Cobey Lab
Preface
1
Why we work
2
How we work
2.1
Principles
2.2
Work hours
2.3
Workspace
2.4
Communication
2.5
Weekly check-ins
2.6
Lab meetings
2.7
Daily “Standup”
2.8
Reproducible research
3
Performance
3.1
Reviews
3.2
My commitments
3.3
Basic expectations
3.4
Graduate researchers
3.5
Postdoctoral researchers
4
So you wanna…
4.1
Join the lab
4.2
Do some research
4.3
Code well and efficiently
4.4
Write good
4.4.1
General advice
4.4.2
Initial submissions
4.4.3
“Mature” papers
4.5
Email like a pro
4.6
Make nice figures
4.7
Keep up with the literature
4.8
Get funded
4.9
See our funding
4.10
Review your peers
4.11
Have productive meetings
4.11.1
Research meetings
4.11.2
Seminar speakers
4.12
Book travel
4.13
Be happy doing research
4.13.1
Time management
4.13.2
Imposter syndrome
4.13.3
Mental health and medical problems
4.13.4
Unwelcome environment
4.14
Give a good talk
4.15
Interview someone
4.16
Contribute to the handbook
4.17
Win at conferences
4.18
Negotiate authorship
4.19
Engage with the public
5
Coding Handbook
5.1
Justification
5.2
Coding Culture
5.2.1
Cultural practices
5.3
Complexity
5.4
Why writing code is easier than reading it
5.4.1
Science and Software
5.5
Indirection, Abstraction, and Generalization
5.5.1
Example:
The Weasel Algorithm
5.6
Debugging
5.7
Functional Programming
5.8
Unit Testing
5.8.1
Limitations to Unit Tests
5.8.2
Testability
5.9
Modules and Modularity
5.10
Statistics and other Modeling
5.11
Guidelines for Writing Code
5.12
Standards
5.13
Lab Systems
5.13.1
Version Control
5.13.2
Midway
5.13.3
Running Jobs on Midway
5.13.4
SLURM tricks
5.13.5
Other Midway items to keep track of
6
Onboarding
References
Cobey Lab Handbook
References