modMine release 17
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.
The ongoing effort to create a Quality Control catalog of commercial antibodies that are reliable, sensitive and specific enough for chromatin immunoprecipitation experiments (led by Susan Strome and Gary Karpen) has just been updated and is available here:
http://www.modencode.org/docs/hmav.html
modMine release 16
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 documentation on the use of modMine is now available from the drop down menu of our blog.
Under the tag modMine you can find a general overview followed by an introductory video and a general help page with more detailed subsections devoted to the analysis of fly and worm data.
Nucleic Acids Res. 2009 Dec 4. [Epub ahead of print]
Ooi SL, Henikoff JG, Henikoff S.
PMID: 19966274
Curr Biol. 2009 Nov 17;19(21):1777-87. Epub 2009 Oct 22.
Ercan S, Dick LL, Lieb JD.
PMID: 19853451
modMine release 15
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 modENCODE project (modencode.org) is seeking an accomplished and
motivated Drosophila or C. elegans scientist to act as the scientific
manager for modENCODE integrative analysis. Applicants should have a
strong scientific and leadership background, with experience both in
large-scale data integration and in the management and coordination of
large scientific groups.
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
modMine release 14
New full release with 588 submissions.
This release contains a snapshot of all fly data for analysis (data analysis freeze).
New front page with simplified layout and improved overview of experiments.
New experiment pages, with summary of experimental factors and access to related features, GBrowse tracks, submissions, submitted files.
A set of fly data has been frozen for analysis. It comprises 560 submissions and bulk downloads of the data are available from the Download Site.
The modMine data warehouse will be available shortly.