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.

• HPC – http://hpc.ilri.cgiar.org/
• Bioinformatics (Old) – http://bioinfo.ilri.cgiarad.org/
• LIMS – https://lims.ilri.cgiar.org/
• Sybil – http://sybil.ilri.cgiar.org/
• DAGRIS – http://bioinfo.ilri.cgiarad.org/dagris/
• CGIAR Media Unit – http://192.168.5.4/media/
• GMOD – http://172.26.0.168 (Visendi's TParvaDB)
• biovbox – 172.26.0.200
• biovboxtest – 172.26.0.205
• biovm – 172.26.16.247
• eBioKit – 172.26.100.111 http://ebiokit.ilri.cgiar.org
• Roche 454 cluster – 172.26.0.118

• Server upgrade notes / documentation
• Scheduling software for the cluster
• R Statistics package
• Genome Assemblers
• Investigate root mailbox and logs
• Configure IDEA
• Configure HPC mail to send to ILRI mailserver
• PASA web interface
• WebLab
• OpenMPI
• Pathogen Profiling Pipeline
• mod_perl
• 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.

• Scripting/programming
• Statistics software
• Genome assembly
• Alignment software

• Install new console for servers?
• RAID on HPC
• Investigate high speed network design
• Consolidate servers using virtualization
• Move Bioinfo server to new server (Manatee + data)
• Active Directory integration (for ssh logins using CGIAR-wide AD credentials)
• Backup strategy
• UPS auto shutdown using acupsd for HPC

• 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

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