[Biojava-dev] Biojava-Mapreduce paradigm...

[Mark Fortner]

Hi Prasanna,
The project sounds interesting.  A few questions occurred to me:

   - Were you planning on submitting this as a GSOC project?
   - Were you planning on using GATE for items 1 & 2?
   - Would there be ways to plugin different ontologies (such as the NCI
   Metathesaurus)?
   - What types of network formats were you planning on supporting?
   - Are you planning on supporting both visual representations of networks
   as well as network graph data?


Cheers,

Mark



On Wed, Mar 27, 2013 at 12:48 PM, Prasanna Bala <balkiprasanna1984 at gmail.com
> wrote:

> Hi All...
>
> I am Prasanna. I am working in the area of Machine Learning for more than 5
> years. I have certain clarifications regarding contribution to Biojava
> community. I have experience in mapreduce programming for more than 2
> years. I have used it for applying various machine learning algorithms
> using distributed computing. I have also used Mahout for various projects
> from Stochastic Gradient Descent to Bayesian networks. I have lot of
> interested and fascinating concepts I would like to contribute to
> Bio-community. I am very much interested in implementing mapreduce
> algorithms in the current field of Bioinformatics. It will be very useful
> for people who are pursuing research in the area of Big data analytics. I
> want to develop and release libraries like Mahout that uses Hadoop for
> distributed computing. This can reduce the complexity of running the code
> in Amazon Elastic MapReduce for large scale datasets.
>
> Biomedical Text mining (Rule based and ML algorithms CRF, Maximum Entropy
> Model, HMM):
> 1) Name Entity Recognition.
> 2) Information extraction.
> 3) Building networks and pathways from literature.
>
> I have many more ideas regarding using ML algorithms in the Bioinformatics
> domain. Would like to know if we can contribute our ideas using this
> architecture.
>
> Cheers,
> Prasanna.
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