Category Archives: Improvements

ISAcreator 1.7.11 now available

Today we announce the release of ISAcreator 1.7.11.

This release updates ISAcreator to work with Java 9.

You can download ISAcreator 1.7.11 from Github here: https://github.com/ISA-tools/ISAcreator/releases/tag/v1.7.11

If you’re an ISAcreator user, or use any of the other ISA-tools suite, please let us know and we can list you as being part of the ISAcommons community.

If you have any questions or any problems with using ISAcreator, please drop the ISA Team an email to isatools@googlegroups.com or to the ISA community forum.

ISAcreator 1.7.10 available now

Today we announce the release of ISAcreator 1.7.10.

Included in this release are several bug fixes primarily relating to Windows 10 file system issues that have been reported by the user community.

Above adapted from original photo by Robert Lee under Attribution-NonCommercial 2.0 Generic (CC BY-NC 2.0).

You can download ISAcreator 1.7.10 from Github here: https://github.com/ISA-tools/ISAcreator/releases/tag/1.7.10

If you’re an ISAcreator user, or use any of the other ISA-tools suite, please let us know and we can list you as being part of the ISAcommons community.

If you have any questions or any problems with using ISAcreator, please drop the ISA Team an email to isatools@googlegroups.com or to the ISA community forum.

Investigation/Study/Assay, Hacks/Coffee/Cakes

In this post, Dr David Johnson gives his reflection on an ISA specification hackathon held in July 2015, in advance of joining the ISA team at Oxford as a research software engineer.

Last week I joined my prospective colleagues at the Oxford University e-Research Centre (OeRC) with some of their collaborators to thresh out an evolution of the ISA (Investigation/Study/Assay) metadata tracking framework. I will be joining the ISA development team at Oxford from September this year, which is a new phase in my career that I am very much looking forward to.

ISA consists of a model specification that describes its key concept elements and structure, while implementations of the specification are also developed by the ISA team. The framework aims to facilitate standards-compliant collection, curation, management and reuse of datasets in the life sciences. The first version of the specification, a Release Candidate from 2008, is implemented as the ISA-Tab (tabular) format – a table-based format that many working in the life sciences are used to, where data is abundantly stored and manipulated in spreadsheets. More recently ISA can also be converted to RDF via linkedISA.

While I have yet to officially join the ISA team (I am currently on a short sabbatical since leaving a research post at Imperial College London) I was invited to attend a 3-day workshop in Oxford to review and make new amendments to the ISA specification towards a version 2.0 release. The workshop, an ELIXIR UK event, was billed as the “ISA as a FAIR research object” Hack-the-Spec event. We were joined by representatives from The Genome Analysis Centre, the European Bioinformatics Institute, Leiden, Manchester and Birmingham universities and even a group visiting from my home-town of Hong Kong, from the GigaScience journal that was launched by Beijing Genomics Institute in 2012. We also were joined online by a number of researchers dialling in via Google hangouts from various sites in Europe.

As a workshop report will come out in due course I won’t get into the detail of the outcomes, but broadly the discussions focused around:

  • Evolving ISA to enable FAIR (Findable, Accessible, Interoperable, Reusable) research objects
  • Fixing ambiguities, missing structures and elements in ISA 1.0
  • Enabling integration of standard identification schemes such as ORCID
  • Redefining the spec to define the ‘core’ ISA elements and separating out domain specific ‘extensions’
  • Specifying conventions, mechanisms, and best practices for developing extensions to this new ‘ISA core’.

What was clear was that there was plenty of scope for evolving ISA from various parts of the user community. By abstracting out the core ISA specification, what we need now is contributions from a diverse range of exemplar projects to ensure that the core is truly interoperable. To this end, we are now encouraging communities to share their ISA templates along with exemplar experiments and start building a repository of extensions in the ISA commons website. In the meantime the ISA team will be formalising the ISA core and developing new reference implementations in tabular and JSON formats and supporting tools. We hope to have a draft specification presented to the community in the fall of 2015.

Apart from the 3 days of discussions fuelled by much coffee and cake, we did also find some time in the evenings to get out to enjoy the sunshine and enjoy a couple of Oxford’s wonderful restaurants…

One of my key takeaways from the workshop, apart from having a crash course into the ISA spec that I will be working on in the coming months, is the importance of going through the community engagement process when developing a data specification. As with engineering software, we need to make sure we are building the right thing. Soliciting feedback is not a vanity exercise or even a political exercise, but an essential part of a carefully-managed process to ensure we evolve the specification to fulfil the changing needs of the people that matter – the user community.

Find out more about ISA here at www.isa-tools.org and about the wider community’s efforts at isacommons.org

Catch up tweets about this ISA 2.0 specification workshop by searching the hashtags #isa_hack and#ElixirNodeUK

ISAcreator available in GenomeSpace

ISAcreator has supported access to GenomeSpace since release 1.7.0. and it is now also available through the GenomeSpace online interface.

GenomeSpace is a framework supporting cloud-based interoperability of genomics analysis tools. By providing access to multiple tools through their interface, and supporting file transfers in the cloud, GenomeSpace provides a bridge among the tools, allowing users    Some of the tools available through GenomeSpace are: Cytoscape, Galaxy, GenePattern, Genomica, Integrative Genomics Viewer (IGV), and the UCSC Genome Table Browser. Find out more about what is GenomeSpace and what GenomeSpace can do for you.

I will now describe the functionality ISAcreator supports for GenomeSpace.

You can launch ISAcreator from your desktop or you can launch it once you are logged in to GenomeSpace (after registering to their service). For launching ISAcreator from within GenomeSpace, just hover over the ISAcreator icon and select ‘Launch’:

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If you launch ISAcreator from GenomeSpace, you will be prompted to download ISAcreator and will see the following pop-up window (after you accept to download the file):

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When running ISAcreator (either from your desktop or following the GenomeSpace route), you will notice that it now has a third mode of operation (apart from the previously available light and normal modes) that corresponds to GenomeSpace. With this third method of operation, ISAcreator supports opening ISA-TAB files stored on the cloud environment provided by GenomeSpace and also, saving files into GenomeSpace storage facilities.

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If you choose the GenomeSpace mode, you will have to enter your GS user credentials in the ISAcreator login page:

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Then you will load the configuration files, as usual, and get to the main menu where you can choose to load an existing ISA-TAB file. If it is not the first time you are loading files, you will see the previously loaded files and also have the option to search GenomeSpace for more files:

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As an example, you can find the publicly available BII-I-1 ISA-TAB dataset in GenomeSpace under Public/agbeltran/ISA-TAB-datasets, and select it to load:

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After loading an ISA-TAB dataset, you can save it to GenomeSpace (even if it is a local dataset that you want to store in GenomeSpace):

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GenomeSpace also provides documentation about ISAcreator in this page and a guide about using ISAcreator in this other page.

As always, send us comments or questions contacting:

  • the ISA team at isatools [at] googlegroups [dot] com, 
  • the ISA user forum at isaforum [at] googlegroups [dot] com

or send us feature requests or bug reports through the issue tracker in Github:

  • https://github.com/ISA-tools/ISAcreator/issues

New developments: publication search UI improvements

I’ve never really liked the Publication locator utilities user interface much, so whilst at BioCurator, in the spare time I had, I redid the interface to make it clearer, faster and more informative to users. The result of the improvements are shown in the screenshots below!

Search by pubmed id – like the last version, only nicer 🙂

 

Publication information is now clearer, and you can easily access a previous search via the last result button in the top panel.

I might make some more improvements to the UI in the next few hours, but for now I think it’s much better than it was!