Koch Institute

Turning Biologists into Bioinformaticists

A Practical Approach

Charlie Whittaker, AJ Bhutkar and Sebastian Hoersch

The David H. Koch Institute for Integrative Cancer Research at MIT
Bioinformatics and Computing Core Facility
Microsoft Researchhttp://research.microsoft.com/en-us/default.aspx We are grateful to Microsoft Corporation and Microsoft Research for their generous support of our educational activities. Microsoft



Topic 1 – Advanced Excel Usage Topic 2 – Genomics Topic 3 – Gene Annotation
Topic Materials Topic Materials Topic Materials
Databases:
NetAffx (registration required)
UniProt
NCBI Protein
IPI

Tools:
Compare 2 Lists
Draw Venn Diagrams
DAVID
Links:
UCSC Genome Informatics
Galaxy
Galaxy Screencast Tutorials
Ensembl
The Broad Institute
DOE Joint Genome Institute (JGI)
NCBI Entrez
Links:
Argo
Topic 4 – Multiple Sequence Alignment and Phylogenetic Analysis Topic 5 – Protein Domain and Motifs Topic 6 – Functional Annotation
Topic Materials
Introductory Presentation
Topic Materials Topic Materials
Links:
Uniprot
Clustal
Web-Based Clustalw
NJ Plot2) andaa
(
Phylip
Links:
SMART
InterPro
Scansite

Links:
GO Tree Machine
Biobase Bioknowledge Library
DAVID
GSEA
Topic 7 - Relational Databases Topic 8 - Unix Utilities Topic 9 - Perl Scripts
Topic Materials Topic Materials Topic Materials
Links:
Galaxy
MySQL
Wikipedia Join Entry
Links:
Emacs
EMBOSS
Blastall


Links:
Perl
Wikipedia Perl Entry
Topic 10 - R Topic 11 - Bioconductor Topic 12 - Microarray Data Processing
Topic Materials Topic Materials Topic Materials
Links:
R
Harvard-MIT Data Center
Links:
Bioconductor

Links:
Public Repositories of Array Data
GenePattern
Biobase Explain