modENCODE Blog

modENCODE Data Access Webinar Apr 5th 2012

peter — Wed, 28 Mar 2012 15:48:15 +0000

“Understanding transcription in Drosophila sister species”. This webinar will discuss the data produced in Brian Oliver’s lab for several Drosophila species. Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. More details and the schedule are at http://wiki.modencode.org/project/index.php/DCC_Usability_webinars

MODENCODE DATA ACCESS WEBINAR Mar 1st 2012

peter — Fri, 24 Feb 2012 14:56:20 +0000

“Understanding worm and fly transcriptome data”, scheduled for Thursday Mar 1, 12:00 EST.
This webinar will introduce the participant to the transcriptome analysis data generated in Robert Waterston’s lab (C. elegans) and Susan Celniker’s lab (D. melanogaster). Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. More details and the schedule are at http://wiki.modencode.org/project/index.php/DCC_Usability_webinars

modMine release 28

sergio — Wed, 01 Feb 2012 16:46:47 +0000

modMine release 28

Release 28 consists of 1835 submissions, organised in 72 experiments divided in 12 categories.

It features an improved overlapping feature search.

modENCODE Data Access Webinar Feb 2nd 2012

peter — Wed, 18 Jan 2012 19:19:29 +0000

Next webinar held by Data Coordination Center for modENCODE is scheduled on Thursday Feb 2, 12:00 EST Topic: “Using modENCODE tools: GBrowse and modMINE”. This webinar will discuss the web tools for data retrieval and analysis – data mining interface (modMINE) and genome browser (GBrowse), both accessible via www.modencode.org. Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. More details and the schedule are at http://wiki.modencode.org/project/index.php/DCC_Usability_webinars

modMine release 27

sergio — Wed, 07 Dec 2011 18:52:14 +0000

modMine release 27

Release 27 of modMine contains all the submissions validated by the end of November 2011 (corresponding to the submission freeze of the 31st of October). Release 27 incorparates 1765 submissions, organised in 72 experiments which in turn are divided in 12 categories.

There are 1224 fly submissions (1201 D. melanogaster) and 541 concern C. elegans.

Fall 2011 modENCODE publications

paul — Thu, 01 Dec 2011 22:16:03 +0000

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.

Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M.
PLoS Computational Biology. 2011 Nov;7(11):

modMine: flexible access to modENCODE data.
Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.
Nucleic Acids Research. 2011 Nov 12

Evidence of abundant stop codon readthrough in Drosophila and other metazoa.
Jungreis I, Lin MF, Spokony R, Chan CS, Negre N, Victorsen A, White KP, Kellis M.
Genome Research. 2011 Nov 2

Synthetic spike-in standards for RNA-seq experiments.
Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B.
Genome Research. 2011 Sep;21(9):1543-51

modENCODE Data Access Webinar Dec 1st 2011

peter — Mon, 07 Nov 2011 21:44:47 +0000

modENCODE project aims to provide the biological research community with a comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D.melanogaster. Data Coordination Center for modENCODE is conducting a series of webinars with the next one, “Understanding worm and fly chromatin modification data” scheduled on Thursday Dec 1, 12:00 EST (Eastern US time). This online webinar will introduce participants to the data obtained in experimental studies of various histone modification marks and chromatin binding proteins, also showing how to visualize and download these data from the modENCODE web site/FTP. Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. More details and the schedule are at http://wiki.modencode.org/project/index.php/DCC_Usability_webinars

modMine release 26

sergio — Fri, 28 Oct 2011 15:39:29 +0000

modMine release 26

Release 26 of modMine contains all the submissions of release 25, with the addition of 3 submissions for the MacAlpine project (D. melanogaster) and 2 for the Snyder one (C. elegans).

Release 26 now contains links to orthologues (human, mouse, rat) for both worm and fly. Lists of submissions present more detailed information on the grouped submissions.

modENCODE Data Access Webinars Resume

peter — Fri, 07 Oct 2011 14:55:25 +0000

modENCODE Data Coordination Center is announcing a new series of 5 webinars
which we are planning to have in 2011/2012 using WebEx teleconference technology.
The first webinar in the series is on Thursday Nov 3, 12:00 EST (Eastern US time)
“Understanding worm and fly transcription factor binding data” (updated).
This online webinar will introduce participants to the data obtained in studies of
transcription factor binding sites in D.melanogaster and C.elegans

and describe how to visualize and download these data from the modENCODE
web site/FTP. Space is limited so advance registration is necessary.

modMine release 25

sergio — Mon, 26 Sep 2011 11:22:36 +0000

modMine release 25

Release 25 of modMine contains all the submissions validated by the end of August 2011. There are 1664 submissions, organised in 69 experiments which in turn are divided in 12 categories.

There are 1185 submissions regarding D. melanogaster, 464 concern C. elegans, and there is also a small number of submssions for other Drosophila species:

D. mojavensis	4
D. pseudoobscura	4
D. simulans	4
D. ananassae	1
D. virilis	1
D. yakuba	1

New in this release.

- Ensembl Compara

The Ensembl Compara data set has been used to get homologues information.

- Easier exploration of other mines

Links to other mines (RatMine, FlyMine, metabolicMine,ZFINMine, YeastMine) are available on reposrt and list report pages and allows exploration of orthologues genes.