brsynth/rpthermo repository overview

⁠rpThermodynamics

Galaxy tool that reads a single or collection of rpSBML files, parses the SMILES or InChI structures to calculate the formation energy of the molecules. Either calculates the Gibbs free energy using databases derived from Equilibrator⁠ or Alberty et al.⁠. Since the retosynthesis algorithm generates chemical species without corss-references to databases, the tool falls back to the Component Contribution⁠ method to estimate the Gibbs free energy of a reaction.

⁠Information Flow

⁠Input

Required information:

• Input rpSBML: Either tar.xz collection of rpSBML or single rpSBML file

Advanced options:

• Name of the heterologous pathway: (default: rp_pathway) Groups ID of the heterologous pathway
• IP address of the rpFBA REST service: IP address of the REST service

⁠Output

• rpThermo: The output is a tar.xz archive containing a list of rpSBML files or a single SBML file

⁠Installing

To build the image using the Dockerfile, use the following image:

docker build -t brsynth/rpthermo-rest:dev .

To run the service as localhost use the following service:

docker run -p 8883:8888 brsynth/rpthermo-rest:dev

⁠Algorithm

The thermodyamics is calculated using the Component Contribution⁠ method

⁠Prerequisites

• Docker - Install⁠
• libSBML - Anaconda library⁠
• Component Contribution - Git to the project⁠

⁠Contributing

TODO

⁠Versioning

Version 0.1

⁠Authors

• Melchior du Lac

⁠License

This project is licensed under the MIT License - see the LICENSE.md⁠ file for details

⁠Acknowledgments

• Thomas Duigou
• Joan Hérisson

⁠How to cite rpThermodynamics?

TODO