Bioinformatics  

Bioinformatics.org

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

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• Neuroscience & Cognitive Science
  

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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 Division of Health Sciences and Technology (HST)
• 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

Don't miss out on all of MIT Libraries' life science related IAP sessions. For more information and all the MIT Libraries' IAP sessions go here:http://student.mit.edu/iap/nslib.html

Bioinformatics for Beginners
Wed Jan 11, 10-11:30am, 14N-132 (DIRC)
Tue Jan 17, 03-04:30pm, 14N-132 (DIRC)

Learn to use IPA during IAP
Wed Jan 18, 01-04:00pm, 14N-132 DIRC

Protocols and Methods: Recipes for Successful Research
Wed Jan 18, 05-06:00pm, 14N-132

BrainNavigator: Hands-On Introduction and Demo
Thu Jan 19, 10-11:30am, 14N-132 (DIRC)

Big Docs in Word: Tips and Tricks to Format your Thesis
Tue Jan 24, 11am-12:30pm, DIRC (14N-132)

Practically Genomic
Mon Jan 23, Wed Jan 25, Fri Jan 27, 11am-1:00pm, DIRC (14N-132)

BIOBASE Knowledge Library and Explain Analysis System Training
Thu Jan 26, 11am-01:30pm, 14N-132 DIRC

Biotech Business Information for Engineers and Scientists
Wed Feb 1, 02-03:00pm, 14N-132 (DIRC)

Get the most from your "omics" analysis: GeneGo MetaCore Software Training 
Thu Feb 2, 02-04:00pm, 14N-132 DIRC

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.

USE THE "MORE TOOLS" TAB
    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.

Go to Vera to search for more electronic journals.

Bioinformatics

Journal of Computational Biology

BMC Bioinformatics

PLoS Computational Biology

Nucleic Acids Research

Structure

Nature Genetics

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.