Welcome to Bioinformatics Wiki Site in Division of Biology and Medicine at Brown University

Here you will find tutorials on how to use some popular bioinformatics software, mainly related to Illumina sequence data analysis,  and information about ongoing sequencing projects at Brown University. 

The WIKI site is based on software and hardware environment on the high performance computing cluster managed by CCV. All BioMed premium users have full access to 256 core with 'normal' priority. EPSCoR sponsored users also have access to additional 256 cores with 'highest' priority. All users have access to the 40+ bioinformatics software packages installed and tested on the system. 

Disk storage for data storage is the responsibility of the users. 

Raw data generated by the sequencer will be kept for one year, and get deleted after a warning email to users one week before deleting.

To be eligible as an EPSCoR sponsored user, please contact Ed Hawrot with an explanation of how your research relates to the effect of climate variability on marine life or other EPSCoR themes (www.riepscor.org). 

We request that users of this bioinformatics WIKI site please use this statement when acknowledging its contribution to your research work: "This research is supported in part by the bioinformatics infrastructure enabled by National Science Foundation EPSCoR Grant No. EPS-1004057, and the Division of Biology and Medicine, Brown University.” 

For those users benefiting from the new (as of early June 2011) 10 Gbps connectivity between Brown's main campus (e.g., CCV) and the facilities at 70 Ship Street, 121 South Main Street, and the Medical Education Building, please use this statement:  "This research is supported in part by the cyber-infrastructure enabled by National Science Foundation RII-C2 EPSCoR Grant No. EPS-1005789."

Users should also be encouraged to submit to us copies of published papers containing such acknowledgments.

Information is included on Illumina technology, FAQs
, basic steps for Illumina sequence analysis and detailed tutorials on how to use our high performance computer cluster to perform data analysis using different software systems.

Please click related the link to find the information you need or contact us for any question or support issues.

This is the software installed in our cluster either under /gpfs/runtime or  /gpfs/runtime/bioinfo: