Resources

Consider this a public bookmark bar. These are resources I've found useful or think might be one day.

Disclaimers: still in progress, definitely not comprehensive, links may not work, and in no particular order.

I welcome any additions, suggestions, or corrections! Feel free to create a pull request or send me an email.

I've found a good portion of this from links other folks have shared on Twitter. Thanks, y'all. Also a very big thank you to everyone who created the original content.

Python
R
GitHub
AMPL
Julia
Other languages
General coding
Math prog. software
Math prog. resources
Operations research-adjacent material
Data viz
Datasets
Communication
Healthcare
Jobs and summer schools
Funding
Teaching
Anti-racism
Blogs I like (and read occasionally)
Various advice
Eclectic

Python

Overview
- Whirlwind tour from @jakevdp
- Overview from @drvinceknight
- Scipy lecture notes
  - Getting started
- Targeted
  - Python for Mathematicians (drvincekinght)
  - Python for Epidemiologists (pzivich)
Free Textbooks
- Think Python by @AllenDowney, beginners guide, programming exp. not necessary
- Python Data Science Handbook by @jakevdp
- Intro to Machine Learning in Python by @amueller
- Bayesian Methods for Hackers (Pilon)
- Modeling and Simulation in Python by @AllenDowney, targeted towards intro undergrads
Community
- Slack channel to learn data science in Python
Overall tutorial
- Python Software Foundation
Topics/packages
- Pandas (data processing)
  - Beginner tutorial from @gjreda
  - Intermediate tutorial from @tomaugspurger
- Networks
  - Package: NetworkX
    - Tutorial: network analysis using humanities data
    - Tutorial: Chinese postman problem
    - Network simplex
  - Package: SNAP
    - Analysis of graphs and networks
    - Claims often faster and able to solve larger problems than NetworkX
- Simulation
  - Discrete-event
    - Package: SimPy
      - Google group
      - Book chapter by Barry Nelson
    - Package: Ciw (for open queueing networks)
  - Agent-based modeling
    - Package: Mesa, general purpose
      - Tutorial
    - Package: ABCE, economic modeling
- List of operations-research-related packages
- Optimization
  - Overview (Ted Ralphs)
  - Modeling languages
    - Package: gurobipy
      - Walk-through of building simple model
      - Walk-through of semi-complex model
      - Example models
        
        List
        
        Guided tour
    - Package: PuLP, linear programs
    - Package: Pyomo, all-purpose
      - How to run models
      - Example models
    - Package: Pysp, extends Pyomo for stochastic programming
  - Solvers & algorithms
    - Package: scipy.optimize
    - Package: CVXPY, convex opt
      - Short-course
    - Package: Optimist, SDDP in water systems
    - Package: PyBnB, parallel branch-and-bound
    - Package: StochOPy, stochastic optimization
    - Package: StOpt, stochastic control (written in C++, Python bindings)
    - Package: py-lapsolver, fast linear assignment problems
    - Package: munkres, Hungarian algorithm
    - Library: PyMaxFlow, Max flow/min cut
    - Package: PyPSA, power systems analysis
    - Package: PySCIPOpt
      - Book
  - Plot convex hull
  - Examples
    - Optimization tutorial (ekhoda)
    - TSP
      - Implement TSP, Video
      - A few algos tutorial (Norvig)
    - Genetic algo (Stoltz)
    - Facility location problems (SCIP)
- Dimensionality reduction
  - Package: umap, uniform manifold approx. and projection
- Game theory (source)
  - Software: Gambit
  - Package: Nashpy, 2-player games/compute equilibria, paper
  - Package: Axelrod, iterated prisoner's dilemma
  - Package: PyNFG, network form games
  - Library: lrslib, lrsnash can be used to compute Nash equilibria
  - Within SageMath, games: cooperative with finite players; matching; normal form with N players
- Math
  - SageMath textbook: Computational Mathematics with SageMath, Zimmermann et al.
- Machine learning
  - Flowchart, choosing the right estimator
  - Sklearn tutorial from @jakevdp
  - Checklist before releasing (Almeida)
- Statistics
  - Package: lifelines, survival analysis
- Supply chain
  - Package: Supplychainpy
- Webscraping
  - Tutorial (by Agarwal)
- Convert PDF to html
  - Package: PDFMiner, then can be used to parse
- Other fields
  - Package: CobraPy, biological network modeling - constraints/optimization
  - ChemE code, optimize process simulators
- Visualization / figures
  - Python Graph Gallery - lots of examples with code
  - Overview of plotting for exploratory analysis (Hopper)
  - Seaborn Examples
  - Altair
    - Example code, notebooks
    - Video tutorial from @jakevdp
  - R-style graphing
    - Package: plotnine
    - Package: ggplot
  - Funny
    - XKCD-style figures
Notebooks
- Package nbdime - version control with notebooks
- Reproducible data analysis, (videos, VanderPlas)
- "I don't like notebooks" (slides, Joel Grus)
- "I like notebooks: Response to Joel Grus" (slides, Hopper)
How to...
- Run code
- Set up
  - Add Python to PATH: medium post
  - Install packages that aren't available via conda: stackoverflow
  - Install TensorFlow: medium post
  - Manage/use environments:
    - conda docs
    - tutorial
- Export to file
  - Strings
  - Numpy array to txt
  - Numpy array to csv
- Write unit tests, SciPy
  - FIRST principle
What's a...
- Generator? stackoverflow
- pycache file? answer 1, answer 2
Humor
- xkcd 353
- xkcd 1987

R

Reference
- Free Textbooks
  - An Introduction to R
  - Hands-On Programming with R (Grolemund)
  - R for Data Science by @hadley and @garrettgman
    - Some solutions (Arnold)
  - R Programming for Data Science (Peng, 2019)
  - Advanced R (Wickham)
    - Some solutions (Grosser et al.)
  - R Packages (Wickham)
  - Text Mining with R by @juliasilge and @dgrtwo
  - Exploratory Data Analysis with R(Peng, 2016)
  - Efficient R Programming (Gillespie, Lovelace, 2016)
  - Functional programming and unit testing for data munging with R (Rodrigues, 2017)
  - R Markdown: The Definitive Guide (Xie et al., 2019)
- Cheat sheets
  - Base R
  - ggplot2: Two pages; Longer
  - Syntax comparison: base R vs. formula vs. tidyverse
- Styleguides
  - From Google
  - Tidyverse
- R Cookbook
Search engine for R help
Learn R
- Handbook - Intro to R for Decision Modelers (Pechlivanoglou et al)
- Seminar code - Intro to R seminar code (IDRE)
- Compilation of resources
  - Arnholt
- Courses & collection of tutorials
  - UC Business Analytics
  - Coding club, Univ. of Edinburgh
  - Stat 545, R course with many materials online
- Websites
  - R-bloggers
  - R FAQ on StackOverflow
  - R Weekly, new R resources every week
Communities/fora
- Tidy Tuesdays, a weekly data viz project
  - Package: TidyTuesdayR - to help download data
  - See results from each week: TidyTuesdayRocks (Grantham)
- Community to walk through R for Data Science book together
- R-Ladies community on Slack
- RStudio Community
Packages/topics
- Package: EpiModel
  - Short course resources, slides
  - Gallery of extensions
- dplyr
  - Joins
    - Cheatsheet (Stat 545)
    - Gifs of join types (gadenbuie)
  - Tutorials
- Bootstrapping
  - Package: slipper
  - Package: boot
    - How to use
- Package: reprex
  - Prep short bits of code (e.g., to post on StackOverflow)
- Webscraping
  - Tutorial by Watts, for journalists
  - Tutorial by Taback
- K-means
  - Tutorial, UC Business
- Package: sociome - access to social determinants of health data
- Stats
  - Package: precisely - estimate power size based on precision
Operations research
- Paper on using R for OR
- Website with resources
- Package: ompr - mixed-integer LPs
- Package: optplot - plot opt models
Simulation
- Microsimulation tutorial (Krijkamp et al.)
Statistics
- Summary
  - Package: summarytools, e.g., view(dfSummary(iris))
- Principal component analysis tutorial (Hayden)
- Survival analysis
  - Package: survival, base analysis
  - Package: survminer, improved visuals
    - Cheatsheet
  - Tutorial
Health economics
- Package: hesim, simulation
- Package: dampack, decision-analytic models
Math
- ODEs: Package: odin
Visualizations
- Examples - R Graph Gallery
- Create figures
  - Package: ggplot2
  - Package: ggpubr - wrapper around ggplot
    - Intended to be easier to create pub-ready figures
- Package: rvg - export figures to be editable in Powerpoint
- Package: magick, vignette - image processing
- Graphs and networks
  - Tutorial (Ognyanova)
  - Package: DiagrammeR
    - Example (Kalvelagen)
  - Package: Plotly
- Gantt charts
  - Package: GanttR
  - Other options
- Interactive timelines
  - Package: timevis
- Spatial data
  - Package: sf, simple features
- Maps
  - Package: ggmap
    - Using Stamen maps (Tay)
  - Package: urbnmapr, state and county
- Colors / themes
  - Color/fill/transparency in ggplot2 (tidyverse)
  - RColorBrewer
    - Explanation (by chelsea in R)
    - GUI to review options on a map
Markdown/reports
- Thesis template
- knitr html template
- Package: Tufte - in style of Tufte
How to...
- Set up
  - Update R, run in RGui, not RStudio
  - Have your code text you when done running
- Data
  - List factor levels
    - List all including those without observations - levels(), could also use droplevels()
    - Only list those with observations - unique() (Cai)
  - Add rows to dataframe
    - Use list() rather than c() if types are mixed
- Plot things
  - Axes
  - Plot all data in background on faceted ggplot2 figures
  - Change colors
  - Iteratively make plots
    - Using loops
    - Using purrr by @dpananos
  - Plot multiple figures
    - Faceting, must be same plot type
    - Package: cowplot (Claus Wilke)
      - Shared legends
    - Package: GridExtra - paneling ggplot figures
    - Function: Multiplot
    - If using base R
  - Drill-down figures, with plotly
  - Save high resolution figures
- Fit distributions
- Write an R package by @jtleek
What is...
- ::
- Pipe operator %>%
  - Short explanation from @hadley
  - Longer from DataCamp
- Environments, namespaces, etc. (Suraj Gupta)
Humor or fun
- Package: Cowsay, tutorial - make animals say funny things
- Excel 2003 themed figures
- Package: GeomMLBStadiums - draw baseball stadiums in ggplot2

GitHub

Beginner Tutorial
Guide to Git with R
Cheat sheets
Binder - Convert Jupyter notebooks to executables
How to...
- Install git
- Undo
- Save credentials (i.e., username/password)
- Exit git log (soln: type 'q')
- Revert to older version (use new branch)
- Repos
  - Clone a repo
  - Use cloned repo
- Manage branches
  - Merge
  - Delete
- Forking
  - Tutorial
- Deal with errors:
  - Local changes being overwritten
  - Unlink of file - essentially, had to close AMPL, then worked fine
What is...
- a bare repository?
- Travis CI?
Humor:
- xkcd 1597
- xkcd 1296

AMPL

Free textbook: AMPL (Fourer, Gay, and Kernighan)
Intro to AMPL Handout (Krishnamoorthy)
Help forum: Google group
Specifics
- Dynamic set definitions, e.g., AVAIL vs. AVAIL_all
- argmin
- Sampling discrete random variables from uniform distribution

Julia

How to use
Free textbooks
- Think Julia (Lauwens)
- Julia Programming for Operations Research (ver1) (Kwon, code)
Resource compilations
- Many resources (Julia site)
- Lists of packages related to different areas (svaksha) - click on the .md links to see
Fora
Videos
Operations research
- Optimization in Julia - nice summary of solvers at bottom of page
- Modeling languages
  - JuMP - general
  - Convex.jl - disciplined convex
- Solvers/algorithms
  - JuliaStochOpt
    - Including: discrete-time stochastic control
  - SDDP (stochastic dual dynamic prog); tutorials
  - SDDiP (SDDP with integer variables)
  - StructJuMP (2-stage stochastic programs)
  - DSP (stochastic mixed-integer)
  - Complementarity.jl (mixed-complementarity and math programs with equilibrium problems)
  - CLP - COIN-OR LP solver
  - L-shaped solver
- Specifics
  - Rolling horizon
Other math/CS
- Evaluate derivatives
- Differential equations
- Calculus
- Machine learning
  - Tutorial (JPUG)
- Game Theory
  - Tutorial
Plots
- Tutorial (JPUG)
- Tutorial (documentation)
- Formatting and style by backend
Performance
- Tips (from manual; from JPUG)
- Package: TimerOutputs.jl
- Package: BenchmarkTools.jl
Other
- OhMyREPL.jl (syntax highlighting in REPL)
- Parallel computing
  - Overview
  - Tutorial (García-Heredia)
  - parallel_computing.jl (Nassar)
  - Caching pool (odow)
  - Examples
    - Gurobi (odow)
    - [JuMP and Ipopt] (https://discourse.julialang.org/t/running-jump-using-ipopt-in-parallel/9167)
Package dev and workflow
- Create and register a package (attractivechaos)
- Create local package
- Workflow v1.0 (Engheim)
- Patching packages
  - Discourse answer 1 (sdewaele)
  - Discourse answer 2 (CameronBieganek)
- Unit testing
How to:
- Install a package the first time
- Install a specific version of a package (answered within the first section)
- Install a package from github (example)
- Suppress multiple Gurobi license messages - send environment to solver: v1
What is:
- The ! after a function name? answer

Other programming languages

SQL
- Sequel Pro - for Mac
MATLAB
- FAST - Stochastic dual dynamic programming (open-source)
- Optimization (paid)
- Global optimization (paid)

General coding / computation

Overview/best practices
- Overview (slides from @tommlogan)
- Best practices from @marcio-mourao
- Good enough practices (Wilson et al.)
- Best practices (Wilson et al.)
- Coding standards (EECS 280, UM)
Textbooks
- Compilation of free textbooks
- The Turing Way - reproducible data science
Courses
- System and Software Tools (slides)
- Intro to computing for computer scientists (lectures)
  - E.g., Linux, command line, version control, shells, scripting
- Computing for Social Sciences (slides, resources, etc.)
- Data Skills for Reproducible Science (notes, code)
- Software Carpentry ()many resources)
- Intro to Biomedical Data Science (materials)
Command line
- Bash
  - Shell commands
  - Reference manual
- Overview (William Shotts)
- Free textbook: The Linux Command Line (William Shotts)
- Intro (slides, UM CSCAR)
Linux
- Intro course (free online)
Remote computing
- SSH - aka Secure Shell (allows secure remote login even if network insecure)
  - PuTTy
- File transfer
  - WinSCP - Windows
  - Cyberduck - Mac/Windows
  - Large files: Globus
    - Basic version for research/education is free
- Cluster computing
  - PBS overview (batch scripting, 40min video)
  - Unixm
    - Book: The Unix Workbench (Kross)
    - Tutorial for beginners
    - vi commands
Text editors
- Atom
  - Keyboard shortcuts (nwinkler)
- Vim
  - Game to learn Vim: Vim Adventures
- Emacs
- Visual Studio Code
- Sublime
- Nano
Share code
- Carbon - nice formatting for screenshotting code
Parallel computing
- Intro (Barney)
Servers
- The introduction to servers I wish I'd had (Harriet)
What are/is...
- src vs. bin folders?
- the difference between statically and dynamically typed lanugages? stackoverflow; blogpost (From Python Conquers)
How to...
- Add environment variables/PATH

Math programming software

Overviews
- From Math Opt Society (Sept 2017)
- Convex MINLP solver comparison (Jun 2018)
- Benchmarks
  - Linear programs - simplex (Mittelmann)
Solvers
- Commercial
  - CPLEX (free for academics)
  - Gurobi (free for academics)
  - Xpress
  - MOSEK, especially SOCP, SDP
- Non-commercial
  - GLPK (LP, MIP)
  - SCIP (MIP, MINLP, constraint IP)
  - Bonmin (MINLP)
  - Couenne (Non-convex MINLP)
  - MAiNGO (MINLP)
  - NEOS:
    - Server
    - Guide
  - Concorde (TSP - traveling salesman)
  - OpenSolver - Excel add-in, extends standard Excel solver
  - Ipopt (nonlinear, local)
  - BiqBin (Binary quadratic)
  - DSP (Stochastic mixed-integer programs)
  - ECOS (Second-order conic programs), website
  - OSQP (Operator Splitting Quadratic Program)
  - Mini-CP (Constraint programming)
  - Dakota
  - Other code
    - Knapsack, incl COMBO algorithm (Pisinger)
- OR-Tools from Google
Modeling lanugages
- SolverStudio (free) - Excel add-on, useful when OpenSolver not big enough
- AMPL
- OPL
- LP add-on for Google sheets
- MiniZinc (Constraint modeling), docs
- Pyomo (Python)
- JuMP (Julia)
- Gravity (C++)
Application specific
- Facility location
  - SITATION
- Agent-based
  - NetLogo

Math programming resources

Textbooks available for free
- A First Course in Linear Optimization v3.0 by @jon77lee
- Decision Modeling (David M. Tulett, author-provided source) - optimization for undergrads
- Convex Optimization (Stephen Boyd and Lieven Vandenberghe)
- MOSEK Modeling Cookbook
  - Conic optimization, not specific to MOSEK solver
- Foundations and Methods of Stochastic Simulation (Barry Nelson)
- Intro to Applied Linear Algebra (Stephen Boyd and Lieven Vandenberghe)
- Myths and Counterexamples (Harvey Greenberg)
- Iterative Methods in Combinatorial Optimization (Lau et al., 2011)
Communities / forums
- Operations Research Stack Exchange
- No longer in use: OR Exchange
- Google groups
  - AMPL
  - Gurobi
  - AIMMS
  - Pyomo
- Stack Overflow
- Optimization Online (preprint site)
- IE faculty listserv, e.g., job postings, etc.
Overviews
- Glossary
- OR Notes (JE Beasley)
Models
- GAMS model library
Algorithms
- List/explanation from the folks at NEOS
Test sets/libraries
- Compilation: on OR.SE, on GitHub
- MIPLIB
- OR Library
- TSPLIB
- Networks (DIMACS)
- MINLP in AMPL
- VRP-REP - vehicle routing
  - Commonly used (per Laporte 2007): CMT, 1979, GWKC, 1998
- Facility location
  - Bilde-Krarup (Quite old - 1977)
Course resources
- Math Programming (generally)
  - Notes (Bertsimas, Fall 2009)
  - Large-scale opt: Slides (Vandenberghe, 2016)
  - Several courses (Mitchell)
  - Video tutorials (Sharkey, Nurre)
- Linear programming
  - Slides (Vanedenberghe, 2013)
- Combinatorial optimization
  - Lecture notes (Schrijver, 2017)
  - Lecture notes (Goemans, Spring 2004)
  - Notes (Chekuri, Spring 2010)
- Computational methods
  - Notes (Grimmer, Ding 2018)
- Convex Optimization
  - Lectures videos, Convex Opt I & II (Boyd, 2008)
  - Lecture videos (Bazzi, 2019)
  - Slides (Vandenberghe)
  - Slides (Vandenberghe, 2019)
  - Slides (Nedich)
  - Convex Opt II
    - Notes (Boyd and Luo, Fall 2003)
    - Slides, notes (Duchi)
    - Notes (Candes)
- Applied numerical computing
  - Slides, notes (Vandenberghe, 2018)
- Linear dynamical systems
  - Lecture videos (Boyd, 2008)
- Stochastic programming
  - Videos, slides (Papavasiliou)
  - Lecture notes (Shapiro, Dentcheva, Ruszczynski)
  - Readings (Powell, Fall 2017)
- Optimal Learning
  - Various materials (Powell)
- Opt for machine learning
  - Slides (Udell)
- SDP
  - Slides (Parrilo, Lall)
- Scheduling theory and applications
  - Slides and handouts (Shehadeh, 2018)
OR in practice
- Wagner Prize Videos (INFORMS)
Other
- IFORS Developing Countries page - a variety of open-source resources
- OR societies around the world
- COIN-OR Foundation
  - Resources
- INFORMS tutorials (videos)
Topics
- Benders Decomposition
  - Using callbacks to avoid rebuilding the scenario tree by @parubin
  - Examples:
    - In AMPL
    - With callbacks by @vitaut
- Decision diagrams for integer programming
  - Slides (van Hoeve)
- Disjunctive programming
  - Overview from GAMS
  - Video (Ruiz)
- Gradient descent
  - Intro Blogpost (Pigeon)
- MINLP (Mixed-integer nonlinear programming)
  - Overview (Grossmann)
  - Slides (Leyffer and Linderoth, in 2005)
- Nonlinear optimization
  - Slides (Biegler)
  - Short course slides (Wachter)
- Numerical issues
  - Gurobi guidelines
- SDP (Semidefinite programming)
  - Rendl 1, Rendl 2
- Subgradient methods
  - Notes (Boyd) - minimize convex function, non-differentable
- Supply chain
  - XSG game, overview - supply chain simulation game (Salman)
- Variables
  - Semicontinuous (post by Rubin, post by Kalvelagen)
  - Semi-integer (post by Kalvelagen)
How to...
- Linearize product of variables
- Linearize max/max/absolute value
- Linearize max(0,y) by @prubin73
- Incorporate a max in a constraint (Rubin, Contardo)
- Remember primal / dual conversion
  - Sensible-odd-bizarre (SOB) method, citing this paper

Operations research-adjacent material

Linear Algebra
- Videos
  - Intuitive overview (~2hrs, 3Blue1Brown)
  - Intro course lectures (Strang)
- Review and reference (handout, Kolter and Do)
- Intro to matrix algebra (handout, Carey)
- Course notes, exercises, book (Boyd and Vandenberghe)
Economics and game theory
- Game theory
  - Intro course lectures (Ben Polak)
  - Course slides (Nedich)
- Slides from several courses (Fernández-Villaverde)
  - Including: computational methods; tools; macro dynamics; graduate macro; macro uncertainty shocks; equil macro; global econ history; political econ of early America
Networks
- Free textbook: Networks, Crowds, and Markets (Easley, Kleinberg), intro undergrad
- List of resources (briatte)
- Bayes nets
  - Tutorial (Netica)
  - Intro slides (CMU)
Data Science
- How to get started
  - Blog post by @kierisi
  - Plan (Kross)
- Directory of materials (DataSciGuide)
- DataFramed podcast (DataCamp)
- Courses
  - Foundations of Data Science (video, slides, assignments, Berkeley)
    - Textbook (Adhikari, DeNero)
  - Applied data science (course readings from @hadley)
  - Intro to data ethics (course module, Shannon Vallor)
- Examples
  - Work habits and bicycles (VanderPlas)
Machine Learning
- Communities
  - Google group
  - CrossValidated, stackexchange
- Textbooks
  - Intro to Statistical Learning (James et al.)
  - Elements of Statistical Learning (Hastie, Tibshirani, Friedman) - more technical than James et al. book
  - Statistical Learning with Sparsity (Hastie, Tibshirani, Wainwright)
  - A Brief Intro to ML for Engineers (Simeone)
  - Fairness in ML (Barocas, Hardt, Narayanan) - book in progress
- Technical Notes - ML and AI from @chrisalbon
- ML flashcards from @chrisalbon
  - Scrape off Twitter for free (@Dpananos)
- Courses
  - Recordings, slides (@amueller)
  - Recordings, slides (Hastie, Tibshirani)
  - Course notes (Clayton Scott)
  - Notes, slides (Abernathy)
  - Learning with big messy data - Slides (Udell)
- Topics
  - How decision trees work (Rohrer)
  - Taxonomy of reproducibility
  - Monte Carlo tree search
  - Data leakage (Brownlee)
Deep learning
- Slides (EECS 498-598)
Compilations
- From Vodrahalli
- From Finlayson
Statistics
- Communities/forums
  - datamethods - health-related stats forum
  - Talk Stats
  - CrossValidated
- Books
  - Causal Inference (Hernan and Robins)
    - Notes about book (Finlayson)
    - DAGs from book (Finlayson)
  - Advanced Data Analysis from an Elementary Point of View (Shalizi)
- Glossary of Statistical Terms (Harrell)
- 10 rules to use stats (comp biology)
- Essential statistics with R (UVA)
- Document and avoid these problems (biostat)
- StatPrimer (Gerstman)
- Courses
  - Modern regression (Shalizi, notes)
  - Regression modeling strategies (Harrell)
    - Notes
    - 1 day overview
- Tests
  - What test should I use? (Examples in R, Stata, SAS, SPSS)
  - t-tests
- Specific topics
  - Relationships between univariate distributions (Leemis)
  - Odds ratios (Best practices; Norton, Dowd, Maciejewski, paywall)
  - Dirichlet processes (notes by @tdhopper)
  - Experimental design (warning signs, Norvig)
  - Survival analysis (overview, Grace-Martin)
- Same stats for different data
Biomedical data related
- Courses
  - Biomedical data science (Turner, notes)
  - Biostatistics for biomedical research (Harrell)
    - Videos
  - Clinical trials - design/analysis (Penn State, notes)
Probability
- Review (Maleki and Do)
Mathematics
- Primers (Kun)
- Notes (Conrad)
- Compilation of courses (Dhar)
- Boolean functions
  - Lecture videos (O'Donnell)
  - Free textbook: [Analysis of Boolean Functions] (http://www.contrib.andrew.cmu.edu/~ryanod/?page_id=2334) (O'Donnell)
Computer science
- FAQ about C
Ethics and social good
- Mechanism design for social good (Reading list)
- Ethics and policy in data science (syllabus)
Other
- Compilation of lots of resources for students (FrontBench)
- Blockchain overview (2 hr video)
- Gentle intro to graph theory (Joshi)
- Habits of highly mathematical people (Kun)

Data visualization

Free Textbooks
- Fundamentals of Data Visualization by @clauswilke
- Data Visualization: A Practical Introduction by @kjhealy
Course
- Data viz Videos, Ghodsi, U. Waterloo
Color
- Guide to using color (Rost)
- Color oracle - convert screen to what a color blind person would see
Networks
- Overview of software, etc., NC State
- Gephi
  - Tutorial - create citation network, NC State
- Example - citation network (Caren, using Python & d3.js)
- Graphviz (python)
  - Examples
  - Force-directed graph (json/html)
Community
- Data viz book club
  - On Twitter
Various
- Multiple views on how to choose a visualization (Franconeri, 2019)
- Ten simple rules for better figures (Rougier et al., 2014)

Datasets/databases

Note: health-related data is in this section
Search engine
Compilations
- Data.gov
- From Vanderbilt Biostats
- Kaggle
- Public datasets
- Google Public Data Explorer
- Datasets available via R packages
- Open/public datasets for machine learning
  - List 1 (Stanford)
  - List 2 (BigML)
- Network datasets
- Time series
  - From DataMarket
  - Economic (Fed Reserve)
- Good, small datasets (Vicki Boykis)
Specific sources
- Bureau of Labor Statistics, e.g., Consumer Price Index (inflation)
- US Census Bureau
- Pew Research Center: data and how to analyze
- Neighborhood atlas - disparities / deprivation work, perspective about (paywall?)
- FEMA Hazus
- FiveThirtyEight
  - List of available data, data, R package
- European statistics
- IMF
- WHO
- Quandl - financial / economic data - some are free
Literature

Communication/dissemination

Sharing data (guide by @jtleek)
Open-source: How to choose license
Manuscripts
- How to write
  - Your first paper (@jtleek, biostat)
  - 12 steps to writing
  - Writing a paper (Whitesides)
  - Healthcare-focused
    - Prep for a medical journal (Welch, 1999 paper)
    - Writing for Impact (Ibrahim and Dimick)
    - Policy papers in clinical journals (UM CHEAR)
    - Picking a journal
    - Reporting guidelines
- Run a "paper sprint"
- Staying organized
  - Publication planner (Pacheco-Vega)
- Types of reviews (Temple U) - Systematic, scoping, etc.
Visual abstracts
Policy
- How to use research to affect policy (Oxfam)
- Connect research to policy (Quinn)
- More than a press release (Frakt, Videos)
Working with the media
Writing for lay outlets
- For "The Conversation" (slides, Chang and Czuhajewski)
Writing help
- Lots of resources (Purdue)
Reference software
- Zotero
- Mendeley
- EndNote
LaTeX
- Getting started (Johnson, Code)
- Overview (Wilkins)
- Collaboration
  - ShareLaTeX
- Templates
  - Example for journals (Coelho)
  - Thesis templates:
    - From U Wolverhamptom
    - From Michigan
- Beamer tips and tricks (slides, source code, from @paulgp)
- Graphics
  - Tikz and PGF
- Indicating math mode
  - Using /( /) vs $
Writing a book
- Self-publishing (Kun)

Healthcare

Guides
- Healthcare Industry (largely UM students only)
- Health management and policy
- Finding health statistics
  - From UM
  - From Wisconsin-Madison
Datasets / databases
- Medicare Part B
  - National summary files
  - Carrier summary files
  - Not free: CCW
- CDC: data/stats
  - Chronic disease datasets
    - E.g., Maternal and child health
- Critical care database: MIMIC
- Other
- Major surveys
  - NHANES (in person)
  - BRFSS (phone, pronounced "Burfiss")
Methods
- Forums
  - datamethods - health-related stats forum
  - MedStats - google group
- Pharmacy concentration calcs
Newsletters
- CDC's Morbidity and Mortality Weekly Report

Jobs/Summer schools

Jobs
- Compilations
  - Companies that hire operations researchers; from @dirkschumacher
  - United Nations (UN) jobs from from @dirkschumacher
  - Humanitarian logistics orgs (GT CHHS)
  - Math-related (ORFE Princeton)
- Listservs/job boards
  - Inside Higher Ed
  - Academic Jobs Online
  - ChronicleVitae
  - Academic Keys
  - Times Higher Ed
  - California Community Colleges
  - Council for Christian Colleges and Universities
  - Infectious disease dynamics listserv
  - Minority postdoc
  - Twitter feeds with job postings
    - R job listings
    - Data science
- National labs
  - Sandia: fellowships/postdocs
  - National Renewable Energy Lab NREL
    - Director's Postdoc Fellowship
  - Oak Ridge
- Pathways to Science - internships, jobs, etc.
- How to build your portfolio (Harris)
- What can you do with a math degree? Videos - PICMATH
- Schools
  - Summer schools 2019 (Thiago Serra)
- Undergrads
  - MSRI-UP - summer math program for undergrads
  - Job search resources - BIG Math
Career prep
- Questions to think through career goals from @benlangmead
  - Slightly expanded from @jtleek
Academic job search
- OperationsAcademia.org - OR/MS job postings and advice
- University compilations
  - Univ. of Michigan; Berkeley; UPenn; Duke
- Materials checklist (UCSF)
- How to prep app materials (LinkLab, UVA)
- Research statement
  - How to write
    - Jim Austin; Karen Kelsky; UPenn; U. Wash; GSA (Geology); Duke; Med College of Wisc; Cornell
  - Samples
    - UCSF
- Teaching statement
  - Univ. of Michigan, UPenn
    - Guidelines for teaching at MIT
- Diversity statement
  - Univ. of Michigan; UCSD; UNL; Vanderbilt; Cincinnati
- Interviews
  - Overview on phone and on-site interviews (LinkLab, UVA)
  - Commonly asked questions (Vitae)
- Job talk
  - Article - giving an excellent talk (Carpenter, Waters)
  - Article - Tips for a Successful Job Talk (Aguilar)
  - Slides - How to Give a Seminar (Storesletten, econ)
  - Slides - How to present your job market paper (La Ferrara, econ)
- Videos
  - Duke postdoc services
- Articles
  - The hiring process from the other side (Berkeley)
- Example materials
  - From Philip Guo
- Advice
  - Navigating the OR/MS academic job process (Dutta, Çağlayan)

Twitter

Communities I appreciate
- #orms
- #rstats
- #phdchat
- #AcWri
- #scicomm
Hashtags that have included interesting discussions at some point
Other
- CV without Twitter (Auriel Fournier)

Various advice

Grad students
- Picking a PhD advisor (Langin, Science)
- For new grad students (Dorsa Amir)
- Guide to grad school (Adam Marcus, CS)
- Guidebook for succeeding in the PhD (Alex Eble, econ, another link)
- Succeeding in the PhD (Dredze, Wallach; computer science)
- One year to dissertation (McGowan, files)
- Advisor/PhD student dynamics (Nelson)
- For female grad students (political science, compiled by @dianazobrien)
- Attending big conferences (Kieran Healy, sociology)
- 10 tips to win at grad school (Toor)
- Compilations
  - The Professor Is In (Karen Kelsky) - blog with various academic advice
  - Many resources (Pacheco-Vega, polisci/georgraphy)
  - Doing research (Arinivas Akella, CS)
  - Grad school, technical writing, etc. (Mihir Bellare, CS)
Undergrads
- Undergrad in the Lab Blog
- Lots of advice (Pathways to Science)
- Applying to grad school (Klett & Lee)
- 10 rules of good studying (Oakley)
- 10 rules of bad studying (Oakley)
New faculty
- Compliation (Stanford)
- Compilation (Tang)
- The 7 Year Postdoc (Nagpal)
  - Counter thoughts
- Getting started (Whitaker)
- If the 3rd year review goes poorly (Albertson)
- Staying sane on the tenure track (Henderson)
- Faculty Mentoring Handbook (Arizona)
- Running a lab/research group
  - Ten simple rules towards healthier research labs (Maestre, 2019)
  - Making the Right Moves: A Practical Guide to Scientific Management (HHMI) - free book about managing a lab
- Advising students
  - Evaluating OR PhD students (Pasupathy, Hunter)
- Working with research assistants
  - Guidelines (Northwestern)
  - Hire and manage (MacKenzie)
- Mentoring
  - Compliation (AEA, econ)
Job search
- Academic search (Nagi)
- Data science jobs by @robinsones
- Vitae - database, advice, etc.
- Job market mistakes (humanities)
Various
- 8 tips for saying no by @APottegard
- The Pac-Man rule (Holscher) - always leave room for someone to join the group
- Econ prof's work style (Hal Varian)
- Chris Blattman's blog (econ prof, links on right-hand side)
- When your data science project doesn't work
- Blogs for female consultants/bus. travelers
- Business clothes for women (Stern)
- Imposter syndrome resources (Fournier)
- The importance of stupidity in scientific research (Schwartz, 2008)
Skills
- Reading papers
  - Reading papers by @jtleek
  - Technical papers (Nock)
- Writing lit reviews (Raul Pacheco-Vega)
- Organizing data in a spreadsheet (Broman and Woo, open access); not always the best idea, but some tips
- Reviewing papers
  - How to review a paper (Leek - biostat)
  - Being a good reviewer (DiDomenico et al., pharmacy)
- Writing production-level code (Pappakrishnan)
- How to report bugs effectively (Simon Tatham) - perhaps send to your users
- Debugging
  - Infeasible models (Kalvelagen)
  - Rubber ducky method - explain in detail to an inanimate object
  - Wolf-fence algorithm - basically binary search with fun description (original paper, paywall)

Eclectic

CV of failures
- Johannes Haushofer
- WaPo article
Grad school's "hidden curriculum" (Calarco)
Diversity
- Compilation of articles (AstroBetter - Equal Opportunity Astronomy)
Pay your undergrad researchers
- Paper about field techs (Fournier, Bond)
- Other blog posts cited within
Meta - list of "awesome" lists
Azimuth Project
- Collaboration of scientists and engineers who want to save the planet
Guide to Bad Data
- Github
- Article on Quartz
Technical / scientific debt from @dgrtwo
Types of validity (Amy Bucher)
Testing (Kehrer)
Various software
- Digitize it - Convert figure to (x,y) data
- draftable - Compare pdf files
- color oracle - convert screen to what a color blind person would see:
- Poll meeting availability
  - When2Meet
  - When is good
Word
- How to change the Normal template
Fun OR (or related) applications
- 2048 using MDPs from @jdleesmiller
- Chutes & Ladders as a Markov chain @jakevdp
- Mario Kart drivers - Pareto efficiency from @hinnefe2
- Text mining on country music lyrics (Miller)
OR/Programming/etc. in Industry
- Netflix
Examples
- Queueing (Kottke)
Algorithms
- 15 important algorithms (McFadden)
- 100 days of algorithms (Bouda), code
Beer game using AI
Websites
- (Free) Hosted by github
  - Tutorial (Carlos)
  - Themes
    - Simple one for academics
    - Template for labs
- (Free/Paid) Wix
- (Free) Google Sites
Icons - e.g., the Google Scholar logo
Download GoogleMaps to use offline
Math genealogy project
User interfaces
- Explaining UX to kindergartners (Singh)
- Terrible elevator control panels (Bartholdi)
Source code for Apollo 11: code
Humor
- Top 10 Illegitimate Proof Techniques (I think the original version of this list came from Dana Angluin)
- "The best way to write secure and reliable applications"
- Add coffee stains to your LaTeX files (Rein)
- Guide to interpreting faculty feedback
- Spurious correlations (Vigen)
  - Make your own
- Create parody O'Reilly book covers
- Improbable research
- Computer science research topic generator
- Gettysburg address via powerpoint (Norvig)

eltuck / Resources