Updates from January, 2012 Toggle Comment Threads | Keyboard Shortcuts

  • Eamonn Maguire 8:02 pm on January 27, 2012 Permalink | Reply  

    Toward interoperable bioscience data published in Nature Genetics 

    Our commentary, named “Toward interoperable bioscience data” has just been released in Nature Genetics. In it, we focus on working towards an ISA commons, where one day we’ll all be able to share our experimental metadata in one common, easy to use format, supporting minimal information checklists and ontologies (via the ISA-Tab format and respective tools).

    The editor speaks about the paper, paraphrased here:

    “Reformatting data is a full-time job for many researchers, even before the minimum reporting guidelines, terminologies and formats of each field are taken into consideration. In this issue, we present a Commentary and a Perspective suggesting solutions to these problems that have been developed by a process of community consultation and open review to which the journal was a party. In the Commentary, Susanna-Assunta Sansone and colleagues identify one central problem, namely that “most repositories are designed for specific assay types, necessitating the fragmentation of complex datasets,” and they offer a unified view of the metadata formatting that will be needed to ensure that biomedical research datasets become interoperable. This solution is the overarching ISA framework, where the acronym stands for ‘Investigation’ (the project context), ‘Study’ (a unit of research) and ‘Assay’ (analytical measurement) (p 121). This proposal shifts the sets of reporting standards agreed upon by each community into the infrastructure and formatting of the data files themselves. Sansone and colleagues also list a set of participant communities that can pioneer the approach and teach by example.”

    Many thanks to all who contributed to the paper and to the growing success of ISA (commons and tools).

  • Eamonn Maguire 8:48 am on January 21, 2012 Permalink | Reply
    Tags: , Isa, job, recruitment   

    We are hiring a software developer 

    We are hiring! Details are below:

    University of Oxford, UK
    Software Engineer (3 year fixed term) start date April 2012, or asap

    Complete applications must be received by 12 noon on 15th February 2012
    Interviews will held between 22nd and 28th February.

    Salary: £29,099 – £35,788pa (grade 7)
    Location: Oxford e-Research Centre, 7 Keble Road, Oxford, UK
    Projects: http://www.isa-tools.org and http://www.biosharing.org
    Other entitlements: 38 days’ annual leave including public holidays and Christmas closure
    Membership of the University’s Pension Scheme

    We are seeking an enthusiastic, experienced Software Developer to engage in software development and to contribute to successful projects on standards and data sharing infrastructure for management, curation and sharing of bio-investigations.

    The following criteria are considered essential to the post:
    • degree in a relevant field, such as computer science or bioinformatics, ideally with some background knowledge in biology
    • proven professional experience and profound knowledge of Java
    • ability to work efficiently as part of a distributed development team
    • experience in the design and/or implementation of distributed software
    • willingness to work as part of a team and demonstrated flexibility to respond to emerging needs
    The following criteria are considered to be desirable though not essential
    • Oracle, MySQL, JBoss, JBoss Seam, Lucene, AJAX, JAXB, XML schema, RDF, SPARQL, Java Script, PHP, Python
    • experience of development for and testing on Windows, Mac OS X and Linux operating systems
    • understanding of software development lifecycle and agile development methodologies
    • ability to perform user requirements analysis

    More details and link to application form at: https://www.recruit.ox.ac.uk and enter Vacancy ID: 101935

  • Eamonn Maguire 10:18 am on January 11, 2012 Permalink | Reply  

    ISA tools code dashboard 

    We’ve just added a code dashboard to the website so that you easily see the commit activity across all projects (most active projects are at the top and change dynamically). The page is powered by Gitview (http://gitview.logicalcognition.com/).

    ISAcreator dashboard page

    We hope to add extra information to each box about current build status (retrieved from our TeamCity continuous build management system), latest releases and issues currently being reviewed discussed at any point in time.

    Please let me know if you experience any rendering problems in your browser.

    • Geordie Pele 8:44 pm on January 11, 2012 Permalink | Reply

      Deein canny son

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