binarysubstrate / phenotypes

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Contributions

Contributions are welcome!

Requirements

  • numpy
  • h5py
  • scipy
  • theano
  • biopython
  • keras

tensorflow may be additionally required if using Python 2 instead of Python 3.

On Windows, Visual Studio C++ is required. Microsoft Visual C++ 14.0 is required if using Python 3.5 or Microsoft Visual C++ 10.0 is required is Python 3.4.

Installation

Using Anaconda

conda create -n phenotypes python=3 numpy h5py scipy theano biopython
source activate phenotypes
pip install keras

Using pip

pip install -r requirements.txt

Depending on your environment you may have to pip install numpy before pip installing other packages. This will be improved if/when a setup script is created.

References

Sønderby, S. K., Sønderby, C. K., Nielsen, H. & Winther, O. Convolutional LSTM networks for subcellular localization of proteins. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 9199, 68–80 (2015).
https://arxiv.org/abs/1503.01919

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