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@article{Alvarsson:2011fk,
	Abstract = {BACKGROUND:Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a extensible lightweight open system for handling plate design, and validation and preparation of data.RESULTS:A Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves. CONCLUSIONS:Brunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC50 values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources.},
	Author = {Alvarsson, Jonathan and Andersson, Claes and Spjuth, Ola and Larsson, Rolf and Wikberg, Jarl},
	Date-Added = {2011-05-20 11:57:25 +0200},
	Date-Modified = {2011-05-20 11:57:34 +0200},
	Doi = {10.1186/1471-2105-12-179},
	Issn = {1471-2105},
	Journal = {BMC Bioinformatics},
	Number = {1},
	Pages = {179},
	Title = {Brunn: An open source laboratory information system for microplates with a graphical plate layout design process},
	Url = {http://www.biomedcentral.com/1471-2105/12/179},
	Volume = {12},
	Year = {2011},
	Bdsk-Url-1 = {http://www.biomedcentral.com/1471-2105/12/179},
	Bdsk-Url-2 = {http://dx.doi.org/10.1186/1471-2105-12-179}}

@article{Munos:2006vn,
	Abstract = {The low number of novel therapeutics approved by the US FDA in recent years continues to cause great concern about productivity and declining innovation. Can open-source drug research and development, using principles pioneered by the highly successful open-source software movement, help revive the industry?},
	Author = {Munos, Bernard},
	Date-Added = {2011-05-13 15:25:45 -0400},
	Date-Modified = {2011-05-13 15:25:45 -0400},
	Doi = {10.1038/nrd2131},
	Journal = {Nat Rev Drug Discov},
	Journal-Full = {Nature reviews. Drug discovery},
	Mesh = {Clinical Trials as Topic; Databases, Factual; Drug Approval; Drug Design; Humans; Organizational Innovation; Research; Software; Technology, Pharmaceutical},
	Month = {Sep},
	Number = {9},
	Pages = {723-9},
	Pmid = {16915233},
	Pst = {ppublish},
	Title = {Can open-source R\&D reinvigorate drug research?},
	Volume = {5},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrd2131}}

@article{Geldenhuys:2006kx,
	Abstract = {Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process. Among the reviewed software programs are applications programmed in JAVA, Perl and Python, as well as resources including software libraries. These programs might be useful for cheminformatics approaches to drug discovery, including QSAR studies, energy minimization and docking studies in drug design endeavors. Furthermore, this review explores options for integrating available computer modeling open-source software applications in drug discovery programs.},
	Author = {Geldenhuys, Werner J and Gaasch, Kevin E and Watson, Mark and Allen, David D and Van der Schyf, Cornelis J},
	Date-Added = {2011-05-13 15:25:37 -0400},
	Date-Modified = {2011-05-13 15:25:37 -0400},
	Doi = {10.1016/S1359-6446(05)03692-5},
	Journal = {Drug Discov Today},
	Journal-Full = {Drug discovery today},
	Mesh = {Computer-Aided Design; Drug Design; Internet; Quantitative Structure-Activity Relationship; Software},
	Month = {Feb},
	Number = {3-4},
	Pages = {127-32},
	Pmid = {16533710},
	Pst = {ppublish},
	Title = {Optimizing the use of open-source software applications in drug discovery},
	Volume = {11},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S1359-6446(05)03692-5}}

@article{DeLano:2005uq,
	Abstract = {Widespread adoption of open-source software for network infrastructure, web servers, code development, and operating systems leads one to ask how far it can go. Will "open source" spread broadly, or will it be restricted to niches frequented by hopeful hobbyists and midnight hackers? Here we identify reasons for the success of open-source software and predict how consumers in drug discovery will benefit from new open-source products that address their needs with increased flexibility and in ways complementary to proprietary options.},
	Author = {DeLano, Warren L},
	Date-Added = {2011-05-13 15:24:34 -0400},
	Date-Modified = {2011-05-13 15:24:34 -0400},
	Doi = {10.1016/S1359-6446(04)03363-X},
	Journal = {Drug Discov Today},
	Journal-Full = {Drug discovery today},
	Mesh = {Access to Information; Database Management Systems; Diffusion of Innovation; Drug Design; Drug Industry; Software; Software Design},
	Month = {Feb},
	Number = {3},
	Pages = {213-7},
	Pmid = {15708536},
	Pst = {ppublish},
	Title = {The case for open-source software in drug discovery},
	Volume = {10},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S1359-6446(04)03363-X}}

@article{Stahl:2005fk,
	Abstract = {Open-source software will never achieve ubiquity. There are environments in which it simply does not flourish. By its nature, open-source development requires free exchange of ideas, community involvement, and the efforts of talented and dedicated individuals. However, pressures can come from several sources that prevent this from happening. In addition, openness and complex licensing issues invite misuse and abuse. Care must be taken to avoid the pitfalls of open-source software.},
	Author = {Stahl, Matthew T},
	Date-Added = {2011-05-13 15:23:33 -0400},
	Date-Modified = {2011-05-13 15:23:33 -0400},
	Doi = {10.1016/S1359-6446(04)03364-1},
	Journal = {Drug Discov Today},
	Journal-Full = {Drug discovery today},
	Mesh = {Access to Information; Computational Biology; Database Management Systems; Licensure; Software; Software Design},
	Month = {Feb},
	Number = {3},
	Pages = {219-22},
	Pmid = {15708537},
	Pst = {ppublish},
	Title = {Open-source software: not quite endsville},
	Volume = {10},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S1359-6446(04)03364-1}}

@article{Lonie2011,
	Author = {David C. Lonie and Eva Zurek},
	Date-Added = {2011-05-13 15:17:19 -0400},
	Date-Modified = {2011-05-13 15:20:56 -0400},
	Doi = {10.1016/j.cpc.2010.07.048},
	Journal = {Computer Physics Communications},
	Keywords = {XtalOpt, crystal structure, genetic algorithm},
	Number = {2},
	Pages = {372-387},
	Title = {XtalOpt: An open-source evolutionary algorithm for crystal structure prediction},
	Volume = {182},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cpc.2010.07.048}}

@article{Wagener:2009uq,
	Abstract = {Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use.},
	Author = {Wagener, Johannes and Spjuth, Ola and Willighagen, Egon L and Wikberg, Jarl E S},
	Date-Added = {2011-04-20 12:08:46 +0200},
	Date-Modified = {2011-04-20 12:08:46 +0200},
	Doi = {10.1186/1471-2105-10-279},
	Journal = {BMC Bioinformatics},
	Journal-Full = {BMC bioinformatics},
	Mesh = {Computational Biology; Computer Communication Networks; Information Storage and Retrieval; Internet; Software; User-Computer Interface},
	Pages = {279},
	Pmc = {PMC2755485},
	Pmid = {19732427},
	Pst = {epublish},
	Title = {XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services},
	Volume = {10},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2105-10-279}}

@article{Spjuth:2010uq,
	Abstract = {ABSTRACT: BACKGROUND: QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. RESULTS: We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. CONCLUSIONS: Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes it easy to join, extend, combine datasets and hence work collectively, but also allows for analyzing the effect descriptors have on the statistical model's performance. The presented Bioclipse plugins equip scientists with graphical tools that make QSAR-ML easily accessible for the community.},
	Author = {Spjuth, Ola and Willighagen, Egon L and Guha, Rajarshi and Eklund, Martin and Wikberg, Jarl Es},
	Date-Added = {2011-04-20 11:55:12 +0200},
	Date-Modified = {2011-04-20 11:55:12 +0200},
	Doi = {10.1186/1758-2946-2-5},
	Journal = {J Cheminform},
	Journal-Full = {Journal of cheminformatics},
	Month = {Jun},
	Number = {1},
	Pages = {5},
	Pmid = {20591161},
	Pst = {aheadofprint},
	Title = {Towards interoperable and reproducible QSAR analyses: Exchange of datasets},
	Volume = {2},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1758-2946-2-5}}

@misc{bodo,
	Date-Added = {2011-04-20 11:54:31 +0200},
	Date-Modified = {2011-04-20 11:54:31 +0200},
	Note = {\url{http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml}},
	Title = {{The Blue Obelisk Descriptor Ontology}},
	Url = {http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml},
	Bdsk-Url-1 = {http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml}}

@article{Spjuth:2007fk,
	Abstract = {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.},
	Author = {Spjuth, Ola and Helmus, Tobias and Willighagen, Egon L and Kuhn, Stefan and Eklund, Martin and Wagener, Johannes and Murray-Rust, Peter and Steinbeck, Christoph and Wikberg, Jarl E S},
	Date-Added = {2011-04-20 11:45:03 +0200},
	Date-Modified = {2011-04-20 11:45:03 +0200},
	Doi = {10.1186/1471-2105-8-59},
	Journal = {BMC Bioinformatics},
	Journal-Full = {BMC bioinformatics},
	Mesh = {Biochemistry; Computational Biology; Computer Graphics; Genomics; Programming Languages; Software; Software Design; User-Computer Interface},
	Pages = {59},
	Pmc = {PMC1808478},
	Pmid = {17316423},
	Pst = {epublish},
	Title = {Bioclipse: an open source workbench for chemo- and bioinformatics},
	Volume = {8},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2105-8-59}}

@article{Hanson2010,
	Author = {Hanson, Robert M.},
	Citeulike-Article-Id = {7757032},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1107/S0021889810030256},
	Citeulike-Linkout-1 = {http://scripts.iucr.org/cgi-bin/paper?S0021889810030256},
	Doi = {10.1107/S0021889810030256},
	Journal = {Journal of Applied Crystallography},
	Keywords = {cheminformatics, jmol, opensource},
	Month = oct,
	Number = {5 Part 2},
	Pages = {1250--1260},
	Posted-At = {2010-09-02 20:23:55},
	Priority = {5},
	Title = {Jmol - a paradigm shift in crystallographic visualization},
	Url = {http://dx.doi.org/10.1107/S0021889810030256},
	Volume = {43},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1107/S0021889810030256}}

@article{Hull:2006p60,
	Author = {D Hull and K Wolstencroft and R Stevens and C Goble and M. R Pocock and P Li and T Oinn},
	Date-Added = {2009-05-06 16:40:38 +0200},
	Date-Modified = {2009-05-06 16:40:43 +0200},
	Doi = {10.1093/nar/gkl320},
	Journal = {Nucleic Acids Research},
	Local-Url = {file://localhost/Users/steinbeck/Documents/Reading/Papers/2006/Hull/Nucleic%20Acids%20Research%202006%20Hull.pdf},
	Month = {Jul},
	Number = {Web Server},
	Pages = {W729--W732},
	Rating = {0},
	Read = {Yes},
	Title = {Taverna: a tool for building and running workflows of services},
	Uri = {papers://1951507D-4601-4058-AA94-8D6940C9C00F/Paper/p60},
	Volume = {34},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/nar/gkl320}}

@article{Kuhn:2010p4001,
	Author = {Thomas Kuhn and Egon Willighagen and Achim Zielesny and Christoph Steinbeck},
	Date-Added = {2010-07-30 11:00:56 +0200},
	Date-Modified = {2010-07-30 11:00:56 +0200},
	Doi = {10.1186/1471-2105-11-159},
	Journal = {BMC Bioinformatics},
	Language = {en},
	Local-Url = {file://localhost/Users/steinbeck/Documents/Reading/Papers/2010/Kuhn/BMC%20Bioinformatics%202010%20Kuhn-2.pdf},
	Month = {Mar},
	Number = {1},
	Pages = {159},
	Rating = {0},
	Read = {Yes},
	Title = {CDK-Taverna: an open workflow environment for cheminformatics},
	Uri = {papers://1951507D-4601-4058-AA94-8D6940C9C00F/Paper/p4001},
	Url = {http://www.biomedcentral.com/1471-2105/11/159},
	Volume = {11},
	Year = {2010},
	Bdsk-Url-1 = {http://www.biomedcentral.com/1471-2105/11/159},
	Bdsk-Url-2 = {http://dx.doi.org/10.1186/1471-2105-11-159}}

@article{DeMatos:2009p3839,
	Author = {Paula De Matos and Rafael Alcantara and Adriano Dekker and Marcus Ennis and Janna Hastings and Kenneth Haug and Inmaculada Spiteri and Steve Turner and Christoph Steinbeck},
	Date-Added = {2009-11-03 15:04:05 +0100},
	Date-Modified = {2009-11-03 15:04:05 +0100},
	Doi = {10.1093/nar/gkp886},
	Journal = {Nucleic Acids Research},
	Local-Url = {file://localhost/Users/steinbeck/Documents/Reading/Papers/2009/De%20Matos/Nucleic%20Acids%20Research%202009%20De%20Matos.pdf},
	Month = {Oct},
	Pages = {gkp886v1},
	Rating = {0},
	Read = {Yes},
	Title = {Chemical Entities of Biological Interest: an update},
	Uri = {papers://1951507D-4601-4058-AA94-8D6940C9C00F/Paper/p3839},
	Url = {http://nar.oxfordjournals.org/cgi/content/full/gkp886v1},
	Year = {2009},
	Bdsk-Url-1 = {http://nar.oxfordjournals.org/cgi/content/full/gkp886v1},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/nar/gkp886}}

@article{Steinbeck2006,
	Abstract = {The Chemistry Development Kit ({CDK}) provides methods for common tasks in molecular informatics, including {2D} and {3D} rendering of chemical structures, {I/O} routines, {SMILES} parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the {CDK}'s new {QSAR} capabilities and the recently introduced interface to statistical software.},
	Address = {Cologne University Bioinformatics Center (CUBIC), Germany. c.steinbeck@uni-koeln.de},
	Author = {Steinbeck, Christoph and Hoppe, Christian and Kuhn, Stefan and Floris, Matteo and Guha, Rajarshi and Willighagen, Egon L.},
	Citeulike-Article-Id = {1073448},
	Citeulike-Linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/16796559},
	Citeulike-Linkout-1 = {http://www.hubmed.org/display.cgi?uids=16796559},
	Issn = {1381-6128},
	Journal = {Current pharmaceutical design},
	Keywords = {bopaper},
	Number = {17},
	Pages = {2111--2120},
	Pmid = {16796559},
	Posted-At = {2011-04-14 16:29:12},
	Priority = {2},
	Title = {Recent developments of the chemistry development kit ({CDK}) - an open-source java library for chemo- and bioinformatics.},
	Url = {http://view.ncbi.nlm.nih.gov/pubmed/16796559},
	Volume = {12},
	Year = {2006},
	Bdsk-Url-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16796559}}

@article{Steinbeck2003,
	Abstract = {{PMID}: 12653513 The Chemistry Development Kit ({CDK}) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The {CDK} provides methods for many common tasks in molecular informatics, including {2D} and {3D} rendering of chemical structures, {I/O} routines, {SMILES} parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.},
	Address = {Max-Planck-Institute of Chemical Ecology, Jena, Germany. c.steinbeck@uni-koeln.de},
	Author = {Steinbeck, Christoph and Han, Yongquan and Kuhn, Stefan and Horlacher, Oliver and Luttmann, Edgar and Willighagen, Egon},
	Citeulike-Article-Id = {423382},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1021/ci025584y},
	Citeulike-Linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ci025584y},
	Citeulike-Linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12653513},
	Citeulike-Linkout-3 = {http://www.hubmed.org/display.cgi?uids=12653513},
	Day = {1},
	Doi = {10.1021/ci025584y},
	Issn = {0095-2338},
	Journal = {Journal of Chemical Information and Computer Sciences},
	Keywords = {bopaper},
	Month = mar,
	Number = {2},
	Pages = {493--500},
	Pmid = {12653513},
	Posted-At = {2011-04-14 16:27:53},
	Priority = {2},
	Title = {The Chemistry Development Kit ({CDK}): An {Open-Source} Java Library for Chemo- and Bioinformatics},
	Url = {http://dx.doi.org/10.1021/ci025584y},
	Volume = {43},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci025584y}}

@article{RijnbeekS10,
	Abstract = {{BACKGROUND}:Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial {world.RESULTS}:Here we present {OrChem}, an extension for the Oracle {11G} database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. {OrChem} provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data {sets.AVAILABILITY}:{OrChem} is free software and can be redistributed and/or modified under the terms of the {GNU} Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.},
	Author = {Rijnbeek, Mark and Steinbeck, Christoph},
	Citeulike-Article-Id = {5986061},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1186/1758-2946-1-17},
	Citeulike-Linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20298521},
	Citeulike-Linkout-2 = {http://www.hubmed.org/display.cgi?uids=20298521},
	Doi = {10.1186/1758-2946-1-17},
	Issn = {1758-2946},
	Journal = {Journal of Cheminformatics},
	Keywords = {bopaper},
	Number = {1},
	Pages = {17+},
	Pmid = {20298521},
	Posted-At = {2011-04-14 16:27:22},
	Priority = {2},
	Title = {{OrChem} - An open source chemistry search engine for {Oracle(R})},
	Url = {http://dx.doi.org/10.1186/1758-2946-1-17},
	Volume = {1},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1758-2946-1-17}}

@article{Guha2006,
	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.},
	Address = {Pennsylvania State University, University Park, Pennsylvania 16804-3000, Jmol Project, USA.},
	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.},
	Citeulike-Article-Id = {869714},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1021/ci050400b},
	Citeulike-Linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ci050400b},
	Citeulike-Linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16711717},
	Citeulike-Linkout-3 = {http://www.hubmed.org/display.cgi?uids=16711717},
	Day = {1},
	Doi = {10.1021/ci050400b},
	Issn = {1549-9596},
	Journal = {Journal of Chemical Information and Modeling},
	Keywords = {bopaper},
	Month = may,
	Number = {3},
	Pages = {991--998},
	Pmid = {16711717},
	Posted-At = {2011-04-14 15:06:14},
	Priority = {2},
	Title = {The Blue Obelisk - Interoperability in Chemical Informatics},
	Url = {http://dx.doi.org/10.1021/ci050400b},
	Volume = {46},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci050400b}}

@article{Bioclipse2,
	Abstract = {{BACKGROUND}:Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new {tasks.RESULTS}:Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and {alignments.CONCLUSION}:Bioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today's powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked ({Web/Cloud}) services for more demanding calculations or retrieval of data. The fact that Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, making it easy to add new algorithms, visualizations, as well as scripting commands. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative {research.Bioclipse} 2 is released under the Eclipse Public License ({EPL}), a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.},
	Author = {Spjuth, Ola and Alvarsson, Jonathan and Berg, Arvid and Eklund, Martin and Kuhn, Stefan and Masak, Carl and Torrance, Gilleain and Wagener, Johannes and Willighagen, Egon and Steinbeck, Christoph and Wikberg, Jarl},
	Citeulike-Article-Id = {6297196},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1186/1471-2105-10-397},
	Citeulike-Linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799422/},
	Citeulike-Linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19958528},
	Citeulike-Linkout-3 = {http://www.hubmed.org/display.cgi?uids=19958528},
	Day = {3},
	Doi = {10.1186/1471-2105-10-397},
	Issn = {1471-2105},
	Journal = {BMC Bioinformatics},
	Keywords = {bopaper},
	Month = dec,
	Number = {1},
	Pages = {397+},
	Pmcid = {PMC2799422},
	Pmid = {19958528},
	Posted-At = {2011-04-14 15:00:22},
	Priority = {0},
	Title = {Bioclipse 2: A scriptable integration platform for the life sciences},
	Url = {http://dx.doi.org/10.1186/1471-2105-10-397},
	Volume = {10},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2105-10-397}}

@article{OBoyleCinfony2008,
	Abstract = {By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of {OpenBabel}, the {CDK} and the {RDKit}.},
	Author = {O'Boyle, Noel M. and Hutchison, Geoffrey R.},
	Citeulike-Article-Id = {4277552},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1186/1752-153X-2-24},
	Citeulike-Linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646723/},
	Citeulike-Linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19055766},
	Citeulike-Linkout-3 = {http://www.hubmed.org/display.cgi?uids=19055766},
	Doi = {10.1186/1752-153X-2-24},
	Issn = {1752-153X},
	Journal = {Chemistry Central Journal},
	Keywords = {bopaper},
	Pages = {24+},
	Pmcid = {PMC2646723},
	Pmid = {19055766},
	Posted-At = {2011-03-11 15:43:12},
	Priority = {0},
	Title = {Cinfony--combining Open Source cheminformatics toolkits behind a common interface.},
	Url = {http://dx.doi.org/10.1186/1752-153X-2-24},
	Volume = {2},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1752-153X-2-24}}

@article{CurlySMILES,
	Author = {Drefahl, Alex},
	Doi = {10.1186/1758-2946-3-1},
	Journal = {Journal of Cheminformatics},
	Number = {1},
	Title = {CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures},
	Url = {http://dx.doi.org/10.1186/1758-2946-3-1},
	Volume = {3},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1758-2946-3-1}}

@book{iupac_nomenclature_1979,
	Author = {{IUPAC}},
	Keywords = {Name To Structure},
	Publisher = {Pergamon Press, Oxford},
	Title = {Nomenclature of Organic Chemistry},
	Year = {1979}}

@book{iupac_guide_1993,
	Author = {{IUPAC}},
	Keywords = {Name To Structure},
	Publisher = {Blackwell Scientific publications},
	Title = {A Guide to {IUPAC} Nomenclature of Organic Compounds {(Recommendations} 1993)},
	Year = {1993}}

@article{lowe_chemical_2011,
	Abstract = {We have produced an open source, freely available, algorithm {(Open} Parser for Systematic {IUPAC} Nomenclature, {OPSIN)} that interprets the majority of organic chemical nomenclature in a fast and precise manner. This has been achieved using an approach based on a regular grammar. This grammar is used to guide tokenization, a potentially difficult problem in chemical names. From the parsed chemical name, an {XML} parse tree is constructed that is operated on in a stepwise manner until the structure has been reconstructed from the name. Results from {OPSIN} on various computer generated name/structure pair sets are presented. These show exceptionally high precision (99.8\%+) and, when using general organic chemical nomenclature, high recall (98.7-99.2\%). This software can serve as the basis for future open source developments of chemical name interpretation.},
	Author = {Daniel M. Lowe and Peter T. Corbett and Peter {Murray-Rust} and Robert C. Glen},
	Doi = {10.1021/ci100384d},
	Journal = {Journal of Chemical Information and Modeling},
	Keywords = {Name To Structure},
	Month = mar,
	Number = {3},
	Pages = {739--753},
	Shorttitle = {Chemical Name to Structure},
	Title = {Chemical Name to Structure: {OPSIN,} an Open Source Solution},
	Url = {http://dx.doi.org/10.1021/ci100384d},
	Volume = {51},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci100384d}}

@article{ONS2010,
	Abstract = {This book contains the results of the Open Notebook Science Solubility Challenge. All experimental measurements are provided with a link to either the laboratory notebook page where the experiment was carried out or to a literature reference.  The Challenge was sponsored by Submeta, Nature and {Sigma-Aldrich}.},
	Author = {Jean-Claude Bradley and Cameron Neylon and Rajarshi Guha and Antony J. Williams and Bill Hooker and Andrew S. I. D. Lang and Brent Friesen and Tim Bohinski and David Bulger and Matthew Federici and Jenny Hale and Jenna Mancinelli and Khalid B. Mirza and Marshall J. Moritz and Daniel Rein and Cedric Tchakounte and Hai T. Truong},
	Citeulike-Article-Id = {8952460},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1038/npre.2010.4243.3},
	Citeulike-Linkout-1 = {http://precedings.nature.com/documents/4243/version/3},
	Day = {3},
	Doi = {10.1038/npre.2010.4243.3},
	Issn = {1756-0357},
	Journal = {Nature Precedings},
	Month = mar,
	Number = {713},
	Posted-At = {2011-03-07 13:24:06},
	Priority = {2},
	Publisher = {Nature Publishing Group},
	Title = {Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents},
	Url = {http://dx.doi.org/10.1038/npre.2010.4243.3},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/npre.2010.4243.3}}

@article{Overington2009,
	Author = {Overington, John},
	Citeulike-Article-Id = {4019443},
	Citeulike-Linkout-0 = {http://dx.doi.org/10.1007/s10822-009-9260-9},
	Citeulike-Linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19194660},
	Citeulike-Linkout-2 = {http://www.hubmed.org/display.cgi?uids=19194660},
	Citeulike-Linkout-3 = {http://www.springerlink.com/content/kt430778npr45t48},
	Day = {1},
	Doi = {10.1007/s10822-009-9260-9},
	Issn = {1573-4951},
	Journal = {Journal of computer-aided molecular design},
	Keywords = {chembl},
	Month = apr,
	Number = {4},
	Pages = {195--198},
	Pmid = {19194660},
	Posted-At = {2011-02-16 10:22:35},
	Priority = {2},
	Title = {{ChEMBL}. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory ({EMBL}-{EBI}). Interview by Wendy A. Warr.},
	Url = {http://dx.doi.org/10.1007/s10822-009-9260-9},
	Volume = {23},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10822-009-9260-9}}

@article{CDKNewsBO,
	Author = {Murray-Rust, P.},
	Citeulike-Article-Id = {9208527},
	Issn = {1614-7553},
	Journal = {CDK News},
	Number = {2},
	Pages = {43--46},
	Posted-At = {2011-04-26 11:32:35},
	Priority = {2},
	Title = {The Blue Obelisk},
	Volume = {2},
	Year = {2005}}

@book{CDKBook,
	Author = {Egon Willighagen},
	Publisher = {Lulu Enterprises, Morrisville, NC, US},
	Title = {Groovy Cheminformatics with the Chemistry Development Kit},
	Year = {2011}}

@book{JmolBook,
	Author = {Angel Herr{\'a}ez},
	Publisher = {Lulu Enterprises, Morrisville, NC, US},
	Title = {How to use Jmol to study and present molecular structures},
	Volume = 1,
	Year = {2007}}

@book{OpenBabelBook,
	Author = {Geoffrey R. Hutchison and Chris Morley and Noel M. O'Boyle and Craig James and Chris Swain and Hans De Winter and Tim Vandermeersch},
	Publisher = {Lulu Enterprises, Morrisville, NC, US},
	Title = {Open Babel - Official User Guide},
	Year = {2011}}

@article{cclib,
	Author = {Noel M. O'Boyle and Adam L. Tenderholt and Karol M. Langner},
	Journal = {J. Comp. Chem.},
	Number = {5},
	Pages = {839--845},
	Title = {cclib: A library for package-independent computational chemistry algorithms},
	Volume = {29},
	Year = 2008}

@article{Frenking,
	Author = {Stefan Dapprich and Gernot Frenking},
	Doi = {10.1021/j100023a009},
	Journal = {J. Phys. Chem.},
	Month = {Jun},
	Number = {23},
	Pages = {9352--9362},
	Title = {Investigation of Donor-Acceptor Interactions: A Charge Decomposition Analysis Using Fragment Molecular Orbitals},
	Volume = {99},
	Year = {1995},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/j100023a009}}

@article{Rappe:1992um,
	Author = {A. K. Rapp\'e and C. J. Casewit and K. S. Colwell and W. A. Goddard III and W. M. Skiff},
	Journal = {Journal of the American Chemical Society},
	Number = {25},
	Pages = {10024-10035},
	Title = {UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations},
	Volume = {114},
	Year = {1992}}

@article{NWChem,
	Author = {M. Valiev and E. J. Bylaska and N. Govind and K. Kowalski and T. P. Straatsma and H. J. J. {van Dam} and D. Wang and J. Nieplocha and E. Apra and T. L. Windus and W. A. {de Jong}},
	Doi = {10.1016/j.cpc.2010.04.018},
	Journal = {Comput. Phys. Commun.},
	Number = {9},
	Pages = {1477--1489},
	Title = {NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations},
	Volume = {181},
	Year = 2010,
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cpc.2010.04.018}}

@article{smsd,
	Author = {Rahman, S.A. and Bashton, M. and Holliday, G.L. an Schrader, R. and Thornton, J.M.},
	Issue = {12},
	Journal = {J.~Cheminf.},
	Title = {Small Molecule Subgraph Detector ({SMSD}) Toolkit},
	Volume = {1},
	Year = {2009}}

@article{orchem,
	Author = {Rijnbeek, M. and Steinbeck, C.},
	Issue = {17},
	Journal = {J.~Cheminf.},
	Title = {{OrChem} - An Open Source Chemistry Search Engine for Oracle},
	Volume = {1},
	Year = {2009}}

@article{padel,
	Author = {Yap, C.W.},
	Issue = {7},
	Journal = {J.~Comp.~Chem.},
	Pages = {1466--1474},
	Title = {{PaDEL}-Descriptor: An open source software to calculate molecular descriptors and fingerprints},
	Volume = {32},
	Year = {2011}}

@article{Dong:2007aa,
	Author = {Dong, X. and Gilbert, K. and Guha, R. and Heiland, R. and Kim, J. and Pierce, M. and Fox, G. and Wild, D.J.},
	Journal = {J.~Chem.~Inf.~Model.},
	Number = {4},
	Pages = {1303--1307},
	Title = {A Web Service Infrastructure for Chemoinformatics},
	Volume = {47},
	Year = {2007}}

@article{DayEtAl2011,
	Author = {Day N.E. and Murray-Rust P. and Tyrrell S.M.},
	Journal = {J. Appl. Cryst.},
	Volume = {44},
	Number = {3},
	Pages = {628--634},
	Title = {CIFXML: a schema and toolkit for managing CIFs in XML},
	Year = {2011}}
	
@article{HawizyEtAl,
	Author = {Hawizy L. and Jessop D.M. and Adams N. and Murray-Rust P.},
	Journal = {J. Cheminf.},
	Volume = {3},
	Pages = {17},
	Title = {ChemicalTagger: A tool for Semantic Text-mining in Chemistry},
	Year = {2011}}