modENCODE Blog

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.

The mailing list announce@modencode.org will receive notification of any new posting to the modENCODE blog.

If you wish to subscribe (or unsubscribe) please go to the page

http://mailman.modencode.org/mailman/listinfo/announce

and follow the instructions.

The new modmine release 23.1 presents a new displayer for the expression heatmaps. The new displayer uses canvasXpress to perform clustering operations on the data.

The new release is built on the same data of release 23.

modMine release 23

Release 23 of modMine contains all the submissions validated by the end of April 2011. There are 1451 submissions, organised in 61 experiments which in turn are divided in 14 categories. The break down of the number of submissions in term of organism is the following:

New in this release:

• All the worm data has been updated to genomic version 220
• New display for the content pages, allowing a more compact overview of the data available

Past releases of modMine are temporarily unavailable because of works in the computer room. They should be back on line by 26 May 2011.

Please help us make the datasets distributed by the modENCODE project more useful to you:
take the modENCODE community survey!