├── collab.yml ├── pelican-themes ├── content ├── extra │ └── CNAME ├── css │ ├── concept-map-padding.css │ ├── FeedEk.css │ ├── concept-map.css │ └── timeline.css ├── images │ ├── DS3b.jpg │ ├── face-2.png │ ├── origami.png │ ├── spyro.mp4 │ ├── BSM-panel.png │ ├── LHC-panel.png │ ├── Web-panel.png │ ├── GitHub-2016.png │ ├── Higgs-panel.png │ ├── SM-confusion.jpg │ ├── atlas-yy-140.png │ ├── atlas-zz-138.png │ ├── basketball.png │ ├── cms-zz-138.png │ ├── cosmic-rays.jpg │ ├── cosmic_ray.jpg │ ├── crayfis_logo.png │ ├── supersplit.png │ ├── Standard-Model.jpg │ ├── jet-embedding.png │ ├── learnEmbedding.png │ ├── particle-fever.png │ ├── sharing-grief.png │ ├── Detectors-panel.png │ ├── Kyle_Nifty_Fifty.jpg │ ├── Lagrangian-panel.png │ ├── basketball-play.png │ ├── gaussianInfoGeom.png │ ├── interpEmbedding.png │ ├── Kyle_Nifty_Fifty_2.jpg │ ├── standardmodel-standard.jpg │ ├── what-can-750-tell-us.png │ ├── year-in-review-GH-2016.png │ ├── Kyle_Nifty_Fifty-small.jpeg │ ├── stark-seven-deadly-sins.png │ ├── CharlieRose_forweb2-284x300.png │ ├── Kyle_Nifty_Fifty_2-small.jpeg │ ├── atlas-week-group-IMG_7192.JPG │ ├── realineituhedron-coverpage.png │ ├── kyle-andys-party-miras-photo.jpg │ ├── msdse-2015-collaboration-network.png │ ├── Particle-Fever-Standard-Model-Graphic.png │ └── Kyle-Cranmer-headshot-cropped-square-web.jpeg ├── downloads │ ├── .DS_Store │ ├── files │ │ ├── loader.gif │ │ ├── murmuration.mp4 │ │ ├── supersplit_750.pdf │ │ ├── realineituhedron.pdf │ │ ├── scale-separation.png │ │ ├── test_colab.yml │ │ ├── test_projects.yml │ │ ├── test_document.json │ │ ├── test_people.yml │ │ ├── test3.json │ │ ├── test.yml │ │ └── test.json │ ├── notebooks │ │ └── NetworkxD3example.ipynb │ └── code │ │ └── learnEmbedding.py ├── js │ ├── test-FeedEk.js │ ├── test-concept-map.js │ ├── iris-collaboration-map-test.js │ ├── test-collaboration-map.js │ ├── test-FeedEk-minimal.js │ ├── iris-collaboration-map.js │ ├── packages.js │ ├── FeedEk.min.js │ └── FeedEk.js ├── Hotellings-Experiment.md ├── Jupyter Book.md ├── ML4Jets2020.md ├── the-higgs-boson-a-natural-disaster.md ├── facebook-graphseach-and-the-nsa.md ├── recursive-prime-decomposition.md ├── a-d3-test-post-using-iframe.md ├── scale-separation.md ├── TheoristsMakeDataToo.md ├── Philae.md ├── DS3.md ├── next-up-flask.md ├── Supersplit.md ├── OpenScienceMeetup.md ├── iris-map.md ├── bicep2-software-carpentry.md ├── ML4PS2020.md ├── feedEk.md ├── thebe.md ├── roofit-statistical-modeling-language-in-ipython-notebook-c2-b6.md ├── murmuration-gp.md ├── ridge-map.md ├── pelican-cite.md ├── DecomposingMixtureSlides.md ├── pages │ ├── Home.md │ └── projects.md ├── The-Reallineituhedron.md ├── USA-science-engineering-festival.md ├── inspire-api.md ├── Recast.md ├── visualizing-information-geometry-with-multidimensional-scaling.md ├── looking-back-on-2015.md ├── iris-map-test.md ├── projects-from-july-2013.md ├── collaboration-map.md ├── enabling-data-sharing-citation-and-discovery.md ├── a-fresh-look-for-the-standard-model.md ├── kyle-10authors-2020.bib ├── Testing.md ├── SoftwareCitation.md ├── visiting-my-high-school-in-arkansas.md ├── Crayfis.md ├── Sabbatical.md └── timeline.md ├── Tipue Search 7.0 ├── pelican-plugins ├── .DS_Store ├── cache ├── PagesGenerator-Readers └── ArticlesGenerator-Readers ├── .gitignore ├── README ├── convert.py ├── convert_json_yml.py ├── publishconf.py ├── pip.freeze.oldmbp ├── requirements.txt ├── fabfile.py ├── extra_header_minimal.html ├── develop_server.sh ├── Makefile ├── pelicanconf.py └── _nb_header_minimal.html /collab.yml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pelican-themes: -------------------------------------------------------------------------------- 1 | ../pelican-themes -------------------------------------------------------------------------------- /content/extra/CNAME: 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#!/usr/bin/env python 2 | import sys 3 | import json 4 | import yaml 5 | 6 | print(yaml.dump(yaml.load(json.dumps(json.loads(open(sys.argv[1]).read()))), default_flow_style=False)) -------------------------------------------------------------------------------- /convert_json_yml.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import sys 3 | import json 4 | import yaml 5 | 6 | print(yaml.dump(yaml.load(json.dumps(json.loads(open(sys.argv[1]).read()))), default_flow_style=False)) -------------------------------------------------------------------------------- /content/js/test-FeedEk.js: -------------------------------------------------------------------------------- 1 | $('#divRss').FeedEk({ 2 | FeedUrl:'http://inspirehep.net/rss?ln=en&p=a%3AK.S.Cranmer.1', 3 | MaxCount : 5, 4 | ShowDesc : true, 5 | ShowPubDate:true, 6 | TitleLinkTarget:'_blank', 7 | DateFormat: 'MM/DD/YYYY', 8 | DateFormatLang:'en' 9 | }); -------------------------------------------------------------------------------- /content/Hotellings-Experiment.md: -------------------------------------------------------------------------------- 1 | Title: Hotelling's Experiment 2 | date: 2014-04-11 10:53 3 | Slug: Hotelling-Experiment 4 | Category: Blog 5 | Tags: python, Statistics 6 | Authors: Kyle Cranmer 7 | 8 | {% notebook downloads/notebooks/HotellingsExperiment.ipynb %} 9 | -------------------------------------------------------------------------------- /content/js/test-concept-map.js: -------------------------------------------------------------------------------- 1 | $(function(){ 2 | plotConceptMap(); 3 | }); 4 | function plotConceptMap() 5 | { 6 | d3.json("/downloads/files/collaboration.json", function(dataJson) { 7 | var plot = new ConceptMap("graph", "graph-info", dataJson); 8 | }); 9 | } 10 | -------------------------------------------------------------------------------- /content/js/iris-collaboration-map-test.js: -------------------------------------------------------------------------------- 1 | $(function(){ 2 | plotCollaborationMap(); 3 | }); 4 | function plotCollaborationMap() 5 | { 6 | d3.json("/downloads/files/test.json", function(dataJson) { 7 | var plot = new CollaborationMap("graph", "graph-info", dataJson); 8 | }); 9 | } 10 | -------------------------------------------------------------------------------- /content/js/test-collaboration-map.js: -------------------------------------------------------------------------------- 1 | $(function(){ 2 | plotCollaborationMap(); 3 | }); 4 | function plotCollaborationMap() 5 | { 6 | d3.json("/downloads/files/collaboration.json", function(dataJson) { 7 | var plot = new CollaborationMap("graph", "graph-info", dataJson); 8 | }); 9 | } 10 | -------------------------------------------------------------------------------- /content/js/test-FeedEk-minimal.js: -------------------------------------------------------------------------------- 1 | $('#divRss-minimal').FeedEk({ 2 | FeedUrl:'http://inspirehep.net/rss?ln=en&p=a%3AK.S.Cranmer.1', 3 | MaxCount : 5, 4 | ShowDesc : false, 5 | ShowPubDate:false, 6 | DescCharacterLimit:500, 7 | TitleLinkTarget:'_blank', 8 | DateFormat: 'MM/DD/YYYY', 9 | DateFormatLang:'en' 10 | }); -------------------------------------------------------------------------------- /content/js/iris-collaboration-map.js: -------------------------------------------------------------------------------- 1 | $(function(){ 2 | plotCollaborationMap(); 3 | }); 4 | function plotCollaborationMap() 5 | { 6 | // d3.json("/downloads/files/test2.json", function(dataJson) { 7 | d3.json("/downloads/files/collaboration-iris.json", function(dataJson) { 8 | var plot = new CollaborationMap("graph", "graph-info", dataJson); 9 | }); 10 | } 11 | -------------------------------------------------------------------------------- /content/Jupyter Book.md: -------------------------------------------------------------------------------- 1 | Title: Jupyter Book 2 | date: 2020-01-26 3 | Slug: Jupyter Book 4 | Category: Blog 5 | Tags: python, Physics, statistics 6 | Authors: Kyle Cranmer 7 | 8 | I've just started to collect material that I use for a class at NYU into a Jupyter book. 9 | It's here: 10 | 11 | [https://cranmer.github.io/intro-exp-phys-book/introduction](https://cranmer.github.io/intro-exp-phys-book/introduction) -------------------------------------------------------------------------------- /content/downloads/files/test_colab.yml: -------------------------------------------------------------------------------- 1 | collaborations: 2 | - name: ATLAS 3 | - name: CMS 4 | - name: LHCb 5 | - name: DOMA 6 | - name: Analysis Systems 7 | - name: Innovative Algorithms 8 | - name: SSL 9 | - name: Blueprint 10 | - name: Executive Board 11 | - name: Steering Board 12 | - name: Advisory Board 13 | - name: Training, Education and Outreach 14 | - name: OSG 15 | - name: SCAILFIN 16 | - name: DIANA 17 | - name: DASPOS 18 | -------------------------------------------------------------------------------- /content/ML4Jets2020.md: -------------------------------------------------------------------------------- 1 | Title: ML4Jets 2020 2 | date: 2020-01-15 3 | Slug: ML4Jets 2020 4 | Category: Blog 5 | Tags: Machine Learning, Physics 6 | Authors: Kyle Cranmer 7 | 8 | We held [ML4Jets](https://indico.cern.ch/event/809820/overview) at NYU January 15-17, 2020. 9 | We had about 115 in attendance. 10 | 11 | -------------------------------------------------------------------------------- /content/css/FeedEk.css: -------------------------------------------------------------------------------- 1 | .feedEkList{width:450px; list-style:none outside none;background-color:#FFFFFF; border:1px solid #D3CAD7; padding:4px 6px; color:#3E3E3E;} 2 | .feedEkList li{border-bottom:1px solid #D3CAD7; padding:5px;} 3 | .feedEkList li:last-child{border-bottom:none;} 4 | .itemTitle a{font-weight:bold; color:#4EBAFF !important; text-decoration:none } 5 | .itemTitle a:hover{ text-decoration:underline } 6 | .itemDate{font-size:11px;color:#AAAAAA;} -------------------------------------------------------------------------------- /content/the-higgs-boson-a-natural-disaster.md: -------------------------------------------------------------------------------- 1 | Title: The Higgs Boson: A Natural Disaster! 2 | Date: 2014-02-07 16:02 3 | Author: cranmer 4 | Category: Blog 5 | Tags: Physics, Higgs, Communication 6 | Slug: the-higgs-boson-a-natural-disaster 7 | 8 | See my blog post over at QuantumDiaries on an analogy about the fine 9 | tuning problem related to the Higgs boson. 10 | 11 | 12 | ["The Higgs Boson: A Natural Disaster!" ](http://www.quantumdiaries.org/2014/02/01/the-higgs-boson-a-natural-disaster/) 13 | 14 | -------------------------------------------------------------------------------- /content/downloads/files/test_projects.yml: -------------------------------------------------------------------------------- 1 | projects: 2 | - name: pyhf 3 | - name: func_adl 4 | - name: Coffea 5 | - name: uproot 6 | - name: Awkward Array 7 | - name: Recast 8 | - name: REANA 9 | - name: MadMiner 10 | - name: Scikit-Hep 11 | - name: Histogram projects 12 | - name: Ampgen 13 | - name: particle 14 | - name: xcache 15 | - name: iDDS 16 | - name: third party copy 17 | - name: modeling data workflows 18 | - name: ServiceX 19 | - name: acts 20 | - name: fast-pid 21 | - name: mkfit 22 | - name: ML on FPGAs 23 | - name: PV-finder 24 | - name: ML for Jets 25 | -------------------------------------------------------------------------------- /content/facebook-graphseach-and-the-nsa.md: -------------------------------------------------------------------------------- 1 | Title: Facebook GraphSearch and the NSA 2 | Date: 2013-07-13 03:49 3 | Author: cranmer 4 | Category: Blog 5 | Slug: facebook-graphseach-and-the-nsa 6 | 7 | It was worth a shot.  The funny thing is that Mark Zuckerburg is a 8 | friend of my friend and he is being followed by an NSA employee. 9 | 10 |   11 | 12 | [![GraphSearchNSA][]][GraphSearchNSA] 13 | 14 | And for good measure 15 | 16 | ![][] 17 | 18 |   19 | 20 | [GraphSearchNSA]: http://wordpress.theoryandpractice.org/wp-content/uploads/2013/07/GraphSearchNSA.png 21 | []: http://i.imgur.com/XLQIsnH.gif 22 | -------------------------------------------------------------------------------- /content/recursive-prime-decomposition.md: -------------------------------------------------------------------------------- 1 | Title: My favorite way to write numbers 2 | date: 2016-03-27 3 | Slug: My favorite way to write numbers 4 | Category: Blog 5 | Tags: mathematics, python 6 | Authors: Kyle Cranmer 7 | 8 | 9 | **Warning** I need to fix some css problems with pelican-bootstrap3 and embeded notebooks. 10 | 11 | You might want to [view the notebook with nbviewer instead](http://nbviewer.jupyter.org/github/cranmer/play/blob/master/misc/recursive%20prime%20decomposition.ipynb). 12 | 13 | 14 | 15 | ---- 16 | 17 | {% notebook downloads/notebooks/recursive-prime-decomposition.ipynb %} 18 | 19 | 20 | -------------------------------------------------------------------------------- /publishconf.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- # 3 | from __future__ import unicode_literals 4 | 5 | # This file is only used if you use `make publish` or 6 | # explicitly specify it as your config file. 7 | 8 | import os 9 | import sys 10 | sys.path.append(os.curdir) 11 | from pelicanconf import * 12 | 13 | SITEURL = 'https://theoryandpractice.org' 14 | RELATIVE_URLS = False 15 | 16 | FEED_ALL_ATOM = 'feeds/all.atom.xml' 17 | CATEGORY_FEED_ATOM = 'feeds/%s.atom.xml' 18 | 19 | DELETE_OUTPUT_DIRECTORY = True 20 | 21 | # Following items are often useful when publishing 22 | 23 | #DISQUS_SITENAME = "" 24 | #GOOGLE_ANALYTICS = "" 25 | -------------------------------------------------------------------------------- /content/a-d3-test-post-using-iframe.md: -------------------------------------------------------------------------------- 1 | Title: A D3 Test post using iframe 2 | Date: 2013-06-28 18:21 3 | Author: cranmer 4 | Category: Blog 5 | Tags: Data, Physics, Statistics 6 | Slug: a-d3-test-post-using-iframe 7 | 8 | A quick test of inserting an HTML file with some [D3 magic][] into a 9 | wordpress post using the iframe trick I found [here][] 10 | 11 |   12 | - - - 13 |   14 | 15 | 16 | 17 | [D3 magic]: http://d3js.org/ 18 | [here]: http://charlesmartinreid.com/wordpress/2012/08/d3-and-wordpress/ 19 | -------------------------------------------------------------------------------- /content/scale-separation.md: -------------------------------------------------------------------------------- 1 | Title: Scale Separation 2 | date: 2019-05-01 3 | Slug: Scale Separation 4 | Category: Blog 5 | Tags: python 6 | Authors: Kyle Cranmer 7 | 8 | While preparing for my talk at [Gotham Phyiscs X ML](https://sites.google.com/view/physicsxml/schedule?authuser=0) I made my first word cloud pun using Andreas Mueller's [word_cloud](https://github.com/amueller/word_cloud) tool. 9 | 10 |
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15 | 16 | ### Code: 17 | 18 | {% notebook downloads/notebooks/scale-separation-word-cloud.ipynb cells[0:2] %} 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /content/TheoristsMakeDataToo.md: -------------------------------------------------------------------------------- 1 | Title: Theorists Make Data Too 2 | date: 2015-11-11 13:53 3 | Slug: Theorists Make Data Too 4 | Category: Blog 5 | Tags: physics, communication 6 | Authors: Kyle Cranmer 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 |
-------------------------------------------------------------------------------- /content/Philae.md: -------------------------------------------------------------------------------- 1 | Title: Physics of Philae 2 | date: 2014-10-13 13:53 3 | Slug: Philae 4 | Category: Blog 5 | Tags: physics, communication 6 | Authors: Kyle Cranmer 7 | 8 | My first storify. Some physics based on the information of the Philae's big bounce in [this article](http://www.bbc.com/news/science-environment-30034060) 9 | 10 |
-------------------------------------------------------------------------------- /content/DS3.md: -------------------------------------------------------------------------------- 1 | Title: Launch of DS3 2 | date: 2019-10-15 3 | Slug: DS3 4 | Category: Blog 5 | Tags: data science 6 | Authors: Kyle Cranmer 7 | 8 | I took over has Executive Director of the Moore Sloan Data Science Environment (MSDSE) in late 2018. 9 | One of my major initiatives in 2019 was the launch of [Data Science and Software Services (DS3](https://cds.nyu.edu/ds3/)) at NYU. 10 | 11 | The Data Science & Software Services (DS3) creates a central service for faculty and research staff to access expertise in data science and statistical methodology as well as software engineering aligned with research goals. DS3 aims to enhance the research capacity of NYU by providing highly skilled labor for funded projects and increasing the competitiveness of grant proposals. 12 | 13 | DS3 is a joint undertaking of the Center for Data Science Moore-Sloan Data Science Environments (MSDSE) project, the NYU Libraries, NYU IT Research Technology, and the PRIISM Center, with connections to affiliated services such as Data Services, High Performance Computing (HPC), NYU IT Teaching and Learning with Technology (TLT), and more. 14 | 15 | -------------------------------------------------------------------------------- /content/next-up-flask.md: -------------------------------------------------------------------------------- 1 | Title: Next up, Flask 2 | Date: 2013-06-28 19:56 3 | Author: cranmer 4 | Category: Blog 5 | Slug: next-up-flask 6 | 7 | I was a big fan of [Zope][] early on (late 90's) and always wanted to do 8 | some fun web-based projects.  One of the more successful ones was 9 | [LaTeXWiki][], which was one of the first wiki plugins where you could 10 | write LaTeX.    Unfortunately, I was always sufficiently confused about 11 | some aspect of Zope that most of my projects only worked out with the 12 | help of friends like Sean, Joe, Jeff, Bob, and Stephen. 13 | 14 | The [old theoryandpractice][] site ran on Zope, but it hasn't been 15 | touched in years.  I spent so much time getting a 3-collumn CSS layout 16 | back in the early CSS days that it basically killed my interest.  Now 17 | I'm rebooting theoryandpractice.org (love that name) with wordpress and 18 | I'm hoping to tinker with some of the new technologies like D3 19 | and [Flask][].  Wish me luck! 20 | 21 | [Zope]: http://www.zope.org 22 | [LaTeXWiki]: https://github.com/eaudeweb/EionetProducts/tree/master/ZWiki/plugins/latexwiki 23 | [old theoryandpractice]: http://old.theoryandpractice.org 24 | [Flask]: http://flask.pocoo.org 25 | -------------------------------------------------------------------------------- /content/Supersplit.md: -------------------------------------------------------------------------------- 1 | Title: Supersplit Supersymmetry and the 750 GeV Diphoton Excess 2 | date: 2016-04-01 10:53 3 | Slug: Supersplit-750 4 | Category: Blog 5 | Tags: physics 6 | Authors: Kyle Cranmer 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | Well I caught the fever for the 750 GeV excess too. While ATLAS policies prevent me from submitting a paper to the arXiv about a preliminary result, I couldn't help but write up [these thoughts](http://bit.ly/1Y34QbT) on the excess in the context of Supersplit Supersymmetry. Note, they do not represent any offical view of the ATLAS collaboration. 15 | 16 | 17 | 18 | 19 | 20 | 21 | We clearly need more data, but these are exciting times. The analysis in the paper reveals many interesting and subtle statistical considertions. On the face of it, supersplit supersymmetry is excluded with 2-3$\sigma$ confidence. However, I also go so far as to propose a new *phenothropic principle* that explains this tension as a new form of tuning with a non-anthropic selection mechnaism. 22 | -------------------------------------------------------------------------------- /content/OpenScienceMeetup.md: -------------------------------------------------------------------------------- 1 | Title: Open Science Meetup 2 | date: 2015-5-01 15:53 3 | Slug: NYC Open Science Meetup 4 | Category: Blog 5 | Tags: physics, open science 6 | Authors: Kyle Cranmer 7 | 8 | After a colloquium at Renaissance Technologies and sitting on Daniel Foreman-Mackey's thesis defense I gave a [fun talk](http://dx.doi.org/10.6084/m9.figshare.1399147) for the [inagural NYC Open Science Meetup](http://www.meetup.com/ny-openscience/events/221735680/?a=uc1_te) sponsored by [authorea](http://authorea.com). 9 | 10 | 11 |

Our NYC #OpenScience meetup yesterday: @KyleCranmer showing how to detect Cosmic Rays on your smartphone pic.twitter.com/SA18UPTXvh

— Authorea (@authorea) April 30, 2015
12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /content/iris-map.md: -------------------------------------------------------------------------------- 1 | Title: Map of IRIS-HEP 2 | date: 2019-05-05 3 | Slug: collaboration-map-iris 4 | Category: Blog 5 | Tags: visualization 6 | Authors: Kyle Cranmer 7 | JavaScripts: d3.min.js, packages.js, collaboration-map.js, iris-collaboration-map.js 8 | Stylesheets: concept-map.css, concept-map-padding.css 9 | 10 | This is a variation on the other [Collaboration map](/2016/12/collaboration-map/) aimed at IRIS-HEP. 11 | 12 | * people: with description that links to their homepage. 13 | * projects: specific projects or perhaps topics of discussion 14 | * collaborations: groups of people brought together with some common goal, theme, or for some other organizational reason 15 | 16 | One nice thing about this appraoch is that the [input is JSON](/downloads/files/collaboration.json) (here's an example on GitHub [link](https://github.com/cranmer/TheoryAndPractice/blob/javascript/content/downloads/files/collaboration.json) ), so it should be easy to collaboratively guild this collaboration graph. 17 | 18 | I'd like to make something easier to edit with yaml and then convert it to JSON, but I'll leave that for another day. 19 | 20 | The interactive visualization at the top is my first try at a collaboration map. 21 | 22 | 23 |
24 |
25 | 26 |
27 | - - - 28 | 29 | -------------------------------------------------------------------------------- /content/bicep2-software-carpentry.md: -------------------------------------------------------------------------------- 1 | Title: Bicep2 and Software Carpentry 2 | Date: 2014-03-17 16:47 3 | Author: cranmer 4 | Category: Blog 5 | Tags: Data, python, Statistics, physics, open science 6 | Slug: bicep2-software-carpentry 7 | 8 | 9 | This week NYU hosted a [Software Carpentry Bootcamp](http://software-carpentry.org/bootcamps/index.html) along with Berkeley and U. Washington (the other institutes in the Moore-Sloan data science environment). I sat in on the python classes (there were also classes in R). However, on Monday, there was a _huge_ announcement from the [BICEP2](http://bicepkeck.org) collaboration about the observation of B-mode polarization in the CMB, which is considered a smoking gun for primordial gravitational waves predicte by inflation. That made it hard to concentrate on python, but I tried to merge the two. I noticed that BICEP2 made their likelihood curve public. I also noticed that they got a bit mixed up with their Bayesian and Frequentist statistics (at least the terminology), so that gave me an idea. 10 | Here's a link to my [iPython notebook on alternate BICEP2 error analysis](http://nbviewer.ipython.org/url/cranmer.github.io/downloads/notebooks/BICEP2_likelihood.ipynb?create=1) 11 | 12 | For convenience, embedded below (using the pelican liquid notebook plugin) 13 | 14 | - - - 15 | 16 | {% notebook downloads/notebooks/BICEP2_likelihood.ipynb %} -------------------------------------------------------------------------------- /content/downloads/files/test_document.json: -------------------------------------------------------------------------------- 1 | { 2 | "ditems": [ 3 | { 4 | "name": "Pete Elmer", 5 | "description": "", 6 | "links": [ 7 | "CMS", 8 | "DIANA", 9 | "Executive Board", 10 | "Innovative Algorithms", 11 | "Analysis Systems" 12 | ], 13 | "date": "2020-01-01 00:00:00", 14 | "slug": "ditem", 15 | "type": "ditem", 16 | "ditem": 1 17 | }, 18 | { 19 | "name": "Brian Bockelman", 20 | "links": [ 21 | "DOMA", 22 | "DIANA", 23 | "OSG", 24 | "Executive Board", 25 | "xcache", 26 | "iDDS", 27 | "third party copy" 28 | ], 29 | "date": "2020-01-01 00:00:00", 30 | "slug": "ditem", 31 | "description": "", 32 | "type": "ditem", 33 | "ditem": 2 34 | } 35 | ], 36 | "collaborations": [ 37 | { 38 | "name": "ATLAS", 39 | "description": "ATLAS is an experiment at CERN designed to explore the secrets of the universe.", 40 | "date": "2020-01-01 00:00:00", 41 | "slug": "slug", 42 | "group": 1, 43 | "type": "collaboration", 44 | "count": 1 45 | }, 46 | { 47 | "name": "CMS", 48 | "description": "CMS is an experiment at CERN designed to explore the secrets of the universe.", 49 | "date": "2020-01-01 00:00:00", 50 | "slug": "slug", 51 | "group": 1, 52 | "type": "collaboration", 53 | "count": 2 54 | } 55 | ] 56 | } -------------------------------------------------------------------------------- /content/js/packages.js: -------------------------------------------------------------------------------- 1 | (function() { 2 | packages = { 3 | 4 | // Lazily construct the package hierarchy from class names. 5 | root: function(classes) { 6 | var map = {}; 7 | 8 | function find(name, data) { 9 | var node = map[name], i; 10 | if (!node) { 11 | node = map[name] = data || {name: name, children: []}; 12 | if (name.length) { 13 | node.parent = find(name.substring(0, i = name.lastIndexOf("."))); 14 | node.parent.children.push(node); 15 | node.key = name.substring(i + 1); 16 | } 17 | } 18 | return node; 19 | } 20 | 21 | classes.forEach(function(d) { 22 | find(d.name, d); 23 | }); 24 | 25 | return map[""]; 26 | }, 27 | 28 | // Return a list of imports for the given array of nodes. 29 | imports: function(nodes) { 30 | var map = {}, 31 | imports = []; 32 | 33 | // Compute a map from name to node. 34 | nodes.forEach(function(d) { 35 | map[d.name] = d; 36 | }); 37 | 38 | // For each import, construct a link from the source to target node. 39 | nodes.forEach(function(d) { 40 | if (d.imports) d.imports.forEach(function(i) { 41 | imports.push({source: map[d.name], target: map[i]}); 42 | }); 43 | }); 44 | 45 | return imports; 46 | } 47 | 48 | }; 49 | })(); 50 | -------------------------------------------------------------------------------- /content/js/FeedEk.min.js: -------------------------------------------------------------------------------- 1 | /*! FeedEk jQuery RSS/ATOM Feed Plugin v3.1.1 2 | * https://jquery-plugins.net/FeedEk/FeedEk.html https://github.com/enginkizil/FeedEk 3 | * Author : Engin KIZIL */ 4 | !function (r) { r.fn.FeedEk = function (t) { var a, i = r.extend({ MaxCount: 5, ShowDesc: !0, ShowPubDate: !0, DescCharacterLimit: 0, TitleLinkTarget: "_blank", DateFormat: "", DateFormatLang: "en" }, t), e = r(this).attr("id"), n = ""; r("#" + e).empty(), null != i.FeedUrl && (r("#" + e).append(''), r.ajax({ url: "https://feed.jquery-plugins.net/load?url=" + encodeURIComponent(i.FeedUrl) + "&maxCount=" + i.MaxCount + "&dateCulture=" + i.DateFormatLang + "&dateFormat=" + i.DateFormat, dataType: "json", success: function (t) { r("#" + e).empty(), null != t.data && (r.each(t.data, function (t, e) { n += '
  • ' + e.title + "
    ", i.ShowPubDate && (a = new Date(e.publishDate), n += '
    ', 0 < r.trim(i.DateFormat).length ? n += e.publishDateFormatted : n += a.toLocaleDateString(), n += "
    "), i.ShowDesc && (n += '
    ', 0 < i.DescCharacterLimit && e.description.length > i.DescCharacterLimit ? n += e.description.substring(0, i.DescCharacterLimit) + "..." : n += e.description, n += "
    ") }), r("#" + e).append('")) } })) } }(jQuery); 5 | -------------------------------------------------------------------------------- /content/ML4PS2020.md: -------------------------------------------------------------------------------- 1 | Title: ML4PS2020 2 | date: 2020-12-15 3 | Slug: ML4PS2020 4 | Category: Blog 5 | Tags: machine learning, Physics 6 | Authors: Kyle Cranmer 7 | 8 | We held the third Machine Learning for Physical Sciences workshop at NeurIPS2020 on December 11, 2020. 9 | 10 | * Website: [Machine Learning for Physical Sciences](http://ml4physicalsciences.github.io) 11 | * Some live tweets: [#ML4PS2020](https://twitter.com/hashtag/ML4PS2020?src=hashtag_click) 12 | 13 | We had more than 150 posters and more than 200 people attend the poster session on Gather Town. Gather Town worked surprisingly well. 14 | 15 |

    We've updated our the website for Machine Learning in the Physical Sciences with the schedule and more than 150 contributed papers! Many thanks to @glouppe and @atilimgunes for the website updates, all the organizers and all the reviewers! #ML4PS2020 https://t.co/4Gx5Q8Bczn pic.twitter.com/FtbhZaycYM

    — Kyle Cranmer (@KyleCranmer) December 4, 2020
    -------------------------------------------------------------------------------- /pip.freeze.oldmbp: -------------------------------------------------------------------------------- 1 | appnope==0.1.0 2 | asn1crypto==0.24.0 3 | attrs==19.1.0 4 | backcall==0.1.0 5 | bcrypt==3.1.5 6 | beautifulsoup4==4.7.1 7 | bleach==3.1.0 8 | blinker==1.4 9 | certifi==2019.3.9 10 | cffi==1.11.5 11 | cryptography==2.4.2 12 | decorator==4.4.0 13 | defusedxml==0.6.0 14 | docutils==0.14 15 | entrypoints==0.3 16 | fabric==2.4.0 17 | feedgenerator==1.9 18 | ghp-import==1.0.0 19 | idna==2.8 20 | invoke==1.2.0 21 | ipykernel==5.1.0 22 | ipython==7.5.0 23 | ipython-genutils==0.2.0 24 | ipywidgets==7.4.2 25 | jedi==0.13.3 26 | Jinja2==2.10.1 27 | jsonschema==3.0.1 28 | jupyter==1.0.0 29 | jupyter-client==5.2.4 30 | jupyter-console==6.0.0 31 | jupyter-core==4.4.0 32 | latexcodec==2.0.1 33 | Markdown==3.0.1 34 | MarkupSafe==1.1.1 35 | mistune==0.8.4 36 | nbconvert==5.5.0 37 | nbformat==4.4.0 38 | notebook==5.7.8 39 | pandocfilters==1.4.2 40 | paramiko==2.4.2 41 | parso==0.4.0 42 | pelican==3.7.1 43 | pexpect==4.7.0 44 | pickleshare==0.7.5 45 | prometheus-client==0.6.0 46 | prompt-toolkit==2.0.9 47 | ptyprocess==0.6.0 48 | pyasn1==0.4.5 49 | pybtex==0.23.0 50 | pycparser==2.19 51 | Pygments==2.3.1 52 | PyNaCl==1.3.0 53 | pyrsistent==0.14.11 54 | python-dateutil==2.8.1 55 | pytz==2018.9 56 | PyYAML==5.3.1 57 | pyzmq==18.0.0 58 | qtconsole==4.4.3 59 | Send2Trash==1.5.0 60 | six==1.12.0 61 | smartypants==2.0.1 62 | soupsieve==1.8 63 | terminado==0.8.2 64 | testpath==0.4.2 65 | tornado==6.0.2 66 | traitlets==4.3.2 67 | typogrify==2.0.7 68 | Unidecode==1.0.23 69 | wcwidth==0.1.7 70 | webencodings==0.5.1 71 | widgetsnbextension==3.4.2 72 | -------------------------------------------------------------------------------- /content/downloads/files/test_people.yml: -------------------------------------------------------------------------------- 1 | ditems: 2 | - name: Peter Elmer 3 | links: 4 | - CMS 5 | - DIANA 6 | - Executive Board 7 | - Steering Board 8 | - Innovative Algorithms 9 | - name: Brian Bockelman 10 | links: 11 | - DOMA 12 | - DIANA 13 | - OSG 14 | - Executive Board 15 | - xcache 16 | - iDDS 17 | - third party copy 18 | - name: Gordon Watts 19 | links: 20 | - ATLAS 21 | - Analysis Systems 22 | - Executive Board 23 | - Steering Board 24 | - func_adl 25 | - name: David Lange 26 | links: 27 | - CMS 28 | - Innovative Algorithms 29 | - Executive Board 30 | - acts 31 | - name: Heather Gray 32 | links: 33 | - ATLAS 34 | - Innovative Algorithms 35 | - Executive Board 36 | - acts 37 | - name: Frank Wuerthwein 38 | links: 39 | - CMS 40 | - OSG 41 | - Executive Board 42 | - modeling data workflows 43 | - name: Sudhir Malik 44 | links: 45 | - CMS 46 | - Training, Education and Outreach 47 | - Executive Board 48 | - name: Rob Gardner 49 | links: 50 | - ATLAS 51 | - SSL 52 | - Executive Board 53 | - name: Mark Neubaeur 54 | links: 55 | - ATLAS 56 | - Blueprint 57 | - Analysis Systems 58 | - Innovative Algorithms 59 | - Executive Board 60 | - ML on FPGAs 61 | - name: Kyle Cranmer 62 | links: 63 | - Analysis Systems 64 | - Innovative Algorithms 65 | - Executive Board 66 | - Recast 67 | - pyhf 68 | - MadMiner 69 | - REANA 70 | - ML for Jets 71 | - ATLAS 72 | - INSPIRE 73 | - HEPData 74 | - MSDSE 75 | - DIANA 76 | - DASPOS 77 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | appnope==0.1.0 2 | asn1crypto==0.24.0 3 | attrs==19.1.0 4 | backcall==0.1.0 5 | bcrypt==3.1.5 6 | beautifulsoup4==4.7.1 7 | bleach==3.1.0 8 | blinker==1.4 9 | certifi==2019.3.9 10 | #cffi==1.11.5 11 | cryptography==2.4.2 12 | decorator==4.4.0 13 | defusedxml==0.6.0 14 | docutils==0.14 15 | entrypoints==0.3 16 | fabric==2.4.0 17 | feedgenerator==1.9 18 | ghp-import==1.0.0 19 | idna==2.8 20 | invoke==1.2.0 21 | ipykernel==5.1.0 22 | ipython==7.5.0 23 | ipython-genutils==0.2.0 24 | ipywidgets==7.4.2 25 | jedi==0.13.3 26 | Jinja2==2.10.1 27 | jsonschema==3.0.1 28 | jupyter==1.0.0 29 | jupyter-client==5.2.4 30 | jupyter-console==6.0.0 31 | jupyter-core==4.4.0 32 | latexcodec==2.0.1 33 | Markdown==3.0.1 34 | MarkupSafe==1.1.1 35 | mistune==0.8.4 36 | nbconvert==5.5.0 37 | nbformat==4.4.0 38 | notebook==5.7.8 39 | pandocfilters==1.4.2 40 | paramiko==2.4.2 41 | parso==0.4.0 42 | pelican==3.7.1 43 | pexpect==4.7.0 44 | pickleshare==0.7.5 45 | prometheus-client==0.6.0 46 | prompt-toolkit==2.0.9 47 | ptyprocess==0.6.0 48 | pyasn1==0.4.5 49 | pybtex==0.23.0 50 | pycparser==2.19 51 | Pygments==2.3.1 52 | PyNaCl==1.3.0 53 | pyrsistent==0.14.11 54 | python-dateutil==2.8.1 55 | pytz==2018.9 56 | PyYAML==5.3.1 57 | #pyzmq==18.0.0 58 | pyzmq 59 | qtconsole==4.4.3 60 | Send2Trash==1.5.0 61 | six==1.12.0 62 | smartypants==2.0.1 63 | soupsieve==1.8 64 | terminado==0.8.2 65 | testpath==0.4.2 66 | tornado==6.0.2 67 | traitlets==4.3.2 68 | typogrify==2.0.7 69 | Unidecode==1.0.23 70 | wcwidth==0.1.7 71 | webencodings==0.5.1 72 | widgetsnbextension==3.4.2 73 | -------------------------------------------------------------------------------- /content/feedEk.md: -------------------------------------------------------------------------------- 1 | Title: FeedEk 2 | date: 2016-12-29 3 | Slug: FeedEk 4 | Category: Blog 5 | Tags: visualization 6 | Authors: Kyle Cranmer 7 | JavaScripts: https://code.jquery.com/jquery-1.9.1.min.js, FeedEk.js, FeedEk.min.js, test-FeedEk.js, test-FeedEk-minimal.js 8 | Stylesheets: FeedEk.css 9 | 10 | 11 | I've been a bit annoyed with [feed.mikle.com](https://feed.mikle.com/), the RSS feed widget I'm using on my homepage. 12 | Sometimes it doesn't update, and while it is convenient, I can't modify the code to be able to tweak it. In particular, 13 | I'd like to get mathjax to work on the titles of the papers. 14 | 15 | I was looking around earlier, and I found [FeedEK](http://jquery-plugins.net/FeedEK/FeedEK.html), which looks pretty nice. 16 | Now that I've enabled [pelican_javascript](https://github.com/mortada/pelican_javascript), it's pretty easy. I did this first for the [Collaboration Map](/2016/12/collaboration-map/) and this time it only took me about five minutes to add the [javascript](https://github.com/cranmer/TheoryAndPractice/tree/master/content/js) and [css](https://github.com/cranmer/TheoryAndPractice/tree/master/content/css). I'm pointing the feed to my INSPIRE profile: `http://inspirehep.net/rss?ln=en&p=a%3AK.S.Cranmer.1`. 17 | 18 | All I had to do in my markdown/html was add 19 | 20 | ```html 21 |
    22 | ``` 23 | 24 | 25 | I'm still not sure how to get mathjax to render the LaTeX, but it seems more plausible now. 26 | 27 | ### Here's the minimal feed: 28 | 29 | - - - 30 | 31 |
    32 | 33 | ### Here's the detailed feed: 34 | 35 | - - - 36 | 37 |
    38 | -------------------------------------------------------------------------------- /content/thebe.md: -------------------------------------------------------------------------------- 1 | Title: Testing interactive blog post 2 | date: 2016-01-18 3 | Slug: Testing interactive blog post! 4 | Category: Blog 5 | Tags: physics, machine learning, statistics 6 | Authors: Kyle Cranmer 7 | 8 | Recently I've been learning more about docker and all the things it can do for us. 9 | My student Lukas Heinrich has been working on the [Recast](http://recast.perimeterinstitute.ca) 10 | project and using docker heavily. In parallel, [Tim Head](http://betatim.github.io/) and I have 11 | been talking a lot about projects like [binder](http://mybinder.org) and [everware](http://everware.xyz), 12 | which let you run Jupyter notebooks in a GitHub repository with custom requirements encapsulated in 13 | a docker image. 14 | 15 | Most recently, Tim had [this awesome blog post](http://betatim.github.io/posts/really-interactive-posts/) 16 | on interactive blog posts using static html. It's all powered via [`thebe`](https://github.com/oreillymedia/thebe). 17 | 18 | I want to turn this example into one that uses a custom docker image that has [george](http://dan.iel.fm/george/current/) 19 | installed, but so far I've not been successful with that. So just so I can feel like I've accomplished something, 20 | here's an example from a recent blog post on [Hotelling's experiment](/2014/04/Hotelling-Experiment/). 21 | The point here is that you have a static blog post that you can execute (and modify). 22 | The last cell uses python2.7 syntax for the `print` statements in a python3 session, so it won't work. 23 | But you can edit it accoridngly (comment out or change to `print(...)`. 24 | 25 | Have fun, now let's embed the interactive notebook: 26 | 27 | - - - 28 | 29 | {% thebe HotellingsExperiment.ipynb %} 30 | 31 | 32 | -------------------------------------------------------------------------------- /fabfile.py: -------------------------------------------------------------------------------- 1 | from fabric.api import * 2 | import fabric.contrib.project as project 3 | import os 4 | 5 | # Local path configuration (can be absolute or relative to fabfile) 6 | env.deploy_path = 'output' 7 | DEPLOY_PATH = env.deploy_path 8 | 9 | # Remote server configuration 10 | production = 'root@localhost:22' 11 | dest_path = '/var/www' 12 | 13 | # Rackspace Cloud Files configuration settings 14 | env.cloudfiles_username = 'my_rackspace_username' 15 | env.cloudfiles_api_key = 'my_rackspace_api_key' 16 | env.cloudfiles_container = 'my_cloudfiles_container' 17 | 18 | 19 | def clean(): 20 | if os.path.isdir(DEPLOY_PATH): 21 | local('rm -rf {deploy_path}'.format(**env)) 22 | local('mkdir {deploy_path}'.format(**env)) 23 | 24 | def build(): 25 | local('pelican -s pelicanconf.py') 26 | 27 | def rebuild(): 28 | clean() 29 | build() 30 | 31 | def regenerate(): 32 | local('pelican -r -s pelicanconf.py') 33 | 34 | def serve(): 35 | local('cd {deploy_path} && python -m SimpleHTTPServer'.format(**env)) 36 | 37 | def reserve(): 38 | build() 39 | serve() 40 | 41 | def preview(): 42 | local('pelican -s publishconf.py') 43 | 44 | def cf_upload(): 45 | rebuild() 46 | local('cd {deploy_path} && ' 47 | 'swift -v -A https://auth.api.rackspacecloud.com/v1.0 ' 48 | '-U {cloudfiles_username} ' 49 | '-K {cloudfiles_api_key} ' 50 | 'upload -c {cloudfiles_container} .'.format(**env)) 51 | 52 | @hosts(production) 53 | def publish(): 54 | local('pelican -s publishconf.py') 55 | project.rsync_project( 56 | remote_dir=dest_path, 57 | exclude=".DS_Store", 58 | local_dir=DEPLOY_PATH.rstrip('/') + '/', 59 | delete=True 60 | ) 61 | -------------------------------------------------------------------------------- /content/roofit-statistical-modeling-language-in-ipython-notebook-c2-b6.md: -------------------------------------------------------------------------------- 1 | Title: RooFit statistical modeling language demo in an IPython notebook 2 | Date: 2014-03-04 21:01 3 | Author: cranmer 4 | Category: Blog 5 | Tags: Data, python, Statistics 6 | Slug: roofit-statistical-modeling-language-in-ipython-notebook 7 | 8 | Particle physicisits primarily use [ROOT][] for the data analysis 9 | framework. Part of that framework is a package 10 | called [RooFit][] statistical modeling and fitting package. I have 11 | contributed to this package and added a layer on top 12 | called [RooStats][] that provides with statistical inference in both 13 | frequentist and Bayesian paradigms based on statistical models made with 14 | RooFit. These are the tools that were used to claim the discover the 15 | Higgs boson, and those [statistical models get pretty complicated][]. 16 | 17 | I created [a little IPython notebook](http://nbviewer.ipython.org/url/theoryandpractice.org/downloads/notebooks/BasicRooFitExample.ipynb?create=1) to demonstrate a simple example of RooFit's ability to create a statistical model, generate 18 | some simulated data, fit that data, create the profile likelihood, and 19 | provide a covariance matrix from the likelihood fit.  Enjoy! 20 | 21 | For convenience, here it is embeded 22 | - - - 23 | {% notebook downloads/notebooks/BasicRooFitExample.ipynb %} 24 | 25 | [ROOT]: http://root.cern.ch/ 26 | [RooFit]: http://root.cern.ch/drupal/content/users-guide#roofit 27 | [RooStats]: https://twiki.cern.ch/twiki/bin/view/RooStats/WebHome 28 | [statistical models get pretty complicated]: http://blogs.discovermagazine.com/cosmicvariance/2011/12/08/making-the-higgs-sausage/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+CosmicVariance+%28Cosmic+Variance%29#.UxFW0NyrvlI 29 | -------------------------------------------------------------------------------- /extra_header_minimal.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 91 | 92 | 135 | 136 | 137 | 156 | -------------------------------------------------------------------------------- /content/timeline.md: -------------------------------------------------------------------------------- 1 | Title: Creating a timeline 2 | date: 2020-12-23 3 | Slug: timeline 4 | Category: Blog 5 | Tags: website 6 | Authors: Kyle Cranmer 7 | Stylesheets: timeline.css 8 | 9 | While updating this website, I considered migrating it to Sphinx based on [Chris Holdgraf's blog post](https://predictablynoisy.com/posts/2020/sphinx-blogging/) and my recent experience with JupyterBooks for [Statistics and Data Science for Physicists](http://theoryandpractice.org/stats-ds-book/intro.html). Chris has this nice [timeline](https://predictablynoisy.com/about/) on his about page. 10 | 11 | I'm not ready to migrate this website away from pelican, so I looked into making a timeline. I found this [list of CSS timelines](https://freefrontend.com/bootstrap-timelines/) and this one with a [horizontal timeline](https://bootsnipp.com/snippets/a3BjR). I'm just copy-pasting that code into this blog post and the CSS in timeline.css which I can include with `Stylesheets: timeline.css` at the top of the markdown for this post. Let's see... 12 | 13 | Well it works, but I needed to remove `class="container"` from the surrounding `
    ` or it spilled out over the navigation on the right. Cool! 14 | 15 | **Update** In the vertical timeline at the bottom I experimented with adding altmetric embeds in the timeline. 16 | 17 |
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      Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC

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      September 2012

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      Observing Ultra-High Energy Cosmic Rays with Smartphones

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      June 2016

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