Updates from July, 2011 Toggle Comment Threads | Keyboard Shortcuts

  • Eamonn Maguire 5:53 pm on July 28, 2011 Permalink | Reply  

    ISAcreator 1.4.1 release 

    In response to the discovery of a bug when creating a new study in ISAcreator 1.4, we’ve released a minor version 1.4.1 to address this issue! Sorry for any inconvenience caused! The error slipped our glare after changing the ISA overview tree slightly before release of version 1.4.

    You can download the new versions from our tools page!

  • Eamonn Maguire 5:45 pm on July 28, 2011 Permalink | Reply  

    Akka – very cool for distributed, concurrent systems in Java 

    Sub-paragraphing from their website.

    Akka is the platform for the next generation event-driven, scalable and fault-tolerant architectures on the JVM

    We believe that writing correct concurrent, fault-tolerant and scalable applications is too hard. Most of the time it’s because we are using the wrong tools and the wrong level of abstraction.

    Akka is here to change that…

    It has a Java and Scala API.

    Thanks to Matthew Pocock for bringing it to my attention!

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

    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!

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