Software

• Iris
  Data visualization framework for bioinformatics.


• CMap
  Originally created for the Gramene project, CMap is a web-based genetic and comparative map visualizer. It is now part of the Generic Model Organism Database (GMOD) project, and is freely available from Sourceforge.net.


• HTML::GMap
  This module provides an easy-to-use way to build interactive web-based geographical maps that utilize the Google Maps API.


• Generic Search Page Framework
  This package consists of WebForm::SearchPage and WebForm::ParamField Perl modules, which are used to represent web search pages running on top of a relational database. This framework can be used to write search pages that query a database, independent of the database schema. The modules provide common functionality typically needed for search pages, reducing development time and standardizing interfaces.


• Generic Search Page Framework - Panzea Search Pages
  This package contains code for Panzea search pages built on top of the Generic Search Page Framework. This code runs on the Panzea schema.


• Look-Align Alignment Viewer
  This is an interactive web-based application for displaying pre-computed multiple sequence alignments. Software is written in Perl and uses readily available open-source components. It supports data retrieval from GDPDM-based MySQL databases or flat files.


• SQL::Translator
  SQL::Translator was created while working on CMap as a means to translate a MySQL schema to Oracle, PostgreSQL and Sybase. It has since grown into a healthy, open-source project with 20 developers actively working on new functionality. SQL::Translator is freely available on the Comprehensive Perl Archive Network (CPAN).


• Text::RecordParser
  This module was also created while writing CMap as a simple way to parse delimited text files. The code is freely available on CPAN.


• Bio::GenBankParser
  A Parse::RecDescent-based grammar parser for GenBank records. Very flexible and extensible.