical modeling, available in terminal window. Only two user licenses for site so you may have to coordinate this with others.Type 'matlab' at command line.
  • Maple 14: type 'maple' at command line ('quit' to leave maple). 'xmaple' starts the graphical user interface.
  • Mathematica: type 'mathematica' at command line.
  • R an open source statistical package: type 'R' at command line.
  • tellurium: type 'tellurium' at command line. A Python Environment for Reproducible Dynamical Modeling of Biological Networks. More info at tellurium.analogmachine.org

     

  • COPASI: type 'copasi' at the command line. COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard.
  • CellDesigner: type 'celldesigner' at command line. A graphical modeling tool of biochemical networks. See: CellDesigner website
    CellDesigner Startup Guide (pdf)3.26 MB

Graphical and text editors:

  • Gimp: Type 'gimp' at the command line. Used for image manipulation.
  • LibreOffice: For documents, spreadsheets, presentations (Reasonably MS Office compatible).
  • Text editors (your choice): gedit, vi, emacs, pico, Others may be available.
  • RStudio: 'rstudio' at the command line. Useful for running R, using Rmarkdown and LaTeX to generate manuscripts. More Info at website.
  • Lyx: type: 'lyx' at the command line. LaTeX editor and document processor. LyX combines the power and flexibility of TeX/LaTeX with the ease of use of a graphical interface.

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.