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{"name":"MSDK","tagline":"Mass Spectrometry Development Kit","body":"### What is MSDK?\r\n\r\nMSDK is a Java library of algorithms for processing mass spectrometry data. The goals of the library are to provide a flexible data model with Java interfaces for mass-spectrometry related objects (including raw spectra, processed data sets, identification results etc.) and to integrate the existing algorithms that are currently scattered around various Java-based graphical tools, such as (in alphabetical order):\r\n* [Guineu](https://code.google.com/p/guineu/)\r\n* [JDAMP](http://software.iab.keio.ac.jp/jdamp/)\r\n* [Maltcms](http://maltcms.sourceforge.net)\r\n* [MassCascade](https://bitbucket.org/sbeisken/masscascade/)\r\n* [Mass-Up](http://sing.ei.uvigo.es/mass-up/)\r\n* [Maui-VIA](http://bimsbstatic.mdc-berlin.de/kempa/software/kempaSoftware.html)\r\n* [msInspect](http://proteomics.fhcrc.org/CPL/msinspect/index.html)\r\n* [mzMatch](http://mzmatch.sourceforge.net)\r\n* [MZmine](http://mzmine.github.io)\r\n* [OpenChrom](https://www.openchrom.net)\r\n* [ProteoSuite](https://code.google.com/p/proteo-suite/)\r\n* [SIRIUS](http://bio.informatik.uni-jena.de/sirius2/)\r\n\r\n### Why do we need MSDK?\r\n\r\nWhile competition among various algorithms is beneficial for the progress of research, the absence of a common data model and development platform makes it difficult and laborious to evaluate the results and performance of different algorithms. MSDK addresses this issue for the Java platform, while other projects such as [OpenMS](http://open-ms.sourceforge.net) or [ProteoWizard](http://proteowizard.sourceforge.net) address this issue in C/C++. The advantages of Java are its multi-platform nature and easy, rapid development in a higher-level language compared to C/C++.\r\n\r\n### Usage\r\n\r\n#### API\r\n\r\nPlease see the complete [MSDK API](http://msdk.github.io/api/).\r\n\r\n#### Maven artifacts\r\n\r\nMSDK jars are automatically deployed to Maven Central. In order to use MSDK, simply add the following dependency to your pom.xml:\r\n\r\n```\r\n <dependency>\r\n    <groupId>io.github.msdk</groupId>\r\n    <artifactId>msdk-all</artifactId>\r\n    <version>0.0.3</version>\r\n </dependency>\r\n```\r\n\r\n### Java version\r\n\r\nMSDK requires Java runtime (JRE) version 1.7 or newer.\r\n\r\n### License\r\n\r\nMSDK binaries and source codes are dual-licensed under either the terms of the [Eclipse Public License v1.0](http://www.eclipse.org/legal/epl-v10.html) as published by the Eclipse Foundation\r\n \r\n  or (per the licensee's choosing)\r\n \r\nunder the terms of the GNU [Lesser General Public License version 2.1](http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html) as published by the Free Software Foundation.\r\n\r\n### Contributors\r\n\r\nPlease use GitHub's [statistics](https://github.com/msdk/msdk/graphs/contributors) to see who has contributed to this project so far. The [Git Blame](https://help.github.com/articles/using-git-blame-to-trace-changes-in-a-file) feature can be used to track the authorship of each individual line in the source codes.\r\n\r\n### How to join this project\r\n\r\nPlease join our [Google Group](https://groups.google.com/forum/#!forum/msdk-devel) and tell us about your ideas. Contributions to MSDK can be made through GitHub's standard [Pull Request](https://help.github.com/articles/using-pull-requests/) mechanism. If you are not familiar with this mechanism, please read our brief [tutorial](pull-request-tutorial.html). Before creating a Pull Request, please make sure that you agree with your code being distributed as part of MSDK under the above-mentioned license.\r\n\r\n### How to report problems\r\n\r\nYou can report problems and bugs through the GitHub's [Issues tracker](https://github.com/msdk/msdk/issues) or through our [Google Group](https://groups.google.com/forum/#!forum/msdk-devel). Please do so [constructively](http://www.chiark.greenend.org.uk/~sgtatham/bugs.html).\r\n\r\n### Source codes\r\n\r\nMSDK source codes are available from our [GitHub repository](https://github.com/msdk/msdk). To clone the source code tree, you can use this command:\r\n```\r\n$ git clone https://github.com/msdk/msdk.git\r\n```\r\n\r\n[Apache Maven](http://maven.apache.org) is required to build MSDK. To compile the source codes, run the following command in the source code directory:\r\n```\r\n$ mvn package\r\n```\r\n","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}