How%20to%20use%20the%20web%20for%20bioinformatics

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How to use the web for bioinformatics

• Molecular Technologies
• October 14, 2006
• Ethan Strauss
• ethan.strauss_at_promega.com
• 274-4330 X 1171
• http//q7.com/ethan

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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.

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How to find all those dang URLs!

• http//q7.com/ethan/molbio/2004.html

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Outline

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

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How to use a Browser

• Search on the text of a page
• Downloading files
• Transfer of data to and from browser windows.

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How to use a Browser

• Reading and dissecting URLs
• Protocol http//
• Domainhttp//www.promega.com/
• Pathhttp//www.promega.com/search/
• Specific Filehttp//www.promega.com/search/Defaul
  t.aspx
• Query Stringhttp//www.promega.com/search/Default
  .aspx?querywizardindexes0page1

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How to Find General Information

• Search Engines
• Categorized by a human (Yahoo)
• Fewer sites.
• Better Index
• Straight text search (Google)
• More Sites
• More Complete index
• Scientific (Scirus)
• Looks good.

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Exercise 1

• Try to determine my fathers occupation.
• My name is Ethan Strauss
• I work at Promega
• If you have time, pick apart this URL
• http//q7.com/ethan/molbio/2006.html

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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 searchs of full text of many journals.
• Very good for finding protocols and uses of
  specific products.
• Individual journal sites
• General Searches

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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 Promegas Dual Luciferase Assay System
• Compare these results with those from MedLine

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How to find Biological InformationProtocols

• Bioprotocol
• BioTechniques Molecular Biology Techniques
  Forums
• Molecular Biology Protocols
• Google

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Biological InformationLimitations of the web

• Proprietary Information
• Old Information
• Too old to be on the web.
• Information that is no longer correct.
• Unpublished Information

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Biological InformationLimitations of the web

• Incorrect Information
• Blatant
• Subtle
• Biased Information
• Consider anything on a commercial web page to be
  an advertisement.
• Compare www.whitehouse.org and www.whitehouse.gov

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How to find Biological InformationBiological
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

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How to find Biological Information DNA Sequence
Databases

• General
• Genbank (NCBI)
• EMBL
• DBJJ
• Species Specific
• Yeast
• Human
• C. elegans
• E. coli
• Meta Sites

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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

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How to cite information from the web

• Information from journalsAuthor(s) (year of
  publication) Title Journal Name Volume, pages
• Information from databasesDatabase name with
  release number, ID number of specific information
  if appropriate, Date retrieved, URL (generally
  for database, not specific entry).
• Information from arbitrary web sitesWeb 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)

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Homework Due in 2 weeks (October 28th)

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, different
   organisms (other than human, mouse, or rat),
   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.
5. Send to ethan.strauss_at_promega.com and place a
   copy in MyWebSpace