Web-based information systems

1. Informatics
   1. Growth of data
   2. Knowledge pyramid
2. Basis of Bioinformatics
   1. Biology
      1. Reason for being
   2. Related to computational biology
      1. Computational chemistry
         1. Molecular biology
   3. Statistics/mathematics/probability
      1. Data mining
   4. Computer science/Algorithms
   5. Informatics
      1. Information science
      2. Database
      3. Web-based information systems
      4. Ontologies
3. Web theory
   1. Communication
      1. TCP
      2. HTTP
   2. 3-tier
      1. Client
         1. Browser
      2. App server/web server
         1. HTTP server
         2. Java engine
         3. Script engine
      3. DB Server
         1. RDBMS
         2. Tables/Relations
            1. Versus files
            2. Versus other designs
         3. Search facilities
         4. Schema
            1. Chado
   3. Languages
      1. Perl
      2. Java
         1. J2EE
      3. .NET
      4. Python
      5. Ruby
      6. HTML
      7. XML
      8. XHTML
      9. PHP
      10. Javascript
      11. Java Applets
   4. Not as fast as languages like C/Fortran used for algorithmic and/or statistical programming, scientific programming
      1. Speed
         1. Faster CPU ... clock speed
         2. More CPU's
         3. More cores
         4. Cluster computing
         5. Grid computing
         6. Super computing
         7. Optimized algorithms/efficiency or approximation (good enough)
   5. Use of Free/Open Source/Open Standards
      1. 3WC
      2. IETF
   6. Services
      1. Content
         1. Sequence data
         2. Annotation
      2. Sequence data upload facilities
      3. Curtation
      4. Provenance
      5. Search/Download
      6. Viewers/Visualization
      7. Online Analysis
      8. Literature/papers
      9. Educational materials
4. Examples
   1. http://en.wikipedia.org/wiki/Bioinformatics#Software_tools
   2. http://en.wikipedia.org/wiki/Biological_databases
   3. http://www.kokocinski.net/bioinformatics/databases.php
   4. NCBI
      1. http://www.ncbi.nlm.nih.gov/
         1. About
         2. http://www.ncbi.nlm.nih.gov/About/index.html
      2. http://www.ncbi.nlm.nih.gov/Genbank/index.html
   5. EBI/EMBL
      1. http://www.ebi.ac.uk/
      2. http://www.ebi.ac.uk/embl/index.html
   6. NIG/DDBJ
      1. http://www.nig.ac.jp/index-e.html
      2. http://www.ddbj.nig.ac.jp/
   7. Specialized databases
      1. VectorBase
         1. http://www.vectorbase.org/
      2. Ensembl
         1. http://www.ensembl.org/
      3. FlyBase
         1. http://flybase.org/
      4. WormBase
         1. http://wormbase.org/
      5. KEGG
         1. http://www.genome.ad.jp/
      6. SWISS-PROT
         1. http://ca.expasy.org/sprot/
      7. PIR
         1. http://pir.georgetown.edu/
      8. PRF
         1. http://www4.prf.or.jp/en/
   8. Site Maps
      1. http://www.ncbi.nlm.nih.gov/Sitemap/index.html
      2. http://www.ebi.ac.uk/Information/sitemap.html
   9. Ontologies
      1. GO
         1. http://www.geneontology.org/
         2. SiteMap
            1. http://www.geneontology.org/GO.site.map.shtml
      2. GOA
         1. http://www.ebi.ac.uk/GOA/
   10. Development tools/software
       1. Open Bioinformatics Foundation
          1. http://open-bio.org/
       2. Bioinformatics.org
          1. http://bioinformatics.org/
       3. SourceForge
          1. Search on bioinformatics
       4. EMBOSS
          1. http://emboss.sourceforge.net/what/
       5. BioPerl
          1. http://bioinformatics.org/
          2. BioJava
             1. http://biojava.org/
          3. BioPython
             1. http://biopython.org/
          4. BioRuby
             1. http://bioruby.org/
       6. BioDAS
          1. http://biodas.org/
       7. GMOD
          1. http://gmod.sourceforge.net/
       8. BioMOBY
          1. http://biomoby.org/
       9. myGrid
          1. http://www.mygrid.org.uk/
   11. Analysis tools/software
       1. NCBI
          1. http://www.ncbi.nlm.nih.gov/Ftp/
       2. EMBL-EBI
          1. ftp://ftp.ebi.ac.uk/pub/software/
       3. TIGR
          1. http://www.tigr.org/software/

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