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

• ipython (SciPy) - interactive, MATLAB like environment for python, with access to scipy. This is my preferred platform for doing everything, mainly because of the flexibility of python and the large number of packages available. The exception might be statistical analysis, where R seems to have the edge.
• MATLAB - Default platform for doing anything with control systems.
• Mathematica - I use this quite a bit for examples that are going to go into textbooks, since I can manipulate symbolic equations and output things in LaTeX format. The main limitation for me is getting plots into the form I want for books.
• R - programming language tuned to statistical analysis. I haven't done that much with it yet, but it looks like it has the packages that I need for working with data sets.

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.

Lab software

This is some of the software that I have used for supporting experimental work in the lab.

• Notebook - Software for creating lab notebooks. Has good support for time-tagging, importing images, etc. Mainly useful for things you would put in a lab notebook (as opposed to other types of notes).
• aPE - Plasmid editing software. I use this for viewing and annotating sequencies

General purpose software

• Evernote - I use this for tacking notes on various topics. Uploads notes to the cloud and does handwriting recognition on scanned notes and blackboard photos.
• Papers (Mac) - this is what I used to keep track of all of my technical papers.
• TimeLog (Mac) - I use this to track my time on different tasks, including consulting.
• Things (Mac) - keep track of action items and tasks that I need to remember to do

Unused software

I've downloaded quite a few software packages that I don't seem to use very much (yet).

• EnzymeX - Software from mekentosj for working with restriction enzymes (I don't do this all that often and have used NEBcutter for this purpose)
• LabAssistant - Software from mekentosj for planning out experiments. I've found it easier to just write out what I want to do in my lab notebook (printed or electronic)