* [Caml-list] Bioinformatics Js_of_ocaml GSoC project
@ 2014-03-03 17:11 Ashish Agarwal
2014-03-04 11:26 ` Florent Monnier
2014-03-04 16:37 ` Kristopher Micinski
0 siblings, 2 replies; 6+ messages in thread
From: Ashish Agarwal @ 2014-03-03 17:11 UTC (permalink / raw)
To: Biocaml, Caml List, ocsigen
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Dear students,
I'd like to announce a Biocaml [1] project for the Google Summer of Code
[2], which is being hosted under the Open Bioinformatics Foundation [3,4].
Please get in touch with me if you are interested! Feel free to propose
other project ideas as I'm happy to mentor any project involving
Bioinformatics and OCaml. See here [5] for an up-to-date announcement, but
I've also pasted the announcement below.
Project: Bioinformatics Js_of_ocaml Visualization Toolkit
Rationale: OCaml is a strong statically typed functional programming
language. Usually one does not consider such languages for front-end
development, but the Js_of_ocaml compiler is causing OCaml to be more
widely used for building websites. Js_of_ocaml compiles OCaml code to pure
Javascript and the generated Javascript has very good performance. On the
other hand, bioinformatics data analysis needs to be conducted by a broader
range of users, which requires more elegant user interfaces with high
quality data visualization.
Approach: Write an OCaml library that can be used to visualize large data
sets efficiently and interactively in the browser. The library should be
smart enough to work on the client side when possible, but make server side
calls when necessary. You may want to use Eliom for this purpose. You can
connect to parsers and data structures available in Biocaml as needed. As
demonstration of success, it should be possible to create genome
visualizations like that of the UCSC genome browser and protein interaction
networks like that of Cytoscape.
Difficulty and needed skills: This project is for intermediate to advanced
programmers. You will need to be already familiar with OCaml (or closely
related languages like F# and Haskell) and have a basic understanding of
Javascript and client/server programming.
[1] http://biocaml.org
[2] http://code.google.com/soc
[3] http://www.open-bio.org/wiki/
[4] http://www.open-bio.org/wiki/Google_Summer_of_Code
[5] http://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas#Biocaml
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^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [Caml-list] Bioinformatics Js_of_ocaml GSoC project
2014-03-03 17:11 [Caml-list] Bioinformatics Js_of_ocaml GSoC project Ashish Agarwal
@ 2014-03-04 11:26 ` Florent Monnier
2014-03-04 16:45 ` Ashish Agarwal
2014-03-04 16:37 ` Kristopher Micinski
1 sibling, 1 reply; 6+ messages in thread
From: Florent Monnier @ 2014-03-04 11:26 UTC (permalink / raw)
To: Ashish Agarwal; +Cc: Biocaml, Caml List, ocsigen
2014-03-03 18:11 UTC+01:00, Ashish Agarwal wrote:
> Dear students,
>
> I'd like to announce a Biocaml [1] project for the Google Summer of Code
> [2], which is being hosted under the Open Bioinformatics Foundation [3,4].
> Please get in touch with me if you are interested! Feel free to propose
> other project ideas as I'm happy to mentor any project involving
> Bioinformatics and OCaml. See here [5] for an up-to-date announcement, but
> I've also pasted the announcement below.
>
> Project: Bioinformatics Js_of_ocaml Visualization Toolkit
>
> Rationale: OCaml is a strong statically typed functional programming
> language. Usually one does not consider such languages for front-end
> development, but the Js_of_ocaml compiler is causing OCaml to be more
> widely used for building websites. Js_of_ocaml compiles OCaml code to pure
> Javascript and the generated Javascript has very good performance. On the
> other hand, bioinformatics data analysis needs to be conducted by a broader
> range of users, which requires more elegant user interfaces with high
> quality data visualization.
>
> Approach: Write an OCaml library that can be used to visualize large data
> sets efficiently and interactively in the browser. The library should be
> smart enough to work on the client side when possible, but make server side
> calls when necessary. You may want to use Eliom for this purpose. You can
> connect to parsers and data structures available in Biocaml as needed. As
> demonstration of success, it should be possible to create genome
> visualizations like that of the UCSC genome browser and protein interaction
> networks like that of Cytoscape.
>
> Difficulty and needed skills: This project is for intermediate to advanced
> programmers. You will need to be already familiar with OCaml (or closely
> related languages like F# and Haskell) and have a basic understanding of
> Javascript and client/server programming.
>
> [1] http://biocaml.org
> [2] http://code.google.com/soc
> [3] http://www.open-bio.org/wiki/
> [4] http://www.open-bio.org/wiki/Google_Summer_of_Code
> [5] http://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas#Biocaml
>
> --
> Caml-list mailing list. Subscription management and archives:
> https://sympa.inria.fr/sympa/arc/caml-list
> Beginner's list: http://groups.yahoo.com/group/ocaml_beginners
> Bug reports: http://caml.inria.fr/bin/caml-bugs
Hi Ashish,
I'm not a student, but just an unemployed person seeking for a job.
Is it possible to participate to a Google Summer of Code ?
--
Florent
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [Caml-list] Bioinformatics Js_of_ocaml GSoC project
2014-03-04 11:26 ` Florent Monnier
@ 2014-03-04 16:45 ` Ashish Agarwal
0 siblings, 0 replies; 6+ messages in thread
From: Ashish Agarwal @ 2014-03-04 16:45 UTC (permalink / raw)
To: Florent Monnier; +Cc: Biocaml, Caml List, ocsigen
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On Tue, Mar 4, 2014 at 6:26 AM, Florent Monnier
<monnier.florent@gmail.com>wrote:
I'm not a student, but just an unemployed person seeking for a job.
> Is it possible to participate to a Google Summer of Code ?
>
Hi Florent. Unfortunately, it seems [1] you must be at least a part-time
student.
[1]
http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2014/help_page#2._Whos_eligible_to_participate_as_a
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^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [Caml-list] Bioinformatics Js_of_ocaml GSoC project
2014-03-03 17:11 [Caml-list] Bioinformatics Js_of_ocaml GSoC project Ashish Agarwal
2014-03-04 11:26 ` Florent Monnier
@ 2014-03-04 16:37 ` Kristopher Micinski
2014-03-04 16:48 ` Ashish Agarwal
1 sibling, 1 reply; 6+ messages in thread
From: Kristopher Micinski @ 2014-03-04 16:37 UTC (permalink / raw)
To: Ashish Agarwal; +Cc: Biocaml, Caml List, ocsigen
This is wicked cool, and I'd like to keep track of this and
potentially help out. I'm not interested as a GSOC student (I'm a
grad student) but am using js_of_ocaml for visualization right now,
and I'd be interested in having discussions with whoever works on
this.
Kris
On Mon, Mar 3, 2014 at 12:11 PM, Ashish Agarwal <agarwal1975@gmail.com> wrote:
> Dear students,
>
> I'd like to announce a Biocaml [1] project for the Google Summer of Code
> [2], which is being hosted under the Open Bioinformatics Foundation [3,4].
> Please get in touch with me if you are interested! Feel free to propose
> other project ideas as I'm happy to mentor any project involving
> Bioinformatics and OCaml. See here [5] for an up-to-date announcement, but
> I've also pasted the announcement below.
>
> Project: Bioinformatics Js_of_ocaml Visualization Toolkit
>
> Rationale: OCaml is a strong statically typed functional programming
> language. Usually one does not consider such languages for front-end
> development, but the Js_of_ocaml compiler is causing OCaml to be more widely
> used for building websites. Js_of_ocaml compiles OCaml code to pure
> Javascript and the generated Javascript has very good performance. On the
> other hand, bioinformatics data analysis needs to be conducted by a broader
> range of users, which requires more elegant user interfaces with high
> quality data visualization.
>
> Approach: Write an OCaml library that can be used to visualize large data
> sets efficiently and interactively in the browser. The library should be
> smart enough to work on the client side when possible, but make server side
> calls when necessary. You may want to use Eliom for this purpose. You can
> connect to parsers and data structures available in Biocaml as needed. As
> demonstration of success, it should be possible to create genome
> visualizations like that of the UCSC genome browser and protein interaction
> networks like that of Cytoscape.
>
> Difficulty and needed skills: This project is for intermediate to advanced
> programmers. You will need to be already familiar with OCaml (or closely
> related languages like F# and Haskell) and have a basic understanding of
> Javascript and client/server programming.
>
> [1] http://biocaml.org
> [2] http://code.google.com/soc
> [3] http://www.open-bio.org/wiki/
> [4] http://www.open-bio.org/wiki/Google_Summer_of_Code
> [5] http://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas#Biocaml
>
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [Caml-list] Bioinformatics Js_of_ocaml GSoC project
2014-03-04 16:37 ` Kristopher Micinski
@ 2014-03-04 16:48 ` Ashish Agarwal
2014-03-04 17:03 ` Kristopher Micinski
0 siblings, 1 reply; 6+ messages in thread
From: Ashish Agarwal @ 2014-03-04 16:48 UTC (permalink / raw)
To: Kristopher Micinski; +Cc: Biocaml, Caml List, ocsigen
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On Tue, Mar 4, 2014 at 11:37 AM, Kristopher Micinski <krismicinski@gmail.com
> wrote:
I'd be interested in having discussions with whoever works on this.
The best way to keep up-to-date will be to subscribe to the Biocaml mailing
list [1]. If the project is selected, it is a requirement that regular
updates are provided on a public mailing list, which will be that of
Biocaml and OBF.
[1] https://groups.google.com/d/forum/biocaml
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^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [Caml-list] Bioinformatics Js_of_ocaml GSoC project
2014-03-04 16:48 ` Ashish Agarwal
@ 2014-03-04 17:03 ` Kristopher Micinski
0 siblings, 0 replies; 6+ messages in thread
From: Kristopher Micinski @ 2014-03-04 17:03 UTC (permalink / raw)
To: Ashish Agarwal; +Cc: Biocaml, Caml List, ocsigen
Okay, will do,!,
Kris
On Tue, Mar 4, 2014 at 11:48 AM, Ashish Agarwal <agarwal1975@gmail.com> wrote:
> On Tue, Mar 4, 2014 at 11:37 AM, Kristopher Micinski
> <krismicinski@gmail.com> wrote:
>
>> I'd be interested in having discussions with whoever works on this.
>
>
> The best way to keep up-to-date will be to subscribe to the Biocaml mailing
> list [1]. If the project is selected, it is a requirement that regular
> updates are provided on a public mailing list, which will be that of Biocaml
> and OBF.
>
> [1] https://groups.google.com/d/forum/biocaml
^ permalink raw reply [flat|nested] 6+ messages in thread
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2014-03-03 17:11 [Caml-list] Bioinformatics Js_of_ocaml GSoC project Ashish Agarwal
2014-03-04 11:26 ` Florent Monnier
2014-03-04 16:45 ` Ashish Agarwal
2014-03-04 16:37 ` Kristopher Micinski
2014-03-04 16:48 ` Ashish Agarwal
2014-03-04 17:03 ` Kristopher Micinski
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