Release 23.0

In Release 23.0 we have updated data from FlyBase to release FB2010_02 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.

  • NEW – links to Reactome’s skypainter
  • UPDATED – dataset names, links updated
  • FIX – fixed bug preventing querying genes with a list of affy probes
  • FIX – fixed list links to FlyBase, FlyExpress and ModMine
  • FIX – widget rounding error
  • FIX – several performance improvements to querying and list analysis pages.
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Release 22.0

In Release 22.0 we have updated data from FlyBase to release FB2009_10 and updated several data sets to their most recent versions.  In addition we have added GO annotation for protein domains from InterPro and a microRNA widget to list analysis pages which shows enrichment of microRNAs targetting the genes in a list.  Please see the data section of FlyMine for more details.

Data

  • NEW – GO annotation for protein domains (from interpro)

WebApp

  • NEW:  microRNA widget on list analysis pages, showing enrichment of microRNAs targetting the genes in a list.

FlyMine Funding

Good News – FlyMine is now funded by the NHGRI and so will continue to be updated and developed until at least 2011.  Please continue to give us your ideas and feedback.

Future of FlyMine

Dear FlyMine users,
We regret to announce that FlyMine will only be updated until December 2008/ January 2009. After that the final version will be kept live for as many years as it is still significantly used. Condolences would be appreciated and can be sent to support@flymine.org!
There are a couple of reasons for this change. Currently there is a great opportunity to develop a medically-focussed database using the InterMine system developed during the FlyMine project: we plan to generate a resource valuable to the broader biomedical research community and for which there will be little overlap with other resources worldwide. In addition, our most recent funding reviewers expressed concern at perceived overlap with FlyBase, leading us to re-evaluate where we could most effectively contribute.
Fortunately, FlyBase is keen to cover the loss of functionality provided to the Drosophila community either by adopting InterMine or by developing similar functionality themselves. In order to assess priorities for users we will be carrying out a survey jointly with FlyBase and encourage you to take part.
Drosophila data will still be available through the InterMine platform as part of the modENCODE project. In addition, the NIH is reviewing an application to incorporate InterMine functionality as part of the yeast (SGD), rat (RGD) and zebrafish (ZFIN) model organism databases.
During the FlyMine project our group developed the open source InterMine system, which is software used to create data warehouses with a flexible web interface. InterMine reduces the effort needed to build and maintain both small and large-scale data warehouses, while providing flexible querying, powerful operations on lists and integrated analysis tools.
InterMine has become a successful project in its own right and is being adopted by a growing number of groups for their own database projects. It has made real progress in enabling the creation of integrated databases and providing biologists with advanced functionality, and we will continue its development. We thank all users of FlyMine for contributing to this success by providing feedback and suggestions.
The FlyMine/ InterMine Team

FlyMine workshop

We are running a half day workshop on using FlyMine in Cambridge UK on June 20th. This is part of a joint workshop with FlyBase, half a day will be devoted to each. The workshop is free of charge, for more information and to sign up see here.