[GSoC] Any project initiative in NGS

Sat Mar 1 01:58:04 EST 2014

Hello All,
         I am Devang Varia, and i am interested in any projects that are concerning to Next Generation Sequencing Data Analysis. I have a deep sense of understanding biological data and a good grip in java(core + swing), Perl and bioinformatics algorithms. I am also open to any kind of naive idea's i can make a difference in. 
Regards,
Devang Varia


> On 28-Feb-2014, at 22:30, gsoc-request at lists.open-bio.org wrote:
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> Today's Topics:
> 
>   1. Re: GSOC OBF & GMOD (Pjotr Prins)
>   2. Re: GSOC OBF & GMOD (Fields, Christopher J)
>   3. biocaml projects under O|B|F GSoC (Ashish Agarwal)
>   4. Re: biocaml projects under O|B|F GSoC (Pjotr Prins)
>   5. Re: biocaml projects under O|B|F GSoC (Peter Cock)
>   6. Re: biocaml projects under O|B|F GSoC (Ra)
>   7. biojs projects (Andy Jenkinson)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 27 Feb 2014 22:04:32 +0100
> From: Pjotr Prins <pjotr2014 at thebird.nl>
> Subject: Re: [GSoC] GSOC OBF & GMOD
> To: "Fields, Christopher J" <cjfields at illinois.edu>
> Cc: Robin Haw <robin.haw at oicr.on.ca>,    "gsoc at lists.open-bio.org"
>    <gsoc at lists.open-bio.org>,    Amelia Ireland <amelia.ireland at gmod.org>
> Message-ID: <20140227210432.GA32348 at thebird.nl>
> Content-Type: text/plain; charset=us-ascii
> 
>> On Thu, Feb 27, 2014 at 07:46:01PM +0000, Fields, Christopher J wrote:
>> Ah yes, but then I believe Amelia?s point is whether this is something that the Biojavascript folks (who aren?t officially one of the OBF Bio* but have been accepted as their own GSoC org) might be a better fit.  Which very well could be ?yes? depending on their view of things.  Maybe someone can reach out to them and ask?
> 
> If you read the BioJS paper, you'll see that they are mostly working
> on visualisation components for the browser.
> 
> We are talking Client-server here - different ball game. If we were to
> start a serious project in Javascript we should talk about that. We
> should not fear mixing programming languages. We have gotten beyond
> that point by now. I currently write code in Ruby, D, Python and
> Javascript. Apparently LISP I can't get around either. I don't think I
> am that special. Main thing is to find mentors that take an active
> interest in maintaining such a code base. Without a mentor we won't
> get anywhere.
> 
> Javascript + Nodejs makes a pretty enticing server environment, these
> days. And more and more students are learning Javascript before Perl
> or Python. Now if there is an eager mentor...
> 
> Pj.
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 27 Feb 2014 22:15:01 +0000
> From: "Fields, Christopher J" <cjfields at illinois.edu>
> Subject: Re: [GSoC] GSOC OBF & GMOD
> To: Pjotr Prins <pjotr2014 at thebird.nl>
> Cc: Robin Haw <robin.haw at oicr.on.ca>,    "gsoc at lists.open-bio.org"
>    <gsoc at lists.open-bio.org>,    Amelia Ireland <amelia.ireland at gmod.org>
> Message-ID: <1DD889FA-58A8-479B-ADF0-318BF5C4AB55 at illinois.edu>
> Content-Type: text/plain; charset="Windows-1252"
> 
>> On Feb 27, 2014, at 3:04 PM, Pjotr Prins <pjotr2014 at thebird.nl> wrote:
>> 
>>> On Thu, Feb 27, 2014 at 07:46:01PM +0000, Fields, Christopher J wrote:
>>> Ah yes, but then I believe Amelia?s point is whether this is something that the Biojavascript folks (who aren?t officially one of the OBF Bio* but have been accepted as their own GSoC org) might be a better fit.  Which very well could be ?yes? depending on their view of things.  Maybe someone can reach out to them and ask?
>> 
>> If you read the BioJS paper, you'll see that they are mostly working
>> on visualisation components for the browser.
>> 
>> We are talking Client-server here - different ball game. If we were to
>> start a serious project in Javascript we should talk about that. We
>> should not fear mixing programming languages. We have gotten beyond
>> that point by now. I currently write code in Ruby, D, Python and
>> Javascript. Apparently LISP I can't get around either. I don't think I
>> am that special. Main thing is to find mentors that take an active
>> interest in maintaining such a code base. Without a mentor we won't
>> get anywhere.
>> 
>> Javascript + Nodejs makes a pretty enticing server environment, these
>> days. And more and more students are learning Javascript before Perl
>> or Python. Now if there is an eager mentor...
>> 
>> Pj.
> 
> I?m not disagreeing, actually.  I just want to make sure these go to the right place, whether it be OBF or elsewhere.
> 
> 
> chris
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 27 Feb 2014 17:52:19 -0500
> From: Ashish Agarwal <agarwal1975 at gmail.com>
> Subject: [GSoC] biocaml projects under O|B|F GSoC
> To: gsoc at lists.open-bio.org
> Message-ID:
>    <CAMu2m2JL66E_GCQFUZYB05RKxL04CxJ_cg=kfwfiPtkcSoxEXg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi all,
> 
> I'm a bit late to the conversation. Can I still propose some Biocaml [1]
> projects under the O|B|F organization or am I too late? I will have time to
> mentor and have a couple of project ideas:
> 
> * Provide a high-performance client side visualization library. The code
> would be written in pure OCaml and compiled to pure Javascript using
> js_of_ocaml [2]. Thus it is an OCaml project, not Javascript, though
> knowledge of Javascript will certainly be needed. If a student is
> interested, we could also use FRP (functional reactive programming) to
> implement the interactivity.
> 
> * Use Mirage OS [3] to implement bioinformatics algorithms scalable to
> arbitrary numbers of VMs. Mirage code is written in pure OCaml. Actually,
> I'm not sure how feasible this would be, and I would benefit from a
> co-mentor with deeper knowledge about bioinformatics algorithms. This could
> potentially be joint with the Xen organization, which was also accepted for
> GSoC [4]. (Is that allowed?)
> 
> [1] http://biocaml.org
> [2] http://ocsigen.org/js_of_ocaml/
> [3] http://www.openmirage.org/
> [4] http://openmirage.org/blog/applying-for-gsoc2014
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 28 Feb 2014 08:12:40 +0100
> From: Pjotr Prins <pjotr2014 at thebird.nl>
> Subject: Re: [GSoC] biocaml projects under O|B|F GSoC
> To: Ashish Agarwal <agarwal1975 at gmail.com>
> Cc: gsoc at lists.open-bio.org
> Message-ID: <20140228071240.GA2050 at thebird.nl>
> Content-Type: text/plain; charset=us-ascii
> 
> Sounds good to me! These are the type of projects that attract
> brilliant students.
> 
> Pj.
> 
>> On Thu, Feb 27, 2014 at 05:52:19PM -0500, Ashish Agarwal wrote:
>> Hi all,
>> 
>> I'm a bit late to the conversation. Can I still propose some Biocaml [1]
>> projects under the O|B|F organization or am I too late? I will have time to
>> mentor and have a couple of project ideas:
>> 
>> * Provide a high-performance client side visualization library. The code
>> would be written in pure OCaml and compiled to pure Javascript using
>> js_of_ocaml [2]. Thus it is an OCaml project, not Javascript, though
>> knowledge of Javascript will certainly be needed. If a student is
>> interested, we could also use FRP (functional reactive programming) to
>> implement the interactivity.
>> 
>> * Use Mirage OS [3] to implement bioinformatics algorithms scalable to
>> arbitrary numbers of VMs. Mirage code is written in pure OCaml. Actually,
>> I'm not sure how feasible this would be, and I would benefit from a
>> co-mentor with deeper knowledge about bioinformatics algorithms. This could
>> potentially be joint with the Xen organization, which was also accepted for
>> GSoC [4]. (Is that allowed?)
>> 
>> [1] http://biocaml.org
>> [2] http://ocsigen.org/js_of_ocaml/
>> [3] http://www.openmirage.org/
>> [4] http://openmirage.org/blog/applying-for-gsoc2014
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Fri, 28 Feb 2014 10:07:18 +0000
> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [GSoC] biocaml projects under O|B|F GSoC
> To: Pjotr Prins <pjotr2014 at thebird.nl>
> Cc: OBF GSoC <gsoc at lists.open-bio.org>, OBF Board <board at open-bio.org>
> Message-ID:
>    <CAKVJ-_5GqMLOLZoHVndyco57KV82UGDUMiETjtAh2VD+doAxfw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Ashish,
> 
> Regarding Biocaml, the OBF doesn't yet have a formal project affiliation
> process, but there is a draft here if you have any thoughts on this?
> https://github.com/OBF/obf-docs/blob/unratified-drafts/Affiliated-Project-Policy.md
> 
> I presume you have some specific biological visualization tasks and
> algorithms in mind? If so, then this could be made to fit under the OBF
> for GSoC 2014.
> 
> With regards to joint projects with two GSoC organisations - I don't
> think that is possible (although you may wish to circulate the project
> idea to both communities to find co-mentors and potential students).
> I think for Google's paperwork there has to be just one organisation...
> but best checking on the official mailing list to be sure.
> 
> For the Miraga VM based project, perhaps talk to Brad Chapman
> (who does Biopython, CloudBioLinux, etc) for ideas about potential
> co-mentors? See e.g. Brad's blog http://bcbio.wordpress.com/
> 
> Peter
> 
> 
>> On Fri, Feb 28, 2014 at 7:12 AM, Pjotr Prins <pjotr2014 at thebird.nl> wrote:
>> 
>> Sounds good to me! These are the type of projects that attract
>> brilliant students.
>> 
>> Pj.
>> 
>>> On Thu, Feb 27, 2014 at 05:52:19PM -0500, Ashish Agarwal wrote:
>>> Hi all,
>>> 
>>> I'm a bit late to the conversation. Can I still propose some Biocaml [1]
>>> projects under the O|B|F organization or am I too late? I will have time
>> to
>>> mentor and have a couple of project ideas:
>>> 
>>> * Provide a high-performance client side visualization library. The code
>>> would be written in pure OCaml and compiled to pure Javascript using
>>> js_of_ocaml [2]. Thus it is an OCaml project, not Javascript, though
>>> knowledge of Javascript will certainly be needed. If a student is
>>> interested, we could also use FRP (functional reactive programming) to
>>> implement the interactivity.
>>> 
>>> * Use Mirage OS [3] to implement bioinformatics algorithms scalable to
>>> arbitrary numbers of VMs. Mirage code is written in pure OCaml. Actually,
>>> I'm not sure how feasible this would be, and I would benefit from a
>>> co-mentor with deeper knowledge about bioinformatics algorithms. This
>> could
>>> potentially be joint with the Xen organization, which was also accepted
>> for
>>> GSoC [4]. (Is that allowed?)
>>> 
>>> [1] http://biocaml.org
>>> [2] http://ocsigen.org/js_of_ocaml/
>>> [3] http://www.openmirage.org/
>>> [4] http://openmirage.org/blog/applying-for-gsoc2014
>>> _______________________________________________
>>> GSoC mailing list
>>> GSoC at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/gsoc
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Fri, 28 Feb 2014 11:59:56 +0100
> From: Ra <ilpuccio.febo at gmail.com>
> Subject: Re: [GSoC] biocaml projects under O|B|F GSoC
> To: Peter Cock <p.j.a.cock at googlemail.com>
> Cc: OBF GSoC <gsoc at lists.open-bio.org>, Pjotr Prins
>    <pjotr2014 at thebird.nl>,    OBF Board <board at open-bio.org>
> Message-ID:
>    <CACQsWTM_D1Qb5Q258h=0oHuzzCv8qeeFmaQ_3nwNQ88GvXaA0w at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Ashish,
> formally having 1 project and mentoring from two different orgs is not
> possible but you can always collaborate or contribute with Xen informally,
> we did the same with JRuby.
> 
> 
> 
> On Fri, Feb 28, 2014 at 11:07 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
> 
>> Hi Ashish,
>> 
>> Regarding Biocaml, the OBF doesn't yet have a formal project affiliation
>> process, but there is a draft here if you have any thoughts on this?
>> 
>> https://github.com/OBF/obf-docs/blob/unratified-drafts/Affiliated-Project-Policy.md
>> 
>> I presume you have some specific biological visualization tasks and
>> algorithms in mind? If so, then this could be made to fit under the OBF
>> for GSoC 2014.
>> 
>> With regards to joint projects with two GSoC organisations - I don't
>> think that is possible (although you may wish to circulate the project
>> idea to both communities to find co-mentors and potential students).
>> I think for Google's paperwork there has to be just one organisation...
>> but best checking on the official mailing list to be sure.
>> 
>> For the Miraga VM based project, perhaps talk to Brad Chapman
>> (who does Biopython, CloudBioLinux, etc) for ideas about potential
>> co-mentors? See e.g. Brad's blog http://bcbio.wordpress.com/
>> 
>> Peter
>> 
>> 
>>> On Fri, Feb 28, 2014 at 7:12 AM, Pjotr Prins <pjotr2014 at thebird.nl> wrote:
>>> 
>>> Sounds good to me! These are the type of projects that attract
>>> brilliant students.
>>> 
>>> Pj.
>>> 
>>>> On Thu, Feb 27, 2014 at 05:52:19PM -0500, Ashish Agarwal wrote:
>>>> Hi all,
>>>> 
>>>> I'm a bit late to the conversation. Can I still propose some Biocaml
>> [1]
>>>> projects under the O|B|F organization or am I too late? I will have
>> time
>>> to
>>>> mentor and have a couple of project ideas:
>>>> 
>>>> * Provide a high-performance client side visualization library. The
>> code
>>>> would be written in pure OCaml and compiled to pure Javascript using
>>>> js_of_ocaml [2]. Thus it is an OCaml project, not Javascript, though
>>>> knowledge of Javascript will certainly be needed. If a student is
>>>> interested, we could also use FRP (functional reactive programming) to
>>>> implement the interactivity.
>>>> 
>>>> * Use Mirage OS [3] to implement bioinformatics algorithms scalable to
>>>> arbitrary numbers of VMs. Mirage code is written in pure OCaml.
>> Actually,
>>>> I'm not sure how feasible this would be, and I would benefit from a
>>>> co-mentor with deeper knowledge about bioinformatics algorithms. This
>>> could
>>>> potentially be joint with the Xen organization, which was also accepted
>>> for
>>>> GSoC [4]. (Is that allowed?)
>>>> 
>>>> [1] http://biocaml.org
>>>> [2] http://ocsigen.org/js_of_ocaml/
>>>> [3] http://www.openmirage.org/
>>>> [4] http://openmirage.org/blog/applying-for-gsoc2014
>>>> _______________________________________________
>>>> GSoC mailing list
>>>> GSoC at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>> _______________________________________________
>>> GSoC mailing list
>>> GSoC at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/gsoc
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> 
> 
> -- 
> Ra
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Fri, 28 Feb 2014 10:00:58 -0500
> From: Andy Jenkinson <andy.jenkinson at ebi.ac.uk>
> Subject: [GSoC] biojs projects
> To: "gsoc at lists.open-bio.org" <gsoc at lists.open-bio.org>
> Message-ID: <EDBF7E9F-3E40-4635-9E26-732FD78D2315 at ebi.ac.uk>
> Content-Type: text/plain; charset=us-ascii
> 
> I just wanted to mention, given the discussion about BioJS, that there seem to be a remarkable number of potential students already showing their interest.
> 
> Cheers,
> Andy
> 
> 
> ------------------------------
> 
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
> 
> 
> End of GSoC Digest, Vol 21, Issue 8
> ***********************************