The following software and database for which it would be useful to have
agents. This list is obviously larger than necessary but it is meant to
show the range of data types, data organization and tools we will have
to deal with.

  ---------------- --- ------------------------------------------------------------------------------------------ ---------- -------
  Name                 URL                                                                                        Category   Have
                                                                                                                             code?

  CONTENT          2   <http://www.riaca.win.tue.nl/CAN/SystemsOverview/Special/DiffEqns/Content/GCbody.html>     BS         Y

  CanDYS               <http://www.agnld.uni-potsdam.de/~wolfgang/candys.html>                                    BS         Y

  AUTO             1   http://indy.cs.concordia.ca/auto/main.html                                                 BS         Y

  BLAST            1   <http://www.ncbi.nlm.nih.gov/BLAST/>                                                       DA         N

  ACEAlign         1   <http://atlas.med.harvard.edu/>                                                            MA         N

  Scanalyze        1   <http://rana.lbl.gov/EisenSoftware.htm>                                                    MA         N

  MAExplore        3   <http://www.lecb.ncifcrf.gov/MAExplorer/hmaeDocD.html>                                     MA         N

  Clustal          1   <http://members.tripod.com/~mhoenicka/clustalw.html>                                       DA/PE      N

  GCG              1   <http://www.accelrys.com/products/gcg_wisconsin_package/v10p2_highlights.html>             MB         N

  DSSP             1   <http://www.cmbi.kun.nl/swift/dssp/>                                                       SA         N

  WPDB             2   <http://www.sdsc.edu/pb/wpdb/wpdb.htm>                                                     SA         N

  Sequence Space   2   <http://industry.ebi.ac.uk/SeqSpace/UG.html>                                               SA         N

  JAMBW            1   <http://www.embl-heidelberg.de/JaMBW/>                                                     MB         N

  Kinemage         1   <http://kinemage.biochem.duke.edu/>                                                        SV         N

  EMotif           1   <http://motif.stanford.edu/emotif/emotif-scan.html>                                        DA         N

  WebGen           1   <http://genome.c.kanazawa-u.ac.jp/~webgen/webgen.html>                                     TH         N

  BIND             1   <http://genome.c.kanazawa-u.ac.jp/~webgen/webgen.html>                                     DB         Y

  DIP              1   http://dip.doe-mbi.ucla.edu/                                                               DB         N

  Curagen Yeast    1   <http://portal.curagen.com/extpc/com.curagen.portal.servlet.PortalYeastList?modeIn=List>   DB         Y

  KEGG             1   http://www.genome.ad.jp/kegg/                                                              DB         Y

  BRENDA           1   http://www.brenda.uni-koeln.de/                                                            DB         N

  EMP              1   http://www.empproject.com/                                                                 DB         Y

  Subtlist         1   http://genolist.pasteur.fr/SubtiList/                                                      DB         N

  YPD              1   http://www.proteome.com/databases/index.html                                               DB         N

  NCBI             1   http://www.ncbi.nlm.nih.gov/                                                               DB         Y

  Stanford             http://genome-www5.stanford.edu/MicroArray/SMD/                                            DB         N
  Microarray                                                                                                                 
  Database                                                                                                                   

  PDB              1   http://www.rcsb.org/pdb/                                                                   DB         Y

  BBID             3   http://bbid.grc.nia.nih.gov/                                                               DB         N

  Transfac         1   <http://transfac.gbf.de/TRANSFAC/>                                                         DB         N

  NETLIB           1   <http://www.netlib.org/> (ODEPACK, MINPACK, LAPACK, etc)                                   SI/FI/BS   Y

  R                1   <http://www.r-project.org/>                                                                ST         Y

  Witten/Machine   1   http://www.cs.waikato.ac.nz/ml/weka/                                                       ML         Y
  Learning                                                                                                                   
  ---------------- --- ------------------------------------------------------------------------------------------ ---------- -------

DA- Sequence Analysis

DV- Sequence Visualization

SA- Structure Analysis

SV- Structure Visualization

MB- Molecular Biological Support

PE- Phylogeny/Evolutionary Biology

MA- Microarray Analysis

TD- Two-D gel analysis

TH- Two Hybrid analysis

SI- Simulation

FI- Fitting

ST- Statistics

ML- Machine Learning

NA- Network Analysis

NV- Network Visualization

BS- Bifurcation Theory and Sensitivity Analysis

DB- Database

Other instances of tools that people use

<http://www.tigr.org/softlab/>

<http://www.geocities.com/CapeCanaveral/1957/software.html>

<http://www.public.iastate.edu/~pedro/research_tools.html>

<http://www.hgmp.mrc.ac.uk/Research/Microarray/dataanalysis.jsp>

<http://www.embl-heidelberg.de/~toldo/JaMBW.html>

Some basic Molecular Biological Functions we could probably emulate
quickly to hook biologists on the software: See:

Incogen

Pathcalling