Bioinformatics  

Bioinformatics.org

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

Check out the How Do I? Tab

• Biology
• Medicine
• Neuroscience & Cognitive Science
  

Books
Bioinformatics @ MIT
BIOBASE
GeneGo MetaCore
How Do I?

Have you checked out Star? MIT's homegrown Software Tools for Academics and Researchers.

• Broad Institute of MIT and Harvard
• Whitehead Institute for Biomedical Research
• Computational and Systems Biology at MIT (CSBi)
• Harvard-MIT Health Science and Technology (HST) program
• National Center for Biotechnology Information (NCBI)
• National Institutes of Health (NIH)
• The Harvard Clinical and Translational Science Center
• The David H. Koch Institute for Integrative Cancer Research at MIT

No classes are currently scheduled, but here's a list of past classes:

• Bioinformatics for Beginners
• Learn to use IPA during IAP
• Protocols and Methods: Recipes for Successful Research
• BrainNavigator: Hands-On Introduction and Demo
• Big Docs in Word: Tips and Tricks to Format your Thesis
• BIOBASE Knowledge Library and Explain Analysis System Training
• Biotech Business Information for Engineers and Scientists
• Get the most from your "omics" analysis: GeneGo MetaCore Software Training 

Have a request? email crummett@mit.edu

Have you checked out the Online Bioinformatics Resource Collection (OBRC) 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.

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.

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

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.

LigerCat is a PubMed search tool that uses tag clouds to show important concepts and trends. LigerCat aggregates multiple articles in PubMed, summing their MeSH descriptors and presenting them in a cloud, weighted by frequency.

MeSH is PubMed's controlled vocabulary.