DownloadsBookmarks

1
Downloads/Bookmarks

• BIOL/CHEM 4900

2
Websites to Bookmark

• Make a Biocomputing favorites folder in your
  normal internet browser
• Add these sites to the Biocomputing folder
• Galileo http//galileo.peachnet.edu
• Interlibrary Loan http//adminservices.clayton.ed
  u/library/illcopy.htm
• Biology Workbench http//workbench.sdsc.edu/
• Specialized search engines
• http//biol.net/
• http//us.expasy.org/BioHunt/
• NCBI (Entrez/Pubmed/etc) http//www.ncbi.nlm.nih
  .gov/
• Entrez http//www.ncbi.nlm.nih.gov/Entrez/
• Tutorial for Entrez http//www.ncbi.nlm.nih.gov/
  entrez/query/static/help/entrez_tutorial_BIB.pdf

3
More Websites to Bookmark

• KEGG http//www.genome.ad.jp/kegg/
• Expasy http//us.expasy.org/
• Swiss-Prot http//us.expasy.org/sprot/
• PIR http//pir.georgetown.edu/pirwww/search/textp
  sd.shtml
• GenBANK http//www.ncbi.nlm.nih.gov/Genbank/index
  .html
• EMBL http//www.ebi.ac.uk/embl/index.html
• DDJB http//www.ddbj.nig.ac.jp/
• Protein Data Bank http//www.rcsb.org/pdb/
• ORF Finder http//www.ncbi.nlm.nih.gov/gorf/gorf.
  html
• GENSCAN http//genes.mit.edu/GENSCAN.html

4
Software to Download

• You should have the following
• Clayton State University e-mail account (CHECK IT
  DAILY)
• Microsoft Office (from the Hub Software Center)
• Adobe Acrobat Reader www.acrobat.com

5
Software to Download

• You will also need Firefox http//www.mozilla.com
  /en-US/firefox/
• Click on Firefox 3 free download, Run, Run
  (again), Setup wizard (next, next, next, install,
  finish)
• Import bookmarks, etc., if you are going to use
  this as your default browser
• Installing the Chime plug-in (npchime.dll) for
  Firefox
• You must register at MDL to get the Chime plug-in
  (http//www.mdl.com/my_account/register1.jsp)
• A password will be sent to your email address.
  Write this password down (case sensitive).
• Log in to MDL (http//www.mdl.com/my_account/index
  .jsp?urlreturn/products/framework/chime/index.jsp
  )
• From the Downloads menu on the bar near the top,
  select Download Products.
• Select MDL Chime 2.6 SP6 for Windows (make sure
  it is SP6, not SP7) or 2.6 SP3 for Macintosh
• Click Start Download. Save the installer program
  in a place where you can find it.
• Start MDLChimeSP6.exe, click run to install,
  click next until done.
• Copy the file npchime.dll from c\Program
  Files\Internet Explorer\Plugins to c\Program
  Files\Mozilla Firefox\plugins. The other three
  "chime" files in the plugins directory are
  unnecessary chime.html is the Chime release
  notes chime26.isu and ChimeShim.dll are
  obsolete.
• Close all Firefox browser windows. This is
  necessary since browsers load new plugins only
  when starting.
• Start Firefox. Clicking this link (ATP) should
  display a wireframe rendering of an ATP molecule.
  Here is another Chime test site. If these don't
  work, please ask for help.

6
Does Protein Explorer Work?

• Open Firefox
• Go to Protein Explorer Frontdoor
  http//www.umass.edu/microbio/chime/pe_beta/pe/pro
  texpl/frntdoo2.htm
• Bookmark this site
• Click on Quick-Start Protein Explorer
• You will need to disable pop-up blockers to start
  protein explorer
• PE will check for browser compatibility. Be
  patient.
• Do you see a spinning molecule on the screen? If
  so, PE and Chime are working (woo-hoo!).

7
Biology Workbench

• You have already bookmarked the Biology Workbench
  site http//workbench.sdsc.edu/
• In any web browser, go to Biology Workbench and
  register to set up your account.
• Start the Biology Workbench tutorial
  http//bsw-uiuc.net/tutorials_current/How3.2/

8
Additional Reading

• Hagen, Joel. 2000. The origins of
  bioinformatics. Nature Reviews. 1 231-236.
• Bayat, Ardeshir. 2002. Bioinformatics
  Science, medicine, and the future. BMJ. 324
  1018-1022.
• On reserve in library
• May be reserved under BIOL 3100 or Burnett
• Also on course website