This is the BecA-ILRI Bioinformatics Platform Wiki. Here you'll find information about all things IT for Bioinformatics. Please use this wiki to document all changes you make to servers/services.

• List of servers at ILRI

• Server upgrade notes / documentation
• R Statistics package
• Investigate root mailbox and logs
• Configure IDEA
• Configure HPC mail to send to ILRI mailserver
• PASA web interface
• WebLab
• OpenMPI
• Pathogen Profiling Pipeline
• Interproscan
• ergatis
• Installing Workflow Engine
• Configuring Samba for Windows filesharing
• genvar, a pipeline designed to analyze an annotated genome
• CodonOptTable
• Install PSPP
• Form Tools: Automated form processing and reporting
• Install Mobyle
• Install DIY → Do-It-Yourself! Annotator
• Server monitoring tools
• Chado, the relational database schema
• AMOS, infrastructure for developing assembly tools
• WindowMasker, identify and mask repetitive DNA sequences in a genome
• RepeatMasker, screen DNA sequences for interspersed repeats and low complexity DNA sequences
• GAAS, calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias
• Bio-Linux, a Ubuntu derivative with common Bioinformatics tools
• seqclean, a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.
• Active Directory integration (for ssh logins using CGIAR-wide AD credentials)

• Scripting/programming
• Statistics software
• Scheduling software for the cluster
• Genome Assembly
• Alignment software
• Web servers

• RAID on HPC
• Consolidate servers using virtualization
• Backup strategy
• apcupsd - Auto-shutdown on power failure using acupsd

• Shell tips and tricks
• Perl tips
• Rocks commands
• FreeBSD tips
• RPM tips
• VirtualBox tips
• Kernel compiling
• HPC concepts
• Database
• Project management
• Using Diskutil.app (Mac OS X only)
• Working with Java jar files
• cron-apt – Keeping servers up to date automatically

E-mail questions, comments, or corrections to the maintainers of this wiki:

• Alan Orth: a.orth@cgiar.org
• Etienne de Villiers: e.villiers@cgiar.org