Tools, tips, & resources compiled by fellows of the MIT Biological Engineering Communication Lab
Below is a list of resources compiled for BE Communication Lab fellows relevant to undergraduate, graduate students, and postdocs at MIT. Although there are some MIT-specific resources, this list is also relevant to any STEM student/researcher.
The MIT BE Communication Lab resources are also stored within this repository and are highlighted within the list below. If you have any questions, email us at mitbecl@gmail.com.
This list compiles resources to transform data into a clear message through:
- data analysis and visualization,
- figure design,
- writing and reference management,
- design tools and resources,
- professional resources.
It also includes resources for reproducibility and miscellaneous tools for biological engineering research (e.g. plasmid design, flow cytometry analysis, next-generation sequencing).
- Legend
- Computing
- Data Visualization
- Reproducible Analysis
- Writing
- Figures
- Design Tools & Resources
- Poster Design
- Scientific Software
- Unsorted Weblinks
- Professional Resources
- Miscellaneous & Unsorted
- License
| Symbol | Meaning |
|---|---|
| 🆓 | no upfront cost |
| 🔓 | open source |
| 💵 | small cost |
| 💰 | large cost |
| 📦 | Computing Package |
| 📚 | Resource |
Students typical use the follow resources to analyze and plot data for class and research purposes.
-
Python 🆓 🔓 – general applicability, open-source; commonly used with Anaconda, a package and environment manager
-
R 🆓 🔓 - popular for bioinformatics, genomics, statistics; typically used with RStudio 🆓 using packages from CRAN
- RStudio introduction to R - a good place to start for complete beginners.
- Swirl teaches R within RStudio. A great interactive resource for beginners.
-
MATLAB 💰 - commercial computing environment offered at MIT for affiliates. See Gnu Octave for an open source 🔓 alternative.
-
Other computing languages/platforms used include Julia and Go, but their user bases are much smaller.
Computing clusters are available at MIT and affiliate institutions for use by students and non-affiliates.
-
Athena – computing environment offering remote environments with pre-installed software and file storage
-
TIG - CSAIL group offering computing services
-
AWS, Google Cloud, Microsoft Azure - commercially available services simple to setup with researcher funds
-
C3DDB - Boston-wide resource for life science researchers
-
Koch Institute Bioinformatics & Computing Core - offers a variety of cloud computing resources
-
McGovern Institute Core - Linux-based cluster offering storage and CPU/GPU performance
-
Other institutes (e.g. Broad Institute) and groups offer internal computing resources, inquire directly to gain access
- Trees, Maps, and Theorems: Effective Communication for Rational Minds by Jean-Luc Doumont - The CommLab Bible
- http://serialmentor.com/dataviz/
- https://datavizcatalogue.com/
- http://www.cookbook-r.com/Graphs/
- https://python-graph-gallery.com/
- https://www.data-to-viz.com/
- Grammar of Graphics📚💰 - landmark book on foundations in data visualization
- Plotting One Variable Distributions - BECL-produced resource for plotting bar graphs, boxplots, violin plots, and more. Includes example data set and raw code files.
- matplotlib – the most popular plotting framework
- Pandas - table management
- bokeh – interactive web-based visualization
- seaborn – opinionated plotting framework for statistical visualizations
- plotly – interactive web-based visualization
- altair – straightforward visualization framework, biased towards statistical plotting
- Rpy2 - use R code in jupyter notebook
- BECL notes - BECL-produced resource for python related plotting and getting started.
This is an opinionated summary of key tools for plotting in R, focusing primarily on the tidyverse group of packages📦.
- ggplot2📦🔓 – the most popular plotting framework based on the book, Grammar of Graphics
- plotly📦🔓 – commercially supported interactive web-based visualization tools
- Shiny📦🔓 – interactive charts and applications on the web, great for displaying public data and generating publication website
- reticulate📦🔓 - interface with Python via R
- ggplot2 Cheatsheet sheet📚 - quick overview of ggplot2 plotting functions and aesthetics
- ggplot2 Tutorial📚 - Harvard tutorial on getting started with ggplot2
- R Graph Gallery📚 - gallery of plots generated using R
- R for Data Science📚 - a comprehensive resource to become proficient at using R for all data science needs, written by lead instructors at RStudio
- RAW – fast, easy graphs from Excel or CSV files
- Graphpad Prism – stand-alone plotting program
- Excel – the one and only
- Datawrapper – fast, easy graphs from Excel or CSV files
- Octave – Free version MATLAB
- WebPlotDigitiazer
- Naming files and projects 📓, a slide deck compiled by Jenny Bryan (@JennyBryan), software engineer at RStudio
- drake 📦 – toolkit to build reproducible workflows that scale
- rapport
- knitr - allows to convert markdown, R, and plots/tables to html or PDF files, similar to Jupyter for python
- workflowr
- here - makes it easy for users to set directories and paths
- ROpenSci
- Pandoc - for switching between .doc/.tex/.md/etc file types
- Microsoft Word
- Adobe Illustrator 💰
- Inkscape 🆓 🔓
- Microsoft Powerpoint 💩
- Affinity Designer 💵
- BioRender 🆓
- Adobe Photoshop 💰
- Affinity Designer 💵
- GIMP 🆓 🔓 The GNU Image Manipulation Program
- ImageJ/Fiji 🆓 🔓
- ColorBrewer - web-based color palette tool with accessibility options (R package)
- Palettable - similar to ColorBrewer with customizable color schemes (Python package)
- Adobe Color CC - select color schemes based on color wheel and color harmony
- Ggsci - color themes inspired by scientific journals, science fiction, and media
- Viz-Palette
- GenZ Yellow
- Millenial Pink
- Butterick’s Practical Typography - typography best practices
- Google Fonts - select from fonts based on characteristics
- Canva - font combinations based on starter font
- Font Squirrel - downloadable fonts based on characteristics
- Neue Haas Grotesk
- Noun Project - downloadable icons
- IcoMoon - more icons
- Unsplash - downloadable high-quality images
- Adobe Illustrator 💰
- Inkscape
- Microsoft Powerpoint 💩
- Adobe InDesign 💰
- Horizontal and Vertical Microsoft PowerPoint and Adobe Illustrator Poster Templates 🆓 📚 - by Tyler Toth and Alex Triassi. Takeaway: white-space friendly poster templates to get you started
- Chemical Structures
- Analytical Chemistry
- Protein Structure Visualization
- Plasmid Editors
- Flow Cytometry
- Microscopy Analysis
- BLAST
- TCoffee
- MPI Bioinformatics Toolkit
- HMMER
- ClustalOmega
- GSEA
- Weblogo
- Pfam
- Espript
- Primer3
- Ensembl
- Github Personal Webpage Boilerplate
- PhD/Post-Doctoral website examples
- https://jef.works/ (Harvard, Bioinformatics)
- https://www.nikhitasingh.com/ (MIT Media Lab, AI)
- https://davidlazar.org/ (MIT CSAIL, Computing)
- https://www.anishathalye.com/ (MIT CSAIL, Computing)
- https://slowkow.com/ (Harvard, Immunogenomics)
To the extent possible under law, MIT BECL has waived all copyright and related or neighboring rights to the compilation of this list, but not the resources included.