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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

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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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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

About
Bio Extensions for the Python WS client
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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('^' + ".*" + '

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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

About
Bio Extensions for the Python WS client
www.intermine.org
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

About
Bio Extensions for the Python WS client
www.intermine.org
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

About
Bio Extensions for the Python WS client
www.intermine.org
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7 forks
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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('^' + ".*" + '

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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

About
Bio Extensions for the Python WS client
www.intermine.org
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

About
Bio Extensions for the Python WS client
www.intermine.org
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, '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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= Biological Extensions to the InterMine Webservice Client Library This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It provides a wrapper class interminebio.SequenceQuery that can be used to gain access
to biologically specific data.
== Example
Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
== Who is this for?
InterMine data warehouses are typically constructed to hold
Biological data, and as this library facilitates programmatic
access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services
may find it especially useful:
* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)
These extensions are aimed at bioinformaticians looking to integrate
these sources of data into other workflows.
For details on constructing queries, see the intermine documentation.
== Support
Support is available on our development mailing list: dev@intermine.org
== License
All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license

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Bio Extensions for the Python WS client
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