Tools
From Informatics
Tools
- GForge Project - a group of individual sourceforge nodes.
- (t)wiki - here is a comparison matrix of twiki, media wiki, and confluence: http://www.wikimatrix.org/compare/TWiki+MediaWiki+Confluence
- eclipse - open source IDE.
- Cygwin - linux feel on windows
- Subversion - a cvs alternative.
- RoboForm - remembers form fields (password protects them) so you can "fill out a form in one button click".
- Putty - connect to one of our servers.
- Enterprise Architect - A UML modelling tool. This is the caGrid recommended modelling tool.
Java Specific
- log4j
- JDa decent decompiler. Eclipse plugni is also available. NOTICE! The site does not work properly at this time. The latest working site for Eclipse plugin is http://mchr3k-eclipse.appspot.com/; information is at http://mchr3k.github.com/jdeclipse-realign/
- Classycle Analysing Tools for Java Class and Package Dependencies
- Java5 - Annotations, Generics
- Commons Logging - geWorkbench logging package
- JUnit - Java unit testing framework
- Serialization - Java serialization Discover the secrets of the Java Serialization API
- JNI - Java Native Interface
- Tomcat - Web container
- YourKit - A profiler (we have licenses for this)
- Axis - Tips on using Apache Axis
- XML - Tips on schemas, instance documents, etc.
- JGoodies - recipies
- Swing - tips and tricks
- Install Anywhere - Instructions.
- Performance Tuning
- jar format
- More Java Topics
Others
- Regular Expression
- RESTful
- REST Way a brief but extremely clear explanation of what 'RESTful' means for web services
- steps toward the glory of REST
- Javascript - Setting up your environment for Javascript development.
Grid Specific
- JCog - Java commodity grid toolkit.
- get it here.
Unix Specific
- grep - useful for searching files for patterns
- scp - copy files from your windows box to a linux server
- kill - kill processes
- less - "less is better than more"
- perl - simple but useful commands (ie. find and replace in 1000 different files)
- tar - tarballs, untar & unzip in one command, etc.
- zcat - This is useful for importing data into a mysql database.
Bioinformatics Specific
- RSA - Regulatory Sequence Analysis Tools
- MAGE - http://www.mged.org/index.html
- MPIBLAST - parallelization of NCBI BLAST
- R
Wiki markup
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