From: Konstantin T. <an...@ya...> - 2010-01-26 20:57:01
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Hello, I'd like to setup local database containing reagents used in our laboratory and use JCP for substructure search. Is there any working solution for interaction of JCP with database? What 3rd party software is needed? -- Regards, Konstantin |
From: Rajarshi G. <raj...@gm...> - 2010-01-26 21:05:18
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I'd think that JCP should be independent of any specific DB. On Tue, Jan 26, 2010 at 3:56 PM, Konstantin Tokarev <an...@ya...> wrote: > Hello, > I'd like to setup local database containing reagents used in our laboratory and use JCP for substructure search. Is there any working solution for interaction of JCP with database? What 3rd party software is needed? > -- > Regards, > Konstantin > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > -- Rajarshi Guha NIH Chemical Genomics Center |
From: Konstantin T. <an...@ya...> - 2010-01-26 21:13:18
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Do you mean there's no API for interaction? 26.01.10, 16:05, "Rajarshi Guha" <raj...@gm...>: > I'd think that JCP should be independent of any specific DB. > On Tue, Jan 26, 2010 at 3:56 PM, Konstantin Tokarev wrote: > > Hello, > > I'd like to setup local database containing reagents used in our laboratory and use JCP for substructure search. Is there any working solution for interaction of JCP with database? What 3rd party software is needed? > > -- > > Regards, > > Konstantin > > > > ------------------------------------------------------------------------------ > > The Planet: dedicated and managed hosting, cloud storage, colocation > > Stay online with enterprise data centers and the best network in the business > > Choose flexible plans and management services without long-term contracts > > Personal 24x7 support from experience hosting pros just a phone call away. > > http://p.sf.net/sfu/theplanet-com > > _______________________________________________ > > Cdk-jchempaint mailing list > > Cdk...@li... > > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > > > -- > Rajarshi Guha > NIH Chemical Genomics Center > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint -- Regards, Konstantin Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign |
From: Rajarshi G. <raj...@gm...> - 2010-01-26 21:12:38
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No, I meant that JCP is just for drawing/viewing a structure. Your DB interaction code should be independent of JCP. Depending on how the app is structured, you'd draw a substructure, click a button and the code would pull the SMILES from the JCP instance, connect to the DB, perform the search and then display results. 2010/1/26 Konstantin Tokarev <an...@ya...>: > Do you mean there's no API for interaction? > > 26.01.10, 16:05, "Rajarshi Guha" <raj...@gm...>: > >> I'd think that JCP should be independent of any specific DB. >> On Tue, Jan 26, 2010 at 3:56 PM, Konstantin Tokarev wrote: >> > Hello, >> > I'd like to setup local database containing reagents used in our laboratory and use JCP for substructure search. Is there any working solution for interaction of JCP with database? What 3rd party software is needed? >> > -- >> > Regards, >> > Konstantin >> > >> > ------------------------------------------------------------------------------ >> > The Planet: dedicated and managed hosting, cloud storage, colocation >> > Stay online with enterprise data centers and the best network in the business >> > Choose flexible plans and management services without long-term contracts >> > Personal 24x7 support from experience hosting pros just a phone call away. >> > http://p.sf.net/sfu/theplanet-com >> > _______________________________________________ >> > Cdk-jchempaint mailing list >> > Cdk...@li... >> > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint >> > >> -- >> Rajarshi Guha >> NIH Chemical Genomics Center >> ------------------------------------------------------------------------------ >> The Planet: dedicated and managed hosting, cloud storage, colocation >> Stay online with enterprise data centers and the best network in the business >> Choose flexible plans and management services without long-term contracts >> Personal 24x7 support from experience hosting pros just a phone call away. >> http://p.sf.net/sfu/theplanet-com >> _______________________________________________ >> Cdk-jchempaint mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > > -- > Regards, > Konstantin > > Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign > -- Rajarshi Guha NIH Chemical Genomics Center |
From: Stefan K. <ste...@eb...> - 2010-01-27 09:23:14
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On Tuesday 26 January 2010 21:05:08 Rajarshi Guha wrote: > I'd think that JCP should be independent of any specific DB. Indeed. You would retrieve the structure from JCP in some format (mol or whatever you like) and start your search with that. So JCP has nothing to do with the search as a such. You would need to use some database plugin like the MDL cartridge, Orchem or similar for the search. Stefan > > On Tue, Jan 26, 2010 at 3:56 PM, Konstantin Tokarev <an...@ya...> wrote: > > Hello, > > I'd like to setup local database containing reagents used in our > > laboratory and use JCP for substructure search. Is there any working > > solution for interaction of JCP with database? What 3rd party software is > > needed? -- > > Regards, > > Konstantin > > > > ------------------------------------------------------------------------- > >----- The Planet: dedicated and managed hosting, cloud storage, colocation > > Stay online with enterprise data centers and the best network in the > > business Choose flexible plans and management services without long-term > > contracts Personal 24x7 support from experience hosting pros just a phone > > call away. http://p.sf.net/sfu/theplanet-com > > _______________________________________________ > > Cdk-jchempaint mailing list > > Cdk...@li... > > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint -- Stefan Kuhn B. Sc. M. A. Software Engineer in the Chemoinformatics and Metabolism Team European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2657 Fax +44 (0)1223 494 468 |
From: Egon W. <ego...@gm...> - 2010-01-27 10:09:30
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On Tue, Jan 26, 2010 at 9:56 PM, Konstantin Tokarev <an...@ya...> wrote: > I'd like to setup local database containing reagents used in our laboratory and use JCP for substructure search. Is there any working solution for interaction of JCP with database? What 3rd party software is needed? Are you using MyChem of PgChem, perhaps? I can imagine someone should write a JavaScript (perhaps using jQuery?) library that links JChemPaint to ChemiSQL instances, like the above too, or OrChem by Mark at the EBI... Mark/Stefan, how is ChEBI linking JChemPaint to the ChEBI database substructure searching? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Stefan K. <ste...@eb...> - 2010-01-27 10:13:10
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> how is ChEBI linking JChemPaint to the ChEBI database substructure > searching? Export of structure in mol format to a text field via JavaScript, submission of the form via http and execution of search on server using the mol file. I think this is the only way you can do it in a webapp, since the applet is running on client and the database on the server, so a direct link seems not possible for me. Stefan > > Egon -- Stefan Kuhn B. Sc. M. A. Software Engineer in the Chemoinformatics and Metabolism Team European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2657 Fax +44 (0)1223 494 468 |