modENCODE Blog

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.

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.

modMine release 24

Release 24 of modMine contains all the submissions validated by the end of June 2011. There are 1504 submissions, organised in 61 experiments which in turn are divided in 12 categories.

New in this release.

- A new way of managing users’ lists when transferring them from one release to the next one. The new system makes transparent to the user any update made necessary by the changes on elements of the list in the model organism databases (FlyBase or WormBase).

Usually there will be no changes and no action will need to be taken.  However, if a user’s list needs upgrading, these simple steps need to be followed:

• log in
• go to the “My Mine” section of modMine
• check the status of your lists by visiting the “Lists” page (http://intermine.modencode.org/query/mymine.do).
• Click on the “Upgrade” links that you find in the last column of the table and resolve duplications and conflicts.

The new system allows also a much shorter downtime of modMine when the release is changed.

- Sequence features can be exported as a file or sent to Galaxy in UCSC BED format

- Data labels and column names are configurable now and not tied to the database field names.