Changes between Version 1 and Version 2 of MolgenisProgress2010_1


Ignore:
Timestamp:
2010-09-30T21:16:29+02:00 (14 years ago)
Author:
Morris Swertz
Comment:

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  • MolgenisProgress2010_1

    v1 v2  
    99* MOLGENIS used for noricdb.org ([http://www.ncbi.nlm.nih.gov/pubmed/20664631 Leu et al, Eur J Hum Genetics]) published
    1010
    11 * MOLGENIS used for multiple GEN2PHEN data model pilots (EBI, FIMM, U Leic, shared programmers), paper in draft
     11* MOLGENIS used for multiple GEN2PHEN data model pilots (EBI, FIMM, U Leic, U Groningen/FWN, shared programmers), paper in draft
    1212
    1313* MOLGENIS used for a locus specific database (UMCG), paper in draft
    … …  
    2323== Progress ==
    2424
    25 Find the complete list of progress at http://www.molgenis.org/wiki/ChangeLog + filter
     25Find the complete list of progress at http://www.molgenis.org/timeline
    2626
    2727* Batch upload by name:
    … …  
    6262* Added automated testing suite
    6363Each MOLGENIs now autogenerates an extensive testing suite that is subsequently tested using a permution of values based on the current data model. Both CSV import/export as database add/update/find/remove are extensively tested. This has greatly improved the quality of each MOLGENIS.
    64 After each import these tests are now automatically run on the http://www.molgenis.org/apps/hudson server. Status: released.
     64After each import these tests are now automatically run on the http://gbic.target.rug.nl:8080/hudson/ server. Status: released.
    6565
    6666* Running: authorization and authentication
    … …  
    7070MOLGENIS users can now add jobs to a job manager to be submitted to a PBS compatible cluster. Typical use case is to run R scripts. These R scripts then use the MOLGENIS R/API to read raw data and write back results. A simple meta model has been added to design input/output parameters do that the scripts can be parameterized via the MOLGENIS user interface. This work has been piloted in the XGAP system. Also a parser was made to enable tool model exchange with Galaxy servers; this is however not yet fully functional and will be continuted as planned for the coming 6 months. Status: under development.
    7171
    72 * Running: Index and ontology enhanced search
     72* (Sponsored by NBIC/Biobanking platform) Running: Index and ontology enhanced search
    7373Together with the NBIC/biobank programmers we invested in search (driven by biobank use cases). We have piloted a Lucene indexing method to enable 'google' like searches on whole MOLGENIS instances. Next we devoted effort in the development of OntoCAT (ontocat.org) the open source toolbox that enables simple and uniform access to diverse ontological sources. Currently we are in the process of incorporating this tool to enable semantic query expansion, using ontological relationships to rewrite users query such that more revelent information is found. This project will be further developed in the next 6 months so it can be publically released. Status: under development.
    7474