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https://github.com/cfrioux/fluto
https://github.com/cfrioux/fluto
answer-set-programming bioinformatics flux-balance-analysis gap-filling linear-programming metabolic-models metabolic-network metabolic-reconstruction
Last synced: about 1 month ago
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- Host: GitHub
- URL: https://github.com/cfrioux/fluto
- Owner: cfrioux
- License: gpl-3.0
- Created: 2018-05-15T13:01:13.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2021-10-04T06:41:43.000Z (about 3 years ago)
- Last Synced: 2023-12-11T12:30:17.957Z (about 1 year ago)
- Topics: answer-set-programming, bioinformatics, flux-balance-analysis, gap-filling, linear-programming, metabolic-models, metabolic-network, metabolic-reconstruction
- Language: Python
- Size: 308 KB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# fluto
Metabolic network completion with respect to topological and linear reaction rate constraints based on the stoichiometry.
Tested with Python 3.6.10 and 3.7.6.
So far only level 2 [SBML](http://sbml.org/Documents/Specifications) files are supported.
**If you use Fluto, please cite:**
Frioux, C., Schaub, T., Schellhorn, S., Siegel, A., Wanko, P. (2019), Hybrid metabolic network completion, TPLP, 19(1), 83–108 [https://dx.doi.org/10.1017/s1471068418000455](https://dx.doi.org/10.1017/s1471068418000455)
[PDF of the manuscript](https://www.cs.uni-potsdam.de/wv/publications/DBLP_journals/tplp/FriouxSSSW19.pdf).
## Installation and requirements
A good practice is to perform the Python installations into a [virtualenv](https://virtualenv.pypa.io/en/stable/installation/) or a [conda environment](https://conda.io/docs/user-guide/tasks/manage-environments.html)
Create a conda environment for fluto from the `environment.yml`.
- `conda env create -f environment.yml`
Activate conda environment.
- `conda activate fluto`
### ClingoLP
- `conda install -c potassco -c conda-forge clingo-lp`
### CPLEX
IBM provides a promotional version sufficient to solve the toy example.
- `conda install -c ibmdecisionoptimization cplex`
For the full version follow the [IBM installation procedure](https://www.ibm.com/support/knowledgecenter/SSSA5P_12.10.0/ilog.odms.cplex.help/CPLEX/GettingStarted/topics/set_up/Python_setup.html). e.g.
- `cd /Applications/CPLEX_Studio128/cplex/python/3.6/x86-64_osx/`
- `python setup.py install`
### Package install
Install the Fluto package:
- `python setup.py install`
## Usage
```text
❯ fluto -h
usage: fluto [-h] -m MODEL [-r REPAIRBASE] [-s SEEDS] [-e N | -b | -c]
[--sagot | --fluto1] [--no-accumulation] [--no-fba] [--cplex]
[--json]
Performs hybrid (topological/flux) gap-filling
optional arguments:
-h, --help show this help message and exit
-m MODEL, --model MODEL
organism metabolic model in SBML format
-r REPAIRBASE, --repairbase REPAIRBASE
database of reactions for gap-filling
-s SEEDS, --seeds SEEDS
use topological seeds that are not defined via
reactions in the model, txt file with one seed ID per
line
-e N, --enumerate N enumerate at most N solutions, default is 1, use 0 for
all solutions
-b, --brave compute the union of all solutions
-c, --cautious compute the intersection of all solutions
--sagot use the notion of Sagot & Acuna for the topological
produciblity criterium, default is the scope notion of
Handorf & Ebenhöh
--fluto1 use scope notion of the first fluto version for the
topological produciblity criterium, default is the
scope notion of Handorf & Ebenhöh
--no-accumulation allow the accumulation of metabolites, per default the
accumulation of metabolites is allowed
--no-fba turn off flux balance constraints
--cplex use CPLEX solver
--json produce JSON output
requires Python, ClingoLP and CPLEX packages, see README.md
```
### Example
`fluto -m data/toy/draft.xml -s data/toy/toposeeds.txt -r data/toy/repairdb.xml`
## Publication
- [Hybrid metabolic network completion, Frioux, C., Schaub, T., Schellhorn, S., Siegel, A., Wanko, P. (2019), TPLP, 19(1), 83–108](https://www.cs.uni-potsdam.de/wv/publications/DBLP_journals/tplp/FriouxSSSW19.pdf)