This is the internal 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, and applications.

List of servers at ILRI

Software resources:

• Programming and scripting
• Statistics software
• Scheduling software for managing cluster resources
• Genome Assembly tools
• Alignment software
• Web servers

To move/reorganize:

• Server upgrade notes / documentation
• 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)

• 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