Organization and Brainstorming
Welcome!
This first post is to hold the notes for discussing organization and brainstorming for the Eisen Lab Coding Club. The purpose of this group is to (1) Meet regularly in order to not go crazy and (2) Share computational knowlege. We choose to unify our learning under the theme of “Confocal Image Analysis with Python”, since we all use confocal data to some extent. We will frame the topics of our topics/lessons under this theme, but are open to other topics.
The main languages we are using is Python, with secondary focus on R. We will also likley introduce skills and concepts related to unix/bash, Matlab, html, and css.
See: Google Doc for collaboratively taking notes.
Framework
- Meet weekly? Tuesdays at 12:00.
- Assign a leader and topic for the week.
- This is the theme for the week and we can ask help from everyone based on the weeks topic through Eisen Lab Slack.
- The leader is resonsible for framing the weeks topics, presenting on Tuesday, and writing a summary for the website.
Topic Ideas
Skills
- Eisen lab base skills - Collaboratively make a List of baseline computational skills that for the lab (CM)
- Git
- Jupyter notebook
- markdown
- Python basics
- Within this, a starter-pack on processing MS2 datasets (VB)
- ssh
- programmatic dataframe handling
- Introduction to .csz files and meta data (Jenna)
- Phylogenetics (Marc)
- Branch distance, transcriptome, genomic sequence data
- Figure making → R and matplotlib
- html / github websitehtml / github website
- Evolution of transcription (Ashley)
- Introduction to automating in python
Projects
- Build a script that reads in Czi files and outputting a movie (Ciera, Ashley, Marc)
- Build and maintain a Eisen Lab Coding Club website
- Build a repository with figures/code
Interests
- Evolution of transcription (Ashley)
Other Projects
- Identifying IDRS from the genome? Proteome? (Mike)
- Simulating evolution of IDRs under neutral model