@segrelab

Segrè Lab

README.md

Daniel Segrè Lab at Boston University

Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.

To learn more about the lab, visit our website.

Pinned Loading

  1. cometscometsPublic

    Computation of Microbial Ecosystems in Time and Space

    HTML 28 14

  2. cometspycometspyPublic

    Python interface for running COMETS simulations and analyzing the results

    Python 16 12

  3. comets-toolboxcomets-toolboxPublic

    MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB 2 4

  4. MiCoNEMiCoNEPublic

    The Microbial Co-occurrence Network Explorer

    Python 21 4

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Showing 10 of 47 repositories
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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" + '

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@segrelab

Segrè Lab

README.md
Daniel Segrè Lab at Boston University
Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.
To learn more about the lab, visit our website.

Pinned
Loading
  1. cometscometsPublic
    
Computation of Microbial Ecosystems in Time and Space 
    HTML
28

14

  2. cometspycometspyPublic
    
Python interface for running COMETS simulations and analyzing the results 
    Python
16

12

  3. comets-toolboxcomets-toolboxPublic
    
MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB
2

4

  4. MiCoNEMiCoNEPublic
    
The Microbial Co-occurrence Network Explorer

    Python
21

4


Repositories

Showing 10 of 47 repositories
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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
@segrelab

Segrè Lab

README.md
Daniel Segrè Lab at Boston University
Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.
To learn more about the lab, visit our website.

Pinned
Loading
  1. cometscometsPublic
    
Computation of Microbial Ecosystems in Time and Space 
    HTML
28

14

  2. cometspycometspyPublic
    
Python interface for running COMETS simulations and analyzing the results 
    Python
16

12

  3. comets-toolboxcomets-toolboxPublic
    
MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB
2

4

  4. MiCoNEMiCoNEPublic
    
The Microbial Co-occurrence Network Explorer

    Python
21

4


Repositories

Showing 10 of 47 repositories
View all repositories
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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('^' + ".*" + '

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@segrelab

Segrè Lab

README.md
Daniel Segrè Lab at Boston University
Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.
To learn more about the lab, visit our website.

Pinned
Loading
  1. cometscometsPublic
    
Computation of Microbial Ecosystems in Time and Space 
    HTML
28

14

  2. cometspycometspyPublic
    
Python interface for running COMETS simulations and analyzing the results 
    Python
16

12

  3. comets-toolboxcomets-toolboxPublic
    
MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB
2

4

  4. MiCoNEMiCoNEPublic
    
The Microbial Co-occurrence Network Explorer

    Python
21

4


Repositories

Showing 10 of 47 repositories
View all repositories
Top languages
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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
@segrelab

Segrè Lab

README.md
Daniel Segrè Lab at Boston University
Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.
To learn more about the lab, visit our website.

Pinned
Loading
  1. cometscometsPublic
    
Computation of Microbial Ecosystems in Time and Space 
    HTML
28

14

  2. cometspycometspyPublic
    
Python interface for running COMETS simulations and analyzing the results 
    Python
16

12

  3. comets-toolboxcomets-toolboxPublic
    
MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB
2

4

  4. MiCoNEMiCoNEPublic
    
The Microbial Co-occurrence Network Explorer

    Python
21

4


Repositories

Showing 10 of 47 repositories
View all repositories
Top languages
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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
@segrelab

Segrè Lab

README.md
Daniel Segrè Lab at Boston University
Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.
To learn more about the lab, visit our website.

Pinned
Loading
  1. cometscometsPublic
    
Computation of Microbial Ecosystems in Time and Space 
    HTML
28

14

  2. cometspycometspyPublic
    
Python interface for running COMETS simulations and analyzing the results 
    Python
16

12

  3. comets-toolboxcomets-toolboxPublic
    
MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB
2

4

  4. MiCoNEMiCoNEPublic
    
The Microbial Co-occurrence Network Explorer

    Python
21

4


Repositories

Showing 10 of 47 repositories
View all repositories
Top languages
Loading…
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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
@segrelab

Segrè Lab

README.md
Daniel Segrè Lab at Boston University
Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.
To learn more about the lab, visit our website.

Pinned
Loading
  1. cometscometsPublic
    
Computation of Microbial Ecosystems in Time and Space 
    HTML
28

14

  2. cometspycometspyPublic
    
Python interface for running COMETS simulations and analyzing the results 
    Python
16

12

  3. comets-toolboxcomets-toolboxPublic
    
MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB
2

4

  4. MiCoNEMiCoNEPublic
    
The Microbial Co-occurrence Network Explorer

    Python
21

4


Repositories

Showing 10 of 47 repositories
View all repositories
Top languages
Loading…
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Loading…

, '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
@segrelab

Segrè Lab

README.md
Daniel Segrè Lab at Boston University
Through mathematical modeling and experiments, we study the dynamics and evolution of metabolic networks in living systems. We are interested both in the fundamental principles of biological organization and in applications to environmental sustainability and human health.
To learn more about the lab, visit our website.

Pinned
Loading
  1. cometscometsPublic
    
Computation of Microbial Ecosystems in Time and Space 
    HTML
28

14

  2. cometspycometspyPublic
    
Python interface for running COMETS simulations and analyzing the results 
    Python
16

12

  3. comets-toolboxcomets-toolboxPublic
    
MATLAB scripts and utilities for the COMETS software for spatial DFBA

    MATLAB
2

4

  4. MiCoNEMiCoNEPublic
    
The Microbial Co-occurrence Network Explorer

    Python
21

4


Repositories

Showing 10 of 47 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…