@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo

Open-source genomics data platforms

Project Site | Documentation | Demo Portal | Quickstart

We build software that enables researchers and the public to access, manage and study large amounts of genomics data.

Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.

By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.

Demo Portal

Pinned Loading

  1. arrangerarrangerPublic

    Data portal API and component generation

    TypeScript 32 24

  2. stagestagePublic

    TypeScript 1 5

  3. songsongPublic

    File management system with metadata validation

    Java 14 5

  4. scorescorePublic

    Secure Cloud Object REsource: file transfer microservice

    Java 20 11

  5. lyriclyricPublic

    TypeScript 2 1

  6. lecternlecternPublic

    Data Schema / Dictionary management system

    TypeScript 2 5

Repositories

Showing 10 of 42 repositories
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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" + '

Skip to content
@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo
Open-source genomics data platforms
Project Site |
Documentation |
Demo Portal |
Quickstart
We build software that enables researchers and the public to access, manage and study large amounts of genomics data.
Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.
By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.
Demo Portal

Pinned
Loading
  1. arrangerarrangerPublic
    
Data portal API and component generation

    TypeScript
32

24

  2. stagestagePublic
    TypeScript
1

5

  3. songsongPublic
    
File management system with metadata validation

    Java
14

5

  4. scorescorePublic
    
Secure Cloud Object REsource: file transfer microservice

    Java
20

11

  5. lyriclyricPublic
    TypeScript
2

1

  6. lecternlecternPublic
    
Data Schema / Dictionary management system

    TypeScript
2

5


Repositories

Showing 10 of 42 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
@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo
Open-source genomics data platforms
Project Site |
Documentation |
Demo Portal |
Quickstart
We build software that enables researchers and the public to access, manage and study large amounts of genomics data.
Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.
By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.
Demo Portal

Pinned
Loading
  1. arrangerarrangerPublic
    
Data portal API and component generation

    TypeScript
32

24

  2. stagestagePublic
    TypeScript
1

5

  3. songsongPublic
    
File management system with metadata validation

    Java
14

5

  4. scorescorePublic
    
Secure Cloud Object REsource: file transfer microservice

    Java
20

11

  5. lyriclyricPublic
    TypeScript
2

1

  6. lecternlecternPublic
    
Data Schema / Dictionary management system

    TypeScript
2

5


Repositories

Showing 10 of 42 repositories
View all repositories
Top languages
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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
@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo
Open-source genomics data platforms
Project Site |
Documentation |
Demo Portal |
Quickstart
We build software that enables researchers and the public to access, manage and study large amounts of genomics data.
Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.
By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.
Demo Portal

Pinned
Loading
  1. arrangerarrangerPublic
    
Data portal API and component generation

    TypeScript
32

24

  2. stagestagePublic
    TypeScript
1

5

  3. songsongPublic
    
File management system with metadata validation

    Java
14

5

  4. scorescorePublic
    
Secure Cloud Object REsource: file transfer microservice

    Java
20

11

  5. lyriclyricPublic
    TypeScript
2

1

  6. lecternlecternPublic
    
Data Schema / Dictionary management system

    TypeScript
2

5


Repositories

Showing 10 of 42 repositories
View all repositories
Top languages
Loading…
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Loading…

, '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
@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo
Open-source genomics data platforms
Project Site |
Documentation |
Demo Portal |
Quickstart
We build software that enables researchers and the public to access, manage and study large amounts of genomics data.
Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.
By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.
Demo Portal

Pinned
Loading
  1. arrangerarrangerPublic
    
Data portal API and component generation

    TypeScript
32

24

  2. stagestagePublic
    TypeScript
1

5

  3. songsongPublic
    
File management system with metadata validation

    Java
14

5

  4. scorescorePublic
    
Secure Cloud Object REsource: file transfer microservice

    Java
20

11

  5. lyriclyricPublic
    TypeScript
2

1

  6. lecternlecternPublic
    
Data Schema / Dictionary management system

    TypeScript
2

5


Repositories

Showing 10 of 42 repositories
View all repositories
Top languages
Loading…
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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
@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo
Open-source genomics data platforms
Project Site |
Documentation |
Demo Portal |
Quickstart
We build software that enables researchers and the public to access, manage and study large amounts of genomics data.
Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.
By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.
Demo Portal

Pinned
Loading
  1. arrangerarrangerPublic
    
Data portal API and component generation

    TypeScript
32

24

  2. stagestagePublic
    TypeScript
1

5

  3. songsongPublic
    
File management system with metadata validation

    Java
14

5

  4. scorescorePublic
    
Secure Cloud Object REsource: file transfer microservice

    Java
20

11

  5. lyriclyricPublic
    TypeScript
2

1

  6. lecternlecternPublic
    
Data Schema / Dictionary management system

    TypeScript
2

5


Repositories

Showing 10 of 42 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo
Open-source genomics data platforms
Project Site |
Documentation |
Demo Portal |
Quickstart
We build software that enables researchers and the public to access, manage and study large amounts of genomics data.
Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.
By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.
Demo Portal

Pinned
Loading
  1. arrangerarrangerPublic
    
Data portal API and component generation

    TypeScript
32

24

  2. stagestagePublic
    TypeScript
1

5

  3. songsongPublic
    
File management system with metadata validation

    Java
14

5

  4. scorescorePublic
    
Secure Cloud Object REsource: file transfer microservice

    Java
20

11

  5. lyriclyricPublic
    TypeScript
2

1

  6. lecternlecternPublic
    
Data Schema / Dictionary management system

    TypeScript
2

5


Repositories

Showing 10 of 42 repositories
View all repositories
Top languages
Loading…
Most used topics
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
@overture-stack

Overture

A collection of open-source, extendable solutions for big-data genomic science.
README.md
overture-logo
Open-source genomics data platforms
Project Site |
Documentation |
Demo Portal |
Quickstart
We build software that enables researchers and the public to access, manage and study large amounts of genomics data.
Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data.
By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales.
Demo Portal

Pinned
Loading
  1. arrangerarrangerPublic
    
Data portal API and component generation

    TypeScript
32

24

  2. stagestagePublic
    TypeScript
1

5

  3. songsongPublic
    
File management system with metadata validation

    Java
14

5

  4. scorescorePublic
    
Secure Cloud Object REsource: file transfer microservice

    Java
20

11

  5. lyriclyricPublic
    TypeScript
2

1

  6. lecternlecternPublic
    
Data Schema / Dictionary management system

    TypeScript
2

5


Repositories

Showing 10 of 42 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…