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  • Eamonn Maguire 5:22 pm on August 18, 2011 Permalink | Reply
    Tags: Autocomplete, , , ISAtab, , Swing   

    ISAcreator 1.5 in beta testing phase 

    So here’s what’s been added:
    1) ISAvalidator integrated (hence larger file size ~34mb). Access it from the utilities menu item;

    ISAcreator is calling the ISAvalidator component directly now as well as using the standard validation within ISAcreator itself.

    2) New add assay functionality;

    The old subform has been replaced with a new view of the Assays.

    When you click on Create assay, you are now presented with a new component to help you select which assay(s) you wish to add.

    3) New integration with the study sample sheet to look up sample names in autocomplete mode (featuring a new component to build on top of the Java Swing infrastructure to provide better, more customisable autocomplete). Also, if you have factors in your study sample spreadsheet, attached to the sample, these will be propagated automatically to the assay spreadsheet;

    Autocomplete on study samples.

    4) Same autocomplete component is used in protocol ref columns now to look up the protocol name without the clunky widget that was there before.

    Autocomplete on Protocols.

    If you want to test it (please let us know if you have any problems by reporting them in our issue tracker, please download it here!

  • Eamonn Maguire 7:54 pm on July 6, 2011 Permalink | Reply
    Tags: BII, BioInvestigation Index, European Bioinformatics Institute, , ISA infrastructure, ISAtab, , SCDE, Stem Cell Discovery   

    Big improvements to the BII web application (version 1.4) 

    Performance improvements

    A few weeks ago, we started loading the InnoMed datasets in the EBI instance of the BioInvestigation Index and we started to notice performance problems, especially when accessing the detailed study pages (it was taking almost 70 seconds it to render the pages). We found two problems: the growing number of annotations in the database (1.6 million) were increasing the query space considerably; and 2) the inefficiencies present in Hibernate queries resulted in larger scope queries than we really wanted .

    So, we improved the Lucene index which was generated from the loader and already consumed by the web application to generate the browse view and made it capable of holding all of the assays, factors, characteristics, publications, contacts & their respective content so that we would remove the inefficient queries necessary to generate the study page and therefore make things quicker. Now, everything is quicker and there is no real latency in the page load process. Plus, we’ve also adding server-side caching to further reduce lag. So now, pages such as this one http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-8 load almost instantly, compared to the 90 seconds it took beforehand (obviously completely unacceptable).

    Interface improvements

    If you visit the EBI or Harvard Stem Cell Discovery Engine instances of the BII, you’ll immediately see the improvements to the web application look and feel. We’ve made considerable improvements to clean up the interface and make browsing the content much easier.

    The browse study view

    Log in/register view

    Detail information view

    We still have some plans to even further enhance the web application, so watch this space for version 1.5! You can download version 1.4 from here…you’ll need maven 2.2.1 and JBoss 5 installed first though! There are instructions on our GitHub pages about how to build!

  • Eamonn Maguire 6:03 pm on July 6, 2011 Permalink | Reply
    Tags: Annotator, Bioportal. ISAcreator, ISAtab, , NCBO,   

    In ISAcreator 1.4 we have made a very… 

    In ISAcreator 1.4, we have made a very significant release, improving many aspects of the codebase, solving many of the problems encountered in previous releases, adding new functionality and further improving the user interface. We won’t go into everything here, but will list the major changes:

    Better performance: We’ve tweaked the code, refactored and improved performance and memory load drastically.

    Light mode and advanced mode. Now you can run the creator without the added complication of the wizard or mapper functionalities. If you need them, they are there, but if you don’t then just use the light version.

    New error display: remember the ugly list of errors you had when the ISAtab wasn’t valid? Well, that’s gone, here’s what the new version looks like.

    New ontology lookup interface and the ability to browse within restricted ontologies (e.g. a Label should come from ChEBI) either on the entire ontology level (if no branch of the ontology is specified) or on a specific branch so that the users selections are more targeted.

    Automated annotation of your free text with ontology terms using the NCBO Annotator service.

    You can download it for Mac, Linux and Windows.

  • Eamonn Maguire 4:13 pm on July 6, 2011 Permalink | Reply
    Tags: Bioportal, Configuration, Integration, ISAtab,   

    Mass improvements to the ISA Configurator version 1.3 

    We’ve been working a lot to improve the code base and the usability of our tools! If you start using the ISAconfigurator, you will notice many improvements, not just those listed in this post in terms of reliability, performance and overall look and feel. The new version of the ISAconfigurator is now available for Mac, Linux & Windows.

    New interface

    New menu screen for the configurator.

    Cleaner editing view.

    New Ontology Configuration UI & Performance Improvements

    We have long been providing an easy way to browse across OLS and BioPortal resources, and with our novel configuration tool we are also able to restrict ontology browsing in certain fields to remove burden from the user. Our previous versions weren’t so intuitive to use, so we’ve overhauled the interface to make it easier to restrict ontologies in various fields.

    The configuration interface.

    The cool thing is that the majority of the code used to develop this interface is called as a library from the ISAcreator codebase, so there’s no reason why other Java developers can’t make use of the ISAcreator components in their tools as well!

  • Eamonn Maguire 2:22 pm on June 8, 2011 Permalink | Reply
    Tags: , ISAtab, MAGE to ISAconverter, MAGE-TAB   

    The MAGE to ISA converter takes an ArrayExpress… 

    The MAGE to ISA converter takes an ArrayExpress accession and converts it’s associated MAGE-TAB file to ISAtab.

    Enter a valid ArrayExpress accession, e.g. E-BUGS-65 to get it’s ISAtab counterpart.

    In doing this conversion, this code also cleans up the MAGE-TAB to remove redundant columns, normalise the data structures (split SDRF into a study sample file and assay file) and infer the technologies used in an


    Please test it out and let us know which experiments do not convert for you by emailing us at isatools@googlegroups.com

    This is a beta version. Sometimes the conversion will not work as expected since the files served from ArrayExpress may contain some errors. We can detect and clean most of these errors, but for inference of information such as the measurement being observed and the technology used, it can be very difficult since the MAGE-TAB files may have inconsistent annotations or don’t specify the measurement being performed at all.

    • qwerty 7:23 am on June 9, 2011 Permalink | Reply

      lolled at the accession

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