Coding practices
The BE Communication Lab has resources on Best Practices for Coding, Organization, and Documentation, which include:
- A discussion of Coding Mindsets
- A guide to Coding and Comment Style
- A primer on File Structure
MIT computing resources
- MIT BioMicro Center computing resources: the Center provides a variety of resources and services to members of the Biology and BE departments, as well as the Koch Institute and the Center for Environmental and Health Sciences. These include recurring workshops on various topics and tools in computational biology, informatics consultations, servers and data storage, and computing power through the rous.mit.edu Linux cluster.
- Broad Institute Technology Services: provides members with any kind of Broad Institute affiliation with recurring workshops on various topics and tools in computational biology, informatics consultations, servers and data storage, and computing power through the UGER Linux cluster.
- MIT Athena computing environment: besides administering MIT computers, provides personal and group file storage.
- Scripts@MIT: a hosting service for the MIT community that provides several popular web packages such as MediaWiki and WordPress, as well as CGI script, MySQL, cron, and procmail hosting.
- MIT Information Systems and Technology: provides software licenses, mit.edu domains, and much more for the MIT community
- MIT Student Information Processing Board: volunteer student computing group, improving computing at MIT since 1969. Provides “unofficial computing help”, loans machines, and maintains multiple services (such as scripts, above).
Language-specific resources
Python
- A bioengineer’s guide to Python provides BE specific info on installing Python, helpful libraries, and other tips.
- Anaconda is probably the best way of installing Python, along with multiple standard libraries and tools used in scientific computing such as numpy, pandas, sklearn, and Jupyter Notebooks.
- An introduction to Python bootcamp exercise was prepared for the Fall 2019 20.420 by Pablo Cárdenas, Miranda Dawson, and Eli Karvelis.
- Introduction to virtual environments provides an introduction to virtual environments, including what they are and how to use them in BE.
- Rosalind.info offers introductory Python lessons and a number of learning exercises geared specifically for bioinformatics and sequence processing.
R
- RStudio is an excellent integrated development environment commonly used for R programming.
- Prof. Rafael Irizarry (JHU) has compiled a useful list of R and statistics courses available online.
Matlab
- MathWorks Support provides all the documentation and a number of tutorials for their tools, including MATLAB and SimuLink.