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old_start [2013/04/25 14:35] (current)
aorth created
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 +<​note>​This is the old start page.  As of April 25, 2013 it has been moved here to make room for newer, cleaner content and hierarchical structure</​note>​
  
 +====== ILRI Research Computing ======
 +This is the ILRI Research Computing wiki.  Here you'll find information about all aspects of the research computing infrastructure,​ including tutorials and usage information for users. ​ Please use this wiki to document all changes you make to servers, services, and applications.
 +
 +===== Servers =====
 +[[servers|List of servers at ILRI]]
 +
 +===== Software =====
 +
 +[[software|Software resources]] at ILRI, broken up into loosely-related areas:
 +
 +  * [[software:​programming|Programming and scripting]]
 +  * [[software:​statistics|Statistics]]
 +  * [[software:​scheduling|Scheduling]] -- software for managing cluster resources
 +  * [[software:​genome_assembly|Genome Assembly]]
 +  * [[software:​alignment|Alignment]]
 +  * [[software:​metagenomics|Metagenomics]]
 +  * [[software:​webservers|Web servers]]
 +  * [[software:​internal:​sysadmin|Systems administration]]
 +
 +To move/​reorganize:​
 +  * Configure [[idea|IDEA]]
 +  * [[pasa|PASA]] web interface
 +  * [[WebLab]]
 +  * [[openmpi|OpenMPI]]
 +  * [[PPP|Pathogen Profiling Pipeline]]
 +  * [[Interproscan]]
 +  * [[ergatis]]
 +  * [[workflow engine|Installing Workflow Engine]]
 +  * [[samba|Configuring Samba]] for Windows filesharing
 +  * [[genvar]], a pipeline designed to analyze an annotated genome
 +  * [[Bio::​Tools::​CodonOptTable]]
 +  * Install [[PSPP]]
 +  * [[form_tools|Form Tools]]: Automated form processing and reporting
 +  * Install [[Mobyle]]
 +  * Install [[DIY]] -> Do-It-Yourself! Annotator
 +  * [[server_monitoring|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:​seqclean|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.
 +  * [[ldap_integration|Active Directory integration]] (for ssh logins using CGIAR-wide AD credentials)
 +  * [[Tech Recipes]]
 +  * [[Installing Gbrowse2]]
 +  * [[Uninstalling Perl Modules]]
 +  * [[Monitoring]]
 +
 +===== Hardware =====
 +  * [[RAID]] on HPC
 +  * [[backup|Backups]]
 +  * [[apcupsd]] - Auto-shutdown on power failure using acupsd
 +
 +===== Brainstorms =====
 +Notes from various group brainstorm sessions.
 +  * [[brainstorms|Brainstorming]]
 +
 +====== Tips and tricks ======
 +  * [[shell_tips|Shell tips and tricks]]
 +  * [[perl|Perl]] tips
 +  * [[rocks_commands|Rocks commands]]
 +  * [[FreeBSD]] tips
 +  * [[RPM]] tips
 +  * [[virtualbox|VirtualBox]] tips
 +  * [[Kernel compiling]]
 +  * [[HPC concepts]]
 +  * [[Database]]
 +  * [[Project management]]
 +  * Using [[Diskutil|Diskutil.app]] (Mac OS X only)
 +  * Working with [[Java jar files]]
 +  ​
 +
 +====== Contact ======
 +
 +E-mail questions, comments, or corrections to the maintainers of this wiki:
 +  * [[wiki:​user:​aorth|Alan Orth]]: a.orth@cgiar.org
 +  * [[wiki:​user:​ikahugu|Isaac Kahugu]]: i.kahugu@cgiar.org
old_start.txt · Last modified: 2013/04/25 14:35 by aorth