Graim Lab

Resources

Useful links, etc

TODO Charles Darwin And The Terrible, Horrible, No Good, Very Bad Day

I guess everybody, even the smartest people who ever lived, have days when they feel dumb — really, really dumb. Oct. 1, 1861, was that kind of day for Charles Darwin.

TODO PLoS Collection 10 Simple Rules

A quick, concentrated guides for mastering some of the professional challenges research scientists face in their careers.

Reading and writing papers

TODO Manuscript writing advice

How small changes to a paper can help to smooth the review process.

TODO The Science of Scientific Writing

A guide to revising/improving your scientific writing.

TODO How to read a scientific article

Efficient Reading of Papers in Science and Technology.

TODO Ten simple rules for structuring papers

A short guide to writing scientific papers.

TODO Nature English Communication for Scientists

Nature guide to writing.

TODO NIH Clear Language Guide

This website consists of five sections and a checklist you can print. In each section, you will find a number of cards you can flip through to learn about using plain language in your work. When you are done with the final section, you can print a certificate of completion.

TODO Nature summary paragraph

Color-coded example of how to write an abstract.

TODO Latex equation editor

For when you really need a high quality image of your latex equation and don’t want to screenshot it.

TODO Latex symbol finder

When you can’t remember what the latex name is for a symbol, detexify has your back. It lets you draw the symbol and will show close matches.

TODO Latex table generator

An easy way to create beautiful latex tables.

TODO Scientific Writing Made Easy

A step-by-step guide to writing a scientific manuscript.

TODO How to read a paper

A 3 pass approach to reading journal articles.

Visualizations

TODO Designing an award-winning poster

Blog post describing good poster design principles.

TODO Fundamentals of Data Viz

A textbook and accompanying codebase on data visualization.

TODO Silhouette images

Free silhouette images of animals, plants, etc.

TODO Data To Viz

From Data to Viz leads you to the most appropriate graph for your data. It links to the code to build it and lists common caveats you should avoid.

TODO NIAID BioArt repository

Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, icons, and brushes is freely available within the public domain.

TODO Friends Dont Let Friends Make Bad Graphs

Chenxin Li’s guide to data visualization. Friends don’t let friends make certain types of data visualization - What are they and why are they bad.

TODO Visualization Workshop Slides

Slides from Dan Larremore and Sam Way’s workshop on data visualization.

TODO MatPlotLib Cheatsheets

Tips and cheatsheets by and for MatPlotLib.

TODO ColorHunt Palette Guide

A whole lot of color palettes.

TODO SuperPlots

We provide examples and practical tutorials for creating figures that communicate both the cell-level variability and the experimental reproducibility.

Coding

TODO Good enough practices in scientific computing

This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill.

TODO The Missing Semester of Your CS Education

Learning the command line, data management, and other important CS skills that you may not have learned yet.

TODO Alexs Lemonade Stand Training Modules

This repository is a collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.

TODO Bash tutorials

An introduction to bash scripting.

TODO Data Carpentry Genomics Workshop

This workshop teaches data management and analysis for genomics research.

TODO What they forgot to teach you about R

This book focuses on content intrinsically related to the infrastructure surrounding data analysis in R, but does not delve into the data analysis itself.

TODO DIY.transcriptomics

Best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies.

TODO CCDL Workshop Materials

Workshop materials from the Childhood Cancer Data Lab.

TODO Current Topics in Bioinformatics workshops

Tutorials by the Harvard Chang bioinformatics core.

TODO Posit R snippets

A collection of R code snippets and instructions featuring up-to-date best practices for coding in R

TODO NCI Bioinformatics Training & Education Program

Enabling scientists to understand and analyze their own experimental data by providing instruction and training in bioinformatics software, databases, analyses techniques, and emerging technologies.

TODO scRNA Best Practices Python

This book aims to guide both beginners and experienced professionals in best practices of single-cell sequencing analysis.

TODO scRNA Best Practices Bioconductor

This book will show you how to make use of cutting-edge Bioconductor tools to process, analyze, visualize, and explore scRNA-seq data.

TODO scRNA Best Practices Bioconductor

Tutorials from the 2025 epigenomics workshop.

AI and statistics

TODO Introduction to statistics (original R version)

A introductory book to statistical analysis using R.

TODO Introduction to statistics (python version)

A introductory book to statistical analysis using Python.

TODO Statistical vignette of the day

Interesting statistical anomalies and correlations.

TODO R EasyStats

A collection of R packages for easy statistics and models.

TODO The Elements of Statistical Learning

Recommended textbook on data mining, statistics, and predictive modeling.

TODO Monte Carlo simulations explained

A crash course on how to do Monte Carlo simulations and the basics of running code on a cluster.

TODO R for Data Science

Introduction to R coding for data science applications.

TODO Google Machine Learning Education

Learn to build ML products with Google’s Machine Learning Courses.

TODO Statistical test flowchart

A flowchart to help select which statistical should be used in a variety of common scenarios.

TODO GraphPad Principles of Statistics

The first half of this Guide reviews general principles of statistics, and is not at all specific to GraphPad Prism.

TODO Common statistical tests are linear models

Shows the linear models underlying common parametric and non-parametric tests.

TODO Empowering statistical methods for cellular and molecular biologists

Pollard, Pollard, and Pollard provide guidelines for using statistical methods to analyze the types of experiments reported in cellular and molecular biology journals.

More

TODO Seven year postdoc

The Awesomest 7-Year Postdoc or: How I Learned to Stop Worrying and Love the Tenure-Track Faculty Life

TODO Gender bias calculator

Tool for identifying gendered language in job ads and letters of ref.

TODO Ten simple rules for attending your first conference

Ten simple rules for attending your first conference.

TODO How to schedule a committee meeting

Claus Wilke’s guide to getting 5 faculty into a room at the same time to listen to your annual research update.

TODO UF Graduate School Planning Resources

IDP, roadmap, and other resources for UF graduate students.