Day 2+: Content-specific trainings

In addition to the required basic orientations to lab safety and organization (see Day 0 and Day 1), the lab has put together trainings on topics directly related to our research. Many of these trainings are presented yearly during IAP/Summer, and resources from recent presentations are posted here for reference.

Core lab techniques

The following are core topics/techniques used in our lab. Many are linked to the slides for related training sessions.

Computational skills

General

Github

All lab code is stored on Github for version control and sharing. Check out the following protocols to learn the basics and refer back to as needed:

Data Analysis & Modeling

  • Data analysis tips & common approaches: see the Data Analysis protocols pages, example Jupyter notebooks in the example-training repo (link), and the user guide for the rushd Python package (link)

  • Introduction to gene expression modeling: set of undergrad trainings (Summer 2021)

  • High-performance computing: tutorial for the MIT Engaging cluster (MIT ORCD)

Research reading and writing

Reading literature, communicating your findings, and composing compelling visuals are key research skills to master. The lab has put together several trainings on these science communication topics. A “How to” training series was presented in Summer 2021 (as well as Summer 2023 and Summer 2026), to undergraduates and other interested lab members. Additionally, Katie has put together a Writing Guide relevant for academic writing in diverse forms (papers, proposals, etc.).

To produce high-quality, informative graphics, the lab mainly uses Adobe Illustrator. The best way to learn how to use Illustrator is by making graphics of your own! To get started, check out the following:

Journal clubs are an important component of reading and evaluating primary literature. Past lab journal club presentations are located in this folder. This includes several journal clubs on some of the lab’s papers and review articles (IAP 2024). For a complete list of papers from the lab, see the lab website or Katie’s Google Scholar profile.