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FlyMine 39.0

28 Mar 14 | in News + Release notes by flymine

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.

We have also updated our user documentation and provided better access to our videos:

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

Also, check out the improved pathways displayer on the gene report pages.  Every gene report page includes a chart showing pathways for the gene and for orthologous genes from human and mouse – allowing easy cross-species comparison of pathway data.  For example, see the eyeless gene:

http://www.flymine.org/release-39.0/report.do?id=1058436&trail=|1058436

For a full list of bug fixes see the InterMine documentation (from InterMine 1.3):

https://github.com/intermine/intermine/releases/

The FlyMine Team

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FlyMine 38.0

7 Aug 13 | in News + Release notes by flymine

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

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FlyMine 37.0

9 May 13 | in News + Release notes by flymine

We’ve released an updated version of FlyMine. All of the data sets have been updated, see the “data sources tab for the complete list. We’ve also updated our software with the newest InterMine version (1.2) so there have been lots of bug fixes as well.

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FlyMine 36.0

11 Dec 12 | in Uncategorized by flymine

We’ve released version 36.0 of FlyMine. We’ve fixed a few bugs and updated lots of data sets. Take a look at the “data” tab for more information.

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New video!

10 Dec 12 | in Uncategorized by flymine

Check out our new video giving a quick overview of FlyMine!

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FlyMine 35.0 Released

26 Nov 12 | in News + Release notes by flymine

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.

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FlyMine 34.0

31 Jul 12 | in News + Release notes by flymine

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.

Query Results

We’ve updated the query results in FlyMine. You can now sort your results, filter on any value, add edit or remove columns and much more. See here for the full list.

Widgets

You can now embed FlyMine widgets onto any HTML page. See here for details.

Other

* RNAi screens correctly show up in keyword search results.
* Disease name is now a link so you can click for more information.
* We’ve added links from genes to BioGRID

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Follow InterMine on Twitter!

4 Jun 12 | in News by flymine

InterMine has a new Twitter feed – check it out!

https://twitter.com/#!/intermineorg

Follow it to stay updated on exciting InterMine developments, as well as cool things happening with individual Mines.

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Take SGD with you wherever you go!

17 May 12 | in InterMOD + News by flymine

YeastMine has developed a new iPhone app. See their site for details.

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FlyMine 33.0

29 Feb 12 | in News + Release notes by flymine

Data

New Expression Data

Genome-wide RNA_seq expression data for D. melanogaster have been added.  This data was produced by the modENCODE project (www.modencode.org) and analysed by FlyBase, who calculated a single value for the expression level of each gene at each developmental stage or tissue (see http://flybase.org/reports/FBrf0212041.html for more details).  This data is available on report pages for each gene and can searched through template queries (for example: www.flymine.org/query/template.do?name=Gene_RNA_seq and www.flymine.org/query/template.do?name=RNA_seq_Genes).

Improved RNAi Data

RNAi data for D. melanogaster is now loaded from www.genomernai.org.  This data provides a number of new RNAi experiments and improved phenotype descriptions for both new and existing RNAi experiments.  See the RNAi templates to learn more about this data (for example: www.flymine.org/query/template.do?name=Gene_RNAi&scope=all and www.flymine.org/query/template.do?name=RNAiScreen_genes&scope=all)

Yeast Interactions are back

Due to popular demand, we have put the yeast interaction data back into FlyMine.

Website

List Analysis

  • Your list is automatically mapped to other organisms via orthologs loaded from Ensembl and TreeFam
  • Orthologue and Interactions widgets have been restored (after a user request)

Region Search

  • Extend regions at both sides by entering a value in the new input box
  • Download links are icons
  • Added the option to download chromosome sequence

Export

  • GFF3 export correctly storing parents’ relationship
  • “Hidden” export menu now direct links on results tables
  • FIX – Export works correctly when all columns of an outer join are removed
  • FIX – Missing attributes restored in fasta format

List Upload

  • Specific object types can have a different example list on Bag Upload page, eg. protein accessions displayed if a user selected proteins, gene identifiers displayed if a user selected gene.
  • Go back in history to the filled in form, preserves the input values.
  • “Match on case” – checkbox added to list upload form to toggle case sensitivity

Report page

  • Delay fixed – caching intelligently now
  • Templates displayed in summary also displayed in “Other” category
  • Displayers show nice “No Results” message if data fails to load
  • Displayers by default loaded through AJAX to speed up page loading. Can be set to display immediately without waiting for the DOM to render.
  • Left aligned displayers to make more readable
  • FIX – counts in overlapping features displayer are now correct
  • Protein sequence – added a new displayer
  • Protein Structure ATM: turned into a popup window
  • FIX – links to Reactome correct now

QueryBuilder

  • Add toggle to show/hide empty fields in the QueryBuilder tree
  • Added a button to save/update then run template
  • FIX – if a user clicks [SHOW] in the query builder twice really fast, the field only gets added once
  • FIX – displaying messages too late when the constaint logic is edited
  • FIX – can now build templates with Chrome
  • FIX – deleting a query from query history doesn’t forward user to my mine
  • FIX – prevented name of last saved query becoming the default name in the text box

Query results

  • The values the user selected on the template form are displayed on the results page
  • Updated results table with an exact count of results when available

Template form

  • Show OR logic when appropriate
  • Fixed hyphen breaking on auto-complete in template search on template list page

MyMine

  • Timestamps are now client specific and handle timezones correctly
  • Prompt users if they want to delete a list that’s being used by a query
  • Login/create account page improvements
  • Cookie saved remembering the list order preference(s).
  • Show the new size of a list after upgrade.
  • MyMine table sorting correctly
  • Renaming lists now works as expected

Other

  • FIX – Importing templates with ONE OF constraints works correctly
  • FIX – 4 year old bug which prevented LOOKUP constraints for non-bioentities from working correctly with wildcards
  • FIX – If you remove columns when exporting number of rows returned is not changed

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