1. How to use the web for bioinformatics Molecular Technologies October 15, 2005 Ethan Strauss ethan.strauss@promega.com 274-4330 X 1171 http://www.q7.com/~ethan

2. Objectives At the end of this session you should be able to: Find information on the web about an arbitrary topic. Be aware of pitfalls and problems with information from the web. Be familiar with how to cite information from the web. Use PubMed or a similar tool to search for articles on a given subject.

3. How to find all those dang URLs! http://q7.com/~ethan/molbio/2005lit.htm

4. Outline How to Use a Browser Finding General Information on the Web Pitfalls of web information Finding Biological Information on the Web

5. How to use a Browser Search on the text of a page Downloading files Transfer of data to and from browser windows.

6. How to use a Browser Reading and dissecting URLs http://www.promega.com/search/Default.aspx?query=wizard&indexes=0&page=1 http://www.promega.com/search/Default.aspx?query=wizard&indexes=0&page=1 Protocol http:// Domain http:// www.promega.com/ http:// www.promega.com/ Path http://www.promega.com/search/ http://www.promega.com/search/ Specific File http://www.promega.com/search/Default.aspx http://www.promega.com/search/Default.aspx Query String http://www.promega.com/search/Default.aspx? query=wizard&indexes=0&page=1 For fun, try changing the query, page, or indexes and see what happens. http://www.promega.com/search/Default.aspx? query=wizard&indexes=0&page=1

7. How to Find General Information Search Engines Categorized by a human (Yahoo)Yahoo –Fewer sites. –Better Index Straight text search (Google)Google –More Sites –More Complete index Clusty (Clusty)Clusty –Very new, very hyped! –Seems to be a combination of text and human categorization This is an interesting side note. I put this in for the 2004 version of this lecture. Does anyone use Clusty? Has anyone heard of it? Beware of flashes in pans and changing URLsflashes in pans

8. Exercise 1 Try to determine my father’s occupation. My name is Ethan Strauss I work at Promega If you have time, pick apart this URL http://q7.com/~ethan/molbio/2005lit.html

9. How to find Biological Information Literature PubMed –Quintessential index of medial articles. Agricola –Index of agricultural articles. –Not as easy to use as PubMed HighWire Press –Allows searches of full text of many journals. –Very good for finding protocols and uses of specific products. UW library ( http://www.library.wisc.edu/libraries/distance/biotech/)UW library http://www.library.wisc.edu/libraries/distance/biotech/ Individual journal sites General Searches

10. Exercise 2 A) See if you can find a specific article about any one of the following Your favorite biological topic Viruses of the Dutch Elm disease fungus Ophiostoma ulmi Interactions of cJUN and abl B) Use Highwire to find an article which Uses Promega’s “Dual Luciferase Assay System” Compare these results with those from MedLine

11. How to find Biological Information Protocols Bioprotocol BioTechniques® Molecular Biology Techniques ForumsBioTechniques® Molecular Biology Techniques Forums Molecular Biology Protocols Google

12. Biological Information Limitations of the web Proprietary Information Old Information Too old to be on the web. Information that is no longer correct. Unpublished Information

13. Biological Information Limitations of the web Incorrect Information Blatant Subtle Biased Information Consider anything on a commercial web page to be an advertisement. Compare GM’s view of SUV rollovers with a lawyer’s.GM’s view of SUV rollovers lawyer’s

14. How to find Biological Information Biological Databases There are many biological databases available for free use on the web. DNA Sequence Protein Sequence Transcription Factor Binding site Protein three dimensional structures Biochemical Pathways Taxonomy And many others

15. How to find Biological Information DNA Sequence Databases General –Genbank (NCBI)Genbank –EMBLEMBL –DBJJDBJJ Species Specific –YeastYeast –HumanHuman –C. elegansC. elegans –E. coliE. coli –Meta Sites

16. Exercise 3 Find a gene sequence. –Anything of interest to you –double-stranded RNA virus of a fungus genomic sequence –Human Transforming Growth Factor –bacterial beta-lactamase

17. How to cite information from the web Information from journals Author(s) (year of publication) Title Journal Name Volume, pages Information from databases Database name with release number, ID number of specific information if appropriate, Date retrieved, URL ( generally for database, not specific entry ). Information from arbitrary web sites Web site name or indication, Web page title or name, Date of publication (if available), Date Retrieved, URL (to specific page or main page if more appropriate)

18. Homework Due in 2 weeks (October 30 th ) 1.Find a gene of interest. 2.Find at least three papers which discuss some aspect of this gene in at least three different situations (different cell lines or different organisms or different disease states etc.) 3.Very simply summarize the results of each of these three papers with respect to this gene. 4.Be sure to give citations for the three papers and indicate which paper the information came from.