PyFBA | python implementation of flux balance analysis

by linsalrob Python Version: v2.5-beta License: MIT

X-Ray Key Features Code Snippets Community Discussions Vulnerabilities Install Support

kandi X-RAY | PyFBA Summary

PyFBA is a Python library. PyFBA has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

PyFBA is a Python flux-balance-analysis package that allows you to build models from genomes, gapfill models, and run flux-balance-analysis on that model. The aim of PyFBA is to provide an extensible, python-based platform for FBA work. PyFBA is being developed by Daniel Cuevas, Taylor O'Connell, and Rob Edwards in Rob's bioinformatics group at San Diego State University together with help from Janaka Edirisinghe, Chris Henry, Ross Overbeek and others at Argonne National Labs. You can read more about PyFBA on our github.io pages.

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PyFBA has a low active ecosystem.

It has 18 star(s) with 9 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 1 have been closed. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of PyFBA is v2.5-beta

Quality

PyFBA has 0 bugs and 0 code smells.

Security

PyFBA has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

PyFBA code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

PyFBA is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

PyFBA releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions are available. Examples and code snippets are not available.

It has 6389 lines of code, 341 functions and 110 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed PyFBA and discovered the below as its top functions. This is intended to give you an instant insight into PyFBA implemented functionality, and help decide if they suit your requirements.

Gathers gaps in the given media
Compute the union of all the bounding box
Add roles
Add reactions to the model
Gathers gapfills
Log a message to the global logger
Run FBA
Print a message to stdout
Suggest reactions by compound
Grap gap filling in two media
Parse the SBML file
Create a reaction equation
Load a matrix
Given a list of potential composition of a model composition and a media
Function to minimize gap - filled reactions
Convert a reaction set into a set of reactions
Suggest compounds from the media
Output flux information to FBA
Loads a model
Given a list of Compound and a list of Compound and a list of Compound
Computes the probability of each compound in the given reactions
Returns a set of reactions that minimizes the base reactions
Creates a stoichiometric matrix for each reaction
Parse an SBML file
Calculate the bounds for a set of reactions
Suggest reactions from subsystems

Get all kandi verified functions for this library.

PyFBA Key Features

No Key Features are available at this moment for PyFBA.

PyFBA Examples and Code Snippets

No Code Snippets are available at this moment for PyFBA.

Community Discussions

No Community Discussions are available at this moment for PyFBA.Refer to stack overflow page for discussions.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install PyFBA

Once you have installed GLPK, PyGLPK, and PyFBA, you will most likely want to build a model from a genome, gap fill that model, and test it for growth on different media. We have detailed instructions that walk you through the step-by-step procedures that you need to use to run flux balance analysis on your own genome.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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