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runtime.txt
runtime.txt

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Build StatusBinder

intermine-ws-python-docs

Tutorials for the InterMine Python web client

This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online. You can find the NBViewer service at: https://nbviewer.jupyter.org/

If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages. http://jupyter.readthedocs.io/en/latest/install.html

Table of Contents

Tutorial 0: Registry Features

The utilies of extracting data about mine/organism using registry

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 1: Basics of a Query

The basics that you need to create and run a query.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 2: Adding Constraints

Adding simple constraints to make your queries more useful.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 3: More about constraints

Different types of constraints.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 4: Query Features

Joins and Path Descriptions.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 5: Query Results

Dealing with results of your query.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 6: Advanced Results Management

Filtering and Processing Results

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 7: Templates

Basics of calling a template.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 8: Accessing Templates

Authoring and Accessing your templates.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 9: Lists

Creating and saving lists from identifiers.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 10: Enrichment Calculations

Performing Enrichment calculations on lists.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 11: Combining Lists

Combining lists using set operations.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 12: More to do with queries

Covers additional and useful operations on queries

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 13: Query Manager

Making better queries with Query Manager

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 14: Data Visualisation

Visualising the data using Python client.

  • Try live: Binder
  • Try live (with completed answers): Binder

Tutorial 15: Data Model of Various Mines

Utilising the module to get details about the data model of various mines

  • Try live: Binder
  • Try live (with completed answers): Binder

About

Tutorials for the InterMine Python web client

Resources

Readme
LGPL-2.1 license
Activity
Custom properties

Stars

14 stars

Watchers

12 watching

Forks

19 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

, '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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README.md
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ipynb_check.py
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Repository files navigation
Build StatusBinder
intermine-ws-python-docs
Tutorials for the InterMine Python web client
This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online.
You can find the NBViewer service at: https://nbviewer.jupyter.org/
If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages.
http://jupyter.readthedocs.io/en/latest/install.html
Table of Contents
Tutorial 0: Registry Features
The utilies of extracting data about mine/organism using registry
  • Try live: Binder
  • Try live (with completed answers): Binder
Tutorial 1: Basics of a Query
The basics that you need to create and run a query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 2: Adding Constraints
Adding simple constraints to make your queries more useful.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 3: More about constraints
Different types of constraints.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 4: Query Features
Joins and Path Descriptions.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 5: Query Results
Dealing with results of your query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 6: Advanced Results Management
Filtering and Processing Results
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 7: Templates
Basics of calling a template.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 8: Accessing Templates
Authoring and Accessing your templates.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 9: Lists
Creating and saving lists from identifiers.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 10: Enrichment Calculations
Performing Enrichment calculations on lists.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 11: Combining Lists
Combining lists using set operations.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 12: More to do with queries
Covers additional and useful operations on queries
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 13: Query Manager
Making better queries with Query Manager
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 14: Data Visualisation
Visualising the data using Python client.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 15: Data Model of Various Mines
Utilising the module to get details about the data model of various mines
  • Try live:
Binder
  • Try live (with completed answers):
Binder
About
Tutorials for the InterMine Python web client
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
14 stars
Watchers
12 watching
Forks
19 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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00-tutorial.ipynb
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LICENSE
LICENSE
README.md
README.md
Workshop_Pax6Workflow.ipynb
Workshop_Pax6Workflow.ipynb
ipynb_check.py
ipynb_check.py
requirements.txt
requirements.txt
runtime.txt
runtime.txt
Repository files navigation
Build StatusBinder
intermine-ws-python-docs
Tutorials for the InterMine Python web client
This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online.
You can find the NBViewer service at: https://nbviewer.jupyter.org/
If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages.
http://jupyter.readthedocs.io/en/latest/install.html
Table of Contents
Tutorial 0: Registry Features
The utilies of extracting data about mine/organism using registry
  • Try live: Binder
  • Try live (with completed answers): Binder
Tutorial 1: Basics of a Query
The basics that you need to create and run a query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 2: Adding Constraints
Adding simple constraints to make your queries more useful.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 3: More about constraints
Different types of constraints.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 4: Query Features
Joins and Path Descriptions.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 5: Query Results
Dealing with results of your query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 6: Advanced Results Management
Filtering and Processing Results
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 7: Templates
Basics of calling a template.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 8: Accessing Templates
Authoring and Accessing your templates.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 9: Lists
Creating and saving lists from identifiers.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 10: Enrichment Calculations
Performing Enrichment calculations on lists.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 11: Combining Lists
Combining lists using set operations.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 12: More to do with queries
Covers additional and useful operations on queries
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 13: Query Manager
Making better queries with Query Manager
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 14: Data Visualisation
Visualising the data using Python client.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 15: Data Model of Various Mines
Utilising the module to get details about the data model of various mines
  • Try live:
Binder
  • Try live (with completed answers):
Binder
About
Tutorials for the InterMine Python web client
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
14 stars
Watchers
12 watching
Forks
19 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

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00-tutorial.ipynb
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README.md
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Workshop_Pax6Workflow.ipynb
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ipynb_check.py
requirements.txt
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runtime.txt
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Repository files navigation
Build StatusBinder
intermine-ws-python-docs
Tutorials for the InterMine Python web client
This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online.
You can find the NBViewer service at: https://nbviewer.jupyter.org/
If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages.
http://jupyter.readthedocs.io/en/latest/install.html
Table of Contents
Tutorial 0: Registry Features
The utilies of extracting data about mine/organism using registry
  • Try live: Binder
  • Try live (with completed answers): Binder
Tutorial 1: Basics of a Query
The basics that you need to create and run a query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 2: Adding Constraints
Adding simple constraints to make your queries more useful.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 3: More about constraints
Different types of constraints.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 4: Query Features
Joins and Path Descriptions.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 5: Query Results
Dealing with results of your query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 6: Advanced Results Management
Filtering and Processing Results
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 7: Templates
Basics of calling a template.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 8: Accessing Templates
Authoring and Accessing your templates.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 9: Lists
Creating and saving lists from identifiers.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 10: Enrichment Calculations
Performing Enrichment calculations on lists.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 11: Combining Lists
Combining lists using set operations.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 12: More to do with queries
Covers additional and useful operations on queries
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 13: Query Manager
Making better queries with Query Manager
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 14: Data Visualisation
Visualising the data using Python client.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 15: Data Model of Various Mines
Utilising the module to get details about the data model of various mines
  • Try live:
Binder
  • Try live (with completed answers):
Binder
About
Tutorials for the InterMine Python web client
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
14 stars
Watchers
12 watching
Forks
19 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" + '

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Build StatusBinder
intermine-ws-python-docs
Tutorials for the InterMine Python web client
This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online.
You can find the NBViewer service at: https://nbviewer.jupyter.org/
If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages.
http://jupyter.readthedocs.io/en/latest/install.html
Table of Contents
Tutorial 0: Registry Features
The utilies of extracting data about mine/organism using registry
  • Try live: Binder
  • Try live (with completed answers): Binder
Tutorial 1: Basics of a Query
The basics that you need to create and run a query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 2: Adding Constraints
Adding simple constraints to make your queries more useful.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 3: More about constraints
Different types of constraints.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 4: Query Features
Joins and Path Descriptions.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 5: Query Results
Dealing with results of your query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 6: Advanced Results Management
Filtering and Processing Results
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 7: Templates
Basics of calling a template.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 8: Accessing Templates
Authoring and Accessing your templates.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 9: Lists
Creating and saving lists from identifiers.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 10: Enrichment Calculations
Performing Enrichment calculations on lists.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 11: Combining Lists
Combining lists using set operations.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 12: More to do with queries
Covers additional and useful operations on queries
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 13: Query Manager
Making better queries with Query Manager
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 14: Data Visualisation
Visualising the data using Python client.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 15: Data Model of Various Mines
Utilising the module to get details about the data model of various mines
  • Try live:
Binder
  • Try live (with completed answers):
Binder
About
Tutorials for the InterMine Python web client
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
14 stars
Watchers
12 watching
Forks
19 forks
Report repository
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Used by
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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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ipynb_check.py
requirements.txt
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Build StatusBinder
intermine-ws-python-docs
Tutorials for the InterMine Python web client
This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online.
You can find the NBViewer service at: https://nbviewer.jupyter.org/
If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages.
http://jupyter.readthedocs.io/en/latest/install.html
Table of Contents
Tutorial 0: Registry Features
The utilies of extracting data about mine/organism using registry
  • Try live: Binder
  • Try live (with completed answers): Binder
Tutorial 1: Basics of a Query
The basics that you need to create and run a query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 2: Adding Constraints
Adding simple constraints to make your queries more useful.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 3: More about constraints
Different types of constraints.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 4: Query Features
Joins and Path Descriptions.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 5: Query Results
Dealing with results of your query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 6: Advanced Results Management
Filtering and Processing Results
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 7: Templates
Basics of calling a template.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 8: Accessing Templates
Authoring and Accessing your templates.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 9: Lists
Creating and saving lists from identifiers.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 10: Enrichment Calculations
Performing Enrichment calculations on lists.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 11: Combining Lists
Combining lists using set operations.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 12: More to do with queries
Covers additional and useful operations on queries
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 13: Query Manager
Making better queries with Query Manager
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 14: Data Visualisation
Visualising the data using Python client.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 15: Data Model of Various Mines
Utilising the module to get details about the data model of various mines
  • Try live:
Binder
  • Try live (with completed answers):
Binder
About
Tutorials for the InterMine Python web client
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
14 stars
Watchers
12 watching
Forks
19 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('^' + ".*" + '

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LICENSE
LICENSE
README.md
README.md
Workshop_Pax6Workflow.ipynb
Workshop_Pax6Workflow.ipynb
ipynb_check.py
ipynb_check.py
requirements.txt
requirements.txt
runtime.txt
runtime.txt
Repository files navigation
Build StatusBinder
intermine-ws-python-docs
Tutorials for the InterMine Python web client
This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online.
You can find the NBViewer service at: https://nbviewer.jupyter.org/
If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages.
http://jupyter.readthedocs.io/en/latest/install.html
Table of Contents
Tutorial 0: Registry Features
The utilies of extracting data about mine/organism using registry
  • Try live: Binder
  • Try live (with completed answers): Binder
Tutorial 1: Basics of a Query
The basics that you need to create and run a query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 2: Adding Constraints
Adding simple constraints to make your queries more useful.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 3: More about constraints
Different types of constraints.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 4: Query Features
Joins and Path Descriptions.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 5: Query Results
Dealing with results of your query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 6: Advanced Results Management
Filtering and Processing Results
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 7: Templates
Basics of calling a template.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 8: Accessing Templates
Authoring and Accessing your templates.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 9: Lists
Creating and saving lists from identifiers.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 10: Enrichment Calculations
Performing Enrichment calculations on lists.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 11: Combining Lists
Combining lists using set operations.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 12: More to do with queries
Covers additional and useful operations on queries
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 13: Query Manager
Making better queries with Query Manager
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 14: Data Visualisation
Visualising the data using Python client.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 15: Data Model of Various Mines
Utilising the module to get details about the data model of various mines
  • Try live:
Binder
  • Try live (with completed answers):
Binder
About
Tutorials for the InterMine Python web client
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
14 stars
Watchers
12 watching
Forks
19 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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Workshop_Pax6Workflow.ipynb
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Repository files navigation
Build StatusBinder
intermine-ws-python-docs
Tutorials for the InterMine Python web client
This repository comprises of tutorials to help you get familiarised with the intermine-python package. The tutorials are in the form of Jupyter-Notebooks. You can either install Jupyter on your machine, download the tutorials and then run them on your local machine or you can use Jupyter's notebook viewer facility to view the tutorials online.
You can find the NBViewer service at: https://nbviewer.jupyter.org/
If you already have python installed on your machine, you can pip install Jupyter. If you do not have Python on your machine, you can download and install Anaconda as it would install Python along with Jupyter and many other packages.
http://jupyter.readthedocs.io/en/latest/install.html
Table of Contents
Tutorial 0: Registry Features
The utilies of extracting data about mine/organism using registry
  • Try live: Binder
  • Try live (with completed answers): Binder
Tutorial 1: Basics of a Query
The basics that you need to create and run a query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 2: Adding Constraints
Adding simple constraints to make your queries more useful.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 3: More about constraints
Different types of constraints.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 4: Query Features
Joins and Path Descriptions.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 5: Query Results
Dealing with results of your query.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 6: Advanced Results Management
Filtering and Processing Results
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 7: Templates
Basics of calling a template.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 8: Accessing Templates
Authoring and Accessing your templates.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 9: Lists
Creating and saving lists from identifiers.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 10: Enrichment Calculations
Performing Enrichment calculations on lists.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 11: Combining Lists
Combining lists using set operations.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 12: More to do with queries
Covers additional and useful operations on queries
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 13: Query Manager
Making better queries with Query Manager
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 14: Data Visualisation
Visualising the data using Python client.
  • Try live:
Binder
  • Try live (with completed answers):
Binder
Tutorial 15: Data Model of Various Mines
Utilising the module to get details about the data model of various mines
  • Try live:
Binder
  • Try live (with completed answers):
Binder
About
Tutorials for the InterMine Python web client
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
14 stars
Watchers
12 watching
Forks
19 forks
Report repository
Releases
Packages
Used by
Contributors
Languages