Category: Flymine

New FlyMine build: FlyMine 49, now with added JBrowse!

FlyMine has been updated to the latest version of FlyBase. All other data sets have also been updated to the newest versions, we have fixed a few bugs and made the JBrowse displayer available again. See the data sources page for a full list of the current datasets and their versions.

All data can be accessed through our comprehensive library of template searches or by building your own queries using the query builder.

If you have any questions, please see our docs and do not hesitate
to contact us should you require any further assistance. For help and
feedback please email support@intermine.org or visit our contact page.

[Post originally drafted by Sergio Contrino]

FlyMine 43.0

FlyMine has been updated to the latest version of FlyBase. All other data sets have also been updated to the newest versions and we have fixed a few bugs. See the data sources page for a full list of data and their versions. All data can be accessed through our comprehensive library of template searches or by building your own queries using the query builder.

If you have any questions, please see our docs and videos. Please do not hesitate to contact us should you require any further assistance. For all types of help and feedback email support@flymine.org

New Blog!

We’ve decided to streamline our blogging experience a little bit. Rather than maintaining several separate but mostly similar blogs for HumanMine, FlyMine, and InterMine, this blog will act as a combined stream.

Don’t worry – this doesn’t mean you’ll be forced to view irrelevant updates if you’re only interested in one of the sub categories. WordPress is great about filtering via tag or category. Here are a few quick links:

InterMine-specific updates: https://intermineorg.wordpress.com/category/intermine/

FlyMine-specific updates: https://intermineorg.wordpress.com/category/flymine/

HumanMine-specific updates: https://intermineorg.wordpress.com/category/humanmine/ (It’s empty now, but coming soon!)

FlyMine 41.0

We are pleased to announce that FlyMine has been updated to release 6 of the BDGP sequence assembly and all annotations are now mapped to this sequence version. See FlyBase (http://flybase.org/static_pages/feature/previous/articles/2014_07/FB2014_04.html) for full details of the sequence changes.

All other data sets have also been updated to the newest versions and we have fixed a few bugs.  See the data sources page (link below) for a full list of data and their versions. All data can be accessed through our comprehensive library of template searches or by building your own queries using the query builder.

Also, check out the new interactions network displayer, esyN, now available on gene report and list analysis pages. Editing the network within esyN allows further analysis and exploration of the network, including expansion from any selected node. For an example see:

http://www.flymine.org/flymine/report.do?id=453007817&trail=|453007817

and navigate to Interactions.

Full documentation for FlyMine is available at:

User docs: http://flymine.readthedocs.org
Videos: http://flymine.readthedocs.org/en/latest/videos/Documentationvideos.html

For a full list of data sources see http://www.flymine.org/flymine/dataCategories.do

However, please do not hesitate to contact us should you require any further assistance.

For all types of help and feedback email support@flymine.org

FlyMine 40.0

We are pleased to announce a new release of FlyMine.  We’ve updated all of our data sets to the newest versions and fixed a few bugs.  See the data sources page (link below) for a full list of data and their versions.  All data can be accessed through our comprehensive library of template searches or by building your own queries using the query builder.

Please also take a look at our updated user documentation and videos – here you can also find a cookbook with some more advanced queries explained:

User docs:  http://flymine.readthedocs.org

Videos:  http://flymine.readthedocs.org/en/latest/videos/Documentationvideos.html

However, please do not hesitate to contact us should your require any further assistance.

 

For a list of all changes see http://blog.flymine.org

For a full list of data sources see http://www.flymine.org/release-40.0/dataCategories.do

For all types of help and feedback email support@flymine.org

FlyMine 38.0

We’re pleased to announce a new release of FlyMine! We’ve updated all of our data sets to the newest versions and fixed a few bugs. See the data sources page for a full list of data and their versions. In particular, we have updated the genome annotations from FlyBase to the latest version (FB2013_04) and data from GenomeRNAi version 11.0 is now available. All data can be accessed through our comprehensive library of template searches. For example, find RNAi data for your favourite gene using the template search:

http://www.flymine.org/release-38.0/template.do?name=Gene_RNAi

Also, don’t forget about our other recent changes, for example sharing lists and custom background distributions on analysis widgets:

You can share your lists with your colleagues and collaborators.  Simply add your colleagues email address to your list in ‘MyMine’.  They will be sent an email asking if they would like to accept the list.  Note that the list is still controlled by you – they can just see a copy so only you can modify it.  They can of course create a copy of the list, which will then be theirs to modify. 

You can specify your own background distribution for the enrichment widgets on the list analysis pages.  You need to have your preferred distribution saved as a list.  Each widget then has the option to select the list you wish to use.  If you are logged in you can save this as your default preference.

Please let us know if you would like more information on these or any of our other features.

The FlyMine Team

FlyMine 35.0 Released

We’re happy to announce a new release of FlyMine.  We’ve updated all of our data sets to the newest versions and added lots of exciting features. See the data sources page for a full list of data sources and their versions.

Interactions

We have changed the way we model interactions to make the results of your searches easier for you to understand and analyse.  All the interaction template searches have been updated to use the new model.  In addition, we previously modeled interactions as a ‘matrix expansion’ – which means all possible interactions within a complex would be shown.  We have changed this so that only bait-prey interactions are shown (called a spoke-expansion).  However you can still infer all the possible interactions using the ‘all interactors’ field.  Please email us if you would like more information concerning this.

Sharing Lists

You can now share your lists with your colleagues and collaborators.  Simply add your colleagues email address to your list in ‘MyMine’.  They will be sent an email asking if they would like to accept the list.  Note that the list is still controlled by you – they can just see a copy so only you can modify it.  They can of course, create a copy of the list which will then be theirs to modify.  Again, please email us if you would like more information on this feature.

Background Distribution on Analysis Widgets

You can now specify your own background distribution for the enrichment widgets on the list analysis pages.  You need to have your preferred distribution saved as a list.  Each widget then has the option to select the list you wish to use.  If you are logged in you can save this as your default preference.

Please email us: support@flymine.org for any help on these new features.