diff --git a/README.md b/README.md index a6d25f9..7faa8d9 100644 --- a/README.md +++ b/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). diff --git a/reproducibility_tutorial.pptx b/reproducibility_tutorial.pptx new file mode 100644 index 0000000..7d63485 Binary files /dev/null and b/reproducibility_tutorial.pptx differ