[GSoC] Bionode project idea

[Bruno Vieira]

Thanks Kai! :D

Cheers,
Bruno

On Mon, Feb 15, 2016 at 2:54 PM Kai Blin <kblin at biosustain.dtu.dk> wrote:

> Hi Bruno,
>
> thanks for the proposal, I'll make sure I'll add it to our ideas page.
>
> Cheers,
> Kai
>
> --
> Kai Blin                                           kblin at biosustain.dtu.dk
>
> PostDoc / Scientific Software Engineer
> DTU Biosustain
> http://www.biosustain.dtu.dk/
> Building Thujahuset, room 2.L.09
> DK - 2970 Hørsholm
> Denmark
> mobile: +45 93511306                               twitter: @kaiblin
> ------------------------------
> *From:* GSoC [gsoc-bounces+kblin=biosustain.dtu.dk at mailman.open-bio.org]
> on behalf of Bruno Vieira [mail at bmpvieira.com]
> *Sent:* 15 February 2016 15:35
> *To:* gsoc at mailman.open-bio.org
> *Cc:* Yannick Wurm; Max Ogden; Mathias Buus Madsen
> *Subject:* Re: [GSoC] Bionode project idea
>
> Here's the proposal:
>
> *Bionode workflow engine for streamed data analysis*
>
> Researchers should be able to:
>   * Perform analyses while data are generated (i.e., with “data streams”);
>   * Easily and rapidly update results if input data or analysis
> approaches/parameters change (with minimal recomputation);
>   * Effortlessly change and scale underlying computing platforms while
> pipeline is running;
>   * Easily visualise results.
>
> This is largely impossible because current approaches were developed when
> datasets were simpler and smaller. The student will take advantage of
> recent improvements in generic analysis tools (Node.js Streams &
> asynchronous concurrency) to attain the above objectives.
>
> The student will create a workflow engine for streamed data analysis with
> concurrent pipelining. The main mentors will be Max Ogden and Mathias Buus,
> top Node.js contributors and founders of Dat-data.com, for their experience
> with streaming interfaces. Bruno Vieira (founder of Bionode.io) and Yannick
> Wurm (lecturer in Bioinformatics at QMUL) will co-supervise.
>
> Some work on the data structures and programming interfaces for commonly
> used data sources (e.g., NCBI, Uniprot, Ensembl/Biomart) and data types
> (e.g., VCF, BAM, FASTQ) will be required.
>
> The underlying computational architecture architecture should be
> abstracted. This means that analysis code will run identically using
> different traditional high performance computing system (e.g., Torque, SGE)
> and modern systems (e.g., Hadoop MapReduce).
>
> Some components and proof of concepts required for this project are
> available at http://github.com/bionode
>
> JavaScript skills are required. Node.js and some biology knowledge is a
> plus. Difficulty is medium.
>
> Cheers,
> Bruno
>
> On Mon, Feb 15, 2016 at 1:35 PM Bruno Vieira <mail at bmpvieira.com> wrote:
>
>> Hi all,
>>
>> Would it be possible to propose an idea for the Bionode.io project
>> through OBF?
>> If so, please let me know the proper process to submit, since I saw in
>> another thread that you're having issues with the wiki.
>>
>> Cheers,
>> Bruno
>> bmpvieira.com    bionode.io    wurmlab.github.io
>>
>
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