University of Toronto Chemistry Librarians Workshop June 2012
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University of Toronto Chemistry Librarians Workshop June 2012
- 1. Bioinformatics Databases: Biol3100 Assignment Rajiv Nariani rajivn@yorku.ca Science Librarian York University Libraries 14th June 2012 Chemistry Librarian Workshop (UfT)
- 2. Biology 3100: 2009-2011 • Bioinformatics module has been a part of the 3rd year Biology assignment • Library catalogue, locating articles using STM databases, MeSH headings, critiquing articles, citing references, annotated bibliography, presentations – Bioinformatics assignment is one of the modules – Started with NCBI databases in 2009 – Tetrahymena Genome Database in 2010 – Other tools from EMBL, NCBI & SIB
- 3. Tetrahymena Assignment Open Reading Difference between ciliate mRNA to genomic Frames 6 code and standard alignment (Spidey) (Transeq, NCBI code, (BLAST databases, BLAST [NCBI], European ) Bioinformatics, PubMed) Molecular weight of Homologs, E- protein, isoElectric value (TGD) Point, amino acid Protein domains and composition functions (SIB, European (NCBI, European Bioinformatics) Bioinformatics, SIB) Restriction Enzymes (Enzyme cutters [EBI])
- 4. TGD: Genome, Genes & Proteins
- 6. Basic Local Alignment Search Tool
- 8. T R A S E Q
- 10. Assessment & Marking • Students complete survey of how they found all modules including bioinformatics • Detailed answer sets for 30 TTHERM genes and 30 proteins (Drosophila/Saccharomyces) • TA marks assignment • All students have usually got very high marks for this assignment
- 11. Some survey comments • “Didn’t know all these databases existed” to “I found it very confusing” • “Lot of information” for those who are beginning to “Very simple – did not take too much time” • “Will use it in my other courses – would like advanced courses in bioinformatics”
- 12. Course/Research Guide http://researchguides.library.yorku.ca/biol3100
- 13. SciFinder – Concept Headings
- 14. SciFinder – Concept Headings
- 15. More Resources
Editor's Notes
- Some databases used: NCBI sequencedatabase BLASTEBI Sequence Translation databases (Transeq)SIB (Swiss Institute of Bioinformatics)SWISS-PROT - collection of protein sequencesBioinformatics Resource Portal (http://expasy.org/tools)
- The Department of Biology at York University maintains a page for Core Molecular Biology Facility. This page, http://www.yorku.ca/biocore/, has URLs for many useful programs, tools and databases. Students explore sites and make decisions about options regarding sites to use. These are also used by biochemistry students in 3rd and 4th year.
- BLAST is the tool we use to compare an unknown sequence (amino acids OR nucleotides) against a library of known sequences for the purpose of identifying the unknown sequence. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Compare Transeq sequences derived from Tetrahymena and Standard Code using BLAST and comment on differences.
- Some of the databases used by biochem. students at York Univ.
- Teaching this bioinformatics course has led to developing an expertise and many students have visited the librarian and asked for help in their biochemistry assignments which have bioinformatics components.
- Students who have no knowledge of bioinformatics and genetics to students who have used these tools in other courses.
- Research guide: http://researchguides.library.yorku.ca/biol3100
- http://www.youtube.com/watch?v=nO0wJgZRZJs&feature=youtu.behttp://www.nature.com/scitable/definition/genome-43http://www.ncbi.nlm.nih.gov/guide/howto/find-func-gene/http://www.johnkyrk.com/aminoacid.htmlhttp://nar.oxfordjournals.org/content/40/D1/D1.abstract
- The Canadian Bioinformatics Workshops (CBW) series began offering one and two week short courses in bioinformatics, genomics and proteomics in 1999, in response to an identified need for a skilled bioinformatics workforce in Canada. In partnership with the Canadian Genetics Diseases Network and Human Resources Development Canada, and under the scientific direction of Director, Francis Ouellette, the CBW series was established. For eight years, the series offered short courses in bioinformatics, genomics and proteomics in various cities across Canada. Taught by top faculty from Canada and the US, the courses offered small classes and hands-on instruction. In the fall of 2007, at the third Mentor Network Meeting, a new format and series of exciting workshops were designed. It was recognized that with the introduction of new technologies and scientific approaches to research, having the computational biology capacity and skill to deal with this new data has become an even greater asset. This new series of workshops focuses on training the experts and users of these advanced technologies on the latest approaches being used in computational biology to deal with the new data. The CBW plans to offer these workshops beginning in 2008.The CBW is now hosted by the Ontario Institute for Cancer Research, where Francis Ouellette is Associate Director of Informatics and Biocomputing.
- If you are planning to start a bioinformatics tools and databases course (librarian led) then a good presentation to get ideas: http://chla-absc.ca/2011/sites/default/files/E_How_to_build_a_bioinformatics_service_Clairoux.pdf