# 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

- 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) - OpenCell 4.3: type
**'OpenCell'**at command line. A graphical environment for working on CellML models. See: OpenCell website

- 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.

[This page was last modified 22Mar18, 1:39 pm.]

**Model development and archiving support at
physiome.org 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.