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:
“3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA python library centered on secondary structure elements.” Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev and Ivo L. Hofacker. F1000 Research, in preparation
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 |