Introduction
This page describes some of the software projects that UK CropNet has been involved with. Many of the links below will take you to pages with more information.

A list of software versions we are using can be found here

AceBrowser Enhancements
We have made a significant improvements to many of the standard scripts and displays that come as part of the AceBrowser package. For more details about these enhancements (and for details about how to obtain them), please see our AceBrowser enhancements page.

Java Applet Development
UK CropNet is developing a range of software applications that are designed to be implemented using Java, and thus can be run from most web-browsers. This page outlines some of the recent software developments. Please note that all UK CropNet software is currently being rewritten to conform to a common standard such that future software developments can include current software projects as modules within larger software packages.

CITA: A CORBA Interface to ACEDB databases
CITA provides a simple CORBA interface to one or more ACEDB databases. Currently this interface has been implemented to produce two CITA servers, one written in Perl and one written in C. A number of demo clients are included, to serve as programming examples. Click here for more information about CITA.

GFace: a general Java CITA client
GFace uses CITA to access ACEDB databases and provides a Java display and data browsing environment. The ACEDB query languages are supported (including AQL), and GFace can be extended by the addition of new displays, by using a simple interface. The displays available can be configured on a database by database basis. For more details, click here.

Recombination Viewer
The Recombinant Viewer is a graphical display that aims to highlight areas of particular interest (such as recombination events) in a large group of mapping data. These areas are abstracted out by colour coding the scores according to their identity and the closest unambiguous flanking scores in the same column. The Recombinant Viewer consists of a number of reusable Java components and can be run stand alone or connected to ACEDB.

Recombination Viewer

Grid Map

The Grid Map package was designed to display comparative genome mapping data in a grid format. It is a generic Java version of the Oxford Grid display (written for the ACEDB database software package), but can be used to display any grid object. Jeremy Dickson's version 2.0 of the GridMap is still available, but we strongly recommend you use Moira Priestly's version 3.0.

Pairwise Comparative Map (PCM)

Pairwise Comparative Map (PCM) is a Java bioWidget that shows two genetic maps of any type and species adjacent to each other and draws lines between the homologous loci on each map.  One is able to resize the length of the map, invert a map, and to swap the maps on either side. It is also possible to show a single map on it's own.

Clicking on a locus highlights it along with any homologues on the same map and on the opposite one and all the connecting lines. Double-clicking can fire up a browser with the URL to the database object (locus) if the applet is set up to do so.

A higher-level component called Multi PCM exist where a number of PCMs are placed in a scrollpane. Highlighting a locus in one PCM has the effect of highlighting all the homologues across all of the PCMs. The maps are colour coordinated across the Multi PCM to unify the maps originating from the same database. click here for more information at the John Innes Centre Bioinformatics group.

Comparative Physical and Genetic Map (CPG Map)

CPG Map is a Java graphical programming component for visualising comparative genome mapping data where linkage maps can be displayed alongside physical maps.

Like Grid Map, CPG Map adopts a three-tier design structure whereby CPG Map is only a software component placed on a graphical user interface. CPG Map is not a standalone tool; it is placed within an application or applet which has access to various parameters like whether the CPG Map component should show a zoomed in map or not. The application also very importantly provides CPG Map with data - it doesn't matter where the application gets the data as long as it arranges it in to the correct data structure format. The basic data structure unit in CPG Map is the CPG_Locus class.

Genome Map Viewer (GMV)
A tool for comparing two or more genomes and displaying the results in the form of the concentric ring display of Moore et al. (Grasses, line up and form a circle. 1995 Current Biology 5:737-739), which shows the distribution of the 'building blocks' throughout the grass genomes, each genome being drawn as a separate ring. This and other comparative genetics software is available from the JIC Bioinformatics group software pages.