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 ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
