Skip to content
BranchesTags

Repository files navigation

ETFL

Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7

See ecETFL for an E. coli model.

See also yETFL for a yeast model!

This code is an early release. You will need pyTFA to run it. We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.

Requirements

You will need to have Git-LFS in order to properly download some binary files:

git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull

This module was developed in Python 3.5, and it is recommended to run Python 3.5 to run commercial solvers such as Gurobi and CPLEX. Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)

This module requires pyTFA, as well as COBRApy, and optlang to work properly. The installer should take care of that for you. You might also want to install a dedicated solver. GLPK, CPLEX and Gurobi are supported.

Installation

The module can be installed like any Python package:

git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install

The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.

Running the code

You can run the examples in etfl/tutorials:

cd etfl/tutorials
python test_small.py

You can also run them inside IPython to experiment and play with the objects:

ipython
run test_small.py
m.print_info()

Docker

We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.

Right now, the ETFL Docker is built on top of the pyTFA Docker. If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it. You can install them by following the instructions in pyTFA's Documentation.

More details are available in the Docker folder

License

The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.

About

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

Resources

Readme
Apache-2.0 license
Activity
Custom properties

Stars

18 stars

Watchers

2 watching

Forks

18 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
GitHub - EPFL-LCSB/etfl: ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints · GitHub
Skip to content
BranchesTags
Repository files navigation
ETFL
Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7
See ecETFL for an E. coli model.
See also yETFL for a yeast model!
This code is an early release. You will need pyTFA to run it.
We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
Requirements
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull
This module was developed in Python 3.5, and it is recommended to run Python 3.5
to run commercial solvers such as Gurobi and CPLEX.
Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)
This module requires
pyTFA, as well as
COBRApy, and
optlang to work
properly. The installer should take care of that for you. You might also
want to install a dedicated solver. GLPK, CPLEX and Gurobi are
supported.
Installation
The module can be installed like any Python package:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install
The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.
Running the code
You can run the examples in etfl/tutorials:
cd etfl/tutorials
python test_small.py
You can also run them inside IPython to experiment and play with the
objects:
ipython
run test_small.py
m.print_info()
Docker
We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.
Right now, the ETFL Docker is built on top of the pyTFA Docker.
If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it.
You can install them by following the instructions in pyTFA's Documentation.
More details are available in the Docker folder
License
The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
About
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
18 stars
Watchers
2 watching
Forks
18 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - EPFL-LCSB/etfl: ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints · GitHub
Skip to content
BranchesTags
Repository files navigation
ETFL
Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7
See ecETFL for an E. coli model.
See also yETFL for a yeast model!
This code is an early release. You will need pyTFA to run it.
We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
Requirements
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull
This module was developed in Python 3.5, and it is recommended to run Python 3.5
to run commercial solvers such as Gurobi and CPLEX.
Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)
This module requires
pyTFA, as well as
COBRApy, and
optlang to work
properly. The installer should take care of that for you. You might also
want to install a dedicated solver. GLPK, CPLEX and Gurobi are
supported.
Installation
The module can be installed like any Python package:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install
The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.
Running the code
You can run the examples in etfl/tutorials:
cd etfl/tutorials
python test_small.py
You can also run them inside IPython to experiment and play with the
objects:
ipython
run test_small.py
m.print_info()
Docker
We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.
Right now, the ETFL Docker is built on top of the pyTFA Docker.
If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it.
You can install them by following the instructions in pyTFA's Documentation.
More details are available in the Docker folder
License
The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
About
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
18 stars
Watchers
2 watching
Forks
18 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - EPFL-LCSB/etfl: ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints · GitHub
Skip to content
BranchesTags
Repository files navigation
ETFL
Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7
See ecETFL for an E. coli model.
See also yETFL for a yeast model!
This code is an early release. You will need pyTFA to run it.
We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
Requirements
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull
This module was developed in Python 3.5, and it is recommended to run Python 3.5
to run commercial solvers such as Gurobi and CPLEX.
Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)
This module requires
pyTFA, as well as
COBRApy, and
optlang to work
properly. The installer should take care of that for you. You might also
want to install a dedicated solver. GLPK, CPLEX and Gurobi are
supported.
Installation
The module can be installed like any Python package:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install
The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.
Running the code
You can run the examples in etfl/tutorials:
cd etfl/tutorials
python test_small.py
You can also run them inside IPython to experiment and play with the
objects:
ipython
run test_small.py
m.print_info()
Docker
We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.
Right now, the ETFL Docker is built on top of the pyTFA Docker.
If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it.
You can install them by following the instructions in pyTFA's Documentation.
More details are available in the Docker folder
License
The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
About
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
18 stars
Watchers
2 watching
Forks
18 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - EPFL-LCSB/etfl: ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints · GitHub
Skip to content
BranchesTags
Repository files navigation
ETFL
Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7
See ecETFL for an E. coli model.
See also yETFL for a yeast model!
This code is an early release. You will need pyTFA to run it.
We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
Requirements
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull
This module was developed in Python 3.5, and it is recommended to run Python 3.5
to run commercial solvers such as Gurobi and CPLEX.
Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)
This module requires
pyTFA, as well as
COBRApy, and
optlang to work
properly. The installer should take care of that for you. You might also
want to install a dedicated solver. GLPK, CPLEX and Gurobi are
supported.
Installation
The module can be installed like any Python package:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install
The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.
Running the code
You can run the examples in etfl/tutorials:
cd etfl/tutorials
python test_small.py
You can also run them inside IPython to experiment and play with the
objects:
ipython
run test_small.py
m.print_info()
Docker
We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.
Right now, the ETFL Docker is built on top of the pyTFA Docker.
If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it.
You can install them by following the instructions in pyTFA's Documentation.
More details are available in the Docker folder
License
The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
About
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
18 stars
Watchers
2 watching
Forks
18 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - EPFL-LCSB/etfl: ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints · GitHub
Skip to content
BranchesTags
Repository files navigation
ETFL
Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7
See ecETFL for an E. coli model.
See also yETFL for a yeast model!
This code is an early release. You will need pyTFA to run it.
We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
Requirements
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull
This module was developed in Python 3.5, and it is recommended to run Python 3.5
to run commercial solvers such as Gurobi and CPLEX.
Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)
This module requires
pyTFA, as well as
COBRApy, and
optlang to work
properly. The installer should take care of that for you. You might also
want to install a dedicated solver. GLPK, CPLEX and Gurobi are
supported.
Installation
The module can be installed like any Python package:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install
The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.
Running the code
You can run the examples in etfl/tutorials:
cd etfl/tutorials
python test_small.py
You can also run them inside IPython to experiment and play with the
objects:
ipython
run test_small.py
m.print_info()
Docker
We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.
Right now, the ETFL Docker is built on top of the pyTFA Docker.
If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it.
You can install them by following the instructions in pyTFA's Documentation.
More details are available in the Docker folder
License
The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
About
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
18 stars
Watchers
2 watching
Forks
18 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - EPFL-LCSB/etfl: ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints · GitHub
Skip to content
BranchesTags
Repository files navigation
ETFL
Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7
See ecETFL for an E. coli model.
See also yETFL for a yeast model!
This code is an early release. You will need pyTFA to run it.
We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
Requirements
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull
This module was developed in Python 3.5, and it is recommended to run Python 3.5
to run commercial solvers such as Gurobi and CPLEX.
Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)
This module requires
pyTFA, as well as
COBRApy, and
optlang to work
properly. The installer should take care of that for you. You might also
want to install a dedicated solver. GLPK, CPLEX and Gurobi are
supported.
Installation
The module can be installed like any Python package:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install
The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.
Running the code
You can run the examples in etfl/tutorials:
cd etfl/tutorials
python test_small.py
You can also run them inside IPython to experiment and play with the
objects:
ipython
run test_small.py
m.print_info()
Docker
We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.
Right now, the ETFL Docker is built on top of the pyTFA Docker.
If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it.
You can install them by following the instructions in pyTFA's Documentation.
More details are available in the Docker folder
License
The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
About
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
18 stars
Watchers
2 watching
Forks
18 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
GitHub - EPFL-LCSB/etfl: ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints · GitHub
Skip to content
BranchesTags
Repository files navigation
ETFL
Documentation StatusBuild StatusCodecovCodacy branch gradelicensedoi
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Paper: Salvy, P., Hatzimanikatis, V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nat Commun 11, 30 (2020) doi:10.1038/s41467-019-13818-7
See ecETFL for an E. coli model.
See also yETFL for a yeast model!
This code is an early release. You will need pyTFA to run it.
We recommend using commercial solvers such as CPLEX or Gurobi to run these problems.
Requirements
You will need to have Git-LFS in order to properly download some binary files:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
git lfs install
git lfs pull
This module was developed in Python 3.5, and it is recommended to run Python 3.5
to run commercial solvers such as Gurobi and CPLEX.
Other Python versions (2.7, 3.4) might also work but are not officially supported (see the CI builds)
This module requires
pyTFA, as well as
COBRApy, and
optlang to work
properly. The installer should take care of that for you. You might also
want to install a dedicated solver. GLPK, CPLEX and Gurobi are
supported.
Installation
The module can be installed like any Python package:
git clone https://github.com/EPFL-LCSB/etfl.git /path/to/etfl
cd /path/to/etfl
python3 setup.py install
The installation process should not exceed a minute if the requirements are installed. If they are not, it might take longer as the installer installs them first.
Running the code
You can run the examples in etfl/tutorials:
cd etfl/tutorials
python test_small.py
You can also run them inside IPython to experiment and play with the
objects:
ipython
run test_small.py
m.print_info()
Docker
We recommend the use of Docker to set up a container that will have the proper environment and package version to make ETFL work.
Right now, the ETFL Docker is built on top of the pyTFA Docker.
If you want to use Docker-based install, you will need a working pytfa docker image, with either CPLEX or Gurobi on it.
You can install them by following the instructions in pyTFA's Documentation.
More details are available in the Docker folder
License
The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.
About
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
18 stars
Watchers
2 watching
Forks
18 forks
Report repository
Releases
Packages
Used by
Contributors
Languages