Practically Genomic – Bioinformatics IAP

Day 1 – January 25, 2010, 11 AM - 1 PM
Day 2 – January 27, 2010, 11 AM - 1 PM
Day 3 – January 29, 2010, 11 AM - 1 PM

Location: The DIRC 14N-132 (map)

Charlie Whittaker, AJ Bhutkar, Sebastian Hoersch and Courtney Crummett

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

Setup for the sessions:

The goal of this IAP is to expose attendees to a variety of methods and tools that will facilitate genomics-related research. Please take care of the following preparations prior to the sessions.

1) We will use the supplemental material from the following paper to illustrate different points throughout the sessions and it may be useful to take a look at the paper ahead of time:

Prabhakar et al., 2006 Science 314:786

2) Members of the MIT community have access to the Biobase products. Access the tools by searching Vera with the term "Biobase".

3) A MySQL server is available to members of the MIT commuity. Signup for access HERE.

4) The Gene Ontology Tree Machine and Webgestalt are free tools useful for functional analysis of gene lists. For access register HERE.

5) Affymetrix provides annotations and tools relating to their microarray platforms on their NetAffx website. For access register HERE.

6) Galaxy provides tools for working with genomic data. Create your free account HERE.

Additional Information regarding setup can be found HERE.

Specifically for attendees who will be bringing their own laptops:

Download ClustalX
Download NJplot
Download Argo

Introductory Presentation
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