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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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

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Mechanistic Pan-Cancer Signaling Model

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n 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;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
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About

Documentation Status

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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

About

Mechanistic Pan-Cancer Signaling Model

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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

Repository files navigation

About

Documentation Status

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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

About

Mechanistic Pan-Cancer Signaling Model

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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

Repository files navigation

About

Documentation Status

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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

About

Mechanistic Pan-Cancer Signaling Model

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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

Repository files navigation

About

Documentation Status

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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

About

Mechanistic Pan-Cancer Signaling Model

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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

Repository files navigation

About

Documentation Status

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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

About

Mechanistic Pan-Cancer Signaling Model

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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

Repository files navigation

About

Documentation Status

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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

About

Mechanistic Pan-Cancer Signaling Model

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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

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About

Documentation Status

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. SPARCED is also compatible with cluster running 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.

Instructions & Beginners

A beginner's installation guide of SPARCED for newcomers in computer science is available here

Replicate our results

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

Dependencies

We strongly encourage you 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.

Further information

More information on the model itself can be found in this documentation, in particular in the section dedicated to our papers.

Acknowledgments

SPARCED is a product of the Birtwistle Lab.

We greatly appreciate the help from multiple colloborators, including:

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.

About

Mechanistic Pan-Cancer Signaling Model

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