Skip to content
BranchesTags

Repository files navigation

InterMine

A powerful open source data warehouse system.

InterMine Documentation

In order to improve the chance of continued funding for the InterMine project it would be appreciated if groups that use InterMine or parts of InterMine would let us know (email [info[at]flymine.org](mailto:info flymine.org)).

Getting Started With InterMine

For a guide on getting started with InterMine, please visit: quick start tutorial

Deploying a Demonstration Application

To deploy one of the demonstration applications without going through a tutorial, please enter either the testmodel or biotestmine directory and run the set-up script:

sh setup.sh

This requires that you have all the software dependencies installed and running with the appropriate user permissions (postgres, Tomcat, Java SDK). You will need to have set up usernames and passwords for Tomcat and postgres first, and these can be provided to the setup scripts as PSQL_USER, PSQL_PWD, TOMCAT_USER, and TOMCAT_PWD.

Copyright and Licence

Copyright (C) 2002-2014 FlyMine

See LICENSE file for licensing information.

This product includes software developed by the Apache Software Foundation.

About

A powerful open source data warehouse system

intermine.org

Resources

Readme
License
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

Packages

Contributors

, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
GitHub - stairs/intermine: A powerful open source data warehouse system · GitHub
Skip to content
BranchesTags
Repository files navigation
InterMine
A powerful open source data warehouse system.
InterMine Documentation
In order to improve the chance of continued funding for the
InterMine project it would be appreciated if groups that use
InterMine or parts of InterMine would let us know (email
[info[at]flymine.org](mailto:info flymine.org)).
Getting Started With InterMine
For a guide on getting started with InterMine, please visit:
quick start
tutorial
Deploying a Demonstration Application
To deploy one of the demonstration applications without going
through a tutorial, please enter either the testmodel or
biotestmine directory and run the set-up script:
sh setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as PSQL_USER, PSQL_PWD,
TOMCAT_USER, and TOMCAT_PWD.
Copyright and Licence
Copyright (C) 2002-2014 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation.
About
A powerful open source data warehouse system
intermine.org
Resources
Readme
License
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - stairs/intermine: A powerful open source data warehouse system · GitHub
Skip to content
BranchesTags
Repository files navigation
InterMine
A powerful open source data warehouse system.
InterMine Documentation
In order to improve the chance of continued funding for the
InterMine project it would be appreciated if groups that use
InterMine or parts of InterMine would let us know (email
[info[at]flymine.org](mailto:info flymine.org)).
Getting Started With InterMine
For a guide on getting started with InterMine, please visit:
quick start
tutorial
Deploying a Demonstration Application
To deploy one of the demonstration applications without going
through a tutorial, please enter either the testmodel or
biotestmine directory and run the set-up script:
sh setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as PSQL_USER, PSQL_PWD,
TOMCAT_USER, and TOMCAT_PWD.
Copyright and Licence
Copyright (C) 2002-2014 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation.
About
A powerful open source data warehouse system
intermine.org
Resources
Readme
License
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - stairs/intermine: A powerful open source data warehouse system · GitHub
Skip to content
BranchesTags
Repository files navigation
InterMine
A powerful open source data warehouse system.
InterMine Documentation
In order to improve the chance of continued funding for the
InterMine project it would be appreciated if groups that use
InterMine or parts of InterMine would let us know (email
[info[at]flymine.org](mailto:info flymine.org)).
Getting Started With InterMine
For a guide on getting started with InterMine, please visit:
quick start
tutorial
Deploying a Demonstration Application
To deploy one of the demonstration applications without going
through a tutorial, please enter either the testmodel or
biotestmine directory and run the set-up script:
sh setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as PSQL_USER, PSQL_PWD,
TOMCAT_USER, and TOMCAT_PWD.
Copyright and Licence
Copyright (C) 2002-2014 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation.
About
A powerful open source data warehouse system
intermine.org
Resources
Readme
License
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - stairs/intermine: A powerful open source data warehouse system · GitHub
Skip to content
BranchesTags
Repository files navigation
InterMine
A powerful open source data warehouse system.
InterMine Documentation
In order to improve the chance of continued funding for the
InterMine project it would be appreciated if groups that use
InterMine or parts of InterMine would let us know (email
[info[at]flymine.org](mailto:info flymine.org)).
Getting Started With InterMine
For a guide on getting started with InterMine, please visit:
quick start
tutorial
Deploying a Demonstration Application
To deploy one of the demonstration applications without going
through a tutorial, please enter either the testmodel or
biotestmine directory and run the set-up script:
sh setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as PSQL_USER, PSQL_PWD,
TOMCAT_USER, and TOMCAT_PWD.
Copyright and Licence
Copyright (C) 2002-2014 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation.
About
A powerful open source data warehouse system
intermine.org
Resources
Readme
License
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - stairs/intermine: A powerful open source data warehouse system · GitHub
Skip to content
BranchesTags
Repository files navigation
InterMine
A powerful open source data warehouse system.
InterMine Documentation
In order to improve the chance of continued funding for the
InterMine project it would be appreciated if groups that use
InterMine or parts of InterMine would let us know (email
[info[at]flymine.org](mailto:info flymine.org)).
Getting Started With InterMine
For a guide on getting started with InterMine, please visit:
quick start
tutorial
Deploying a Demonstration Application
To deploy one of the demonstration applications without going
through a tutorial, please enter either the testmodel or
biotestmine directory and run the set-up script:
sh setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as PSQL_USER, PSQL_PWD,
TOMCAT_USER, and TOMCAT_PWD.
Copyright and Licence
Copyright (C) 2002-2014 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation.
About
A powerful open source data warehouse system
intermine.org
Resources
Readme
License
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - stairs/intermine: A powerful open source data warehouse system · GitHub
Skip to content
BranchesTags
Repository files navigation
InterMine
A powerful open source data warehouse system.
InterMine Documentation
In order to improve the chance of continued funding for the
InterMine project it would be appreciated if groups that use
InterMine or parts of InterMine would let us know (email
[info[at]flymine.org](mailto:info flymine.org)).
Getting Started With InterMine
For a guide on getting started with InterMine, please visit:
quick start
tutorial
Deploying a Demonstration Application
To deploy one of the demonstration applications without going
through a tutorial, please enter either the testmodel or
biotestmine directory and run the set-up script:
sh setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as PSQL_USER, PSQL_PWD,
TOMCAT_USER, and TOMCAT_PWD.
Copyright and Licence
Copyright (C) 2002-2014 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation.
About
A powerful open source data warehouse system
intermine.org
Resources
Readme
License
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
GitHub - stairs/intermine: A powerful open source data warehouse system · GitHub
Skip to content
BranchesTags
Repository files navigation
InterMine
A powerful open source data warehouse system.
InterMine Documentation
In order to improve the chance of continued funding for the
InterMine project it would be appreciated if groups that use
InterMine or parts of InterMine would let us know (email
[info[at]flymine.org](mailto:info flymine.org)).
Getting Started With InterMine
For a guide on getting started with InterMine, please visit:
quick start
tutorial
Deploying a Demonstration Application
To deploy one of the demonstration applications without going
through a tutorial, please enter either the testmodel or
biotestmine directory and run the set-up script:
sh setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as PSQL_USER, PSQL_PWD,
TOMCAT_USER, and TOMCAT_PWD.
Copyright and Licence
Copyright (C) 2002-2014 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation.
About
A powerful open source data warehouse system
intermine.org
Resources
Readme
License
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors