Koch Institute - Bioinformatics and Computing Core Facility


	The Swanson Biotechnology Center

Bioinformatics and Computing Core Facility (76-189)

Facility Personnel

Jingzhi Zhu
jingzhi@mit.edu,x4-1728
AJ Bhutkar
arjun@mit.edu
Charlie Whittaker
charliew@mit.edu,x4-0337
Huiming Ding
huiming@mit.edu
Ryan Abo
ryanabo@mit.edu
Vincent Butty
vbutty@mit.edu
Stuart Levine
slevine@mit.edu,x2-2949

Our goal is to make sophisticated bioinformatics tools and methods readily accessible to all KI members. We are available to assist with your experiments in a collaborative-type setting, or we can train you to do the work yourself.

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!
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/28 processor/35 GB RAM mean machine with 4.4 TB 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 Spotfire Decisionsite, a highly interactive graphics-driven data visualization and analysis software. Also, one of the machines runs the Partek Genomics Suite for multi-platform microarray analyses – talk to us about using any of these software packages.
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, variously flavored DNA microarray analyses, and deep sequencing projects – talk to us about working with us!
You may also want to check out our bioinformatics training site "Turning Biologists into Bioinformaticists", covering a wide range of bioinformatics topics from advanced usage of MS Excel to Unix and Perl, from nucleotide and protein sequence analyses to microarray data analysis with R/Bioconductor or GenePattern.

Useful links:

Internal (KI 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
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
GSEA - Gene Set Enrichment Analysis, Broad Institute

External

UCSC genome and table browser, a powerful access point for genome sequence-centered data for multiple species
Galaxy - sophisticated database operations (tailored for genomics use cases!) via web interface
NCBI: Entrez, BLAST, Gene Expression Omnibus, ...
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
GATHER - annotate gene lists by GO, KEGG, Transfac... fast!
Oncomine, a large cancer profiling database
Assess Gene List Overlap Significance
Compare 2 Lists
Generate Venn Diagrams
SRS, a system for unified access to multiple and heterogeneous biological databases

Updated 20091020