[gensc-biodiversity-wg] [Gensc-developers] GSC 14 hackathon Sept 20-21

Philippe proccaserra at gmail.com
Mon Mar 19 15:06:57 UTC 2012 

Well, I am trying to connect the threads of several discussions  :)

P


On 19/03/2012 15:00, Dawn Field wrote:
> are you suggesting a term/ontologies 'centre of gravity' at the
> hackathon? this would be brilliant!
>
>
>
> On Mon, Mar 19, 2012 at 2:58 PM, Philippe<proccaserra at gmail.com>  wrote:
>> Hi Wim, Dawn,
>>
>> Thanks for circulating the minutes. The one thing I noticed in the note is
>> the creation of a CV.
>> Is there a google spreadsheet where things are discussed and where it is
>> possible to contribute?
>> As GSC relies on ENVO, I was wondering if any decision had been made as to
>> which ontological framework that CV could be anchored and where this could
>> be discussed ?
>> There are several reasons why this could matter.
>> 1/ the interplay with existing OBO Foundry resources (I mentioned ENVO) but
>> since Mimarks mentions OBI, it points to several contact points and
>> potential synergies
>> 2/ owing to the growing interest in RDF/OWL, again it seems to be important
>> to look at the amount of work that has been done in OBI (library
>> preparation, nucleic acid extraction, assay, paired end sequencing.....). It
>> seems that a lot of time could be saved and again community cross talk
>> enabled.
>>
>> The key points here are the following:
>> 1. OBI allows the creation of Views:
>> There is tooling available to extract just the classes you need from OBI to
>> serve your needs. So no need to be spooked by the size of OBI.
>> 2. Template creation of metadata loading and creation of defined classes.
>> Again, this can save a lot of time as spreadsheet based tools exist to
>> augment OBI with GSC specific classes while ensuring that enough information
>> about each new class is supplied (typically, a definition, a example of
>> usage, a source for the definition, synonyms and so forth).
>>
>> I would urge looking into all these elements
>>
>> All the best
>>
>> Philippe
>>
>>
>>
>> On 19/03/2012 14:46, Dawn Field wrote:
>>> A key point being to remember that these aren't the only potential
>>> topics (GCDML and MixS/DwC)...just the first two to have
>>> nucleated...For GSC 14 we are talking about a range of ideas -
>>> including high level things like considering website content.  So all
>>> ideas welcomed but let's sort out as soon as possible how the Oxford
>>> and NESCent interests dovetail...
>>>
>>>
>>>
>>> On Mon, Mar 19, 2012 at 2:41 PM, Wim De Smet<Wim.DeSmet at ugent.be>    wrote:
>>>> Yes, caveats certainly apply! Thar be dragons 'ere, etc.
>>>>
>>>> Obviously there is some overlap between both hackatons and groups. In
>>>> reference to Hilmar's email, I think a larger hackaton at NESCent is a
>>>> good
>>>> idea and it should merge both groups in one longer event.
>>>>
>>>> regards,
>>>> Wim
>>>>
>>>>
>>>> On 19-03-12 14:38, Dawn Field wrote:
>>>>> Thanks Wim!  I think there is also a final report being made  - the
>>>>> 'live report' still contains many early notes that could be misleading
>>>>> - as they describe issues that were resolved by further
>>>>> talking/actions at the meeting.
>>>>>
>>>>> GBIF have also posted a news item on the Oxford hackathon
>>>>>
>>>>>
>>>>>
>>>>> http://www.gbif.org/communications/news-and-events/showsingle/article/genomic-data-in-gbif-moves-a-step-closer/
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Mar 19, 2012 at 1:34 PM, Wim De Smet<Wim.DeSmet at ugent.be>
>>>>>   wrote:
>>>>>> Hi,
>>>>>>
>>>>>> The live notes that we used at the (GCDML) mini-hackaton are here:
>>>>>> http://tinyurl.com/7x6v3vm
>>>>>>
>>>>>> I can fill in details on the java bindings (which are started but I
>>>>>> really
>>>>>> need to continue work on). Everybody sort of has their own projects
>>>>>> going,
>>>>>> so ideally we'd all contribute alike to the overview.
>>>>>>
>>>>>> I would propose tying this in with a developer call in a couple of
>>>>>> weeks
>>>>>> and
>>>>>> using that to consolidate a (non-definitive) list of projects for the
>>>>>> next
>>>>>> meeting. Off the top of my head we could use: central documentation on
>>>>>> getting the various tools running, XML documentation, (functional)
>>>>>> tests
>>>>>> of
>>>>>> bindings, extra utility code, tutorials.
>>>>>>
>>>>>> Apologies for cross-posting, should we keep this discussion on
>>>>>> -developers?
>>>>>>
>>>>>> regards,
>>>>>> Wim
>>>>>>
>>>>>>
>>>>>> On 18-03-12 11:43, Dawn Field wrote:
>>>>>>>
>>>>>>> We need to get both up and advertised and will do so with high
>>>>>>> priority!
>>>>>>>
>>>>>>> We propably need a new 'hackathon' page in the Gsc website...
>>>>>>>
>>>>>>> Volunteers from the past hackathons willing to help please come
>>>>>>> forward
>>>>>>> ... I will talk with Peter to get something started
>>>>>>>
>>>>>>> Sent from my iPhone
>>>>>>>
>>>>>>> On 18 Mar 2012, at 02:21, Trish Whetzel<plwhetzel at gmail.com
>>>>>>> <mailto:plwhetzel at gmail.com>>      wrote:
>>>>>>>
>>>>>>>> Excellent news! Is there a write-up or wiki page with the projects
>>>>>>>> from the last hackathon?
>>>>>>>>
>>>>>>>> Trish
>>>>>>>>
>>>>>>>> On Fri, Mar 16, 2012 at 5:12 PM, Dawn Field
>>>>>>>> <<mailto:fiedawn at googlemail.com>fiedawn at googlemail.com
>>>>>>>>
>>>>>>>> <mailto:fiedawn at googlemail.com>>      wrote:
>>>>>>>>
>>>>>>>>     Dear All,
>>>>>>>>
>>>>>>>>     Just a heads up that due to the success of the recent GSC
>>>>>>>>     hackathon/small group meeting within biodiversity, we will be
>>>>>>>> planning
>>>>>>>>     to keep 2 days open after the GSC 14 meeting in Oxford (Sept
>>>>>>>> 17-19,
>>>>>>>>     with hackathon booked for 20-21).
>>>>>>>>
>>>>>>>>     If you would like to use the time to tackle specific development
>>>>>>>>     projects just let us know and we can start to build it into the
>>>>>>>>     planning process for these two days.
>>>>>>>>
>>>>>>>>     We are working on a range of ideas, but we are looking for
>>>>>>>> 'champions'
>>>>>>>>     to put forward specific projects (small or larger) and help
>>>>>>>> organize
>>>>>>>>     getting the right people to the table to make real progress.
>>>>>>>>
>>>>>>>>     best to all,
>>>>>>>>     Dawn
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>     --
>>>>>>>>     Professor Dawn Field
>>>>>>>>     Molecular Evolution and Bioinformatics Group, Head
>>>>>>>>     Centre for Ecology&      Hydrology
>>>>>>>>
>>>>>>>>     Maclean Building
>>>>>>>>     Benson Lane
>>>>>>>>     Crowmarsh Gifford
>>>>>>>>     Wallingford
>>>>>>>>     Oxfordshire
>>>>>>>>     OX10 8BB
>>>>>>>>     T: +44 (0)1491 838800<tel:%2B44%20%280%291491%20838800>
>>>>>>>>     F: +44 (0)1491 692424<tel:%2B44%20%280%291491%20692424>
>>>>>>>>     Direct x2652
>>>>>>>>     Email:<mailto:dfield at ceh.ac.uk>dfield at ceh.ac.uk
>>>>>>>>     <mailto:dfield at ceh.ac.uk>
>>>>>>>>     _______________________________________________
>>>>>>>>     gensc-developers mailing list
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>   <mailto:gensc-developers at lists.gensc.org>gensc-developers at lists.gensc.org
>>>>>>>>     <mailto:gensc-developers at lists.gensc.org>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>   <http://lists.gensc.org/mailman/listinfo/gensc-developers>http://lists.gensc.org/mailman/listinfo/gensc-developers
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> gensc-biodiversity-wg mailing list
>>>>>>> gensc-biodiversity-wg at lists.gensc.org
>>>>>>> http://lists.gensc.org/mailman/listinfo/gensc-biodiversity-wg
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Wim De Smet
>>>>>> http://www.straininfo.net/
>>>>>>
>>>>>> _______________________________________________
>>>>>> gensc-developers mailing list
>>>>>> gensc-developers at lists.gensc.org
>>>>>> http://lists.gensc.org/mailman/listinfo/gensc-developers
>>>>>
>>>>>
>>>>>
>>>> --
>>>> Wim De Smet
>>>> http://www.straininfo.net/
>>>
>>>
>
>

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