Asia Pacific BioGRID Initiative

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APBioBox II - Bioinformatics software and databases in a Box!

APBioBox II Initiative Draft Document

  • Aims
    1. To facilitate the rapid set-up and replication of Bioinformatics resources and services throughout the Asia Pacific through packaging installed and configured software and databases in a box - APBioBox.
    2. To build into the APBioBox a mechanism for keeping the software and databases in an APBioBox-installed resource server up-to-date
    3. To set up the process of keeping the APBioBox current through collaboration and community voluntarism.
  • Potential Collaborators
    1. APBioNet (secretariat) - coordinator
    2. National University of Singapore
    3. Asia Pacific Science and Technology Center, Sun Microsystems
    4. SCS Ltd
    5. Center for Bioinformatics, Peking University
  • Design Features and Philosophy
    1. Pre-configured
    2. Easy, minimum-step installation
    3. Rapid installation
    4. Comprehensive
    5. (Semi)-Automated dynamic update mechanism
    6. in-house and/or shared mode
    7. Wide range of supported platforms: linuxes, solaris
    8. Alternative interfaces: Web form-filling and Java plugin/application
    9. Registry and discovery of BioWeb, BioGrid and other Services
  • Software and Packages
    1. Bioinformatics computational software applicaitions and packages
      1. All-purpose sequence analysis: EMBOSS (emboss-2.7.1)
      2. Phylogenetic inference: PHYLIP (embassy-phylip-3.573c)
      3. Visualisation: Treeview (tv-0.3)
      4. Multiple sequence alignment: CLUSTALW (clustalw-1.83)
      5. abacus-0.63
      6. Sequence homology search: BLAST (blast-2.2.5)
      7. Sequence homology search: fasta3-3.4
      8. cDNA-Genomic DNA alignment: MGALIGN (mgalign-linux-1.3.6)
      9. cDNA-Genomic DNA alignment: embassy-sim4-1.0.0
      10. HMM: (embassy-hmmer-2.1.1)
      11. wise-2.2.0
    2. Bioinformatics GUI and system interfaces
      1. Applications Integration Interface: jEMBOSS
      2. Database Integration Interface: SRS
      3. Workflow Integration gui: KOOPLite (KOOPlatform 3.0 client)
    3. Bioinformatics Web interfaces
      1. W2H
    4. Supporting software packages
      1. Web Server: Apache
      2. SQL Database: MySQL
      3. Programming Language Modules: BioPerl
      4. Programming Language Modules: BioPython
      5. Java: Tomcat
      6. CGI: PHP
      7. Grid Middleware: Globus Grid Toolkit 2.4
      8. Cluster computing: ?
  • Databases
    1. All Bio-Mirror biodatabases
    2. Dynamic updates
  • Intellectual Property Rights and etc
    1. Sensitive to IPR
    2. Public domain or contributed software
    3. Facilitated registration with copyright owner by local implementor

Updated Oct; July; Apr 2004; 4 Dec 2003 (ttw); 16 Sep 2003 - ogs