Computing

General

• Gnome - free software desktop project - usage tips
• PPT to PDF on a Mac
• Process Control
• Software for papers, posters and talks
• VectorNTI
• Perl
• Python
• Ruby
• Emacs
• CGI - Common Gateway Interface
• Cluster
• Subversion (SVN) version control system
• OpenPBS
• Eclipse
• Firefox
• MySQL
• CSS - Cascading Style Sheets
• SSH - Secure Shell
• Shell programming
• DiceWare offers a better way to create a strong, yet easy to remember passphrase for use with encryption and security programs
• Code2HTML converts a program source code to syntax highlighted HTML
• PHP
• Regular Expressions - tutorial and examples in various languages (a.k.a. regexp.info)
• ILoveJackDaniel's - web design and development reference
• Google Code Search helps you find function definitions and sample code by giving you one place to search publicly accessible source code hosted on the Internet
• gotAPI.com - the most comprehensive API collection on the web
• Software Carpentry - this course is an intensive introduction to basic software development practices for scientists and engineers that can reduce the time they spend programming by 20-25%.

Scientific

• In silico protocols on OWW
• Graphing high dimensional data
• MATLAB
  • MATLAB_Computational_Biology_Tools
• R for Statistical Computing
• The Really Easy Statistics Site
• Modeller
• Microfootprinter
• Genamics SoftwareSeek links to biotechnology software
• LIMS - Laboratory Information Management Systems
• bioPIXIE is a novel system for biological data integration and visualization that allows the user to discover interaction networks and pathways in which the user's gene(s)of interest participate
• PerlPrimer - open-source PCR primer design (Windows and Linux)
• BioPerl project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research
• BioJava is an open-source project dedicated to providing a Java framework for processing biological data
• BioPython is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics
• EnzymeX is a program for molecular biologists, developed to help you determine which restriction enzymes you should use to cut your DNA of interest

MIT

• Athena - AFS lockers, Kerberos tickets, user accounts
• BioMicro Center - DNA-NET accounts and file storage
• BioMicro Cluster
• ChemDraw Ultra
  • BioDraw tools for drawing, sharing, and presenting biological pathways are included with ChemDraw. Common pathway elements (membranes, DNA, enzymes, receptors, reaction arrows, etc.) are built in and other elements may be imported.