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Merge pull request #19 from lafita/master
Update the BioJava publication on the website
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‎_config.yml

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# Site settings
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title: BioJava
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description: The open-source Java framework for bioinformatics
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description: The open-source Java library for bioinformatics
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owner: BioJava
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first_published: 2000
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email: biojava-l@biojava.org
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# Release settings
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release:
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version: 5.0.0
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version: 5.2.0
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legacy: 1.9.1
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collections:

‎_includes/citation-2000.md

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**BioJava: open source components for bioinformatics**<br/>
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*Matthew Pocock; Thomas Down; Tim Hubbard* <br/>
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*Matthew Pocock, Thomas Down, & Tim Hubbard* <br/>
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[ACM SIGBIO Newsletter (2000) 20 (2): 10-12.](https://dl.acm.org/citation.cfm?id=360266) <br/>
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[![doi](https://img.shields.io/badge/doi-10.1145%2360262.360266-blue.svg?style=flat)](https://dl.acm.org/citation.cfm?id=360266)
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[![doi](https://img.shields.io/badge/doi-10.1145%2F360262.360266-blue.svg?style=flat)](https://dl.acm.org/citation.cfm?id=360266)

‎_includes/citation-2008.md

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**BioJava: an open-source framework for bioinformatics**<br/>
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*R. C. G. Holland, T. A. Down, M. Pocock, A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer, M. J. Schreiber* <br/>
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*R. C. G. Holland, T. A. Down, M. Pocock, A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer, & M. J. Schreiber* <br/>
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[Bioinformatics (2008) 24 (18): 2096–2097.](https://academic.oup.com/bioinformatics/article/24/18/2096/192730) <br/>
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[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2btn397-blue.svg?style=flat)](https://academic.oup.com/bioinformatics/article/24/18/2096/192730) [![pubmed](https://img.shields.io/badge/pubmed-18689808-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/18689808)
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[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtn397-blue.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btn397) [![pubmed](https://img.shields.io/badge/pubmed-18689808-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/18689808)

‎_includes/citation-2012.md

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**BioJava: an open-source framework for bioinformatics in 2012**<br/>
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*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
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*Andreas Prlic, Andrew Yates, Spencer E. Bliven, Peter W. Rose, Julius Jacobsen, Peter V. Troshin, Mark Chapman, Jianjiong Gao, Chuan Hock Koh, Sylvain Foisy, Richard Holland, Gediminas Rimsa, Michael L. Heuer, H. Brandstatter-Muller, Philip E. Bourne, & Scooter Willis* <br/>
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[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693) <br/>
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[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693) [![pubmed](https://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
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[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](https://doi.org/10.1093/bioinformatics/bts494) [![pubmed](https://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)

‎_includes/citation-2017.md

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**BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank**<br/>
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*Jianjiong Gao, Andreas Prlić, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E Bourne, Peter W Rose* <br/>
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*Jianjiong Gao, Andreas Prlić, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E Bourne, & Peter W Rose* <br/>
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[Bioinformatics (2017) 33 (13): 2047–2049.](https://academic.oup.com/bioinformatics/article/33/13/2047/3002764) <br/>
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[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2btx101-blue.svg?style=flat)](https://academic.oup.com/bioinformatics/article/33/13/2047/3002764) [![pubmed](https://img.shields.io/badge/pubmed-28334105-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/28334105)
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[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtx101-blue.svg?style=flat)](https://academic.oup.com/bioinformatics/article/33/13/2047/3002764) [![pubmed](https://img.shields.io/badge/pubmed-28334105-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/28334105)

‎_includes/citation-2019.md

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**BioJava 5: A community driven open-source bioinformatics library**<br/>
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*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
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[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
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[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)

‎_wiki/AboutBioJava.md

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The BioJava project
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-------------------
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BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of biological sequences and 3D structures. The main goal of the project is to facilitate rapid application development for bioinformatics.
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BioJava is an open-source project dedicated to providing a Java library for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of biological sequences and 3D structures. The main goal of the project is to facilitate rapid application development for bioinformatics.
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We have a <a href="https://wikipedia.org/wiki/BioJava">Wikipedia page</a> (of course!) in case you would like to know more about the project.
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If you use BioJava, please cite:
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{% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
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{% capture my-citation %}{% include citation-2019.md %}{% endcapture %}
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{{ my-citation | markdownify }}
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Other articles include:
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{% capture my-citation %}{% include citation-2017.md %}{% endcapture %}
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{{ my-citation | markdownify }}
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{% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
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{{ my-citation | markdownify }}
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{% capture my-citation %}{% include citation-2008.md %}{% endcapture %}
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{{ my-citation | markdownify }}
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‎_wiki/BioJava_GetStarted.md

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You can now compile and run BioJava programs using the *javac* and
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*java* commands. You might like to look at the developer section on the
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[Main page](http://www.biojava.org/wiki/Main_Page) for documentation,
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[Main page](http://www.biojava.org) for documentation,
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cookbook and tutorials. Finally, you can learn a lot about BioJava by
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trying the demo programs included in the source distribution (see
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below).
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If you want to modify BioJava, you can clone or fork the GitHub repository or obtain the source code from any of the previous releases from the [releases page](https://github.com/biojava/biojava/releases).
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Source releases are distributed in .tar.gz format.
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If you think your modifications can benefit others do not hesitate to submit a [pull request on GitHub](https://github.com/biojava/biojava/pulls). We always welcome new contributions. Here is how you can [get involved]({{site.baseurl}}/getinvolved.html).
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If you think your modifications can benefit others do not hesitate to submit a [pull request on GitHub](https://github.com/biojava/biojava/pulls). We always welcome new contributions. Here is how you can [get involved](GetInvolved).

‎_wiki/FAQs.md

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**Q: Which macromolecular structure formats does BioJava support?**
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A: Currently BioJava supports parsing macromolecular structures in [PDB](https://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html), [MMCIF](https://www.rcsb.org/pdb/static.do?p=file_formats/mmcif/index.html) and, as of version 5+, [MMTF](http://mmtf.rcsb.org/).
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The library also allows conversion between the formats through the same internal representation as `Structure` objects.
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The library also allows conversion between the formats through the same internal representation as `Structure` objects.
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**Q: How often are new versions of BioJava released?**
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A: There is not a fixed schedule for BioJava releases. Minor versions are released when there are important bug fixes to include, and as a fact we have released two major versions in the last six years.
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**Q: I love the library, how can I support you?**
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A: Thanks! We are simple people, so just consider giving us a star in the [GitHub repository](https://github.com/biojava/biojava/stargazers) and [citing the project]({{site.baseurl}}/about.html) if it was useful in your research.
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A: Thanks! We are simple people, so just consider giving us a star in the [GitHub repository](https://github.com/biojava/biojava/stargazers) and [citing one of our publications](About) if it was useful in your research.

‎index.html

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<header class="major">
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<h2>Open source</h2>
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<p>The project is hosted, developed, and maintained on GitHub.</p>
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<a href="https://github.com/biojava/biojava" class="button big">GitHub project</a>
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<a href="https://github.com/biojava/biojava" class="button">GitHub project</a>
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</header>
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</div>
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</section>
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<div class="image"><img src="images/1ihm.png" alt="" /></div><div class="content">
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<h2>Please cite<br />
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</h2>
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{% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
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{% capture my-citation %}{% include citation-2019.md %}{% endcapture %}
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</div>
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</section>
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</header>
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<ul class="actions vertical">
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<li><a href="wiki/BioJava%3AGetStarted" class="button fit special">Get started</a></li>
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<li><a href="https://github.com/biojava/biojava" class="button fit">Get the source</a></li>
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<li><a href="https://github.com/biojava/biojava" class="button fit">Source code</a></li>
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</ul>
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</div>
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</section>

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