https://github.com/mtefagh/qfca
Compressed biological systems of tens of thousands of biochemical reactions by a hierarchical organization of pathways which speeds up the downstream analysis up to 3 times in addition to saving memory and storage space
https://github.com/mtefagh/qfca
fca qfca
Last synced: about 1 year ago
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Compressed biological systems of tens of thousands of biochemical reactions by a hierarchical organization of pathways which speeds up the downstream analysis up to 3 times in addition to saving memory and storage space
- Host: GitHub
- URL: https://github.com/mtefagh/qfca
- Owner: mtefagh
- License: gpl-3.0
- Created: 2017-10-08T23:51:32.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2022-01-05T09:30:05.000Z (over 4 years ago)
- Last Synced: 2024-10-19T05:22:37.966Z (over 1 year ago)
- Topics: fca, qfca
- Language: MATLAB
- Homepage: https://mtefagh.github.io/qfca/
- Size: 2.79 MB
- Stars: 2
- Watchers: 0
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Quantitative Flux Coupling Analysis
====
Introduction
----
*Quantitative flux coupling analysis* (QFCA) is a quantitative approach to identify and remove the redundancies of the steady-state flux cone. The full description and theory of the algorithm implemented by QFCA is discussed in the associated papers. When referencing QFCA, please cite the followings:
- Tefagh, M., & Boyd, S. P. (2019). Quantitative flux coupling analysis. J. Math. Biol., 78(5), 1459-1484. [https://doi.org/10.1007/s00285-018-1316-9](https://doi.org/10.1007/s00285-018-1316-9)
- Tefagh, M., & Boyd, S. P. (2019). Metabolic network reductions. bioRxiv, 499251. [https://doi.org/10.1101/499251](https://doi.org/10.1101/499251)
Quick Start
----
The following example uses the `QFCA` function to compute the table of **flux coupling relations** and the list of **blocked reactions** for the [core *E. coli* model](http://systemsbiology.ucsd.edu/Downloads/EcoliCore) and also returns the **reduced metabolic network**.
```matlab
load('ecoli_core_model.mat');
[reduced_net, fctable, blocked] = QFCA(model, true, 'linprog');
```
The output of the above code is as follows.
```matlab
Original number of:
metabolites = 72; reactions = 95; nonzero elements = 360
Original number of:
reversible reactions = 59; irreversible reactions = 36
Identifying the blocked reactions and removing them from the network: 0.034
Reduced number of:
metabolites = 72; reactions = 95; nonzero elements = 360
Finding the full coupling relations: 0.008
Reduced number of:
metabolites = 34; reactions = 60; nonzero elements = 236
Correcting the reversibility types: 0.037
Finding the directional and partial coupling relations: 0.411
Inferring by the transitivity of full coupling relations: 0.000
Metabolic network reductions postprocessing: 0.001
Reduced number of:
metabolites = 30; reactions = 58; nonzero elements = 224
The number of solved:
linear programs = 54; systems of linear equations = 8
```
Furthermore, the `directionallyCoupled` function can be utilized as a stand-alone function to find **fictitious metabolite** certificates.
License
----
*QFCA* is distributed under the [GNU General Public License v3.0](http://www.gnu.org/copyleft/gpl.html).