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CREDITS
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Credits & Citing
================
This is at least a partial list of contributors to this library:
Main Library Code - CITING
--------------------------
=========== ================ ======================
2015 - 2019 Bernhard Thiel thiel@tbi.univie.ac.at
2012 - 2016 Peter Kerpedjiev pkerp@tbi.univie.ac.at
=========== ================ ======================
**Please Cite:**
Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev and Ivo L.
Hofacker. "3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0,
an RNA python library centered on secondary structure elements.
[version 1; referees: awaiting peer review]".
*F1000Research* 2019, **8**:287
https://doi.org/10.12688/f1000research.18458.1
For the pseudoknot removal code, see citation below.
Contributions
-------------
======= =============== ===========================
2015 Stephan Hammer s.hammer@univie.ac.at
2015 Marcel Kucharik marcel@tbi.univie.ac.at
2016 tcarlile https://github.com/tcarlile
2017-19 Irene Beckmann irene@tbi.univie.ac.at
======= =============== ===========================
ACKNOWLEDGEMENTS
----------------
Third-Party code used (and potentially modified) under the respective licenses
Copyright 2007, Sandra Smit and The Cogent Project
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
We thank Sandra Smit for providing us with the code of the knotted2nested standalone package,
a stripped down version of code available as part of the PyCogent package.
If you use this part of the library, please cite the paper mentioned below.
The full source code is available in the pycogent package under the GPL License:
======== ==================================================================
Used_in forgi._k2n_standalone
URI https://github.com/pycogent/pycogent
License GPL
Year 2007 - 2008
Author Sandra Smit (Sandra.Smit@colorado.edu)
Author Rob Knight (rob@spot.colorado.edu)
Cite Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight,
"From knotted to nested RNA structures: a variety of computational
methods for pseudoknot removal." *RNA* **2008**,
http://dx.doi.org/10.1261/rna.881308
======== ==================================================================
Copyright 2002, David Eppstein
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
======== ======================================================================================
Used_in Convex hulls code in forgi.projection.projection2d
URI http://code.activestate.com/recipes/117225-convex-hull-and-diameter-of-2d-point-sets/
License PSF
Year 2002
Author David Eppstein
======== ======================================================================================
Copyright 2014-2016, Syrtis Major
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
======== ======================================================================================
Used_in plot function in forgi.projection.projection2d
URI http://stackoverflow.com/a/24567352/5069869
License BSD 3-Clause License
Year 2014-2016
Author Syrtis Major
======== ======================================================================================
Copyright Matplotlib development team
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
======== ======================================================================================
Used_in plot function in forgi.projection.projection2d
URI http://matplotlib.org/examples/api/line_with_text.html
License PSF
Year 2008 - 2014
Authors Matplotlib development team
======== ======================================================================================