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 will be presented yearly during IAP/Summer, and resources will be posted here for reference.


Core lab techniques
-------------------

The following are core topics/techniques used in our lab. Many are linked to the slides for the related training session presented 
during IAP 2024.

- `Molecular cloning <https://mitprod.sharepoint.com/:p:/s/GallowayLab/Eehgciq7JzBFn5S0vGZUpCMBsDBGGA4oHPRlX-wvp0IvFw?e=Fde0ZN>`_
- `Mammalian tissue culture <https://mitprod.sharepoint.com/:p:/s/GallowayLab/EZjhWeH-7NRMpHRy8ZdRkE0BvXQ-JOLNJrMfQPxkxwGtOQ?e=pIYlc9>`_
- `Flow cytometry <https://mitprod.sharepoint.com/:p:/s/GallowayLab/Eb6G0dIX5KpLsG1VOLnO9LQB_0yeln_pMnWWWJosOLM5Cg?e=EAAegk>`_
- `Staining and microscopy <https://mitprod.sharepoint.com/:p:/s/GallowayLab/EUmJn0mO1u5FtdCN8u__nBcBuIuvxQxImrUqLOyDxD1LuA?e=g6QD6w>`_
- `Cellular reprogramming <https://mitprod.sharepoint.com/:p:/s/GallowayLab/EQKCUQmj0RNEgr4b1_AVcU4B7MuctnpcJjea-ydXGFGKyw?e=53qAnA>`_
- Genomics


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 a new repository
- :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 
  (`example Jupyter notebook <https://mitprod.sharepoint.com/:u:/s/GallowayLab/Eb7vePShSf1LnHSx13u437YBVE3lMgArRT_wQbcYaDyiPg?e=Ci0kyM>`_ 
  from IAP 2024)
- Introduction to gene expression modeling (:doc:`set of undergrad trainings <../ode_training/index>` from Summer 2021)
- Using the MIT Supercloud (high-performance computing cluster, `tutorial <https://learn.llx.edly.io/course/practical-hpc/>`_)


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 topics. The :doc:`"How to" training series <../training/index>` was presented in Summer 2021 and Summer 2023 to undergraduates 
(and other interested lab members). Additionally, Katie has put together a :doc:`Writing Guide <../../writing_guide/index>` relevant for academic 
writing at all levels (papers, proposals, etc.). 

To produce high-quality, informative graphics, the lab mainly uses Adobe Illustrator. Check out the 
:ref:`Bootcamp Day 0 section <graphics>` for instructions on setting up the software. This `YouTube video <https://www.youtube.com/watch?v=3IuoK07YDds>`_ 
offers a basic tutorial to many of the features relevant for scientific graphics, and the best way to learn how to use Illustrator is by making graphics 
of your own!

Journal clubs are another essential piece 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>`_. Additionally, 
during IAP 2024, lab members will present a series of journal clubs on all papers and review articles published by the lab (*more 
information to be added IAP 2024*). For a complete list of lab papers, see the `lab website <https://gallowaylab.mit.edu/publications/>`_ 
or Katie's `Google Scholar profile <https://scholar.google.com/citations?user=boemvUgAAAAJ&hl=en>`_.