MIT-CCR - Bioinformatics and Computing Core Facility

Bioinformatics and Computing Core Facility, E18-366
	Sebastian Hoersch hoersch@mit.edu, 324-1728 Charlie Whittaker charliew@mit.edu, 324-0337

Our goal is to make sophisticated bioinformatics tools and methods readily accessible to all CCR members. We are available to assist with your experiments in a collaborative-type setting, or we can train you to do the work yourself. -“3rd floor, by the glass wash facility, come on down!!!”

To get in touch with us:

E-mail us: the method of choice in most cases.
Phone us: sometimes, picking up the phone can be the quickest way to solve a problem!
Walk-ins welcome! If we are busy, there’s a couch to make your wait comfortable. Seriously, we welcome walk-ins, but arranging for a meeting ahead of time is probably the most efficient way to go in most cases.

Resources:

Compute cluster LURIA, a 15 node/30 processor/35 GB RAM mean machine with a generous 4.4 TB helping of disk space – talk to us about getting an account on LURIA and fire off your bioinformatics jobs.
Two PC workstations available for general use with an up-to-date version of Spotfire Decisionsite, a highly interactive graphics-driven data visualization and analysis software – talk to us about using Spotfire!
Ourselves: expertise in data manipulation and retrieval, bioinformatics scripting and programming, genome, gene, and protein sequence as well as phylogenetic analysis, protein structure homology modeling, and variously flavored DNA microarray analyses – talk to us about working with us!

A randomish collection of useful links:

Internal (CCR and MIT)

Genome and protein sequence analysis, materials for an introductory workshop we held twice in 2006.
Genome session, slides
Protein session, slides
Genome session, exercises
Protein session exercises
NEW! How-to: BLAT against genomes, in-house
Scansite , a motif scanning tool (Yaffe Lab)
Adhesome annotation resources (Hynes Lab)
Gene analysis tools and homepage of the Burge Lab
Access to cancer datasets by the Broad Institute

External

UCSC genome and table browser, a powerful access point for genome sequence-centered data for multiple species
NCBI: Entrez, BLAST, Gene Expression Omnibus, ...
SRS, a system for unified access to multiple and heterogeneous biological databases
Download ClustalX, the veteran multiple sequence alignment program ClustalW (web version here!) with a GUI (MacOS / Windows) and NJplot for drawing phylogenetic trees.
SMART, protein domain architecture analysis
Oncomine, a large cancer profiling database
Assess Gene List Overlap Significance
Compare 2 Lists
Generate Venn Diagrams

Last update: sh20070102