Day 2+: Content-specific trainings
==================================

In addition to the required basic orientations to lab safety and organization (see :doc:`Day 0 <day_0_setup>` and 
:doc:`Day 1 <day_1_in-lab>`), 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.

- **Molecular cloning:** general introduction (`IAP 2026 <https://mitprod.sharepoint.com/:p:/s/GallowayLab/IQA3vVP3JP5qRbN9GfGuHvU5AQucMAOWycOwvut-UR7X58Y?e=wP9pvO>`__),
  modular Golden Gate assembly (`IAP 2026 <https://mitprod.sharepoint.com/:p:/s/GallowayLab/IQBd38tXyVq9Rbq7-FEZiAfFAejpTyzna_HolRxvQikgSnM?e=Oz6IFk>`__)
- **Mammalian tissue culture:** best practices (`IAP 2026 <https://mitprod.sharepoint.com/:p:/s/GallowayLab/IQAgKhXRx0uiRbabjPYw7oGoAbbs8CY8hp8k0VUlzglbLoY?e=ibijp5>`__),
  cellular reprogramming (`IAP 2025 <https://mitprod.sharepoint.com/:p:/s/GallowayLab/IQBaCEYrFtGLQ6yJTPeuPLW7Ac96vWqtTrysJUB5ZVYJj7s?e=isklZ4>`__)
- **Analytical methods:** flow cytometry (`IAP 2026 <https://mitprod.sharepoint.com/:p:/s/GallowayLab/IQDJKQU0ACzMRJkckaxWEIYqAU5IKlwLuSKH4XubMdEIawY?e=mFVYsc>`__),
  staining and microscopy (`IAP 2026 <https://mitprod.sharepoint.com/:p:/s/GallowayLab/IQCEeRxo0KawS41umxU04aSwAZSE4VzFF9gE_rbtAbGVuWE?e=0EGHPg>`__),
  genomics (:doc:`overview page </protocols/biochem_and_analytics/genomics_sequencing/index>`)


Computational skills
--------------------

General
*******

- Install :doc:`required software <day_0_setup>` and extensions
- :doc:`General software tips and tricks <software_tips_and_tricks>`
- Basics of the :doc:`command line <the_shell>`

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:

- :doc:`Introduction to Git <git_intro>`
- :doc:`Startup checklist <startup_checklist>` for working with Git repositories
- :doc:`Computational environment check <environment_check>` to confirm that you can edit Git repos
- :doc:`Contributor guide <../../contributor_guide>` for editing this protocol site

Data Analysis & Modeling
************************

- **Data analysis tips & common approaches:** see the :doc:`Data Analysis </training/data_analysis/index>` protocols pages, 
  example Jupyter notebooks in the ``example-training`` repo (`link <https://github.com/GallowayLabMIT/example-training>`__),
  and the user guide for the ``rushd`` Python package (`link <https://gallowaylabmit.github.io/rushd/en/main/index.html>`__)
- **Introduction to gene expression modeling:** set of undergrad trainings (:doc:`Summer 2021 </training/ode_training/index>`)
- **High-performance computing:** tutorial for the MIT Engaging cluster (`MIT ORCD <https://orcd-docs.mit.edu/getting-started/>`__)


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 :doc:`"How to" training series </training/how-to/index>` was presented in Summer 2021
(as well as `Summer 2023 <https://mitprod.sharepoint.com/:f:/s/GallowayLab/IgCabz3F-8ZcRYFgF9DnyesTAV1B3twaBrkUFYim1lpEET4?e=aBCbSF>`__ 
and `Summer 2026 <https://mitprod.sharepoint.com/:f:/s/GallowayLab/IgAyMVRnhvKLRoctjrUNiy3YAQfkMzEhhvXRH1zB3gEcWes?e=DAtb9g>`__), 
to undergraduates and other interested lab members. Additionally, Katie has put together a 
:doc:`Writing Guide <../../writing_guide/index>` 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:

  - :ref:`Section on Illustrator <graphics>` in the Onboarding Day 0 page for instructions on setting up the software
  - Illustrator `keyboard shortcuts list <https://mitprod.sharepoint.com/:w:/s/GallowayLab/IQAtam1dK9LiQqfk-UDpyb2bAS8J5FQOKeUqJ94R-dkRs9g?e=VHPmpM>`_ from Graphics & Illustrator training 
    (`IAP 2026 <https://mitprod.sharepoint.com/:f:/s/GallowayLab/IgBqnHBMeeqlTpF_21nT0mweAc7Il02msz5xrXOR2L_5pYA?e=dMaudu>`__)
  - A lab Illustrator tutorial, including slides and video demo (`Summer 2026 <https://mitprod.sharepoint.com/:f:/s/GallowayLab/IgACQyVA1uUKTrsu-DDLHkpfAa-AE8Xvjp6YwBt-zAGldEw?e=cMPzDC>`__)
  - `YouTube video <https://www.youtube.com/watch?v=3IuoK07YDds>`_ for a basic tutorial on many features relevant for scientific graphics

**Journal clubs** are an important component of reading and evaluating primary literature. Past lab journal club presentations are located 
in `this folder <https://mitprod.sharepoint.com/:f:/s/GallowayLab/Eugaj4o4lw5Egeyo9_lQmjIB8un7AnIkFoRDG5BQ0Btwaw?e=OQuJTU>`_. 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 <https://gallowaylab.mit.edu/publications/>`_ 
or Katie's `Google Scholar profile <https://scholar.google.com/citations?user=boemvUgAAAAJ&hl=en>`_.