The increased interest in fingerprint maps has spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and the underlying fingerprint data. For this purpose, we have a new Java-based application called iCE (Internet Contig Explorer) for viewing the fingerprint maps and associated data for all major operating systems. Users can search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers and can load into the software user-generated lists of clones and view their fingerprints. iCE provides access to at the mouse, rat, bovine, C. briggsae and several fungal genome BAC fingerprint maps we have generated in a user-friendly manner, without the need for the user to manage the entire map database.
News
May 9th, 2001 Vancouver - The Genome Sciences Centre is proud to present its public release of the internet Contig Explorer (iCE).
Shown in the screenshots is our Internet accessible, Java based contig viewer, iCE (Internet Contig Explorer). A contig view is shown. As in FPC, contig names are superimposed on a green bar representing clone length. One clone is highlighted in yellow, this clone is also highlighted in the gel display window, allowing the user to examine the actual gel image and bandcalls.
A user can either enter a clone/contig/marker name directly in the text box provided, or can scroll down to the clone/contig/marker of interest.
This view of iCE shows a detailed view of a small region of a contig, along with the some of the gel fingerprints for this region. In the gel fingerprint view, green bands represent bands shared between clones, and red bands represent bands that do not contribute to these runs of conserved bands. In this view, a very tight tolerance was used, the selection of tolerance is a factor critical to the performance of any contig ordering algorithm.
Documentation
The internet Contig Explorer is an application that allows viewing physical map in a convenient manner. All the physical map data you know and love is here: gel fingerprint data, contigs (assemblies of clones), markers and comments associated with clones. The data is stored in SQL relational database which offers other advantages over flat-file formats both in data storage - you don't need the entire database installed on your machine to view one bit of data - and future features such as reports. Contigs (and other data) can be viewed for different data sets - for example, different contigs resulting from different build parameters; different contigs built as fingerprint data is added to the database; contigs resulting from automated contig building versus manual human-assembly.
Source Code
For the utilities, you must get everything, including compiled binaries to ACEDB graphics libraries, and descriptions of SQL tables (see licences embedded in files for distribution restrictions) and utility to populate an SQL database from the FPC database.
Current Release
Internet Contig Explorer (iCE) 3.5
This version of iCE requires you to have the Java Virtual Machine installed.
After downloading execute either "launch-ice" (on Unix-like operating systems) or "launch-ice.bat" (on Microsoft Windows) from the subdirectory ICE that was created.