Web-based tools for Bioinformatics; A (free) introduction to (freely available) NCBI, MUSC and World-wide Bioinformatics Resources.

When and Where---Wednesdays at 1pm Room 438 Library Admin Building Beginning September 10, 2003.


Over the past few years the deployment of Web-based tools for Bioinformatics has exploded. It seems to me that there needs to be a regular introduction and/or review of these materials because they change so rapidly and have become so powerful and generally easy to use. This seminar series is aimed at the first year Graduate Student but all Graduate Students, Research Staff and Faculty are welcome. The seminars will begin with the powerful NCBI resources but will include resources from UCSC, UC Berkeley, EMBL, EXPASY, ENSEMBL, Kyoto, Baylor, MUSC and everywhere else I can find things.

This series is being called a "seminar" but there will be no enrollment or credit. In that regard it will be more like a journal club. Attendees will be welcome to select from the series the sessions that are the most interesting. The sessions will each take an hour to focus on a particular web site or concept. There will be a general introduction, a practical example of the use of the resource and a "take home" example. All of the web-links, and as much of the "how-to" material as possible will be available on a web site as either HTML documents and/or in PDF format.

Please understand that the order and content of these presentations is evolving weekly. I won't place the material on-line until the day of the presentation.

September 10 NCBI overview, Education materials and introduction to ENTREZ. PDF file of Lecture Content.

September 17 Similarity Searching BLAST, FASTA PDF file of Lecture Content.

September 24 DNA analysis Tools Including SeqWeb and W2H. PDF file of Lecture Content.

October 1 Protein analysis Tools Including SeqWeb and W2H. PDF file of Lecture Content.

October 8 Structure Viewers I Cn3D and SwissPDBViewer PDF file of Lecture Content.

October 15 Structure Viewers II RASMOL,Protein Explorer,CHIME, ViewerLite. PDF file of Lecture Content.

October 22Human Genome Tools NCBI Mapviewer. PDF file of Lecture Content.

October 29VISTA tools at UC Berkeley. PDF file of Lecture Content

November 5 UCSC Genome Tools and Viewer PDF file of Lecture Content

November 12 ENSEMBL annotation Project PDF file of Lecture Content

November 19 Non-Human Genome Tools PDF file of Lecture Content

November 26Variation tools OMIM dbSNP PDF file of Lecture Content

December 3 Expression Resources PDF file of Lecture Content

December 10 RNA analysis tools. PDF file of Lecture Content

January 7, 2004 Additional Tools: Spectral Karyotyping and Comparative Genomic Hybridization Database (SKY/CHD),dbMHC, Clone Resources.PDF file of Lecture Content

January 14, 2004 Phylogenetic Tools PDF file of lecture content.

January 21, 2004 Local Proteome Tools MASCOT, Profiles3D, Matchmaker, Modeller

January 28, 2004 Unix-based molecular modeling Tools.

 November 29, 2005 Local and Web-based tools for viewing and discovery of drugs.


Spring 2004 Possible Topics MASCOT, MELANIE for 2D gel analysis, SeqWeb/W2H, Vector NTI Suite, SYBYL, InsightII, Clinical Resources, AMBER, CHEMOFFICE, SciFinderScholar, PERL/BioPERL, Protein Interaction Tools DIP, BRENDA,BIND. . . . The list will be extended into 2004


 

Created by ESH 8-18-2003; updated 11-16-2005 12:41

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