# Welcome to the team!

###### tags: `spring 2022` `biomedical applications` `onboarding` `interns`

# The Team
To see the official list of PSC leadership and staff, click [here](https://www.psc.edu/staff-directory/).

For practical purposes, if you are reading this guide, you will be more than likely working with the best team at PSC, the [Biomedical Applications group](https://www.psc.edu/staff-directory/biomed-group/).

## Brain Image Library
* Alex Ropelewski (supervisor)
* Iván Cao-Berg (direct supervisor)
* Luke Tuite
* Arpit Garg

## HuBMAP
* Philip Blood (supervisor)
* Iván Cao-Berg (direct supervisor)
* Zishen Wen

## XSEDE/Bridges2
* Shawn Brown (supervisor)
* Iván Cao-Berg and Julian Urán (direct supervisors)
* Mason Kim

# Communications
For the duration of this internship you will be expected to communicate with your direct supervisor(s) electronically and work remotely.

There might be opportunities to meet in person for meetings, however these are all constrained to limitations set in place by the university.

:::info
:bulb: In relation to the internship, you are not expected to come to the office or campus if you do not feel comfortable; independently of the restrictions setup by Carnegie Mellon.

For updates on COVID-19, click [here](https://www.cmu.edu/coronavirus/).
:::

## Electronic mail
Depending on the project you are going to be working on, an email in the PSC domain, e.g. `icaoberg AT psc DOT edu`, will be created for you for the duration of the internship. If granted, this account will be used to access resources at PSC like Bridges2, HuBMAP Hive or BIL. If not, then your Andrew ID will be used to access the latter resources.

You will be copied on certain e-mails to keep you in the loop on the projects you are working on. Please read them when posssible.

## Slack workspace
<img src="https://upload.wikimedia.org/wikipedia/commons/thumb/b/b9/Slack_Technologies_Logo.svg/498px-Slack_Technologies_Logo.svg.png" alt="drawing" width="25%"/></br>

You will receive an invitation to our Slack workspace. At the very least, you will be included in the `#biomed-interns` channel.

## Mailing lists
Depending on the project you are going to be working on, you might be included in some mailing list for the duration of the internship.

# Education
## Agile Development
[](https://dilbert.com/)

If you are not familiar with Agile development, then please follow these instructions.

* Visit [LinkedIn Education](https://www.cmu.edu/computing/services/it-professional/training/index.html) and login with your Andrew credentials.
* Search for the course *Agile Software Development: Scrum for Developers* by Shashi Shekhar.


You might also benefit from reading a little bit about [eXtreme programming](https://en.wikipedia.org/wiki/Extreme_programming). The Wikipedia entry should suffice.

### SCRUM
This explanation of [SCRUM](https://www.atlassian.com/agile/scrum) should suffice for now.

## Version Control
[](https://xkcd.com/)

If you are not familiar with version control, then please follow these instructions.

* Visit [LinkedIn Education](https://www.cmu.edu/computing/services/it-professional/training/index.html) and login with your Andrew credentials.
* Search for the course *Version Control for Everyone* by Joe Chellman.


### GitHub
There is a GitHub team page for PSC.

The address is [github.com/pscedu](https://github.com/pscedu). You will be added to the team when you start your internship.

## Continuous Integration
[](https://xkcd.com/)

For basic information about [continuous integration](https://en.wikipedia.org/wiki/Continuous_integration) the Wikipedia entry should suffice.

In practice -at least for the purpose of our team-, what we do is

* write, update, fix code,
* write and verify a test or battery of tests to justify the lines from the step above,
* document the steps above,
* integrate the change into the community branch -or some other branch-,
* repeat and reuse.

This is very naive explanation of the process, but simple enough to understand quickly.

### GitHub Actions for CI
To learn more about GitHub Actions read this [article](https://resources.github.com/devops/tools/automation/actions). For most projects you will work alogn a staff member building these integrations tests for your repository, so reading the article should suffice as an introduction.

## Style Guides

### Google Style Guides

For most projects we will use Google Style Guides because these are robust and well maintained.

* [Python](https://github.com/google/styleguide/blob/gh-pages/pyguide.md)
* [R](https://github.com/google/styleguide/blob/gh-pages/Rguide.md)
* [Shell](https://github.com/google/styleguide/blob/gh-pages/shellguide.md)

## Important Links

* [PSC site](http://www.psc.edu)
* [PSC GitHuB](https://github.com/pscedu/)
* [BIL GitHub]()
* [HuBMAP GitHub](https://github.com/hubmapconsortium/)

# Contributing to this guide

* Only full time developers or staff are allowed to contribute this repository.
* Student research programmers are allowed to contribute to this repository at the end of the experience to facilitate the experience of future interns.