dictyBase: Technical Details

Technical Details

dictyBase runs using two 2 Physical Servers

  1. Application Virtual Server Array-The application server is a Dell PowerEdge 2950 with Dual Quad-Core Xeon 2.66GHz processors and 16GB RAM. This server is running CentOS 5 and VMWare Server. VMWare powers three different virtual machines, each which plays a different role in dictyBase.
    • dictyBase Web Server (Virtual) - This is a web server running Apache 2 on Ubuntu Linux 6.06. Most of the web pages from dictybase.org originate from this server. In addition to serving web pages, all automated data processing tasks are handled on this server. These tasks include searching and importing GenBank and PubMed records, generating BLAST databases, and exporting GFF3, among others. The programming language for dictyBase is Perl.
    • dictyBase Blast Server (Virtual) - This is a web server running Apache 2 on Ubuntu Linux 6.06. This server performs the BLAST analyses performed by users on our BLAST page. Additionally, our curators perform BLAST with this server, and we have automated processes which also utilize our BLAST server. BLAST functionality is exposed to our internal systems via a SOAP interface. BLAST is housed on a separate server to conserve resources and ensure optimum performance of our Web Server.
    • dictyCyc/dictyMart Server (virtual) - This is also an Ubuntu Linux 6.06 server. It runs two third-party web server applications: Pathway tools and BioMart. Pathway Tools is developed at SRI and is the software with which we create dictyCyc. BioMart is jointly developed by European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory
  2. Database Server - The relational database system is Oracle 10g Enterprise Edition running on a Dell PowerEdge 2850 with Dual Dual-Core Xeon 2.80GHz processors and 8 GB RAM. The database server also houses numerous other databases unrelated to dictyBase.
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