Tagged: BioSharing Toggle Comment Threads | Keyboard Shortcuts

  • Eamonn Maguire 6:06 pm on November 14, 2013 Permalink | Reply
    Tags: BioSharing, Open data, ORCID   

    BioSharing Profiles automatically assign data with publications 


    A while ago, we went along to the ORCID codefest at St. Anne’s College, Oxford.

    In the day or two of coding, Alejandra won with her entry in adding ORCID functionalities to ISAcreator.

    In my entry, I created a system that presented article impact metrics from ImpactStory and also automatically pulled ArrayExpress and PRIDE data links for  publications. The advantages being that users don’t have to go looking for the data for a publication across many repositories. Take this example from ArrayExpress, E-GEOD-31453 – from the submission, you’d never know that there were other data submissions directly related to this submission in ArrayExpress or elsewhere, e.g. E-GEOD-27713. The component developed for BioSharing, but could be used by anyone takes a PubMed ID or DOI and finds the data available in public repositories relating to that publication. It’s use is illustrated in one of the profiles for one of our latest BioSharing users, Sheng-Da Hsu. You can see a screenshot of his publications section below, or see it for yourself here.


    Screen Shot 2013-11-14 at 17.41.11

  • Eamonn Maguire 8:48 am on January 21, 2012 Permalink | Reply
    Tags: BioSharing, 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 11:07 am on September 8, 2011 Permalink | Reply
    Tags: BioSharing, Caching, Varnish   

    We just added the Varnish cache (https://www.varnish-cache.org/) to our apache web server for BioSharing (http://www.biosharing.org). Will be interesting to see how it performs. Wikipedia and the BBC are using it, so it must be pretty damn good!

Compose new post
Next post/Next comment
Previous post/Previous comment
Show/Hide comments
Go to top
Go to login
Show/Hide help
shift + esc
%d bloggers like this: