From: <tho...@us...> - 2008-09-09 22:04:30
|
Revision: 12252 http://cdk.svn.sourceforge.net/cdk/?rev=12252&view=rev Author: thomaskuhn Date: 2008-09-09 22:04:23 +0000 (Tue, 09 Sep 2008) Log Message: ----------- Add some citations Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2008-09-09 19:56:24 UTC (rev 12251) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2008-09-09 22:04:23 UTC (rev 12252) @@ -136,7 +136,7 @@ year = {1992}, abstract = {no abstract}, URL = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci00007a012}, -affiliation = {}, +affiliation = {'}, ISSN = {1549-9596} } @article{WeiningerDavid1988, @@ -149,9 +149,58 @@ year = {1988}, abstract = {no abstract}, URL = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci00057a005}, -affiliation = {}, +affiliation = {'}, ISSN = {1549-9596} } +@article{Degtyarenko2008, +author = {Degtyarenko, Kirill and de Matos, Paula and Ennis, Marcus and Hastings, Janna and Zbinden, Martin and McNaught, Alan and Alcantara, Rafael and Darsow, Michael and Guedj, Mickael and Ashburner, Michael}, +title = {ChEBI: a database and ontology for chemical entities of biological interest}, +journal = {Nucl. Acids Res.}, +volume = {36}, +number = {1}, +pages = {344-350}, +doi = {10.1093/nar/gkm791}, +year = {2008}, +abstract = {no abstract}, +URL = {http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D344}, +eprint = {http://nar.oxfordjournals.org/cgi/reprint/36/suppl_1/D344.pdf} +} +@article{IrwinJ2005, +author = {Irwin, J.J. and Shoichet, B.K.}, +title = {ZINC - A Free Database of Commercially Available Compounds for Virtual Screening}, +journal = {Journal of Chemical Information and Modeling}, +volume = {45}, +number = {1}, +pages = {177-182}, +year = {2005}, +abstract = {no abstract}, +URL = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci049714+}, +affiliation = {Department of Pharmaceutical Chemistry, University of California San Francisco, Genentech Hall, 600 16th Street, San Francisco, California 94143}, +ISSN = {1549-9596} +} +@article{DeLano2005, + author = {DeLano, Warren L.}, + year = {2005/2/1}, + title = {The case for open-source software in drug discovery}, + keywords = {Infrastructure;Application programming interfaces;Molecular operating environment;Proprietary software}, + pages = {213-217}, + volume = {10}, + number = {3}, + journal = {Drug Discovery Today} +} +@article{GuhaR2006, +author = {Guha, R. and Howard, M.T. and Hutchison, G.R. and Murray-Rust, P. and Rzepa, H. and Steinbeck, C. and Wegner, J. and Willighagen, E.L.}, +title = {The Blue Obelisk-Interoperability in Chemical Informatics}, +journal = {Journal of Chemical Information and Modeling}, +volume = {46}, +number = {3}, +pages = {991-998}, +year = {2006}, +abstract = {Abstract: The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.}, +URL = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci050400b}, +affiliation = {Pennsylvania State University, University Park, Pennsylvania 16804-3000, Jmol Project, U. S. A., Cornell University, Ithaca, New York 14853, Cambridge University, Cambridge CB2 1TN, Great Britain, Imperial College, London SW7 2AZ, Great Britain, Cologne University Bioinformatics Center (CUBIC), Z\xFClpicher Str. 47, D-50674 K\xF6ln, Germany, University of T\xFCbingen, T\xFCbingen, Germany, and Jmol project, The Netherlands}, +ISSN = {1549-9596} +} @webpage{PipelinePilotWeb, Author = {Accelrys}, Lastchecked = {July 01, 2008}, @@ -192,3 +241,9 @@ Lastchecked = {July 01, 2008}, Url = {\url{http://pgfoundry.org/projects/pgchem/}}, } +@webpage{PubChem, + Author = {NCBI}, + Lastchecked = {September 09, 2008}, + Url = {\url{http://pubchem.ncbi.nlm.nih.gov/}}, +} + This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2009-08-03 21:11:59
|
Revision: 14695 http://cdk.svn.sourceforge.net/cdk/?rev=14695&view=rev Author: egonw Date: 2009-08-03 21:11:46 +0000 (Mon, 03 Aug 2009) Log Message: ----------- Fixed syntax: and between each author Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-03 20:17:30 UTC (rev 14694) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-03 21:11:46 UTC (rev 14695) @@ -212,7 +212,7 @@ ISSN = {1549-9596} } @article{Carpenter1991, - author = {Carpenter, G.A., Grossberg, S. und Rosen, D.}, + author = {Carpenter, G.A. and Grossberg, S. and Rosen, D.}, year = {1991}, title = {ART 2-A: an adaptive resonance algorithm for rapid categorylearning and recognition.}, pages = {493-504}, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ste...@us...> - 2009-08-10 14:11:16
|
Revision: 14707 http://cdk.svn.sourceforge.net/cdk/?rev=14707&view=rev Author: steinbeck Date: 2009-08-10 14:11:07 +0000 (Mon, 10 Aug 2009) Log Message: ----------- Removed duplicat entry for Bioclipse pub Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-10 14:09:09 UTC (rev 14706) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-10 14:11:07 UTC (rev 14707) @@ -9,7 +9,7 @@ title = {Bioclipse: An open rich client workbench for chemo- and bioinformatics}, volume = {8}, issue = {59}, -year = {2007}, +year = {2007} } @ARTICLE{Steinbeck2004a, @@ -304,22 +304,5 @@ howpublished = "\url{http://www.opensource.org/docs/osd}" } -@article{Spjuth2007, - abstract = {BACKGROUND:There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS:Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSIONS:Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.}, - author = {Spjuth, Ola and Helmus, Tobias and Willighagen, Egon and Kuhn, Stefan and Eklund, Martin and Wagener, Johannes and Rust, Peter M. and Steinbeck, Christoph and Wikberg, Jarl}, - citeulike-article-id = {1117873}, - citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-8-59}, - citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17316423}, - citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17316423}, - doi = {10.1186/1471-2105-8-59}, - journal = {BMC Bioinformatics}, - keywords = {bioinformatics, cheminformatics, opensource, papers}, - number = {1}, - posted-at = {2007-06-09 09:27:50}, - priority = {0}, - title = {Bioclipse: An open source workbench for chemo- and bioinformatics}, - url = {http://dx.doi.org/10.1186/1471-2105-8-59}, - volume = {8}, - year = {2007} -} + This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2009-08-13 22:46:54
|
Revision: 14720 http://cdk.svn.sourceforge.net/cdk/?rev=14720&view=rev Author: egonw Date: 2009-08-13 22:46:40 +0000 (Thu, 13 Aug 2009) Log Message: ----------- Removed use of \url{} which does not work for this journal Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-13 22:43:28 UTC (rev 14719) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-13 22:46:40 UTC (rev 14720) @@ -231,64 +231,64 @@ @webpage{PipelinePilotWeb, Author = {Accelrys}, Lastchecked = {August 10, 2009}, - Url = {\url{http://accelrys.com/}}, + Url = {http://accelrys.com/}, } @webpage{InforSenseWeb, Author = {InforSense}, Lastchecked = {August 10, 2009}, - Url = {\url{http://www.inforsense.com/}}, + Url = {http://www.inforsense.com/}, } @webpage{KNIMEWeb, Author = {KNIME}, Lastchecked = {August 10, 2009}, - Url = {\url{http://www.knime.org/}}, + Url = {http://www.knime.org/}, } @webpage{MavenWeb, Author = {Maven}, Lastchecked = {August 10, 2009}, - Url = {\url{http://maven.apache.org/}}, + Url = {http://maven.apache.org/}, } @webpage{SOAPWeb, Author = {SOAP}, Lastchecked = {August 10, 2009}, - Url = {\url{http://www.w3.org/TR/soap/}}, + Url = {http://www.w3.org/TR/soap/}, } @webpage{WSDLWeb, Author = {WSDL}, Lastchecked = {August 10, 2009}, - Url = {\url{http://www.w3.org/TR/wsdl}}, + Url = {http://www.w3.org/TR/wsdl}, } @webpage{PostgreSQLWeb, Author = {PostgreSQL}, Lastchecked = {August 10, 2009}, - Url = {\url{http://www.postgresql.org/}}, + Url = {http://www.postgresql.org/}, } @webpage{PGChemWeb, Author = {Schmid, Ernst-Georg}, Lastchecked = {August 10, 2009}, - Url = {\url{http://pgfoundry.org/projects/pgchem/}}, + Url = {http://pgfoundry.org/projects/pgchem/}, } @webpage{PubChem, Author = {NCBI}, Lastchecked = {August 10, 2009}, - Url = {\url{http://pubchem.ncbi.nlm.nih.gov/}}, + Url = {http://pubchem.ncbi.nlm.nih.gov/}, } @webpage{ChEMBL, Author = {ChEMBL team}, Lastchecked = {August 10, 2009}, - Url = {\url{http://www.ebi.ac.uk/chembl}}, + Url = {http://www.ebi.ac.uk/chembl}, } @webpage{GISTWeb, Author = {Teodor Sigaev and Oleg Bartunov}, Lastchecked = {August 12, 2009}, - Url = {\url{http://www.sai.msu.su/~megera/postgres/gist/}}, + Url = {http://www.sai.msu.su/~megera/postgres/gist/}, } @webpage{CDKTavernaBlogWeb, Author = {Thomas Kuhn}, Lastchecked = {August 12, 2009}, - Url = {\url{http://cdktaverna.wordpress.com/2008/09/07/time-evaluation-for-calculating-molecular-descriptors-using-the-cdk/}}, + Url = {http://cdktaverna.wordpress.com/2008/09/07/time-evaluation-for-calculating-molecular-descriptors-using-the-cdk/}, } @PhDThesis{KuhnDissertation, @@ -312,7 +312,7 @@ @MISC{free-software-foundation, title = "The Open Source Definition", publisher = "Open Source Initiative", - howpublished = "\url{http://www.opensource.org/docs/osd}" + howpublished = "http://www.opensource.org/docs/osd" } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <tho...@us...> - 2009-08-29 10:30:45
|
Revision: 14784 http://cdk.svn.sourceforge.net/cdk/?rev=14784&view=rev Author: thomaskuhn Date: 2009-08-29 10:30:35 +0000 (Sat, 29 Aug 2009) Log Message: ----------- Changed the format of the web page entries Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-28 16:24:46 UTC (rev 14783) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-08-29 10:30:35 UTC (rev 14784) @@ -229,96 +229,74 @@ number = {4}, journal = {Neural networks} } - @webpage{PipelinePilotWeb, - Author = {Accelrys}, - Lastchecked = {August 10, 2009}, - Url = {http://accelrys.com/}, + title = {Pipeline Pilot data analysis and reporting platform}, + url = {http://accelrys.com/products/scitegic/} } @webpage{InforSenseWeb, - Author = {InforSense}, - Lastchecked = {August 10, 2009}, - Url = {http://www.inforsense.com/}, + title = {Inforsense Platform}, + url = {http://www.inforsense.com/products/core_technology/inforsense_platform/} } @webpage{KNIMEWeb, - Author = {KNIME}, - Lastchecked = {August 10, 2009}, - Url = {http://www.knime.org/}, + title = {KNIME Konstanz Information Miner}, + url = {http://www.knime.org/} } @webpage{MavenWeb, - Author = {Maven}, - Lastchecked = {August 10, 2009}, - Url = {http://maven.apache.org/}, + title = {Apache Maven}, + url = {http://maven.apache.org/} } @webpage{SOAPWeb, - Author = {SOAP}, - Lastchecked = {August 10, 2009}, - Url = {http://www.w3.org/TR/soap/}, + title = {W3C SOAP Specifications}, + url = {http://www.w3.org/TR/soap/} } @webpage{WSDLWeb, - Author = {WSDL}, - Lastchecked = {August 10, 2009}, - Url = {http://www.w3.org/TR/wsdl}, + title = {W3C Web Service Definition Language (WSDL)}, + url = {http://www.w3.org/TR/wsdl} } @webpage{PostgreSQLWeb, - Author = {PostgreSQL}, - Lastchecked = {August 10, 2009}, - Url = {http://www.postgresql.org/}, + title = {PostgreSQL Database }, + url = {http://www.postgresql.org/} } @webpage{PGChemWeb, - Author = {Schmid, Ernst-Georg}, - Lastchecked = {August 10, 2009}, - Url = {http://pgfoundry.org/projects/pgchem/}, + title = {pgchem::tigress: chemoinformatics extension to the PostgreSQL}, + url = {http://pgfoundry.org/projects/pgchem/} } @webpage{PubChem, - Author = {NCBI}, - Lastchecked = {August 10, 2009}, - Url = {http://pubchem.ncbi.nlm.nih.gov/}, + title = {The PubChem Project}, + url = {http://pubchem.ncbi.nlm.nih.gov/} } - @webpage{ChEMBL, - Author = {{ChEMBL}~team}, - Lastchecked = {August 10, 2009}, - Url = {http://www.ebi.ac.uk/chembl}, + title = {The ChEMBL Group}, + url = {http://www.ebi.ac.uk/chembl} } - @webpage{ChEBIWeb, - Title = {The database of chemical entities of biological Interest (ChEBI)}, - Lastchecked = {August 10, 2009}, - Url = {http://www.ebi.ac.uk/chebi}, + title = {The database of chemical entities of biological Interest (ChEBI)}, + url = {http://www.ebi.ac.uk/chebi} } - @webpage{GISTWeb, - Author = {Teodor Sigaev and Oleg Bartunov}, - Lastchecked = {August 12, 2009}, - Url = {http://www.sai.msu.su/~megera/postgres/gist/}, + title = {GiST Support for PostgreSQL}, + url = {http://www.sai.msu.su/~megera/postgres/gist/} } @webpage{CDKTavernaBlogWeb, - Author = {Thomas Kuhn}, - Lastchecked = {August 12, 2009}, - Url = {http://cdktaverna.wordpress.com/2008/09/07/time-evaluation-for-calculating-molecular-descriptors-using-the-cdk/}, + title = {The CDK-Taverna Blog}, + url = {http://cdktaverna.wordpress.com/2008/09/07/time-evaluation-for-calculating-molecular-descriptors-using-the-cdk/} } @webpage{MyExperiementWFSubstructure, - Author = {Thomas Kuhn}, - Lastchecked = {August 12, 2009}, - Url = {http://www.myexperiment.org/workflows/557/}, + title = {myExperiment - Topological Substructure Workflow}, + url = {http://www.myexperiment.org/workflows/557/} } @webpage{MyExperiementWFSubstructureDB, - Author = {Thomas Kuhn}, - Lastchecked = {August 12, 2009}, - Url = {http://www.myexperiment.org/workflows/555/}, + title = {myExperiment - Substructure Search on Database Workflow}, + url = {http://www.myexperiment.org/workflows/555/} } @webpage{MyExperiementWFQSAR, - Author = {Thomas Kuhn}, - Lastchecked = {August 12, 2009}, - Url = {http://www.myexperiment.org/workflows/563}, + title = {myExperiment - Calculation of molecular descriptors for molecules loaded from database}, + url = {http://www.myexperiment.org/workflows/563/} } @webpage{MyExperiementWFReactionEnum, - Author = {Thomas Kuhn}, - Lastchecked = {August 12, 2009}, - Url = {http://www.myexperiment.org/workflows/567}, + title = {myExperiment - Reaction Enumeration Workflow}, + url = {http://www.myexperiment.org/workflows/567/} } - @PhDThesis{KuhnDissertation, author = {Kuhn, Thomas}, title ={Open Source Workflow Engine for Cheminformatics: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2009-11-07 23:20:10
|
Revision: 15056 http://cdk.svn.sourceforge.net/cdk/?rev=15056&view=rev Author: egonw Date: 2009-11-07 23:19:50 +0000 (Sat, 07 Nov 2009) Log Message: ----------- Removed used of \url{} which showed up as plain text in the bib section Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-11-07 23:18:32 UTC (rev 15055) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2009-11-07 23:19:50 UTC (rev 15056) @@ -312,7 +312,7 @@ author = {Taylor, Ian J. and Deelman, Ewa and Gannon, Dennis B. and Shields, Matthew}, year = {2007}, title = {Workflows for e-Science: Scientific Workflows for Grids}, - url = {\url{http://dx.doi.org/10.1007/978-1-84628-757-2}}, + url = {http://dx.doi.org/10.1007/978-1-84628-757-2}, keywords = {Computer Communication Networks;Computer network architectures;Computer software;Data transmission systems;Operating systems (Computers);Software engineering;Computer Science;Algorithm Analysis and Problem Complexity;Computer Systems Organization and Communication Networks;Input/Output and Data Communications;Operating Systems;Special Purpose and Application-Based Systems;Grid Computing;Online-Publikation}, address = {London}, publisher = {Springer-Verlag London Limited}, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2010-03-03 05:41:07
|
Revision: 15448 http://cdk.svn.sourceforge.net/cdk/?rev=15448&view=rev Author: egonw Date: 2010-03-03 05:41:01 +0000 (Wed, 03 Mar 2010) Log Message: ----------- Fixed the bibtex source (issue->number) to fix the citation of ref 17 Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2010-03-03 05:35:17 UTC (rev 15447) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.bib 2010-03-03 05:41:01 UTC (rev 15448) @@ -8,7 +8,7 @@ journal = {BMC Bioinformatics}, title = {Bioclipse: An open rich client workbench for chemo- and bioinformatics}, volume = {8}, -issue = {59}, +number = {59}, year = {2007} } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |