FlyMine 26.0

We are pleased to announce the release of FlyMine 26.0.  We have added a host of new features, improvements and bug fixes to make your research easier and more productive.  In Release 26.0 we have updated data from FlyBase to release FB2010_08 and updated several data sets to their most recent versions.  Please see the data section of FlyMine for more details.

New, More Powerful Keyword Search

Our simple search has been improved using Lucene to provide comprehensive faceted results over all FlyMine data. It is now faster, more intuitive, and returns more informative results, with the ability to divide the search results into their data categories. This allows you to quickly zoom in on what you are looking for even when you are starting from just a few letters.

Redesigned Homepage

FlyMine’s homepage has been reworked to get you to the data you need faster and more easily.  You can now upload a list of identifiers directly from the homepage, and we’ve separated queries into their different data categories to make it easier to find the query you need.  Template queries are listed in order popularity so the most useful template queries are listed first.

Data Model Update

We’ve done a major overhaul on the FlyMine data model.  The Sequence Ontology, which underpins our data model, has been updated to version 2.4.2.  We’ve removed unused data types and renamed others for easier querying.  Please see here for the entire list of changes.

Exporting Results – Faster and to More Places

Back-end optimisations mean that you can get your results much faster when exporting a set of results to various file formats. Specifically, we now cache your query better, so that we don’t have to repeat it to do the export step.

An addition to our export options is Galaxy, a collection of data analysis tools in the cloud. You can now tie up the huge data stores of FlyMine with Galaxy’s flexible data-processing tools to really make your research easier.

Queries and Templates

We have overhauled the XML format we use, to provide one that is much easier to read – we are still keeping backwards compatibility with pre-0.94 version XML, so if you have any queries floating about in XML, they will still work, see XMLFormatChanges0.94.

We have also added a new constraint type to the searches you can make, called “MultiValue” constraints.  These let you choose, as the name suggests, more than one value for a match, using the operators “ONE OF/NONE OF”.  Subclass constraints (an advanced constraint feature that allows very fine-grained searching) are now much simpler to add.

Templates have seen some major new features too, the most prominent of which is the “optional” constraints, which allow you to build and use more flexible, templates. The template form now has a new, clearer layout.  More customisable too: You can also specify the order constraints are presented to the user of your template simply by dragging and dropping.

Building queries has seen improvements too. Reverse references are now made more obvious to the user, and you will no longer get lost in an endless loop of self-referencing objects, as the links back to identical objects have been disabled. Subclasses are now hopefully much easier to discover and constrain by using the graphical interface, allowing you the precision and control you need to build sophisticated queries. We have also made various changes to the layout and design of this feature focussed on making the process of building a query easier and more intuitive, such as a simple “remove all” button, when you would just like to start over. Like may features of the site,  there is more customisation here too, with custom column headers meaning you can get the data named the way you want.

Gene and Protein Interactions Visualised

We have a new gene visual analysis tool – Cytoscape Web – which allows network analysis of interaction between genes and proteins on their report pages. This uses flash to provide a simple but compelling look at a complex area. The report pages have seen general performance increases, meaning faster more responsive page views.

Web Services API – Automate your queries

Access to our web-services is now even easier. We have a new section of our site dedicated to helping you get started with the query API. Using the API means you can automate repetitive queries and data processing steps, and quickly gather and analyse massive amounts of data. Use of the API does require a little programming knowledge, in either Java or Perl, so we have provided examples for every query you build or run on the site – clicking the links to ‘Perl’ or ‘Java’ source code will provide you with source code you can run now to get the results you want.

Perl Web Service Client – Simpler but More Powerful

Our Perl client modules have been rewritten to provide a simpler interface for you. They are also much easier to download and install, and they have several powerful new features.

The ease of download is thanks to the CPAN, which means you can download, test and install in one simple command, and have your dependencies managed to boot. The new distribution (Webservice::InterMine) also has a set of tutorial how-to‘s that guide you through writing and executing webservice queries.

Boilerplate has been stripped away, meaning you only need to write code that actually does something. Writing a real, functioning query can be done in as little as four or five lines!

The new features that we hope you will make use of include:

  • Access to the template service,  so you can query your favourite templates automatically.
  • Automatic parsing of results into Perl data structures, so you don’t have to. No more splits and regexes when you can use array indices and hash keys. This means you can not just get the results, but more easily do something with them.
  • You can extend the webservice client dynamically, using Roles to provide new functionality and behaviour on a first-class basis.
  • The ability to handle the sub-class and multi-value constraints, means you can write more complex, more powerful queries.

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I make software & yarn things. Heart open*, scifi, cycling, running, veggies. 🇳🇿🇮🇱🇬🇧🇪🇺🏳️‍🌈. @yoyehudi on Twitter, but also @codeisscience & @intermineorg. @softwaresaved Fellow 2018.