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https://github.com/mtefagh/sparseqfca.jl

Developed a registered Julia package which quantifies the redundancies in genome-scale metabolic networks and provides local sparse certificates which are both efficiently verifiable and interpretable
https://github.com/mtefagh/sparseqfca.jl

bioinformatics fca julia qfca systems-biology

Last synced: 28 days ago
JSON representation

Host: GitHub
URL: https://github.com/mtefagh/sparseqfca.jl
Owner: mtefagh
License: gpl-3.0
Created: 2019-01-14T18:09:21.000Z (almost 6 years ago)
Default Branch: master
Last Pushed: 2024-09-27T06:44:12.000Z (about 2 months ago)
Last Synced: 2024-10-09T05:59:56.181Z (about 1 month ago)
Topics: bioinformatics, fca, julia, qfca, systems-biology
Language: Jupyter Notebook
Homepage: https://mtefagh.github.io/sparseQFCA.jl
Size: 6.4 MB
Stars: 1
Watchers: 1
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        # Sparse Quantitative Flux Coupling Analysis

| **Tests** | **Coverage** |

|:---:|:---:|

| [![Build Status](https://travis-ci.com/mtefagh/sparseQFCA.jl.svg?branch=master)](https://app.travis-ci.com/mtefagh/sparseQFCA.jl) | [![Coverage Status](https://coveralls.io/repos/github/mtefagh/sparseQFCA.jl/badge.svg?branch=master)](https://coveralls.io/github/mtefagh/sparseQFCA.jl?branch=master) [![codecov](https://codecov.io/gh/mtefagh/sparseQFCA.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/mtefagh/sparseQFCA.jl)

## sparseQFCA architecture

*sparseQFCA* is a registered [](https://julialang.org/) is a Julia package providing a sparse Quantitative flux coupling analysis(QFCA). It uses parallel processing and is designed for finding flux coupling table and metabolic network reductions, specifically for QuantomeRedNet. Moreover, a Julia implementation of Swift Consistency Checking is also available as a preprocessing subroutine.

![sparseQFCA architecture](/example/sparseQFCA.png "sparseQFCA architecture")

## How to get started

### Prerequisites and requirements

- **Operating system**: Use Linux (Debian, Ubuntu or centOS), MacOS, or Windows

  10 as your operating system. `sparseQFCA` has been tested on these systems.

- **Julia language**: In order to use `sparseQFCA`, you need to install Julia 1.0

  or higher. Download and follow the installation instructions for Julia

  [here](https://julialang.org/downloads/).

- **Hardware requirements**: `sparseQFCA` runs on any hardware that can run Julia,

  and can easily use resources from multiple computers interconnected on a

  network. For processing large datasets, you are required to ensure that the

  total amount of available RAM on all involved computers is larger than the

  data size.

- **Optimization solvers**: `sparseQFCA` uses

  [`JuMP.jl`](https://github.com/jump-dev/JuMP.jl) to formulate optimization

  problems and is compatible with all [`JuMP` supported

  solvers](https://jump.dev/JuMP.jl/stable/installation/#Supported-solvers).

  However, to perform analysis at least one of these solvers needs to be

  installed on your machine. For a pure Julia implementation, you may use e.g.

  [`HiGHS.jl`](https://github.com/jump-dev/HiGHS.jl), but other solvers ([`GLPK.jl`](https://github.com/jump-dev/GLPK.jl),

  [`CPLEX.jl`](https://github.com/jump-dev/CPLEX.jl), [`MosekTools.jl`](https://github.com/jump-dev/MosekTools.jl),...) work just as well.

:bulb: If you are new to Julia, it is advisable to [familiarize yourself with

the environment

first](https://docs.julialang.org/en/v1/manual/getting-started/).  Use the

Julia [documentation](https://docs.julialang.org) to solve various

language-related issues, and the [Julia package manager

docs](https://julialang.github.io/Pkg.jl/v1/getting-started/) to solve

installation-related difficulties. Of course, [the Julia

channel](https://discourse.julialang.org/) is another fast and easy way to find

answers to Julia specific questions.

## Quick Start

To get started, first run `import Pkg; Pkg.add("sparseQFCA")` to install the *sparseQFCA* package.

## License

*sparseQFCA* is distributed under the [GNU General Public License v3.0](http://www.gnu.org/copyleft/gpl.html).