About
We are from the Eisen (Mike) Lab.
The purpose of this group is to (1) meet regularly in order to not go crazy during quarentine times 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.
Current Schedule
Zoom: link
| Date | Time | Lead | Title |
|---|---|---|---|
| Thursday, June 11 | 10:30am | Ciera and Sam | Pipeline Generality |
| Tuesday, June 9 | 11:00am | Ciera | MS2 Pipeline in Python |
| Thursday, May 28 | 10:30am | Ciera | Approaching large Comp Projects |
| Thursday, May 21 | 10:30am | Colleen | HMM part 1 |
| Tuesday, May 19 | 11:00am | Colleen | HMM part 1 |
| Thursday, May 15 | 10:30am | Jenna | Protocol Standards |
| Thuesday, May 12 | 11:00am | All | Where to go next? |
| Thursday, May 7 | 10:30am | Jenna | Protocols and Collaborative Github |
| Tuesday, May 5 | 11:00am | Stadler | Python Classes tutorial |
| Thursday, April 30 | 11:00am | All | Python Classes cont |
| Tuesday, April 23 | 11:00am | All | Lets all learn about Python classes |
| Tuesday, April 21 | 11:00am | Colleen | Parsing GFF Files |
| Tuesday, April 16 | 11:00am | Group | Save for Savio |
| Tuesday, April 14 | 11:00am | Marc | Intro to Image Analysis - Wigets |
| Thursday, April 9 | 11:00am | Jenna | Savio Sign Up! |
| Tuesday, April 7 | 11:00am | Marc | Intro to Image Analysis Pt1 - Slices |
| Thursday, April 2 | 11:00am | Ciera | matplotlib Colors |
| Tuesday, March 31 | 12:00pm | Stadler | Intro to matplotlib |
| Monday, March 30 | 11:00am | Ciera | Making github hosted website Pt 2 |
| Thursday, March 26 | 11:00am | Jenna | Introduction to .czi files Pt 2 |
| Tuesday, March 24 | 12:00pm | Jenna | Introduction to .czi files Pt 1 |
| Monday, March 23 | 11:00am | Ciera | Making github hosted website |
Framework
- Meet 2-3 times a week at 11:00. For 1 hour chunks.
- Assign a leader and topic for the topic and they guide the hour
- Whatever is discussed for the hour will become 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)