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

We are grateful to Microsoft Corporation and Microsoft Research for their generous support of our educational activities.

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 MIT Libraries Video Tutorials OpenHelix UCSC Training Material Galaxy Galaxy Screencast Tutorials Ensembl The Broad Institute DOE Joint Genome Institute (JGI) NCBI Entrez	Links: Argo General Help User Guide
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 MySQL tutorial Wikipedia Join Entry	Links: Emacs Athena emacs instruction 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 Installing Bioconductor Packages	Links: Public Repositories of Array Data NCBI GEO EBI Array Express GenePattern Biobase Explain