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https://github.com/bad-ants-fleet/ribolands

energy landscapes and folding kinetics of nucleic acids

https://github.com/bad-ants-fleet/ribolands

Science Score: 13.0%

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energy landscapes and folding kinetics of nucleic acids

Basic Info
  • Host: GitHub
  • Owner: bad-ants-fleet
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 501 KB
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Created almost 10 years ago · Last pushed over 4 years ago

https://github.com/bad-ants-fleet/ribolands/blob/master/ 

# ribolands - kinetic analysis of nucleic acids

**ribolands** is a Python wrapper for multiple nucleic acid kinetic analysis
programs, currently `Kinfold`, `RNAsubopt`, `barriers` and `treekin`. Those 
programs have to installed separately. 

:warning: Dear users of the cotranscriptional folding simulator
**DrTransformer**, this package provided only a **preliminary version** of the
software which now has been removed. The newest version of **DrTransformer** is
not publicly available yet, but feel free to reach out for beta-testing.
Also, the executable for the cotranscriptional folding software `BarMap` has
been removed (since it is has never been officially released). `BarMap` can be
coded with minimal effort using the ribolands package, feel free to reach out
if you need help.

## Dependencies
`ribolands` uses [RNAsubopt] from the [ViennaRNA package], as well as [barriers]
and [treekin] for landscape computations. Make sure that you have recent
versions installed: 
 - `ViennaRNA>=v2.4.13`
 - `treekin>=v0.5.1`
 - `barriers>=v1.8.1` 


## Installation
```sh
  ~$ python setup.py install
  ~$ python -m pytest tests/ -v -s
```

## Latest changes
 - removed DrTransformer, which will be available soon as a separate python package.
 - removed all other executables in order to focus on library development.
 - lot's of interface changes to build workflows (work in progress)
 - next release (v0.10) planned for early 2022

## License
MIT

[//]: References
[Hofacker et al. (2010)]: 
[ViennaRNA package]: 
[RNAsubopt]: 
[barriers]: 
[treekin]: 
[ribolands]: 
[drtransformer]:

Owner

  • Name: Stefan Badelt
  • Login: bad-ants-fleet
  • Kind: user
  • Location: Vienna
  • Company: Institute for Theoretical Chemistry

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