Skip to content

Update the BioJava publication on the website #19

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 3 commits into from
May 7, 2019
Merged

Update the BioJava publication on the website #19

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
ffeaf16
Add new publication
lafita May 7, 2019
fb6c214
Fix small issues and update citation
lafita May 7, 2019
a076049
Add space
lafita May 7, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions _config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

# Site settings
title: BioJava
description: The open-source Java framework for bioinformatics
description: The open-source Java library for bioinformatics
owner: BioJava
first_published: 2000
email: biojava-l@biojava.org
Expand Down Expand Up @@ -68,7 +68,7 @@ kramdown:

# Release settings
release:
version: 5.0.0
version: 5.2.0
legacy: 1.9.1

collections:
Expand Down
4 changes: 2 additions & 2 deletions _includes/citation-2000.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
**BioJava: open source components for bioinformatics**<br/>
*Matthew Pocock; Thomas Down; Tim Hubbard* <br/>
*Matthew Pocock, Thomas Down, & Tim Hubbard* <br/>
[ACM SIGBIO Newsletter (2000) 20 (2): 10-12.](https://dl.acm.org/citation.cfm?id=360266) <br/>
[![doi](https://img.shields.io/badge/doi-10.1145%2360262.360266-blue.svg?style=flat)](https://dl.acm.org/citation.cfm?id=360266)
[![doi](https://img.shields.io/badge/doi-10.1145%2F360262.360266-blue.svg?style=flat)](https://dl.acm.org/citation.cfm?id=360266)
4 changes: 2 additions & 2 deletions _includes/citation-2008.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
**BioJava: an open-source framework for bioinformatics**<br/>
*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/>
*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/>
[Bioinformatics (2008) 24 (18): 2096–2097.](https://academic.oup.com/bioinformatics/article/24/18/2096/192730) <br/>
[![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)
[![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)
4 changes: 2 additions & 2 deletions _includes/citation-2012.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
**BioJava: an open-source framework for bioinformatics in 2012**<br/>
*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/>
*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/>
[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693) <br/>
[![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)
[![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)
4 changes: 2 additions & 2 deletions _includes/citation-2017.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
**BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank**<br/>
*Jianjiong Gao, Andreas Prlić, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E Bourne, Peter W Rose* <br/>
*Jianjiong Gao, Andreas Prlić, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E Bourne, & Peter W Rose* <br/>
[Bioinformatics (2017) 33 (13): 2047–2049.](https://academic.oup.com/bioinformatics/article/33/13/2047/3002764) <br/>
[![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)
[![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)
4 changes: 4 additions & 0 deletions _includes/citation-2019.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
**BioJava 5: A community driven open-source bioinformatics library**<br/>
*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/>
[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
[![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)
7 changes: 5 additions & 2 deletions _wiki/AboutBioJava.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ permalink: wiki/About
The BioJava project
-------------------

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.
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.

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.

Expand All @@ -15,14 +15,17 @@ Articles

If you use BioJava, please cite:

{% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
{% capture my-citation %}{% include citation-2019.md %}{% endcapture %}
{{ my-citation | markdownify }}

Other articles include:

{% capture my-citation %}{% include citation-2017.md %}{% endcapture %}
{{ my-citation | markdownify }}

{% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
{{ my-citation | markdownify }}

{% capture my-citation %}{% include citation-2008.md %}{% endcapture %}
{{ my-citation | markdownify }}

Expand Down
4 changes: 2 additions & 2 deletions _wiki/BioJava_GetStarted.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ consult your Java vendor.

You can now compile and run BioJava programs using the *javac* and
*java* commands. You might like to look at the developer section on the
[Main page](http://www.biojava.org/wiki/Main_Page) for documentation,
[Main page](http://www.biojava.org) for documentation,
cookbook and tutorials. Finally, you can learn a lot about BioJava by
trying the demo programs included in the source distribution (see
below).
Expand All @@ -77,4 +77,4 @@ Building your own
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).
Source releases are distributed in .tar.gz format.

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).
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).
4 changes: 2 additions & 2 deletions _wiki/FAQs.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@ permalink: wiki/FAQs

**Q: Which macromolecular structure formats does BioJava support?**
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/).
The library also allows conversion between the formats through the same internal representation as `Structure` objects.
The library also allows conversion between the formats through the same internal representation as `Structure` objects.

**Q: How often are new versions of BioJava released?**
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.

**Q: I love the library, how can I support you?**
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.
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.
6 changes: 3 additions & 3 deletions index.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ <h2>{{ site.title }}</h2>
<header class="major">
<h2>Open source</h2>
<p>The project is hosted, developed, and maintained on GitHub.</p>
<a href="https://github.com/biojava/biojava" class="button big">GitHub project</a>
<a href="https://github.com/biojava/biojava" class="button">GitHub project</a>
</header>
</div>
</section>
Expand All @@ -43,7 +43,7 @@ <h2>Biological sequences</h2>
<div class="image"><img src="images/1ihm.png" alt="" /></div><div class="content">
<h2>Please cite<br />
</h2>
{% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
{% capture my-citation %}{% include citation-2019.md %}{% endcapture %}
{{ my-citation | markdownify }}
</div>
</section>
Expand Down Expand Up @@ -116,7 +116,7 @@ <h2><img src="/images/logo/logo_favicon_250.png" height="60" style="vertical-ali
</header>
<ul class="actions vertical">
<li><a href="wiki/BioJava%3AGetStarted" class="button fit special">Get started</a></li>
<li><a href="https://github.com/biojava/biojava" class="button fit">Get the source</a></li>
<li><a href="https://github.com/biojava/biojava" class="button fit">Source code</a></li>
</ul>
</div>
</section>
pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy