Cytoscape Web is a web-based network visualization tool, modeled after Cytoscape, that is open source, interactive, customizable, and easily integrated into websites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF. Availability and Implementation: Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at http://cytoscapeweb.cytoscape.org/

This release contains the same data as release 17  (freeze of 1st of February 2010), with the addition of 9 C. Elegans submissions from the Waterston project that did not make it to the previous release.

Release 18 contains 1031 submissions, 729 for fly and 311 for worm. 2 of the fly submissions relate to Drosophila Pseudoscura.

In this release the display of the expression levels related to a certain feature has been corrected (those were named as ‘experimental features’ in the previous release), a bug related to the association of features common to different submissions of a certain experiment has been fixed (see post) and more feature relationships and properties are now considered.

We also provide a Perl client API that makes it easy to run templates and create custom queries from simple Perl programs.  The download contains some sample code that will connect to modMine and run queries to, for example, fetch details of antibodies and to find modENCODE features located near to gene(s) of interest.

You can download the package at:

http://www.flymine.org/download/modmine/perlAPI

Instructions are in the file http://www.flymine.org/download/modmine/perlAPI/howToInstall

Or for an automated install, which will handle dependencies for you can use pip:

From the commandline run:

pip http://www.flymine.org/download/modmine/perlAPI/InterMine-0.02.tar.gz

Don’t forget you can install pip (the package installer for Perl) with “cpan pip”

For more information on the available positions and how to apply please see

http://www.intermine.org/wiki/NowHiring#SoftwareDevelopers-modENCODEprojectTwoposts

This release represents the data release freeze of 1st of February 2010.

Release 17 contains 1031 submissions, 729 for fly and 302 for worm. 2 of the fly submissions relate to Drosophila Pseudoscura.

There are 37 experiments in the release, and more than 43 millions of genetic features.

http://www.modencode.org/docs/hmav.html

New incremental release with 780 submissions. 568 concern fly, 212 worm.

This release contains a snapshot of all fly and worm data for analysis (data analysis freeze). It has the same data of release 15 with the addition of 10 worm submissions (all from the Lieb project).

A bug affecting the export of data has been solved.

New full release with 770 submissions. 568 concern fly, 202 worm.

This release contains a snapshot of all fly and worm data for analysis (data analysis freeze).

Please note that the submissions for fly of the Henikoff group have been updated respect release 14. The update has increased the number of submissions by 8.

The goal of the modENCODE project (model organism ENCyclopedia of DNA
Elements) is a systematic identification of all functional elements in
fly and worm and their dynamics across development and in multiple
cell lines, through large-scale data generation and integration,
including gene expression, transcription factor binding, chromatin
modifications, histone variants, microRNAs. The project involves
numerous data production centers in both model organisms, each coupled
with an informatics data processing and analysis group.  In addition,
a Data Coordination Center (DCC) is charged with data storage
processing and dissemination, and the newly-funded Data Analysis
Center (DAC) is charged with integrative analysis of the diverse
datasets, forming the Analysis Working Group (AWG) together with
additional biological and informatics members of the various groups.

The scientific manager will co-direct the DAC and AWG and will be
responsible for coordinating all group activities and priorities, both
scientifically and organizationally. This includes: shaping and
executing the vision of the integrative analysis for modENCODE;
planning, coordinating, and contributing to the writing of modENCODE
scientific papers; coordinating analysis activities, milestones, and
deliverables of the various analysis groups; planning and executing
the scientific agenda for both the weekly group scientific phone
conversations of the AWG, and the bi-yearly person-to-person meetings
of the AWG; interaction and coordination with the human ENCODE project
and AWG; interactions with the NIH program managers for the role of
the DAC in review and evaluation of the overall modENCODE project.

Strong background in scientific leadership is required, as well as a
combination of computational and biological background, and
interpersonal and organizational skills.  A Ph.D. in biology or
computational biology is required, with experience in large-scale data
production and/or data integration in the fly, worm, mouse, or human
genomes. Experience in scientific leadership is also required, as a
fellow, senior post-doc, PI, or co-PI. Experience coordinating or
participating in multi-institutional collaborative efforts is also a
big plus, and specifically in the successful writing of
multi-institutional papers.

The position will involve close interactions with the DAC PI (Manolis
Kellis), DAC co-PIs (Mark Gerstein, Peter Park, Shirley Liu, Peter
Bickel, Steve Brenner, Kris Gunsalus), modENCODE PIs (Waterston,
Celniker, White, Snyder, Karpen, Lieb, Henikoff, Lai, Piano,
MacAlpine), the DCC (Stein, Lewis, Micklem), and other members of the
modENCODE consortium production and analysis teams. Position will be
at MIT, in a highly interdisciplinary and highly collaborative
environment at the interface of the MIT Computer Science and
Artificial Intelligence Laboratory and the Broad Institute of MIT and
Harvard.

To apply, please visit: http://compbio.mit.edu/positions.html