MurrayRM:Software notes

This page has some notes on different software packages that I am looking using or considering using. Mainly just a place to collect information and links for me and my collaborators.

General purpose software

Mathematical analysis

• MATLAB
• SciPy
• R

Systems biology software

Modeling and analysis

• CellDesigner
• COPASI
• Simulac
• StochKit

Flow cytometry (FCM)

• FlowJo - FlowJo is a commercial program for reading and displaying FCM data.
• Weasel - Weasel is an open source tool for reading and displaying FCM data.
• Bioconductor/flow (R) - Bioconductor is a suite of software tools for working with bioinformatics data. The flow package is a set of tools that are designed to read, process and view FCM data. The iFlow package provides a GUI style interface to data that is intended for exploration.