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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release

Computation of Microbial Ecosystems in Time and Space

COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.

COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.

Website

The COMETS website is runcomets.org.

Documentation

Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.

Installation

COMETS can be downloaded from https://www.runcomets.org/get-started.

Toolboxes

We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.

Cite us

If you use COMETS in you scientific work, please cite:

Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.

Contributing

Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.

About

Computation of Microbial Ecosystems in Time and Space

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GPL-3.0 license

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Code of conduct

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Contributing
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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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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release
Computation of Microbial Ecosystems in Time and Space
COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.
Website
The COMETS website is runcomets.org.
Documentation
Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.
Installation
COMETS can be downloaded from https://www.runcomets.org/get-started.
Toolboxes
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
Cite us
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributing
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.
About
Computation of Microbial Ecosystems in Time and Space 
Resources
Readme
GPL-3.0 license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
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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('^' + ".*" + '

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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release
Computation of Microbial Ecosystems in Time and Space
COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.
Website
The COMETS website is runcomets.org.
Documentation
Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.
Installation
COMETS can be downloaded from https://www.runcomets.org/get-started.
Toolboxes
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
Cite us
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributing
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.
About
Computation of Microbial Ecosystems in Time and Space 
Resources
Readme
GPL-3.0 license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release
Computation of Microbial Ecosystems in Time and Space
COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.
Website
The COMETS website is runcomets.org.
Documentation
Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.
Installation
COMETS can be downloaded from https://www.runcomets.org/get-started.
Toolboxes
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
Cite us
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributing
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.
About
Computation of Microbial Ecosystems in Time and Space 
Resources
Readme
GPL-3.0 license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
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0 watching
Forks
0 forks
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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
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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release
Computation of Microbial Ecosystems in Time and Space
COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.
Website
The COMETS website is runcomets.org.
Documentation
Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.
Installation
COMETS can be downloaded from https://www.runcomets.org/get-started.
Toolboxes
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
Cite us
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributing
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.
About
Computation of Microbial Ecosystems in Time and Space 
Resources
Readme
GPL-3.0 license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
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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('^' + ".*" + '

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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release
Computation of Microbial Ecosystems in Time and Space
COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.
Website
The COMETS website is runcomets.org.
Documentation
Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.
Installation
COMETS can be downloaded from https://www.runcomets.org/get-started.
Toolboxes
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
Cite us
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributing
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.
About
Computation of Microbial Ecosystems in Time and Space 
Resources
Readme
GPL-3.0 license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
1 star
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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('^' + ".*" + '

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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release
Computation of Microbial Ecosystems in Time and Space
COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.
Website
The COMETS website is runcomets.org.
Documentation
Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.
Installation
COMETS can be downloaded from https://www.runcomets.org/get-started.
Toolboxes
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
Cite us
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributing
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.
About
Computation of Microbial Ecosystems in Time and Space 
Resources
Readme
GPL-3.0 license
Code of conduct
Code of conduct
Contributing
Contributing
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("// 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); }
})();
})();

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COMETSJoin the chat at https://gitter.im/segrelab/cometsGitHub release
Computation of Microbial Ecosystems in Time and Space
COMETS is a software platform for performing computer simulations of spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species using dynamic flux balance analysis, and on a discrete approximation of diffusion. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
COMETS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Comets is developed with non-commercial use in mind and is presented as-is. To inquire about collaborations or commercial usage and development, please contact us at comets@bu.edu.
Website
The COMETS website is runcomets.org.
Documentation
Documentation on how to install and use COMETS is found at https://segrelab.github.io/comets-manual/.
Installation
COMETS can be downloaded from https://www.runcomets.org/get-started.
Toolboxes
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
Cite us
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributing
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.
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Computation of Microbial Ecosystems in Time and Space 
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