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Strategies Website Development Kit (WDK)

Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.

Features include:

  • XML configuration of:

    • Record types (Record Classes)

    • Parameterized searches (Questions)

    • Record-based attributes and data tables

  • Plugin APIs to support:

    • configurable result filters

    • configurable reports/formats

    • asynchronous result analysis (Step Analysis)

    • non-RDBMS search (Process Queries)

    • result type transformation (e.g. genes to pathways)

  • Finding and bookmarking a particular record (Record Pages, Favorites)

  • Saving off a set of records (Baskets)

  • User login and preference storage

  • Widescale result caching

  • Extensible coding APIs for customized websites

Full up-to-date technical documentation (in progress) can be found here.

This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).

Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.

Explore https://plasmodb.org, a large scale production site powered by the WDK.

Original GUS/WDK project description is here.

Legacy documentation can be found here.

About

No description, website, or topics provided.

Resources

Readme
Apache-2.0 license
Activity
Custom properties

Stars

1 star

Watchers

22 watching

Forks

4 forks
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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
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Strategies Website Development Kit (WDK)
Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.
Features include:
  • XML configuration of:
    • Record types (Record Classes)
    • Parameterized searches (Questions)
    • Record-based attributes and data tables
  • Plugin APIs to support:
    • configurable result filters
    • configurable reports/formats
    • asynchronous result analysis (Step Analysis)
    • non-RDBMS search (Process Queries)
    • result type transformation (e.g. genes to pathways)
  • Finding and bookmarking a particular record (Record Pages, Favorites)
  • Saving off a set of records (Baskets)
  • User login and preference storage
  • Widescale result caching
  • Extensible coding APIs for customized websites
Full up-to-date technical documentation (in progress) can be found here.
This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).
Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.
Explore https://plasmodb.org, a large scale production site powered by the WDK.
Original GUS/WDK project description is here.
Legacy documentation can be found here.
About
No description, website, or topics provided.
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
1 star
Watchers
22 watching
Forks
4 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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Strategies Website Development Kit (WDK)
Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.
Features include:
  • XML configuration of:
    • Record types (Record Classes)
    • Parameterized searches (Questions)
    • Record-based attributes and data tables
  • Plugin APIs to support:
    • configurable result filters
    • configurable reports/formats
    • asynchronous result analysis (Step Analysis)
    • non-RDBMS search (Process Queries)
    • result type transformation (e.g. genes to pathways)
  • Finding and bookmarking a particular record (Record Pages, Favorites)
  • Saving off a set of records (Baskets)
  • User login and preference storage
  • Widescale result caching
  • Extensible coding APIs for customized websites
Full up-to-date technical documentation (in progress) can be found here.
This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).
Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.
Explore https://plasmodb.org, a large scale production site powered by the WDK.
Original GUS/WDK project description is here.
Legacy documentation can be found here.
About
No description, website, or topics provided.
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
1 star
Watchers
22 watching
Forks
4 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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Strategies Website Development Kit (WDK)
Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.
Features include:
  • XML configuration of:
    • Record types (Record Classes)
    • Parameterized searches (Questions)
    • Record-based attributes and data tables
  • Plugin APIs to support:
    • configurable result filters
    • configurable reports/formats
    • asynchronous result analysis (Step Analysis)
    • non-RDBMS search (Process Queries)
    • result type transformation (e.g. genes to pathways)
  • Finding and bookmarking a particular record (Record Pages, Favorites)
  • Saving off a set of records (Baskets)
  • User login and preference storage
  • Widescale result caching
  • Extensible coding APIs for customized websites
Full up-to-date technical documentation (in progress) can be found here.
This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).
Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.
Explore https://plasmodb.org, a large scale production site powered by the WDK.
Original GUS/WDK project description is here.
Legacy documentation can be found here.
About
No description, website, or topics provided.
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
1 star
Watchers
22 watching
Forks
4 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
BranchesTags
Repository files navigation
Strategies Website Development Kit (WDK)
Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.
Features include:
  • XML configuration of:
    • Record types (Record Classes)
    • Parameterized searches (Questions)
    • Record-based attributes and data tables
  • Plugin APIs to support:
    • configurable result filters
    • configurable reports/formats
    • asynchronous result analysis (Step Analysis)
    • non-RDBMS search (Process Queries)
    • result type transformation (e.g. genes to pathways)
  • Finding and bookmarking a particular record (Record Pages, Favorites)
  • Saving off a set of records (Baskets)
  • User login and preference storage
  • Widescale result caching
  • Extensible coding APIs for customized websites
Full up-to-date technical documentation (in progress) can be found here.
This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).
Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.
Explore https://plasmodb.org, a large scale production site powered by the WDK.
Original GUS/WDK project description is here.
Legacy documentation can be found here.
About
No description, website, or topics provided.
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
1 star
Watchers
22 watching
Forks
4 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
BranchesTags
Repository files navigation
Strategies Website Development Kit (WDK)
Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.
Features include:
  • XML configuration of:
    • Record types (Record Classes)
    • Parameterized searches (Questions)
    • Record-based attributes and data tables
  • Plugin APIs to support:
    • configurable result filters
    • configurable reports/formats
    • asynchronous result analysis (Step Analysis)
    • non-RDBMS search (Process Queries)
    • result type transformation (e.g. genes to pathways)
  • Finding and bookmarking a particular record (Record Pages, Favorites)
  • Saving off a set of records (Baskets)
  • User login and preference storage
  • Widescale result caching
  • Extensible coding APIs for customized websites
Full up-to-date technical documentation (in progress) can be found here.
This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).
Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.
Explore https://plasmodb.org, a large scale production site powered by the WDK.
Original GUS/WDK project description is here.
Legacy documentation can be found here.
About
No description, website, or topics provided.
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
1 star
Watchers
22 watching
Forks
4 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
BranchesTags
Repository files navigation
Strategies Website Development Kit (WDK)
Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.
Features include:
  • XML configuration of:
    • Record types (Record Classes)
    • Parameterized searches (Questions)
    • Record-based attributes and data tables
  • Plugin APIs to support:
    • configurable result filters
    • configurable reports/formats
    • asynchronous result analysis (Step Analysis)
    • non-RDBMS search (Process Queries)
    • result type transformation (e.g. genes to pathways)
  • Finding and bookmarking a particular record (Record Pages, Favorites)
  • Saving off a set of records (Baskets)
  • User login and preference storage
  • Widescale result caching
  • Extensible coding APIs for customized websites
Full up-to-date technical documentation (in progress) can be found here.
This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).
Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.
Explore https://plasmodb.org, a large scale production site powered by the WDK.
Original GUS/WDK project description is here.
Legacy documentation can be found here.
About
No description, website, or topics provided.
Resources
Readme
Apache-2.0 license
Activity
Custom properties
Stars
1 star
Watchers
22 watching
Forks
4 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); }
})();
})();

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Strategies Website Development Kit (WDK)
Strategies WDK is a powerful Java-based search platform and REST API to access data stored in a relational database. When combined with the WDKClient web client, it provides an online workspace for exposing relational and other data through a pre-configured set of parameterized queries. These queries can be saved, edited, and shared. They can also be combined to form a complex search “strategy”, a tree-based flow of search results.
Features include:
  • XML configuration of:
    • Record types (Record Classes)
    • Parameterized searches (Questions)
    • Record-based attributes and data tables
  • Plugin APIs to support:
    • configurable result filters
    • configurable reports/formats
    • asynchronous result analysis (Step Analysis)
    • non-RDBMS search (Process Queries)
    • result type transformation (e.g. genes to pathways)
  • Finding and bookmarking a particular record (Record Pages, Favorites)
  • Saving off a set of records (Baskets)
  • User login and preference storage
  • Widescale result caching
  • Extensible coding APIs for customized websites
Full up-to-date technical documentation (in progress) can be found here.
This system has proved highly successful in enabling sophisticated data-mining of 'omics' data (e.g. genes, SNPs, studies) by a diverse group of end users. For VEuPathDB, it has primarily been used to mine data in the GUS Schema (Fischer et al. Database 2011), but has recently been updated so as to provide the ability to browse extensive metadata, e.g. clinical epidemiology variables, inspired by the Harvest data discovery platform (Pennington et. al., JAMIA 2014).
Exploiting the GUS/Strategies-WDK system, our group has successfully developed and deployed a system in support of functional genomics data for diverse user communities, including the NIAID VEuPathDB Bioinformatics Resource Center, the NIDDK Beta Cell Biology Consortium Genomics Resource, and the NIA NIAGADS Genomics database. Although thus far used primarily for functional genomics datasets, our system is inherently generalizable beyond omics data, including clinical records.
Explore https://plasmodb.org, a large scale production site powered by the WDK.
Original GUS/WDK project description is here.
Legacy documentation can be found here.
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