Add reproducibility tutorial

README.md

@@ -1,27 +1,52 @@
 # Battle Lab Onboarding Guide
-Welcome to the lab!
 
-### Getting a MARCC account
-To get an account with MARCC, fill out an [account request form](https://www.marcc.jhu.edu/request-access/request-an-account/), and wait for PI approval
-Also check out the *[MARCC website](https://www.marcc.jhu.edu/getting-started/basic/)* and the MARCC folder
+Welcome to the lab! To get started, you should:
+
+- get added to the lab Slack workspace.
+- get added to the lab calendar and determine which meetings to attend.
+- get accounts to access our cloud computing and cluster computing resources.
+
+### Important names
+
+As of Fall 2023, four important names are:
+
+- Rebecca Keener and Josh Weinstock, research scientists. They are a great resource for any kind of problem-solving or planning.
+- Carmen Kiss is the admin for the Battle Lab and is the go-to person for scheduling.
+- Sarah Bailey is the admin for the CCB, handling CCB-wide matters such as Slack access and facilities issues. 
+
+### Slack 
+
+The lab uses Slack for most quick communication, so don't hesitate to direct message anyone in the lab with a question. For starters, ask someone to add you to the private lab channels:  
+
+- `#battle_lab_misc` - the lab's general channel   
+- `#battle_lab_trainee` - often used for MARCC questions  
+- `#battle_journal_club` - the lab has a journal club that usually runs the weeks we don't have joint group meeting  
+- `#battle_lab_random` - the lab's social channel
 
-We also recommend reviewing the [marcc_guide](marcc_guide) for tips on using MARCC, access to `battle-bigmem` etc.
-### Using Slack
 If you're new to Slack, you should download the app on your phone and desktop.  Once you're added to the JHU Genomics Collective Slack group, here's a few public channels to join:  
+
 - `#general` and `#random` (automatically added)  
 - `#joint_group_meeting`  
 - `#jhu_papers`  
 - `#papers`  
 - `#ccb`  
-- `#ccb_students`  
+- `#ccb_students`
 
-The lab uses Slack for most quick communication, so don't hesitate to direct message anyone in the lab with a question.  For starters, ask someone (my username is jpopp) to add you to the private lab channels:  
-- `#battle_lab_misc` - the lab's general channel   
-- `#battle_lab_trainee` - often used for MARCC questions  
-- `#battle_journal_club` - the lab has a journal club that usually runs the weeks we don't have joint group meeting  
-- `#battle_lab_random` - the lab's social channel    
+### Cloud Computing
+
+Look for separate documentation in this repo. 
+
+### Getting a MARCC account
+
+**This is currently out of date: MARCC is out of service and we now use a cluster called Rockfish.**
+
+To get an account with MARCC, fill out an [account request form](https://www.marcc.jhu.edu/request-access/request-an-account/), and wait for PI approval
+Also check out the *[MARCC website](https://www.marcc.jhu.edu/getting-started/basic/)* and the MARCC folder
+
+We also recommend reviewing the [marcc_guide](marcc_guide) for tips on using MARCC, access to `battle-bigmem` etc.
 
 ### Get familiar with the research
-The [lab website](https://battlelab.jhu.edu/) has a *Publications* section that you can check out for a full list of the lab's previous work.  For a longer list of recommended papers in each of the lab's areas of interest, check out [this compiled list of relevant papers](https://docs.google.com/document/d/1mLs9rMtLIp2Xu4z7ChIIcp838jDdPdoYkHoynu_2NBY/edit).
+
+The [lab website](https://battlelab.jhu.edu/) has a *Publications* section that you can check out for a full list of the lab's previous work.  For a longer list of recommended papers in each of the lab's areas of interest, check out [this compiled list of relevant papers](https://docs.google.com/document/d/1mLs9rMtLIp2Xu4z7ChIIcp838jDdPdoYkHoynu_2NBY/edit).