From: Ola S. <ola...@fa...> - 2005-11-23 23:17:13
|
Hi, Sorry for cross-posting, but this concerns both the CDK and Bioclipse projects. I am looking at how the molecular database-plugin for bioclipse (bc_db) should be designed, and I have some thoughts and proposals that I would like comments on. 1) We use Hibernate3 so that we get transparent OORDB-mapping and multiple database support (and follow the standard of EJB3) 2) We provide the functionality to organize molecules in collections (folders) 3) We store XML in a relational database as text (I know, but it IS much faster) 4) We provide HSQLDB with biolipse as an embedded database 5) Connected database-instances show up in the FileViewer (that possibly should be renamed?) 6) A user can do everything with a database object that he can do with a file object now 7) The database supports subsearches, fingerprint-searches, inchi-searches etc. Comments? How much is already done in NMRDB? What about XMLDB? We could provide another plugin to support that, I suppose. What would we gain from using an XMLDB instead of an RDB? Well, just some thoughts. A database-plugin is probably a very nice feature of Bioclipse. Cheers, .../Ola |
From: Stefan K. <ste...@un...> - 2005-11-24 09:19:00
|
Hi Chitti, please see this mails for ideas on the database. I'm not quite sure right= now=20 how this can be integrated with our plans, but I think you should follow = the=20 discussion. Please also subscribe to the bioclipse mailing list via sf.ne= t.=20 Also ask Ola to make you a developer on bioclipse project (tell your sf n= ame=20 for that) so that we can check in your stuff if you finish something. Stefan Am Thursday 24 November 2005 00:18 schrieb Ola Spjuth: > Hi, > > Sorry for cross-posting, but this concerns both the CDK and Bioclipse > projects. > > I am looking at how the molecular database-plugin for bioclipse (bc_db) > should be designed, and I have some thoughts and proposals that I would > like comments on. > > 1) We use Hibernate3 so that we get transparent OORDB-mapping and > multiple database support (and follow the standard of EJB3) > > 2) We provide the functionality to organize molecules in collections > (folders) > > 3) We store XML in a relational database as text (I know, but it IS muc= h > faster) > > 4) We provide HSQLDB with biolipse as an embedded database > > 5) Connected database-instances show up in the FileViewer (that possibl= y > should be renamed?) > > 6) A user can do everything with a database object that he can do with = a > file object now > > 7) The database supports subsearches, fingerprint-searches, > inchi-searches etc. > > Comments? How much is already done in NMRDB? What about XMLDB? We could > provide another plugin to support that, I suppose. What would we gain > from using an XMLDB instead of an RDB? > > Well, just some thoughts. A database-plugin is probably a very nice > feature of Bioclipse. > > Cheers, > > .../Ola > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files for problems? Stop! Download the new AJAX search engine that ma= kes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel --=20 Stefan Kuhn M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=C3=BClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 My public PGP key is available at http://pgp.mit.edu |
From: Stefan K. <ste...@un...> - 2005-11-24 09:37:17
|
Sorry, this was wrong email adress. Please disregard. Stefan Am Thursday 24 November 2005 10:49 schrieb Stefan Kuhn: > Hi Chitti, > please see this mails for ideas on the database. I'm not quite sure rig= ht > now how this can be integrated with our plans, but I think you should > follow the discussion. Please also subscribe to the bioclipse mailing l= ist > via sf.net. Also ask Ola to make you a developer on bioclipse project (= tell > your sf name for that) so that we can check in your stuff if you finish > something. Stefan > > Am Thursday 24 November 2005 00:18 schrieb Ola Spjuth: > > Hi, > > > > Sorry for cross-posting, but this concerns both the CDK and Bioclipse > > projects. > > > > I am looking at how the molecular database-plugin for bioclipse (bc_d= b) > > should be designed, and I have some thoughts and proposals that I wou= ld > > like comments on. > > > > 1) We use Hibernate3 so that we get transparent OORDB-mapping and > > multiple database support (and follow the standard of EJB3) > > > > 2) We provide the functionality to organize molecules in collections > > (folders) > > > > 3) We store XML in a relational database as text (I know, but it IS m= uch > > faster) > > > > 4) We provide HSQLDB with biolipse as an embedded database > > > > 5) Connected database-instances show up in the FileViewer (that possi= bly > > should be renamed?) > > > > 6) A user can do everything with a database object that he can do wit= h a > > file object now > > > > 7) The database supports subsearches, fingerprint-searches, > > inchi-searches etc. > > > > Comments? How much is already done in NMRDB? What about XMLDB? We cou= ld > > provide another plugin to support that, I suppose. What would we gain > > from using an XMLDB instead of an RDB? > > > > Well, just some thoughts. A database-plugin is probably a very nice > > feature of Bioclipse. > > > > Cheers, > > > > .../Ola > > > > > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through lo= g > > files for problems? Stop! Download the new AJAX search engine that > > makes searching your log files as easy as surfing the web. DOWNLOAD > > SPLUNK! http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Cdk-devel mailing list > > Cdk...@li... > > https://lists.sourceforge.net/lists/listinfo/cdk-devel --=20 Stefan Kuhn M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=C3=BClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 My public PGP key is available at http://pgp.mit.edu |