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PythonJupyterDocker

SPARCED, An Aspiring MCF-10A Whole-Cell Model

MaintenanceContributorsForksStargazersIssuesUnlicense License

Table of Contents

Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact

About SPARCED

SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.

  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.

The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.

(back to top)

Getting Started

Systems Biology Modelers

The SPARCED pipeline can be run with few to no previous coding experience. To do so, we strongly encourage you to use the Docker / Singularity containers we provide.

A complete installation guide is available here.

(back to top)

Developpers

We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide. Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.

A detailed installation guide is available here.

(back to top)

Replicate our results

You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.

(back to top)

Usage

The SPARCED model can be used to create and run small to large-scale mechanistic models.

(back to top)

Contributing

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Any contributions you make are greatly appreciated.

  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request

(back to top)

License

Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.

(back to top)

Acknowledgments

SPARCED is a product of the Birtwistle Lab and the Erdem Lab.

We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.

This material is based on work supported by the National Science Foundation under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.

Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Clemson University is acknowledged for their generous allotment of compute time on the Palmetto Cluster.

(back to top)

Contact

(back to top)

About

[Public] [Fork] Mechanistic Pan-Cancer Signaling Model

www.nature.com/articles/s41467-022-31138-1.epdf

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
PythonJupyterDocker
SPARCED, An Aspiring MCF-10A Whole-Cell Model
MaintenanceContributorsForksStargazersIssuesUnlicense License
Table of Contents
Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact
About SPARCED
SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.
  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.
The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.
(back to top)
Getting Started
Systems Biology Modelers
The SPARCED pipeline can be run with few to no previous coding experience.
To do so, we strongly encourage you to use the Docker / Singularity containers we provide.
A complete installation guide is available here.
(back to top)
Developpers
We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide.
Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.
A detailed installation guide is available here.
(back to top)
Replicate our results
You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.
(back to top)
Usage
The SPARCED model can be used to create and run small to large-scale mechanistic models.
(back to top)
Contributing
If you have a suggestion that would make this better, please fork the repo and create a pull request.
You can also simply open an issue with the tag "enhancement".
Any contributions you make are greatly appreciated.
  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request
(back to top)
License
Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.
(back to top)
Acknowledgments
SPARCED is a product of the Birtwistle Lab and the Erdem Lab.
We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.
This material is based on work supported by the National Science Foundation
under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.
Clemson University is acknowledged for their generous allotment of compute time
on the Palmetto Cluster.
(back to top)
Contact
(back to top)
About
[Public] [Fork] Mechanistic Pan-Cancer Signaling Model
www.nature.com/articles/s41467-022-31138-1.epdf
Resources
Readme
License
Code of conduct
Code of conduct
Activity
Stars
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Watchers
0 watching
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0 forks
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
PythonJupyterDocker
SPARCED, An Aspiring MCF-10A Whole-Cell Model
MaintenanceContributorsForksStargazersIssuesUnlicense License
Table of Contents
Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact
About SPARCED
SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.
  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.
The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.
(back to top)
Getting Started
Systems Biology Modelers
The SPARCED pipeline can be run with few to no previous coding experience.
To do so, we strongly encourage you to use the Docker / Singularity containers we provide.
A complete installation guide is available here.
(back to top)
Developpers
We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide.
Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.
A detailed installation guide is available here.
(back to top)
Replicate our results
You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.
(back to top)
Usage
The SPARCED model can be used to create and run small to large-scale mechanistic models.
(back to top)
Contributing
If you have a suggestion that would make this better, please fork the repo and create a pull request.
You can also simply open an issue with the tag "enhancement".
Any contributions you make are greatly appreciated.
  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request
(back to top)
License
Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.
(back to top)
Acknowledgments
SPARCED is a product of the Birtwistle Lab and the Erdem Lab.
We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.
This material is based on work supported by the National Science Foundation
under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.
Clemson University is acknowledged for their generous allotment of compute time
on the Palmetto Cluster.
(back to top)
Contact
(back to top)
About
[Public] [Fork] Mechanistic Pan-Cancer Signaling Model
www.nature.com/articles/s41467-022-31138-1.epdf
Resources
Readme
License
Code of conduct
Code of conduct
Activity
Stars
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
PythonJupyterDocker
SPARCED, An Aspiring MCF-10A Whole-Cell Model
MaintenanceContributorsForksStargazersIssuesUnlicense License
Table of Contents
Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact
About SPARCED
SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.
  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.
The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.
(back to top)
Getting Started
Systems Biology Modelers
The SPARCED pipeline can be run with few to no previous coding experience.
To do so, we strongly encourage you to use the Docker / Singularity containers we provide.
A complete installation guide is available here.
(back to top)
Developpers
We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide.
Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.
A detailed installation guide is available here.
(back to top)
Replicate our results
You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.
(back to top)
Usage
The SPARCED model can be used to create and run small to large-scale mechanistic models.
(back to top)
Contributing
If you have a suggestion that would make this better, please fork the repo and create a pull request.
You can also simply open an issue with the tag "enhancement".
Any contributions you make are greatly appreciated.
  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request
(back to top)
License
Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.
(back to top)
Acknowledgments
SPARCED is a product of the Birtwistle Lab and the Erdem Lab.
We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.
This material is based on work supported by the National Science Foundation
under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.
Clemson University is acknowledged for their generous allotment of compute time
on the Palmetto Cluster.
(back to top)
Contact
(back to top)
About
[Public] [Fork] Mechanistic Pan-Cancer Signaling Model
www.nature.com/articles/s41467-022-31138-1.epdf
Resources
Readme
License
Code of conduct
Code of conduct
Activity
Stars
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Watchers
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0 forks
Report repository
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
PythonJupyterDocker
SPARCED, An Aspiring MCF-10A Whole-Cell Model
MaintenanceContributorsForksStargazersIssuesUnlicense License
Table of Contents
Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact
About SPARCED
SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.
  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.
The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.
(back to top)
Getting Started
Systems Biology Modelers
The SPARCED pipeline can be run with few to no previous coding experience.
To do so, we strongly encourage you to use the Docker / Singularity containers we provide.
A complete installation guide is available here.
(back to top)
Developpers
We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide.
Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.
A detailed installation guide is available here.
(back to top)
Replicate our results
You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.
(back to top)
Usage
The SPARCED model can be used to create and run small to large-scale mechanistic models.
(back to top)
Contributing
If you have a suggestion that would make this better, please fork the repo and create a pull request.
You can also simply open an issue with the tag "enhancement".
Any contributions you make are greatly appreciated.
  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request
(back to top)
License
Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.
(back to top)
Acknowledgments
SPARCED is a product of the Birtwistle Lab and the Erdem Lab.
We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.
This material is based on work supported by the National Science Foundation
under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.
Clemson University is acknowledged for their generous allotment of compute time
on the Palmetto Cluster.
(back to top)
Contact
(back to top)
About
[Public] [Fork] Mechanistic Pan-Cancer Signaling Model
www.nature.com/articles/s41467-022-31138-1.epdf
Resources
Readme
License
Code of conduct
Code of conduct
Activity
Stars
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
PythonJupyterDocker
SPARCED, An Aspiring MCF-10A Whole-Cell Model
MaintenanceContributorsForksStargazersIssuesUnlicense License
Table of Contents
Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact
About SPARCED
SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.
  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.
The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.
(back to top)
Getting Started
Systems Biology Modelers
The SPARCED pipeline can be run with few to no previous coding experience.
To do so, we strongly encourage you to use the Docker / Singularity containers we provide.
A complete installation guide is available here.
(back to top)
Developpers
We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide.
Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.
A detailed installation guide is available here.
(back to top)
Replicate our results
You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.
(back to top)
Usage
The SPARCED model can be used to create and run small to large-scale mechanistic models.
(back to top)
Contributing
If you have a suggestion that would make this better, please fork the repo and create a pull request.
You can also simply open an issue with the tag "enhancement".
Any contributions you make are greatly appreciated.
  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request
(back to top)
License
Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.
(back to top)
Acknowledgments
SPARCED is a product of the Birtwistle Lab and the Erdem Lab.
We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.
This material is based on work supported by the National Science Foundation
under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.
Clemson University is acknowledged for their generous allotment of compute time
on the Palmetto Cluster.
(back to top)
Contact
(back to top)
About
[Public] [Fork] Mechanistic Pan-Cancer Signaling Model
www.nature.com/articles/s41467-022-31138-1.epdf
Resources
Readme
License
Code of conduct
Code of conduct
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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PythonJupyterDocker
SPARCED, An Aspiring MCF-10A Whole-Cell Model
MaintenanceContributorsForksStargazersIssuesUnlicense License
Table of Contents
Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact
About SPARCED
SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.
  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.
The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.
(back to top)
Getting Started
Systems Biology Modelers
The SPARCED pipeline can be run with few to no previous coding experience.
To do so, we strongly encourage you to use the Docker / Singularity containers we provide.
A complete installation guide is available here.
(back to top)
Developpers
We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide.
Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.
A detailed installation guide is available here.
(back to top)
Replicate our results
You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.
(back to top)
Usage
The SPARCED model can be used to create and run small to large-scale mechanistic models.
(back to top)
Contributing
If you have a suggestion that would make this better, please fork the repo and create a pull request.
You can also simply open an issue with the tag "enhancement".
Any contributions you make are greatly appreciated.
  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request
(back to top)
License
Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.
(back to top)
Acknowledgments
SPARCED is a product of the Birtwistle Lab and the Erdem Lab.
We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.
This material is based on work supported by the National Science Foundation
under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.
Clemson University is acknowledged for their generous allotment of compute time
on the Palmetto Cluster.
(back to top)
Contact
(back to top)
About
[Public] [Fork] Mechanistic Pan-Cancer Signaling Model
www.nature.com/articles/s41467-022-31138-1.epdf
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
PythonJupyterDocker
SPARCED, An Aspiring MCF-10A Whole-Cell Model
MaintenanceContributorsForksStargazersIssuesUnlicense License
Table of Contents
Contents
  1. About SPARCED
  2. Getting Started
  3. Replicate our results
  4. Usage
  5. Contributing
  6. License
  7. Acknowledgments
  8. Contact
About SPARCED
SPARCED is a simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models.
  • With minimal set-up, users can configure small-scale experiments on their local machines, is it through pure Python scripts or Jupyter Notebooks.
  • Both Docker and Singularity containers are provided.
  • SPARCED is also compatible with High Performance Computing and parallelization.
The acronym SPARCED stands for SBML, Proliferation, Apoptosis, Receptor signaling, Cell cycle, Expression & DNA damage, which are sub-models of the large-scale mechanistic model.
(back to top)
Getting Started
Systems Biology Modelers
The SPARCED pipeline can be run with few to no previous coding experience.
To do so, we strongly encourage you to use the Docker / Singularity containers we provide.
A complete installation guide is available here.
(back to top)
Developpers
We recommend to use Anaconda and create a conda environment based on the environment.yml file we provide.
Otherwise, you may base yourself on the requirements.txt file we provide for the minimal required versions.
A detailed installation guide is available here.
(back to top)
Replicate our results
You will find specific instructions on how to run the model (including previousversions) as described in each of our published papers here.
(back to top)
Usage
The SPARCED model can be used to create and run small to large-scale mechanistic models.
(back to top)
Contributing
If you have a suggestion that would make this better, please fork the repo and create a pull request.
You can also simply open an issue with the tag "enhancement".
Any contributions you make are greatly appreciated.
  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request
(back to top)
License
Distributed under the GNU General Public License v2.0. See LICENSE.txt for more information.
(back to top)
Acknowledgments
SPARCED is a product of the Birtwistle Lab and the Erdem Lab.
We greatly appreciate the help from multiple colloborators, including the Hasenauer Lab.
This material is based on work supported by the National Science Foundation
under Grant Nos. MRI# 2024205, MRI# 1725573, and CRI# 2010270.
Any opinions, findings and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.
Clemson University is acknowledged for their generous allotment of compute time
on the Palmetto Cluster.
(back to top)
Contact
(back to top)
About
[Public] [Fork] Mechanistic Pan-Cancer Signaling Model
www.nature.com/articles/s41467-022-31138-1.epdf
Resources
Readme
License
Code of conduct
Code of conduct
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages