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Re: position in cancer informatics

From: Jakub Kotowski <jakubkotowski@gmx.net>
Date: Fri, 20 Jul 2012 11:40:03 +0200
Message-ID: <50092773.9050800@gmx.net>
To: Stefan Decker <stefan.decker@deri.org>
CC: Helena Deus <helena.deus@deri.org>, Melvin Carvalho <melvincarvalho@gmail.com>, "nathan@webr3.org" <nathan@webr3.org>, Michael Hausenblas <michael.hausenblas@deri.org>, "semantic-web@w3.org" <semantic-web@w3.org>, "public-lod@w3.org" <public-lod@w3.org>, "www-rdf-interest@w3.org" <www-rdf-interest@w3.org>, "protege-discussion@lists.stanford.edu" <protege-discussion@lists.stanford.edu>, "semanticweb@yahoogroups.com" <semanticweb@yahoogroups.com>, "dbworld@cs.wisc.edu" <dbworld@cs.wisc.edu>, "machine-learning@egroups.com" <machine-learning@egroups.com>, "taverna-users@lists.sourceforge.net" <taverna-users@lists.sourceforge.net>, "bbb@bioinformatics.org" <bbb@bioinformatics.org>
It seems to me that more than a computational infrastructure you would
need an efficient way to coordinate a community (communication, resource
(file, software?, ...) sharing and a common way of describing each used
methodology and set of results in order to facilitate subsequent result
validation and aggregation. But maybe that's what you mean by
computational infrastructure? Or are you aiming for something more
automated?

Best,

Jakub


On 07/20/2012 11:22 AM, Stefan Decker wrote:
> The discussion seem to point to a deeper question: how to enable crowd
> sourcing of the analysis of these kind of data sets? This may involve
> running of analysis code or maybe even manual work.
> What kind of computational infrastructure would we need to enable this?
> And how do we validate and aggregate results?
> 
> On Thursday, 19 July 2012, Helena Deus wrote:
> 
>     An on a related topic and the reason why doing cancer informatics is
>     so exciting in this area: a happy story where exploring data
>     patterns enabled curing a cancer which had a 4-5% survival chance
>     - http://www.nytimes.com/2012/07/08/health/in-gene-sequencing-treatment-for-leukemia-glimpses-of-the-future.html?_r=1
> 
> 
> 
>     On Jul 19, 2012, at 7:41 PM, Melvin Carvalho wrote:
> 
>>
>>
>>     On 17 July 2012 22:27, Nathan <nathan@webr3.org <javascript:_e({},
>>     'cvml', 'nathan@webr3.org');>> wrote:
>>
>>         Can you open this right up for everybody to be involved?
>>
>>         I know I for one would be happy to invest free time to looking
>>         at these datasets to find patterns - are they open and
>>         available online, any pointers to get started, anything at all
>>         that would enable me (and hopefully others skilled here) to
>>         work on this?
>>
>>         It sounds like less of a "position" and more of a global need
>>         we who can should all be pumping time in to.
>>
>>
>>     Maybe related:
>>
>>     15-Year-Old Maker Astronomically Improves Pancreatic Cancer Test
>>
>>     http://blog.makezine.com/2012/07/18/15-year-old-maker-astronomically-improves-pancreatic-cancer-test/
>>
>>     He gleaned information on the topic from his “good friend Google,”
>>     and began his research. Yes, he even got in trouble in his science
>>     class for reading articles on carbon nanotubes instead of doing
>>     his classwork. When Andraka had solidified ideas for his novel
>>     paper sensor, he wrote out his procedure, timeline, and budget,
>>     and emailed 200 professors at research institutes. He got 199
>>     rejections and one acceptance from Johns Hopkins: “If you send out
>>     enough emails, someone’s going to say yes.”
>>
>>
>>         Best,
>>
>>         Nathan
>>
>>
>>         Helena Deus wrote:
>>
>>             Dear all,
>>             We have an exciting research assistant position open at
>>             DERI for a chance to work with Cancer Informatics! We are
>>             looking for an enthusiastic developer who is familiar with
>>             bioinformatics concepts. Your role will be exploring
>>             cancer related datasets and looking for pattern (applying,
>>             for example, machine learning techniques) that can be used
>>             for personalized medicine.
>>             Please don't hesitate to Fw. this to whomever you think
>>             might be interested.
>>             To apply or to ask for more information, please reply to
>>             me (helena.deus@deri.org <javascript:_e({}, 'cvml',
>>             'helena.deus@deri.org');>) with CV + motivation letter
>>             Kind regards, Helena F. Deus, PhD
>>             Digital Enterprise Research Institute
>>             helena.deus@deri.org <javascript:_e({}, 'cvml',
>>             'helena.deus@deri.org');>
>>
>>
>>
>>
>>
>>
>>
> 
> 
> 
> -- 
> Professor Stefan Decker
> Director, Digital Enterprise Research Institute,
> Professor of Digital Enterprise
> National University of Ireland, Galway. Ireland.
> Tel: +353.91.495011
> E-mail: stefan.decker@deri.org <mailto:stefan.decker@deri.org>
> Web: http://www.deri.ie
> Personal: http://www.stefandecker.org
Received on Friday, 20 July 2012 09:40:37 UTC

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