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Genotype Specification Language (GSL) Core library

Amyris domain specification language for rapidly specifying genetic designs

Community

Documentation

Documentation in the repo is sparse currently, but you can find

This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.

NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.

About

Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.

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bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology

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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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Genotype Specification Language (GSL) Core library
Amyris domain specification language for rapidly specifying genetic designs
Community
Documentation
Documentation in the repo is sparse currently, but you can find
This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.
NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.
About
Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
Topics
bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology
Resources
Readme
License
Activity
Custom properties
Stars
24 stars
Watchers
0 watching
Forks
9 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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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This repository was archived by the owner on Jul 29, 2025. It is now read-only.

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Genotype Specification Language (GSL) Core library
Amyris domain specification language for rapidly specifying genetic designs
Community
Documentation
Documentation in the repo is sparse currently, but you can find
This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.
NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.
About
Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
Topics
bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology
Resources
Readme
License
Activity
Custom properties
Stars
24 stars
Watchers
0 watching
Forks
9 forks
Report repository
Releases
Packages
Used by
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('^' + ".*" + '

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This repository was archived by the owner on Jul 29, 2025. It is now read-only.

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Genotype Specification Language (GSL) Core library
Amyris domain specification language for rapidly specifying genetic designs
Community
Documentation
Documentation in the repo is sparse currently, but you can find
This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.
NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.
About
Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
Topics
bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology
Resources
Readme
License
Activity
Custom properties
Stars
24 stars
Watchers
0 watching
Forks
9 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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

This repository was archived by the owner on Jul 29, 2025. It is now read-only.

BranchesTags
Repository files navigation
Genotype Specification Language (GSL) Core library
Amyris domain specification language for rapidly specifying genetic designs
Community
Documentation
Documentation in the repo is sparse currently, but you can find
This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.
NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.
About
Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
Topics
bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology
Resources
Readme
License
Activity
Custom properties
Stars
24 stars
Watchers
0 watching
Forks
9 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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

This repository was archived by the owner on Jul 29, 2025. It is now read-only.

BranchesTags
Repository files navigation
Genotype Specification Language (GSL) Core library
Amyris domain specification language for rapidly specifying genetic designs
Community
Documentation
Documentation in the repo is sparse currently, but you can find
This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.
NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.
About
Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
Topics
bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology
Resources
Readme
License
Activity
Custom properties
Stars
24 stars
Watchers
0 watching
Forks
9 forks
Report repository
Releases
Packages
Used by
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('^' + ".*" + '

Skip to content

This repository was archived by the owner on Jul 29, 2025. It is now read-only.

BranchesTags
Repository files navigation
Genotype Specification Language (GSL) Core library
Amyris domain specification language for rapidly specifying genetic designs
Community
Documentation
Documentation in the repo is sparse currently, but you can find
This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.
NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.
About
Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
Topics
bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology
Resources
Readme
License
Activity
Custom properties
Stars
24 stars
Watchers
0 watching
Forks
9 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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

This repository was archived by the owner on Jul 29, 2025. It is now read-only.

BranchesTags
Repository files navigation
Genotype Specification Language (GSL) Core library
Amyris domain specification language for rapidly specifying genetic designs
Community
Documentation
Documentation in the repo is sparse currently, but you can find
This library provides all core modules of the compiler, template code for constructing an application, and a set of plug-ins providing basic core functionality.
NB: the actual compiler front end is in this repository and can be built from a distributed packaged version of GslCore without building this repository.
About
Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
Topics
bioinformaticsbiologycompilergeneticsgenotype-specification-languagegslsynthetic-biology
Resources
Readme
License
Activity
Custom properties
Stars
24 stars
Watchers
0 watching
Forks
9 forks
Report repository
Releases
Packages
Used by
Contributors
Languages