Lab communication

Overall, it’s important to ask for help. We try to follow the advice from the you must try, and then you must ask blog post. Also try to ask in a Slack channel where others might be able to benefit from your answers in the future. If enough people ask about something, we’ll try to write a blog post as advised here by David Robinson.

GitHub

• LieberInstitute is our GitHub organization account. After you’ve made your GitHub account let Andrew E Jaffe or Leonardo Collado-Torres know about your username through Slack so they can add you to our team.
• GitHub issues are a useful way to specify tasks for a given project. As an example, check the libdRSE project.
• git to know git: an 8 minute introduction LIBD rstats blog post by Amy Peterson.
• Happy Git and GitHub for the useR book by Jenny Bryan, Jim Hester and other TAs.
• Videos by Jacob Fiksel on how to use Git for Windows and Mac.
• BFG Repo-Cleaner for fixing GitHub repositories that have data files (example, large files) that you want to delete from your history. Use the JHPCE LIBD module for bfg with module load bfg.
• Commit together with co-authors such that everyone gets recognized GitHub activity for joint work.
• Closing issues using keywords in commit messages.
• Merging a pull request. Also check this comment by Yihui Xie on how to best submit pull requests. Yihui Xie wrote two blog posts related to that particular series of pull requests here.
• Syncing a fork.
• How can I undo git reset –hard HEAD~1?.
• Contributing to the LIBD rstats club blog post if you want to write another LIBD rstats blog post or use blogdown.

Slack

• We have multiple Slack workspaces, though the main one we use is the JHU Genomics Slack. Ask Andrew E Jaffe or Leonardo Collado-Torres to add you to that slack workspace. Our main lab channel is #jaffe_lab_group.
• Using Slack for Academic Departmental Communication blog post written by Leo and Stephanie Hicks.
• Preferably ask questions on a project channel such that others involved in the project are able to contribute answers. If it’s a more general question, try asking in the #jaffe_lab_group channel. Beyond our lab, you might want to ask for R help at #rstats and JHPCE help at #jhpce. You might also want to check out #jobs, #jhu_papers, #general, #funding, #diversity, #conferences, #random, #langmead_rss.
• For a new project, create a private channel with the prefix jaffe_ or libd_ then invite the lab members who are working on the project or might be able to help.
• To integrate a GitHub repository with a Slack channel type in the channel the command /github subscribe LieberInstitute/RepoName.
• Slack supports Markdown syntax for your messages, in particular we use a lot the backtick for inline code and the code chunk syntax for multi-line code. Examples:

   `inline code` example
    
    ```
    multi
    line
    code
    example
    ```

renders into:

inline code example

multi
line
code
example

Lab calendar

• We have a Google lab calendar. Ask Emily E Burke or Leonardo Collado-Torres via Slack to add you to the calendar with your Google account email address (could be your libd one or could be a gmail account). The calendar is linked to the #jaffe_lab_group Slack channel and sends reminders to that channel 30 minutes before an event happens.

Twitter

• Tackling Twitter as a Graduate Student blog post by Brianna Barry.