MIT Libraries Research Guides - Bioinformatics

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Find computational resources and programs; online training in Computer Science, Computational Biology and Applied Math & staticsts, established online community.

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Bioinformatics @ MIT
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Bioinformatics Training @ MIT Libraries

Need more information about training? Email me: crummett@mit.edu

Need GeneGo Training? Click Here.

Mon, Jan 04th, 2010: Get the most from your "omics" analysis: GeneGo Training
9:30 AM - 12:30 AM DIRC (14N-132) Learn how to work with different types of data (genomics, proteomics, metabolomics and interaction data) beginning with how to upload gene lists and expression data.
Wed, Jan 06th, 2010: Bioinformatics for Beginners
11AM -12PM DIRC (14N-132) Class attendees will learn organization of key NCBI databases, understand database record structure, and work with the BLAST search tool. Hands-on practicum and excellent starting point.
Mon, Jan 11th, 2010: BIOBASE software training
2-5 PM DIRC (14N-132) Learn how to use the BIOBASE Knowledge Library (BKL) and Human Gene Mutation Database (HGMD) bioinformatics tools licensed by MIT Libraries. Interested in systems biology, biomarkers, drug target discovery, and high-throughput data
Tue, Jan 12th, 2010: Bioinformatics for Beginners
3-4 PM DIRC (14N-134) Class attendees will learn organization of key NCBI databases, understand database record structure, and work with the BLAST search tool. Hands-on practicum and excellent starting point.
Tue, Jan 19th, 2010: Using NCBI's BLAST
11AM-12PM DIRC (14N-132) Learn how to use NCBI resources and optimize your BLAST protein searches to get the most out of your results. Attendance at Bioinformatics for Beginners and familiarity with BLAST are recommended.
Mon, Jan 25th, 2010: Practically Genomic
Three 2 hour sessions. M, W, F 11AM-1PM DIRC (14N-134)
TBD

Resource Highlight!

Have you checked out the Online Bioinformatics Resource Collection (ORBC) brought to you by the University of Pittsburgh's Health Sciences Library System?

The OBRC is a manually curated collection of biolnformatics databases and software tools. Search for topic or tool of interest among the annotations and links for 2440 bioinformatics databases and software tools. Need to find out what tools can be used for phosphorylation? Enter the term and see what you get!

Click here for a short tutorial on how to use the OBRC.

Bioinformatics News

MIT Libraries now have access to the Human Gene Mutation Database (HGDM)

MIT Libraries has obtained a license for the Human Gene Mutations Database (HGMD). HGMD represents a comprehensive collection of data available on germ-line mutations in nuclear genes underlying or associated with human inherited disease.

Search for newly identified gene lesions to determine whether or not they are novel; search by gene to get an overview of the known mutational spectrum for that gene; and search for a type of mutation in a specific location.

HGMD is integrated with other bioscience resources such as OMIM, Entrez Gene and the Human Gene Nomenclature Committee. The free version of HGMD only contains 3 year old data while the licensed version contains current data and a better search interface, so take advantage of this great resource!

NCBI now has a pathway tool available FREE!

NCBI BioSystems Database

Use this to investigate both molecular and disease biosystems.
Contains biological pathways from two source databases, KEGG and the EcoCyc subset of BioCyc
Developed as a collaborative and complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data.
Detailed diagrams and annotations for individual biosystems are then available on the web sites of the source databases.

Bioinformatics Databases and Tools

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TO SEE MORE DATABASES AND TOOLS

NCBI (National Center for Biotechnology Information) -- collection public databases for research in computational biology, genome data, and biomedical information.

BIOBASE (MIT only) -- biological systems analysis tool that includes Proteomics, TransFac, TransPath, and Explain.

Ensembl -- software system which produces and maintains automatic annotation on selected eukaryotic genomes.

GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.

BLAST -- analysis tool that finds regions of similarity between biological sequences.