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    1. BioNetFit2 BioNetFit2Public

      Forked from richardposner/BioNetFit2

      C++

    2. RuleHub RuleHubPublic

      Forked from RuleWorld/RuleHub

      A repository of rule-based models. Could this be the start of something great?

    3. PyBNF PyBNFPublic

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      An application for fitting systems biology models using metaheuristic algorithms

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    6. RuleBuilder RuleBuilderPublic

      Forked from RuleWorld/RuleBuilder

      A tool for graphical construction and visualization of BioNetGen graphs

      Java

    , 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
     blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
emitra17 (Eshan Mitra) · GitHub
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      1. 
BioNetFit2
BioNetFit2Public
        
Forked from richardposner/BioNetFit2
        C++
      2. 
RuleHub
RuleHubPublic
        
Forked from RuleWorld/RuleHub
        
A repository of rule-based models. Could this be the start of something great?

      3. 
PyBNF
PyBNFPublic
        
Forked from lanl/PyBNF
        
An application for fitting systems biology models using metaheuristic algorithms

        Python
      4. 
BioNetFit
BioNetFitPublic
        
Forked from RuleWorld/BioNetFit
        
An application for fitting BioNetGen models using a genetic algorithm

        Perl
      5. 
TRuML
TRuMLPublic
        
Forked from lanl/TRuML
        Python
      6. 
RuleBuilder
RuleBuilderPublic
        
Forked from RuleWorld/RuleBuilder
        
A tool for graphical construction and visualization of BioNetGen graphs

        Java
      
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
emitra17 (Eshan Mitra) · GitHub
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        Achievements
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        Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
        
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Popular repositories
Loading
        1. 
BioNetFit2
BioNetFit2Public
          
Forked from richardposner/BioNetFit2
          C++
        2. 
RuleHub
RuleHubPublic
          
Forked from RuleWorld/RuleHub
          
A repository of rule-based models. Could this be the start of something great?

        3. 
PyBNF
PyBNFPublic
          
Forked from lanl/PyBNF
          
An application for fitting systems biology models using metaheuristic algorithms

          Python
        4. 
BioNetFit
BioNetFitPublic
          
Forked from RuleWorld/BioNetFit
          
An application for fitting BioNetGen models using a genetic algorithm

          Perl
        5. 
TRuML
TRuMLPublic
          
Forked from lanl/TRuML
          Python
        6. 
RuleBuilder
RuleBuilderPublic
          
Forked from RuleWorld/RuleBuilder
          
A tool for graphical construction and visualization of BioNetGen graphs

          Java
        
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
emitra17 (Eshan Mitra) · GitHub
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          Achievements
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          Achievements
          Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
          
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Popular repositories
Loading
          1. 
BioNetFit2
BioNetFit2Public
            
Forked from richardposner/BioNetFit2
            C++
          2. 
RuleHub
RuleHubPublic
            
Forked from RuleWorld/RuleHub
            
A repository of rule-based models. Could this be the start of something great?

          3. 
PyBNF
PyBNFPublic
            
Forked from lanl/PyBNF
            
An application for fitting systems biology models using metaheuristic algorithms

            Python
          4. 
BioNetFit
BioNetFitPublic
            
Forked from RuleWorld/BioNetFit
            
An application for fitting BioNetGen models using a genetic algorithm

            Perl
          5. 
TRuML
TRuMLPublic
            
Forked from lanl/TRuML
            Python
          6. 
RuleBuilder
RuleBuilderPublic
            
Forked from RuleWorld/RuleBuilder
            
A tool for graphical construction and visualization of BioNetGen graphs

            Java
          
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
emitra17 (Eshan Mitra) · GitHub
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            Achievements
            Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
            Achievements
            Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
            
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Popular repositories
Loading
            1. 
BioNetFit2
BioNetFit2Public
              
Forked from richardposner/BioNetFit2
              C++
            2. 
RuleHub
RuleHubPublic
              
Forked from RuleWorld/RuleHub
              
A repository of rule-based models. Could this be the start of something great?

            3. 
PyBNF
PyBNFPublic
              
Forked from lanl/PyBNF
              
An application for fitting systems biology models using metaheuristic algorithms

              Python
            4. 
BioNetFit
BioNetFitPublic
              
Forked from RuleWorld/BioNetFit
              
An application for fitting BioNetGen models using a genetic algorithm

              Perl
            5. 
TRuML
TRuMLPublic
              
Forked from lanl/TRuML
              Python
            6. 
RuleBuilder
RuleBuilderPublic
              
Forked from RuleWorld/RuleBuilder
              
A tool for graphical construction and visualization of BioNetGen graphs

              Java
            
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
emitra17 (Eshan Mitra) · GitHub
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            4
followers
 · 0
following

              Achievements
              Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
              Achievements
              Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
              
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Popular repositories
Loading
              1. 
BioNetFit2
BioNetFit2Public
                
Forked from richardposner/BioNetFit2
                C++
              2. 
RuleHub
RuleHubPublic
                
Forked from RuleWorld/RuleHub
                
A repository of rule-based models. Could this be the start of something great?

              3. 
PyBNF
PyBNFPublic
                
Forked from lanl/PyBNF
                
An application for fitting systems biology models using metaheuristic algorithms

                Python
              4. 
BioNetFit
BioNetFitPublic
                
Forked from RuleWorld/BioNetFit
                
An application for fitting BioNetGen models using a genetic algorithm

                Perl
              5. 
TRuML
TRuMLPublic
                
Forked from lanl/TRuML
                Python
              6. 
RuleBuilder
RuleBuilderPublic
                
Forked from RuleWorld/RuleBuilder
                
A tool for graphical construction and visualization of BioNetGen graphs

                Java
              
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
emitra17 (Eshan Mitra) · GitHub
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              4
followers
 · 0
following

                Achievements
                Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
                Achievements
                Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
                
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Popular repositories
Loading
                1. 
BioNetFit2
BioNetFit2Public
                  
Forked from richardposner/BioNetFit2
                  C++
                2. 
RuleHub
RuleHubPublic
                  
Forked from RuleWorld/RuleHub
                  
A repository of rule-based models. Could this be the start of something great?

                3. 
PyBNF
PyBNFPublic
                  
Forked from lanl/PyBNF
                  
An application for fitting systems biology models using metaheuristic algorithms

                  Python
                4. 
BioNetFit
BioNetFitPublic
                  
Forked from RuleWorld/BioNetFit
                  
An application for fitting BioNetGen models using a genetic algorithm

                  Perl
                5. 
TRuML
TRuMLPublic
                  
Forked from lanl/TRuML
                  Python
                6. 
RuleBuilder
RuleBuilderPublic
                  
Forked from RuleWorld/RuleBuilder
                  
A tool for graphical construction and visualization of BioNetGen graphs

                  Java
                
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
emitra17 (Eshan Mitra) · GitHub
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                  Achievements
                  Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
                  Achievements
                  Achievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2
                  
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Popular repositories
Loading
                  1. 
BioNetFit2
BioNetFit2Public
                    
Forked from richardposner/BioNetFit2
                    C++
                  2. 
RuleHub
RuleHubPublic
                    
Forked from RuleWorld/RuleHub
                    
A repository of rule-based models. Could this be the start of something great?

                  3. 
PyBNF
PyBNFPublic
                    
Forked from lanl/PyBNF
                    
An application for fitting systems biology models using metaheuristic algorithms

                    Python
                  4. 
BioNetFit
BioNetFitPublic
                    
Forked from RuleWorld/BioNetFit
                    
An application for fitting BioNetGen models using a genetic algorithm

                    Perl
                  5. 
TRuML
TRuMLPublic
                    
Forked from lanl/TRuML
                    Python
                  6. 
RuleBuilder
RuleBuilderPublic
                    
Forked from RuleWorld/RuleBuilder
                    
A tool for graphical construction and visualization of BioNetGen graphs

                    Java