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 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.

modMine release 22

Release 22 of modMine contains 1220 submissions, organised in 57 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:

• Network displayer for the Worm Regulatory Network, where you explore the network and access reports on all the genes involved. The network displayer enliven the graph of Figure 3 in the paper “Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. (2010) Science 330: 1775-1787. [DOI:10.1126/science.1196914]“
• Now features of the type ‘binding site’ are associated to their source file, i.e. the submitted file containing the given feature. When in a submission this type of features derive form more than a single data file, they are displayed also in the summaries.

modMine release 21

Release 21 of modMine contains the same data of release 20, with the addition of the data concerning the hierarchical view of the Drosophila Regulatory Network (see “Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE”, 2010, Science 330: 1787-1797).

New in this release:

• Network displayer for the Drosophila Regulatory Network, where you explore the network and access reports on all the genes involved.
• An improved front page.