https://github.com/mtefagh/swiftcore
Accelerated the state-of-the-art in genome-scale metabolic network reconstruction more than 10 times by convex optimization techniques such as factorization, approximation, and regularization
https://github.com/mtefagh/swiftcore
context-specific reconstruction
Last synced: 7 months ago
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Accelerated the state-of-the-art in genome-scale metabolic network reconstruction more than 10 times by convex optimization techniques such as factorization, approximation, and regularization
- Host: GitHub
- URL: https://github.com/mtefagh/swiftcore
- Owner: mtefagh
- License: gpl-3.0
- Created: 2018-10-02T14:00:07.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2022-03-03T15:48:36.000Z (over 3 years ago)
- Last Synced: 2024-10-19T05:22:38.192Z (12 months ago)
- Topics: context-specific, reconstruction
- Language: HTML
- Homepage: https://mtefagh.github.io/swiftcore/
- Size: 5.13 MB
- Stars: 5
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# swiftcc
## Introduction
[swiftcc](https://github.com/mtefagh/swiftcore/blob/master/src/swiftcc.m) is a tool for finding the largest flux consistent subnetwork of the original metabolic network. [swiftccTest](https://github.com/mtefagh/swiftcore/blob/master/test/swiftccTest.m) provides a benchmark to compare its performance against [fastcc](https://wwwen.uni.lu/research/fstc/life_sciences_research_unit/research_areas/systems_biology/software). When referencing SWIFTCC, please cite the following:
- Tefagh, M., & Boyd, S. P. (2020). SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks. BMC Bioinformatics, 21(1), 1-14. [https://doi.org/10.1186/s12859-020-3440-y](https://doi.org/10.1186/s12859-020-3440-y)
## Usage
### `consistent = swiftcc(S, rev [, solver])`
### Inputs:
* `S`: the associated sparse **stoichiometric matrix**
* `rev`: the 0-1 vector with 1's corresponding to the **reversible reactions**
### Optional inputs
* `solver`: the **LP solver** to be used; the currently available options are _gurobi_, _linprog_, and _cplex_ with the default value of _linprog_. It fallbacks to the COBRA LP solver interface if another supported solver is called.
### Outputs:
* `consistent`: the 0-1 indicator vector of the reactions constituting the maximum **flux consistent metabolic subnetwork**
***
# swiftcore
## Introduction
[swiftcore](https://github.com/mtefagh/swiftcore/blob/master/src/swiftcore.m) is a tool for the context-specific reconstruction of genome-scale metabolic networks. [swiftcoreTest](https://github.com/mtefagh/swiftcore/blob/master/test/swiftcoreTest.m) and [weightedTest](https://github.com/mtefagh/swiftcore/blob/master/test/weightedTest.m) provide a benchmark to compare its performance against [fastcore](https://wwwen.uni.lu/research/fstc/life_sciences_research_unit/research_areas/systems_biology/software). When referencing SWIFTCORE, please cite the following:
- Tefagh, M., & Boyd, S. P. (2020). SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks. BMC bioinformatics, 21(1), 1-14. [https://doi.org/10.1186/s12859-020-3440-y](https://doi.org/10.1186/s12859-020-3440-y)
## Usage
### `[reconstruction, reconInd, LP] = swiftcore(model, coreInd, weights, tol, reduction [, solver])`
### Inputs
1. `model`: the **metabolic network** with fields:
* `.S` - the associated sparse **stoichiometric matrix**
* `.lb` - **lower bounds** on reaction rates
* `.ub` - **upper bounds** on reaction rates
* `.rxns` - the cell array of **reaction abbreviations**
* `.mets` - the cell array of **metabolite abbreviations**
2. `coreInd`: the set of indices corresponding to the **core reactions**
3. `weights`: the **weight vector** for the penalties associated with each reaction
4. `tol`: **zero-tolerance**, i.e., the smallest flux value considered nonzero
5. `reduction`: boolean enabling the **metabolic network reduction** preprocess
### Optional inputs
6. `solver`: the **LP solver** to be used; the currently available options are _gurobi_, _linprog_, and _cplex_ with the default value of _linprog_. It fallbacks to the COBRA LP solver interface if another supported solver is called.
### Outputs
1. `reconstruction`: the **flux consistent metabolic network** reconstructed from the core reactions
2. `reconInd`: the 0-1 **indicator vector** of the reactions constituting the reconstruction
3. `LP`: the number of **solved LPs**
# Requirements
To run the test files in the `test` folder, one needs to download the [FASTCORE](http://wwwen.uni.lu/recherche/fstc/life_sciences_research_unit/research_areas/systems_biology/software) package and the [Recon3D](https://www.vmh.life/files/reconstructions/Recon/3D.01/Recon3D_301.zip) model and add them to the Matlab path.
# License
The *swift* family is distributed under the [GNU General Public License v3.0](http://www.gnu.org/copyleft/gpl.html).