The current release of modMine is back and under observation after a hardware problem.
There is a hardware problem that is blocking the current release of modMine (32).
We are trying to solve it: in the meantime please use the archived releases (click on ‘History’ button on www.modencode.org).
Apologies for the inconvenience.
modMine release 32
Release 32 of modMine contains all the submissions validated by the 12 of December 2012. There 2385 submissions, organised in 98 experiments which in turn are grouped in 13 categories. There are 1683 fly submissions (1660 D. melanogaster) and 702 worm ones (672 C. elegans).
This release is based on the new InterMine release 1.1 (see release notes).
modMine release 31
Release 31 of modMine contains all the submissions validated by the end of august 2012. This amount to 2342 submissions, organised in 96 experiments which in turn are grouped in 13 categories. There are 1665 fly submissions (1642 D. melanogaster) and 677 worm ones (647 C. elegans).
This release features a new implementation of the result tables, which allows a much more interactive exploration of the data.
modMine release 30
Release 30 of modMine contains all the submissions validated by the end of May 2012. This amount to 2185 submissions, organised in 84 experiments which in turn are grouped in 12 categories.
There are 1494 fly submissions (1471 D. melanogaster) and 691 worm ones (661 C. elegans).
This release corrects the treatment of chromatin states, now available as sequence features, allows direct access to quality control images, and improves the detection of experimental factors.
modMine release 28
Release 28 consists of 1835 submissions, organised in 72 experiments divided in 12 categories.
It features an improved overlapping feature search.
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.
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
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.
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:
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.