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<big>'''MediaWiki has been successfully installed.'''</big>
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<big>The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics.
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It is now developed by more than 50 developers all over the world and used in more than 10 different academic as well as industrial projects world wide.</big>
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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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= About the Chemistry Development Kit (CDK) =
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== Getting started ==
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The CDK design originated from a meeting on September 27-29 2000, [http://www.ebi.ac.uk/steinbeck Christoph Steinbeck], [http://chem-bla-ics.blogspot.com/ Egon Willighagen] and [http://www.nd.edu/gezelter/ Dan Gezelter]
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* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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met at [http://www.nd.edu/ Notre Dame University], South Bend, USA, to [http://sourceforge.net/apps/mediawiki/cdk/index.php?title=Image:100-0694.jpg discuss the architecture of the package].
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* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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The first actual implementation very much relied on the on the earlier work by the [http://www.ebi.ac.uk/steinbeck lab of Christoph Steinbeck] and his older CompChem libraries, which urgently needed a rewrite. On the flight back to Europe, a first draft of the data classes were written.
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* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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== Project Logo ==
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[[10th Anniversary]]!
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Click on [[Image:Logo.png]] to upload a PNG Logo image.
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In the following years, the CDK library evolved into a fully blown open source and open development chemoinformatics package with code reaching from QSAR descriptor
 +
calculations to 2D and 3D model building. Programs like the 2D structure editor [[JChemPaint]], [http://www.nmrshiftdb.org/ NMRShiftDB],
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a database of organic molecules and their NMR spectra, and [http://www.bioclipse.net/ Bioclipse] are based on or use the CDK. You can learn about these and others on the page [[Software using CDK]]. A full list of [[Features|features]] is available.
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= Download CDK Releases =
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Currently, the CDK releases are available in two flavors: a stable series of CDK 1.4.x releases is available ([https://sourceforge.net/projects/cdk/files/cdk/ latest on Sourceforge]), as well as a development
 +
series, which is currently accesible via [[Development with Git | Git]]. Nightly builds of the development branch are also [http://pele.farmbio.uu.se/nightly/ available]. Maintainance of these release branches has been in the hands [http://chem-bla-ics.blogspot.com/ Egon Willighagen]. See [[CDK Releases]]. [[Maven repositories]] are also available.
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More information about using CDK can be found in the [[Documentation]] section of this website.
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= Getting Involved =
 +
 
 +
People interested in the CDK development are
 +
encouraged to check out the [[Development]] section as well. Some people might want to go directly to the [http://www.sourceforge.net/projects/cdk Sourceforge pages] of the Chemistry Development Kit to [http://sourceforge.net/tracker/?group_id=20024&atid=120024 submit a bug], [http://sourceforge.net/mail/?group_id=20024 subscribe to a mailing list] or [http://sourceforge.net/project/showfiles.php?group_id=20024 download a release].
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If you have any questions about CDK, please see the [[Contact]] section for information on how to reach the CDK developers. The list of source code
 +
contributors is long and can be viewed from the [[List of Contributors]].
 +
 
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If you are looking for things to do, you can either go to [http://sourceforge.net/tracker2/?group_id=20024&atid=997721 Junior tasks], which are simple things which can be done directly by everybody with basic Java knowledge (or some even without, e. g. relating to documentation) or you can view the [[Missing Features]] page. Things here would be great to have, but would need some research, algorithms to be worked out etc.
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Last but not least, check out the [[CDK:Current events|current events]] page for any upcoming community events to join and meet CDK people in person.
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= CDK Publications =
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The two main publications are listed below. If you use the CDK in peer-reviewed work, we kindly ask you to cite either one of these
 +
two articles:
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* "The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics". Steinbeck C., Han Y., Kuhn S., Horlacher O., Luttmann E., Willighagen E.L., ''J. Chem. Inf. Comput. Sci.'' 2003 Mar-Apr; '''43'''(2):493-500  (DOI: [http://dx.doi.org/10.1021/ci025584y 10.1021/ci025584y])
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* "Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics". Steinbeck C., Hoppe C., Kuhn S., Floris M., Guha R., Willighagen E.L., ''Curr. Pharm. Des.'' 2006; '''12'''(17):2111-2120 (DOI: [http://dx.doi.org/10.2174/138161206777585274 10.2174/138161206777585274])
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More extensive list of [[Literature | CDK Literature]].
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The CDK has also been cited in a number of articles and a list of citations can be found at [[Citations]].
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= Sub Projects =
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[[JChemPaint]], [[CDK-XWS]], [http://www.cdk-taverna.de/ CDK-Taverna]
 +
 
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= YourKit support =
 +
 
 +
YourKit is kindly supporting open source projects with its full-featured Java Profiler.
 +
YourKit, LLC is creator of innovative and intelligent tools for profiling
 +
Java and .NET applications. Take a look at YourKit's leading software products:
 +
[http://www.yourkit.com/java/profiler/index.jsp YourKit Java Profiler] and
 +
[http://www.yourkit.com/.net/profiler/index.jsp YourKit ASP Profiler]

Revision as of 07:45, 22 August 2011

The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics. It is now developed by more than 50 developers all over the world and used in more than 10 different academic as well as industrial projects world wide.

Contents

About the Chemistry Development Kit (CDK)

The CDK design originated from a meeting on September 27-29 2000, Christoph Steinbeck, Egon Willighagen and Dan Gezelter met at Notre Dame University, South Bend, USA, to discuss the architecture of the package. The first actual implementation very much relied on the on the earlier work by the lab of Christoph Steinbeck and his older CompChem libraries, which urgently needed a rewrite. On the flight back to Europe, a first draft of the data classes were written.

10th Anniversary!

In the following years, the CDK library evolved into a fully blown open source and open development chemoinformatics package with code reaching from QSAR descriptor calculations to 2D and 3D model building. Programs like the 2D structure editor JChemPaint, NMRShiftDB, a database of organic molecules and their NMR spectra, and Bioclipse are based on or use the CDK. You can learn about these and others on the page Software using CDK. A full list of features is available.

Download CDK Releases

Currently, the CDK releases are available in two flavors: a stable series of CDK 1.4.x releases is available (latest on Sourceforge), as well as a development series, which is currently accesible via Git. Nightly builds of the development branch are also available. Maintainance of these release branches has been in the hands Egon Willighagen. See CDK Releases. Maven repositories are also available.

More information about using CDK can be found in the Documentation section of this website.

Getting Involved

People interested in the CDK development are encouraged to check out the Development section as well. Some people might want to go directly to the Sourceforge pages of the Chemistry Development Kit to submit a bug, subscribe to a mailing list or download a release.

If you have any questions about CDK, please see the Contact section for information on how to reach the CDK developers. The list of source code contributors is long and can be viewed from the List of Contributors.

If you are looking for things to do, you can either go to Junior tasks, which are simple things which can be done directly by everybody with basic Java knowledge (or some even without, e. g. relating to documentation) or you can view the Missing Features page. Things here would be great to have, but would need some research, algorithms to be worked out etc.

Last but not least, check out the current events page for any upcoming community events to join and meet CDK people in person.

CDK Publications

The two main publications are listed below. If you use the CDK in peer-reviewed work, we kindly ask you to cite either one of these two articles:

  • "The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics". Steinbeck C., Han Y., Kuhn S., Horlacher O., Luttmann E., Willighagen E.L., J. Chem. Inf. Comput. Sci. 2003 Mar-Apr; 43(2):493-500 (DOI: 10.1021/ci025584y)
  • "Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics". Steinbeck C., Hoppe C., Kuhn S., Floris M., Guha R., Willighagen E.L., Curr. Pharm. Des. 2006; 12(17):2111-2120 (DOI: 10.2174/138161206777585274)

More extensive list of CDK Literature.

The CDK has also been cited in a number of articles and a list of citations can be found at Citations.

Sub Projects

JChemPaint, CDK-XWS, CDK-Taverna

YourKit support

YourKit is kindly supporting open source projects with its full-featured Java Profiler. YourKit, LLC is creator of innovative and intelligent tools for profiling Java and .NET applications. Take a look at YourKit's leading software products: YourKit Java Profiler and YourKit ASP Profiler

Personal tools