Re: [BlueObelisk-discuss] Best wishes from the COD team!
On Mon, Feb 10, 2014 at 11:37 AM, Saulius Gražulis grazu...@ibt.lt wrote: Dear colleagues, during the two very exciting weeks of hacking with Peter Murray-Rust, in Vilnius, he suggested that I join the Blue Obelisk community and the mailing list. And I awarded Saulius a Blue Obelisk in recognition of the massive contribution to chemical Open Data that COD has made. We are about to see this expand even further. Let me introduce myself: I am currently heading the Vilnius team of the Crystallography Open Database, and maintain the database site at the Vilnius University Institute of Biotechnology (http://www.crystallography.net). As such, I am very interested in (co)-developing free software for chemistry and crystallography, and sharing data. You are cordially invited to use COD, to download COD and to contribute to its development if you wish. Saulius and colleagues have built a superb server which can update crystallography on a daily basis and publish it to the whole world. There is also a strong tradition of COD members reviewing structures and I have seen some structures with several curatorial events. Another project which we have started recently, and which I would like to discuss and coordinate with you, is the Theoretical Crystallography Open Database (TCOD, http://www.crystallography.net/tcod/). After our successful development of COD (which contains experimental crystal structures), and after several requests from a community, we have started TCOD to collect published structures, computed using DFT and other methods. This should be of great value to those who either compute crystal structures for predictive purpose or to compute properties. Peter has told me that the NWChem group, who is present on this mailing list :), has done a large work in developing ontologies to describe various computational methods and encode (meta)data in CML. It seems to me like a good idea to join our efforts, to make a set of descriptions and quality criteria endorsed by computational community, and to have a comprehensive representation of computation results in TCOD. The BO community is indebted to all authors of fully Open source code (FLOSS) of which NWChem is one. The NWChem community has also been presented with an obelisk because of not only open-sourcing the code but their commitment to community development of vocabularies. I'm looking forward to hear from you! Sincerely, Saulius Note that we have transferred the CrystalEye data and software to Vilnius so that it will be continually enhanced by Nick Day's great work on extracting molecules from crystal structures and adding chemistry with software. P -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Best wishes from the COD team!
Saulius, Welcome! Do you know about all the cool crystallographic capabilities of Jmol? Latest is incommensurately modulated structures. Let's talk! Bob Hanson On Mon, Feb 10, 2014 at 5:37 AM, Saulius Gražulis grazu...@ibt.lt wrote: Dear colleagues, during the two very exciting weeks of hacking with Peter Murray-Rust, in Vilnius, he suggested that I join the Blue Obelisk community and the mailing list. Let me introduce myself: I am currently heading the Vilnius team of the Crystallography Open Database, and maintain the database site at the Vilnius University Institute of Biotechnology (http://www.crystallography.net). As such, I am very interested in (co)-developing free software for chemistry and crystallography, and sharing data. You are cordially invited to use COD, to download COD and to contribute to its development if you wish. Another project which we have started recently, and which I would like to discuss and coordinate with you, is the Theoretical Crystallography Open Database (TCOD, http://www.crystallography.net/tcod/). After our successful development of COD (which contains experimental crystal structures), and after several requests from a community, we have started TCOD to collect published structures, computed using DFT and other methods. Peter has told me that the NWChem group, who is present on this mailing list :), has done a large work in developing ontologies to describe various computational methods and encode (meta)data in CML. It seems to me like a good idea to join our efforts, to make a set of descriptions and quality criteria endorsed by computational community, and to have a comprehensive representation of computation results in TCOD. I'm looking forward to hear from you! Sincerely, Saulius P.S. In a short while, I'll post another message regarding presentation of TCOD at the IUCr 2014 Congress in Montreal. -- Dr. Saulius Gražulis Vilnius University Institute of Biotechnology, Graiciuno 8 LT-02241 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 mobile: (+370-684)-49802, (+370-614)-36366 -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Androidtrade; apps run on BlackBerryreg;10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Best wishes from the COD team!
Hi everyone, On Feb 10 2014, Peter Murray-Rust wrote: On Mon, Feb 10, 2014 at 11:37 AM, Saulius Gražulis grazu...@ibt.lt wrote: Dear colleagues, during the two very exciting weeks of hacking with Peter Murray-Rust, in Vilnius, he suggested that I join the Blue Obelisk community and the mailing list. And I awarded Saulius a Blue Obelisk in recognition of the massive contribution to chemical Open Data that COD has made. We are about to see this expand even further. Welcome Saulius! Although I am myself not a frequent author on this mailing list, I've noticed COD before and liek it! Peter has told me that the NWChem group, who is present on this mailing list :), has done a large work in developing ontologies to describe various computational methods and encode (meta)data in CML. It seems to me like a good idea to join our efforts, to make a set of descriptions and quality criteria endorsed by computational community, and to have a comprehensive representation of computation results in TCOD. The BO community is indebted to all authors of fully Open source code (FLOSS) of which NWChem is one. The NWChem community has also been presented with an obelisk because of not only open-sourcing the code but their commitment to community development of vocabularies. @Peter and others: does NWChem write CML? I was planning to do some work on a NWChem parser in cclib (which will export CML itself), but if NWChem already writes CML that would not be a priority. Cheers, Karol -- written by Karol M. Langner Mon Feb 10 13:40:55 EST 2014 -- Androi apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Best wishes from the COD team!
On Mon, Feb 10, 2014 at 6:45 PM, Karol M. Langner karol.lang...@gmail.comwrote: Hi everyone, @Peter and others: does NWChem write CML? I was planning to do some work on a NWChem parser in cclib (which will export CML itself), but if NWChem already writes CML that would not be a priority. Bert de Jong will be able to tell you the exact poisition - but it's in the pipeline. I have written logfile2CML parsers for about 10 compchem codes and they are in http://bitbucket.org/petermr/jumbo-converters. Their goal is to extract all information from logfiles into semantic form. Bert is coordinating the effort to create vocabularies for compchem (Bert - what is your new email address??) Cheers, Karol -- written by Karol M. Langner Mon Feb 10 13:40:55 EST 2014 -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Best wishes from the COD team!
On Feb 10 2014, Peter Murray-Rust wrote: On Mon, Feb 10, 2014 at 6:45 PM, Karol M. Langner karol.lang...@gmail.comwrote: Hi everyone, @Peter and others: does NWChem write CML? I was planning to do some work on a NWChem parser in cclib (which will export CML itself), but if NWChem already writes CML that would not be a priority. Bert de Jong will be able to tell you the exact poisition - but it's in the pipeline. I have written logfile2CML parsers for about 10 compchem codes and they are in http://bitbucket.org/petermr/jumbo-converters. Their goal is to extract all information from logfiles into semantic form. Bert is coordinating the effort to create vocabularies for compchem (Bert - what is your new email address??) Thanks Peter, I've contacted Saulius off-list. -- written by Karol M. Langner Mon Feb 10 16:18:01 EST 2014 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Best wishes from the COD team!
On 02/10/2014 07:38 PM, Robert Hanson wrote: Do you know about all the cool crystallographic capabilities of Jmol? Yes, we do use Jmol extensively! Thanks for great software! Latest is incommensurately modulated structures. These I have not used yet. Very interesting! -- Dr. Saulius Gražulis Vilnius University Institute of Biotechnology, Graiciuno 8 LT-02241 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 mobile: (+370-684)-49802, (+370-614)-36366 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
