An NHGRI grant that funded a collaboration between  InterMine and three of the major Model Organism Databases (MODs) has been renewed and expanded.

The new InterMOD funding is for three years and now includes  MGI (mouse) and  WormBase (worm) who will each set up and host an InterMine instance. These will work alongside the existing InterMine developments at  SGD (yeast),  RGD (rat) and  ZFIN (zebrafish).

A major aim of the new project is to provide stronger links and cross organism querying between the MODs involved.

 TargetMine is an InterMine data warehouse that is now publicly available at the National Institute of Biomedical Innovation (NIBIO), Japan. TargetMine was built to aid prioritisation of candidate genes in drug discovery. Try it out  here.

They have also published a  paper on TargetMine.

YeastMine has now been officially released at SGD, the S. cerevisiae model organism database.

It can be used to query genes, proteins, GO, literature, phenotypes and interactions from the SGD data collection.

Try  YeastMine

InterMine 0.95 is now available. New features include an improved home page layout, better integration of the web service API and template ranking by popularity.

See release notes and upgrade information.

We're running an InterMine workshop in Cambridge on November 15th-16th.

The workshop is split into a one day guide to setting up a new InterMine system (15th) and a half-day workshop on advanced querying with the QueryBuilder and Perl/Java? web service programming (16th).

Registration details are here:

•  InterMine setup
•  Web service

A beta version of  YeastMine is now up at SGD. This is the second InterMine hosted at Model Organism Database,  RatMine was released at RGD late last year.

Also see a  YeastMine video tutorial at OpenHelix. This talks about interoperability between Mines, we have a lot more features to come in this area.

The upcoming InterMine 0.94 release will include a fast, flexible keyword search over the entire database. Check out some details and a demo.

We're hiring a Web Developer/Designer? with great user interface design skills to work on InterMine and our new Wellcome Trust funded metabolicMine project.

For more information see vacancy details?.

The closing date for applications is 13th August 2010.

We've released InterMine 0.93, there is a new subversion branch and tar.gz. We have done a large amount of internal refactoring of code to make the core functionality more robust. In addition there are several bug fixes, validation improvements and a new 'hints' help system.

See the release notes and details on upgrading.

We have four vacancies on InterMine related projects at The University of Cambridge, UK. We are looking for a Web Developer, Bioinformatics Software Developers and a Java Developer.

For more information see vacancy details?.

The closing date for applications is 2nd April 2010.

The Rat Genome Database (RGD) have released an InterMine containing rat genome, protein and SNP data:  http://ratmine.mcw.edu/ratmine. They have also made a  great video which introduces the functionality of RatMine and InterMine in general.

RatMine was built as part of a joint project between InterMine  RGD (rat),  SGD (yeast) and  ZFIN (zebrafish) to deploy an InterMine at each of the model organism database sites and develop new methods of interoperability for cross-organism research.

FlyTF  http://www.flytf.org is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly. They have just released version 2 which now uses InterMine to add flexible querying and analysis of lists to their site.

A paper describing FlyTF has just been published in the  NAR Database Issue.

We've released InterMine 0.92, there is a new subversion branch and tar.gz. The main changes are some improvements to the way integration keys and priorities are configured and validated, a BioPax parser, performance enhancements and some webapp fixes.

See the release notes and details on upgrading.

We will run an InterMine workshop on November 16th - 17th 2009. The training is aimed at software developers who wish to learn how to set up biological databases with the InterMine software. The two day course will step through creating a new Mine, integrating real data and deploying and customising the web application.

The workshop will be held in the Genetics Department in Cambridge and is free to attend.

Sign up here:  http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html

If you have any questions please contact richard@….

We've released InterMine 0.91, there is a new subversion branch and tar.gz. The main changes are fixes to some QueryBuilder features, occasional export issues and improved password security.

See the release notes and details on upgrading.

InterMine is at ISMB in Stockholm. We have a poster (E39) and a live demonstration on Thursday 2nd July at 10.45am in room K2. Hope to see you there!

We have a new public mailing list dev@… for all support, development discussion and suggestions. This replaces the old flymine-dev mailing list.

 Subscribe to dev@intermine.org

A new stable release of InterMine is available. New features include 'outer join' style queries, an update to the QueryBuilder interface, simplified configuration and many performance improvements.

See details on checking out 0.9.

See details on upgrading your existing Mine and source to 0.9.

Gos Micklem recently gave a platform presentation on InterMine at Genome Informatics in Cambridge, UK. The talk was very well received, thanks for all the questions! You can find slides here.

We will be running a two day workshop that will allow participants to build a new InterMine data warehouse with some real data and query it. It will cover Java/Perl? data integration APIs, releasing and configuring the web application, creating new widgets and running queries with the API. The workshop will be held in Cambridge and is free to attend. For more details see  workshop registration.

We gave a live demo of InterMine at the International Symposium for Integrative Bioinformatics (IB08) in Lutherstadt Wittenberg, Germany in August. We were very pleased that the demo ran perfectly and there was lots of interest. Slides and details of other recent talks are available here.

We recently presented InterMine as a live demo in the ISMB technology track and as a platform presentation at BOSC (Bioinformatics Open Source Conference), both in Toronto. We also talked about using InterMine with chado databases at the GMOD community meeting. Slides can be found here. Thanks to everyone who attended and asked lots of questions!

FlyMine release 10.0 is now out, see the  release notes for major changes.

There is a new stable branch of InterMine: branches/flymine_release_10_0_branch.

We have updated and added a lot of documentation, please let us know if there is anything you can't find or if you have suggestions for documents to add. The links on the home page now take you to a contents pages for each section.

Our trac installation is now at  www.intermine.org.