Did you know you can run queries in FlyMine using a web service from Perl/Java code? We have a half day workshop in Cambridge on November 16th that will show you how. More details here:
In Release 25.0 we have updated data from FlyBase to release FB2010_04 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.
- NEW – Stocks from FlyBase
- FIX – Feature type on genes corrected
- FIX – Clones loaded from FlyBase and BDGP merge
- FIX – `query` link in breadcrumbs
- FIX – occasional lag on list analysis page fixed
- FIX – outputting raw HTML for protein structure.alignment fixed
- FIX – removed confusing message on query history page
- would output pathquery object if it was a bad query
- FIX -MicroArrayAssay.name is a dropdown now
- FIX -Removed obsolete Experiment.interactionDetectionMethod from model
- FIX – can use quicksearch with galaxy
- FIX – constraint form on querybuilder works correctly now
In Release 24.0 we have updated data from FlyBase to release FB2010_03 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.
- NEW – Homologues from KEGG
- NEW – added links to RatMine from pathway, GOTerm, protein domain
- UPDATE – QueryBuilder – removed tag filtering from constraint form.
- UPDATE – QueryBuilder – advanced options now open by default
- FIX – Sanger’s datasource name
- FIX – Can now customise the column titles for embedded templates
- UPDATE – Make Bonferroni algorithm less strict, see widgets for more details.
- FIX – Corrected data bug that was duplicating a limited set of interactions.
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.
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.
- NEW – GO annotation for protein domains (from interpro)
- NEW: microRNA widget on list analysis pages, showing enrichment of microRNAs targetting the genes in a list.
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.
Dear FlyMine users,
We regret to announce thatÂ 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 toÂ email@example.com!
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 theÂ 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 sourceÂ 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