Egon Willighagen
2016-03-01 13:49:43 UTC
Hi all,
the NRNB is an USA-based organization around Cytoscape and
WikiPathways, the latter involving PathVisio. You may know that
Cytoscape has a plugin that used the CDK (by Scooter Morris et al.,
UCSF) and here in Maastricht we have been working on PathVisio plugins
for metabolites also using the CDK.
Now, the NRNB has been accepted to the Google Summer of Code and there
are at least two projects where the CDK is related too:
1. https://github.com/nrnb/GoogleSummerOfCode/issues/46
The following project idea is using Java and would involve the CDK directly:
https://github.com/nrnb/GoogleSummerOfCode/issues/46
Here, the idea is integrating a 2D visualization plugin and the
outcome of work by Rianne Fijten for metabolite data (e.g. using the
CDK-based HOSE/NMR prediction stack). These plugins need updating and
integration.
2. https://github.com/nrnb/GoogleSummerOfCode/issues/47
The second idea is in JavaScript where I envision use of remote
services that can convert SMILES and/or identifiers to SVG images of
2D depictions. John's CDKDepict would be a good candidate, but I would
not mind a flexible system that can use other services too, like
perhaps AMBIT.
Now, Noel asked about a JS translation of the CDK stack. That would be
a lot more work, and not sure if it is entirely feasible, but I'm more
than happy to discuss that with the student applicant and co-mentor.
So, if you are a student or know one, please check out these ideas. Of
course, applying does not mean you will get the 5000 dollar to work
for three months during the summer holidays. That's because the NRNB
organization will pick the best proposal (which the students will have
to write). The project ideas are just suggestions, and students are
invited to tune to their interest (though commonly in collaboration
with the anticipated mentor(s)).
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
ImpactStory: https://impactstory.org/EgonWillighagen
the NRNB is an USA-based organization around Cytoscape and
WikiPathways, the latter involving PathVisio. You may know that
Cytoscape has a plugin that used the CDK (by Scooter Morris et al.,
UCSF) and here in Maastricht we have been working on PathVisio plugins
for metabolites also using the CDK.
Now, the NRNB has been accepted to the Google Summer of Code and there
are at least two projects where the CDK is related too:
1. https://github.com/nrnb/GoogleSummerOfCode/issues/46
The following project idea is using Java and would involve the CDK directly:
https://github.com/nrnb/GoogleSummerOfCode/issues/46
Here, the idea is integrating a 2D visualization plugin and the
outcome of work by Rianne Fijten for metabolite data (e.g. using the
CDK-based HOSE/NMR prediction stack). These plugins need updating and
integration.
2. https://github.com/nrnb/GoogleSummerOfCode/issues/47
The second idea is in JavaScript where I envision use of remote
services that can convert SMILES and/or identifiers to SVG images of
2D depictions. John's CDKDepict would be a good candidate, but I would
not mind a flexible system that can use other services too, like
perhaps AMBIT.
Now, Noel asked about a JS translation of the CDK stack. That would be
a lot more work, and not sure if it is entirely feasible, but I'm more
than happy to discuss that with the student applicant and co-mentor.
So, if you are a student or know one, please check out these ideas. Of
course, applying does not mean you will get the 5000 dollar to work
for three months during the summer holidays. That's because the NRNB
organization will pick the best proposal (which the students will have
to write). The project ideas are just suggestions, and students are
invited to tune to their interest (though commonly in collaboration
with the anticipated mentor(s)).
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
ImpactStory: https://impactstory.org/EgonWillighagen