Major improvements and release changes

GenDB 2.4 is an intermediate internal release that enhances the functionality in several areas:

• further improvements and extensions on the data model (194 classes)
• extended search interface, PatScan search for protein sequences
• new tools: Gismo, TransportDB, RFAM, TransTerm
• added support for more types of regions, e.g. oligos, terminators, RNAs, mutations
• numerous bug fixes and improvements of the GenDB web interface
• updated documentation of GenDB CORE API for extending GenDB and writing your own scripts
• more documentation for users and programmers in GenDB Wiki
• several new modules: sequence viewer, comparative genome annotator, SNP detection, gene annotation update checker, etc.
• integration with the SEED genome annotation system: gene cluster viewer, mapping of subsystems
• new scheduler that optimizes job submission and stores current jobs persistently

GenDB 2.2 is the first public release of the new system that greatly enhances the functionality in many areas:

• further improvements and extensions on the data model (189 classes)
• BLAST classes redesigned including support for bi-directional searches
• management of project members via General Project Management System (GPMS) web interface
• numerous bug fixes and improvements of the GenDB web interface
• documentation of GenDB CORE API for extending GenDB
• more documentation for users and programmers in GenDB Wiki
• additional modules for genomic plots, genome comparison, synteny, etc.
• scheduling of jobs via DRMAA interface
• easy to use installation system

GenDB 2.0 was a substantial redesign of the original system using a new version of O2DBI implemented by Burkhard Linke that also supports class inheritance. Due to limited man power GenDB 2.0 was only used in-house for the annotation of more than 20 microbial genomes.

• improved and extended data model (126 classes)
• complex pipelines for gene calling and automated functional annotation,
  based on various state of the art tools
• high-throughput design for compute cluster
• user friendly web interface for browsing and annotating genomes
• well defined API for extending GenDB
• additional modules for genomic plots, genome comparison, syntheny, repeat analysis

GenDB 1 was a very simple system that we implemented as a proof of concept - it has only 13 classes! Nevertheless, we sent the tarball with version 1.1.1 to more than 50 interested users and institutions.

• a lot of bugfixes and improvements
• support for tRNAs
• more and updated tools
  • Blast 2
  • InterPRO-Scan
  • TMHMM
  • Signal-P
• data exchange
  • Import and export of EMBL formatted data
  • Import and export of GenBank formatted data