[BlueObelisk-discuss] Google Summer of Code 2014 options?

[Egon Willighagen]

Hi all,

another year, another Google Summer of Code. And again it is possible
to work on Open Source tools in the area of chemistry.

Below are a few things that I have spotted. What else is out there?

* NRNB mentoring organization [0]
- Cytoscape has a chemical structure viz plugin based on the CDK that
needs updating
- PathVisio has a chemical structure viz plugin based on the CDK that
needs updating
- There is a project idea to integrate Cytoscape into Bioclipse
- There is a project idea to integrate PathVisio into Bioclipse
* VTK mentoring organization [1]
- various chemistry related ideas
* ScaffoldHunter (GPLv3) [2]
- no specific ideas, but based on the CDK, and could use updating to CDK 1.5

Anything else?

Egon

0.http://nrnb.org/gsoc/index.html#ideas-tab
1.http://www.vtk.org/Wiki/VTK/GSoC
2.http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=project_ideas

[Peter Murray-Rust]

Is this still possible (I was invited to a phylogenetic project but told
that it wasn't funded). So has the deadline passed?


On Sat, Mar 1, 2014 at 11:41 PM, Egon Willighagen <

Post by Egon Willighagen
Hi all,
another year, another Google Summer of Code. And again it is possible
to work on Open Source tools in the area of chemistry.
Below are a few things that I have spotted. What else is out there?
* NRNB mentoring organization [0]
- Cytoscape has a chemical structure viz plugin based on the CDK that
needs updating
- PathVisio has a chemical structure viz plugin based on the CDK that
needs updating
- There is a project idea to integrate Cytoscape into Bioclipse
- There is a project idea to integrate PathVisio into Bioclipse
* VTK mentoring organization [1]
- various chemistry related ideas
* ScaffoldHunter (GPLv3) [2]
- no specific ideas, but based on the CDK, and could use updating to CDK 1.5
Anything else?
Egon
0.http://nrnb.org/gsoc/index.html#ideas-tab
1.http://www.vtk.org/Wiki/VTK/GSoC
2.http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=project_ideas
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
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[Egon Willighagen]

Dear Peter,

Post by Peter Murray-Rust
Is this still possible (I was invited to a phylogenetic project but told
that it wasn't funded). So has the deadline passed?

The deadline for mentoring organizations has passed. I did not have
time to try and see if we good bootstrap something for the Blue
Obelisk. Though I think we're in a better position than the previous
time.

Now, it's time for students to propose something. Peter, a full list
of projects is found here:

http://www.google-melange.com/gsoc/org/list/public/google/gsoc2014

In the past, I was mentor via a non-chemistry project, KDE (one of the
major linux desktop experiences), on a data extractor called Strigi.

If you know good students (B.Sc/M.Sc *of* PhD student), please make
them aware of things.

For pathways (the NRNB project) there is a lot of potential text
mining that can be done. This is done in our group by Andra
Waagmeester. One area of interest is CYP metabolism (think xmetdb.org)
and finding literature that actually gives information on CYP
metabolism of drugs is hard to access and assess. For example, I am
now trying to figure out how they determined the CYP metabolism of the
2013 top 1 drug aripiprazole and after some initial (2 hour)
gscholaring I end up with references to posters and internal reports,
but nothing that tells me how they determined what specific CYPs are
showing activity for this drug.

A second area where text mining may interest me, is text mining of
nanomaterial toxicity information. I drew up recently two biological
pathways that may be involved here:
http://www.wikipathways.org/index.php/Portal:Nanomaterials Here too,
text mining as a starting point for searching literature would be very
valuable.

But, it starts with finding a good student, then contacting the host
organization to find a mentor (the above two ideas I would certainly
like to co-mentor), discuss the project with the mentor, and have the
student write a good proposal, and hope it gets selected...

Egon

[Peter Murray-Rust]

understood. It may be wroth posting on OKFN open-science

Post by Egon Willighagen
Dear Peter,

Post by Peter Murray-Rust
Is this still possible (I was invited to a phylogenetic project but told
that it wasn't funded). So has the deadline passed?

The deadline for mentoring organizations has passed. I did not have
time to try and see if we good bootstrap something for the Blue
Obelisk. Though I think we're in a better position than the previous
time.
Now, it's time for students to propose something. Peter, a full list
http://www.google-melange.com/gsoc/org/list/public/google/gsoc2014
In the past, I was mentor via a non-chemistry project, KDE (one of the
major linux desktop experiences), on a data extractor called Strigi.
If you know good students (B.Sc/M.Sc *of* PhD student), please make
them aware of things.
For pathways (the NRNB project) there is a lot of potential text
mining that can be done. This is done in our group by Andra
Waagmeester. One area of interest is CYP metabolism (think xmetdb.org)
and finding literature that actually gives information on CYP
metabolism of drugs is hard to access and assess. For example, I am
now trying to figure out how they determined the CYP metabolism of the
2013 top 1 drug aripiprazole and after some initial (2 hour)
gscholaring I end up with references to posters and internal reports,
but nothing that tells me how they determined what specific CYPs are
showing activity for this drug.
A second area where text mining may interest me, is text mining of
nanomaterial toxicity information. I drew up recently two biological
http://www.wikipathways.org/index.php/Portal:Nanomaterials Here too,
text mining as a starting point for searching literature would be very
valuable.
But, it starts with finding a good student, then contacting the host
organization to find a mentor (the above two ideas I would certainly
like to co-mentor), discuss the project with the mentor, and have the
student write a good proposal, and hope it gets selected...
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286