[BlueObelisk-discuss] Fwd: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties
FYI -- Forwarded message -- From: P.Canepa pc...@kent.ac.uk Date: Mon, Oct 25, 2010 at 10:09 AM Subject: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net, jmol-develop...@list.sourceforge.net jmol-develop...@list.sourceforge.net Dear all, I would like to inform you that I have released my first project, which entirely relies on Jmol. Its name is J-ICE which stand for: a Jmol interface for crystallographic and electronic properties. J-ICE allows users to visualize, to build and to manipulate complex input/output results (deriving from modelling) entirely via a web-server, i.e. without the burden of installing complex packages. At present J-ICE focuses only on rendering and handling crystal structures and their properties as resulting from the application of modern programs such as CRYSTAL09, CASTEP, FHI-aims, QUANTUM ESPRESSO, VASP, Wien2K, etc.. J-ICE is released under the GNU agreement and its project page can be browsed at http://j-ice.sourceforge.net/. The application it self is available for browsing at the this address http://j-ice.sourceforge.net/ondemand/index.html. Alternatively you can download it at https://sourceforge.net/projects/j-ice/ . I would also like to express my gratitude to Bob Hanson, Angel Herraez and Jonathan Gutow for their endless patience, helpfulness and competence during the development of such interface . Comments an ds suggestion are welcomed. Best regards, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456 --- -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Jmol-users mailing list jmol-us...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk
On Sun, Oct 24, 2010 at 10:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps we can collaborate with reusing/extending existing OpenTox REST services with similar functionality and sharing experience with development of web services based on RDF . Perhaps as a start the data can just be pulled and put in one of the current OpenTox servers? Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk
On 25 October 2010 12:07, Egon Willighagen egon.willigha...@gmail.comwrote: On Sun, Oct 24, 2010 at 10:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps we can collaborate with reusing/extending existing OpenTox REST services with similar functionality and sharing experience with development of web services based on RDF . Perhaps as a start the data can just be pulled and put in one of the current OpenTox servers? No problem with this - do you have in mind particular piece of data to start with ? Nina Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 ___ Development mailing list developm...@opentox.org http://www.opentox.org/mailman/listinfo/development -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk
On Mon, Oct 25, 2010 at 11:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps as a start the data can just be pulled and put in one of the current OpenTox servers? No problem with this - do you have in mind particular piece of data to start with ? Check here... http://quixote.wikispot.org/Front_Page And check Peter's blog post today: http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2668 E. -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk
On 25 October 2010 12:16, Egon Willighagen egon.willigha...@gmail.comwrote: On Mon, Oct 25, 2010 at 11:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps as a start the data can just be pulled and put in one of the current OpenTox servers? No problem with this - do you have in mind particular piece of data to start with ? Check here... http://quixote.wikispot.org/Front_Page OK, thanks. OpenTox dataset services accepts CML for upload (it's just POST via OpenTox API), so this is trivial. This one http://neptuno.unizar.es/files/public/datasets/Quixote/examples/HCO-L-Ala-NH2.cml is already here http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/5552 It could be GET in several formats , including RDF, CML, MDL SMILES ( HTTP Accept header) For gaussian files it should be feasible as well, does CDK reads gaussian files ? Once uploaded it automatically becomes structure searchable and searchable by any properties in the uploaded file, not mentioning all OpenTox algorithms can be applied. Similarity search as an example http://ambit.uni-plovdiv.bg:8080/ambit2/query/similarity?type=urlsearch=http%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Fcompound%2F163144%2Fconformer%2F506335threshold=0.7feature_uris[]=max=100 And check Peter's blog post today: http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2668 OK. Nina E. -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 ___ Development mailing list developm...@opentox.org http://www.opentox.org/mailman/listinfo/development -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Fwd: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties
Piero This is fantastic. (I haven't had time to visit your site in detail). Two immediate ways of interacting on Open Source and Open data. If you want crystallographic data we have 200,000 crystal structures at: http://wwmm.ch.cam.ac.uk/crystaleye. These are all from the literature. They are present as CIF and CML and Jmol compatible. You might want to consider an interface We have just started a collaborative Open project on a computational knowledgebase for molecules. see http://quixote.wikispot.org/Front_Page . We now intend to develop this for crystalline materials. Your experience and involvement would be great. I have copied in Pablo Echenique. It should be possible to use your approach to browse the knowledgebase P. On Mon, Oct 25, 2010 at 9:15 AM, Egon Willighagen egon.willigha...@gmail.com wrote: FYI -- Forwarded message -- From: P.Canepa pc...@kent.ac.uk Date: Mon, Oct 25, 2010 at 10:09 AM Subject: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net, jmol-develop...@list.sourceforge.net jmol-develop...@list.sourceforge.net Dear all, I would like to inform you that I have released my first project, which entirely relies on Jmol. Its name is J-ICE which stand for: a Jmol interface for crystallographic and electronic properties. J-ICE allows users to visualize, to build and to manipulate complex input/output results (deriving from modelling) entirely via a web-server, i.e. without the burden of installing complex packages. At present J-ICE focuses only on rendering and handling crystal structures and their properties as resulting from the application of modern programs such as CRYSTAL09, CASTEP, FHI-aims, QUANTUM ESPRESSO, VASP, Wien2K, etc.. J-ICE is released under the GNU agreement and its project page can be browsed at http://j-ice.sourceforge.net/. The application it self is available for browsing at the this address http://j-ice.sourceforge.net/ondemand/index.html. Alternatively you can download it at https://sourceforge.net/projects/j-ice/ . I would also like to express my gratitude to Bob Hanson, Angel Herraez and Jonathan Gutow for their endless patience, helpfulness and competence during the development of such interface . Comments an ds suggestion are welcomed. Best regards, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456 --- -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Jmol-users mailing list jmol-us...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] [quixote-qcdb] Re: [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk
Nina, On Mon, Oct 25, 2010 at 12:28 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Mon, Oct 25, 2010 at 10:33 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: For gaussian files it should be feasible as well, does CDK reads gaussian files ? JUMBO does and the transofrmation is designed to be lossless by using a dictionary structure. CDK has only a minimal Gaussian readers, that extracts 3D coordinates, and might actually do vibrations, but nothing much else. I think what we will want to do, is extend the CDK CMLReader to understand the CMLComp conventions... I have not looked at that yet, nor even tried to read one of the Quixote files in Bioclipse, but will try to find some time for that this week... Actually, I will try the Bioclipse-OpenTox downloadDataset() functionality on this data set tonight: http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/5552 Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] [quixote-qcdb] Re: [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk
On Mon, Oct 25, 2010 at 11:47 AM, Egon Willighagen egon.willigha...@gmail.com wrote: Nina, On Mon, Oct 25, 2010 at 12:28 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Mon, Oct 25, 2010 at 10:33 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: For gaussian files it should be feasible as well, does CDK reads gaussian files ? JUMBO does and the transofrmation is designed to be lossless by using a dictionary structure. CDK has only a minimal Gaussian readers, that extracts 3D coordinates, and might actually do vibrations, but nothing much else. I think what we will want to do, is extend the CDK CMLReader to understand the CMLComp conventions... That's exactly the right way to go. A typical CMLComp document (from a log file) might include modules such as init; optimisation, final coords, Hessian, Frequencies, NMR calculations. -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
