GSoC project [Visualisation for BLAST results] [Hiten Chowdhary -> Yannick Wurm / Anurag Priyam]

[Hiten Chowdhary]

I am Hiten. I will be working this summer on extending and improving visualisation of BLAST result in SequenceServer, as part of GSoC under Open Genome Informatics organisation.

About Project: BLAST is a standard tool to compare newly obtained and previously known sequences. The goal of the project is to facilitate interpretation of BLAST results through different visualisations such as: length distribution, circos type visualisation, and dot-plot. The visualisations will be created using d3 and / or Plotly in a reusable manner. The visualisations will be integrated with SequenceServer, a popular BLAST server written in Ruby.

About Me: I am undergraduate student of Department of Mathematics, IIT Kharagpur. I got engaged with Ruby during my college web development event where I learnt about Ruby on Rails. Ruby's simplicity and agility made it so easy to work with.

 It is an great opportunity and I am excited to make the most of it.

--

Regards,

Hiten Chowdhary

Undergraduate Student

Department of Mathematics

IIT Kharagpur

Ph: +919800111032

[Sameer Deshmukh]

Hi,

Nice project. Have you been selected by the Ruby org?

Visualization is always of interest to us. Can you give us an overview of the capabilites of the finished product that you aspire to create and some links where we track your progress?

Also if you could send in a link to your proposal, that would be great.

[Pjotr Prins]

This would be OBF - bioruby.

Pj.

On Wed, May 11, 2016 at 10:06:55AM -0700, Sameer Deshmukh wrote:
> Hi,
> Nice project. Have you been selected by the Ruby org?
> Visualization is always of interest to us. Can you give us an overview of
> the capabilites of the finished product that you aspire to create and some
> links where we track your progress?
> Also if you could send in a link to your proposal, that would be great.
>
> On Wednesday, May 11, 2016 at 3:28:10 PM UTC+5:30, Hiten Chowdhary wrote:
>
> I am Hiten. I will be working this summer on extending and improving

> visualisation of BLAST result in [1]SequenceServer, as part of GSoC

> under Open Genome Informatics organisation.
> About Project: BLAST is a standard tool to compare newly obtained and
> previously known sequences. The goal of the project is to facilitate
> interpretation of BLAST results through different visualisations such
> as: length distribution, circos type visualisation, and dot-plot. The
> visualisations will be created using d3 and / or Plotly in a reusable
> manner. The visualisations will be integrated with SequenceServer, a
> popular BLAST server written in Ruby.
> About Me: I am undergraduate student of Department of Mathematics, IIT
> Kharagpur. I got engaged with Ruby during my college web development
> event where I learnt about Ruby on Rails. Ruby's simplicity and agility
> made it so easy to work with.
>  It is an great opportunity and I am excited to make the most of it.
> --
>
> Regards,
>
> Hiten Chowdhary
>
> Undergraduate Student
>
> Department of Mathematics
>
> IIT Kharagpur
>
> Ph: +919800111032
>

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> References
>
> Visible links
> 1. https://www.sequenceserver.com/
> 2. mailto:sciruby-dev...@googlegroups.com
> 3. https://groups.google.com/d/optout


--

[Yannick Wurm]

Hi all,

thanks Sameer & Pjotr. We indeed have very strong links to the Open Bioinformatics Foundation via Bioruby in particular :)
    (and thanks to OBF's generous funding Priyam will likely be injecting a very ruby-centric mindset to OBF's upcoming BOSC and Codefest events[1,2] which I  strongly recommend)

But actually funding for Hiten's GSoC project has come through the "Open Genome Informatics" group (http://gmod.org). Gmod groups together several widely-used tools for biologist end-users (based on multiple technologies). Our sequenceserver tool is popular and caters to the similar end-users but it seems we're not actually officially part of Gmod...

Our previous student/project (Monica Dragan - gsoc 2013) benefited greatly from interacting with the sciruby community (this is acknowledged in our recent paper resulting from that project [3]). I am similarly hopeful that Hiten & the sciruby group may similarly interact in mutually beneficial manners.


Kind regards,

Yannick


[1]: http://www.open-bio.org/wiki/BOSC_2016
[2]: http://www.open-bio.org/wiki/Codefest_2016
[3]: http://bioinformatics.oxfordjournals.org/content/early/2016/02/26/bioinformatics.btw015.full


---------------------------------------------------------------------------------
https://wurmlab.github.io    y.w...@qmul.ac.uk    Ants, Bees, Genomes & Evolution
skype:yannickwurm +44 207 882 3049
5.21 Fogg, Organismal Biology, Queen Mary U London, Mile End Rd, E14NS London, UK

SequenceServer: BLAST made easy          http://bit.ly/seqserv
GeneValidator: Visualize protein quality http://bit.ly/gvalidator
Arthropod genomics beyond fruit flies    http://bit.ly/ecoevogenomics
Avoid retracting your genomics analysis   http://bit.ly/antiretraction
Ant genomics challenges & opportunities  http://bit.ly/antgenomics
Social supergene affects development     http://bit.ly/supergenedevo

Enter code here...

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>    3. https://groups.google.com/d/optout


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[Pjotr Prins]

Yeah, Monica and mentor was part of our meetings. Maybe we can do the
same for Hiten. It is getting to be a largish group, but we can try.

Pj.

> >    email to [2][1]sciruby-dev...@googlegroups.com.
> >    For more options, visit [3][2]https://groups.google.com/d/optout.
> >
> > References
> >
> >    Visible links
> >    1. [3]https://www.sequenceserver.com/
> >    2. mailto:[4]sciruby-dev...@googlegroups.com
> >    3. [5]https://groups.google.com/d/optout
>
> --

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> 1. javascript:
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[Hiten Chowdhary]

Hi,

Apologies for replying so late. I got a little caught up with trying to wrap up my head around the SequenceServer code ( got 2 PR's merged, 1 reviewed) and refining the project timeline.

Here is link to my current Project Timeline (needs little more work).

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