TWIP Episode 01: We set goals

The excitement was less than papable but showing up is always the hardest step. We outlined how things will go with a focus on incentives and shame. Listen to this weeks goals.


Workflow Standardization

Research Update – Hematodinium Investigation Yesterday’s notebook update focused on my plans to investigate future research questions. This one focuses on my current project – analyzing differential expression in Hematodinium in Grace’s samples. I’m roughly at the same stage as before – I’ve got all my differentialy-expressed GO terms, but realized a few things. The most important of those: for analysis with GO-MWU/GOseq/some other gene enrichment analysis, I need to provide all my genes, not just the differentially-expressed ones. Because of that, I had to start over on my R script that produces a newline-separated file of UniProt accessions. When going through my R script, I realized I’ve learned a lot in the last few months. The script was badly written, and I had to either sub out specific parts each time, or have differnt scripts for different files. Because of that, I decided to rewrite my scripts, and turned…

from Aidan F. Coyle

Project Proposal Idea

Research Update – Future Plans I’ve been somewhat neglecting my notebook duties for the last while – I’ve really been working along two avenues, and felt like I didn’t have enough in either to warrant a full post. Well, until recently, that is! This is going to be a two-part post. The first (this), will focus on how I’m progressing with planning for future research – finding a good question, determining feasibility, diving into the lit, and so on. The second will focus on how I’m progressing with my analysis of differential gene expression in Grace’s hematodinium samples. Alright. So before I begin describing my potential research project, some quick housekeeping. I imported all of Grace’s thesis lit (she kindly shared her folder with me) into PaperPile, and linked each with a PDF. I’m now on the hunt for a good method for tagging and sorting all 250-odd papers! Enough…

from Aidan F. Coyle

R package: usethis

install.packages(“usethis”) #Install packages
usethis::use_course(“hglanz/rworkshop_Jan2021”) #Download materials from GitHub repo ( to machine

Samples Submitted – M.magister MBD-BSseq Libraries to Univ. of Oregon GC3F

Submitted the M.magister MBD-BSseq libraries created 20201124 using the 4nM aliquots created for the MiSeq test run on 20201202 to the Univ. of Oregon GC3F sequencing core.

For library pooling, I used an updated set of calculations determined by Mac to help equalize individual library contributions, based on the results from the MiSeq run:

Sample Volume_4nMsample_toBalance_uL
CH01-06 2.43
CH01-14 3.1
CH01-22 2.58
CH01-38 1.63
CH03-04 1.66
CH03-15 4.03
CH03-33 1.71
CH05-01 2.1
CH05-06 4.38
CH05-21 1.84
CH05-24 2.98
CH07-06 1.79
CH07-11 2.83
CH07-24 2.98
CH09-02 1.36
CH09-13 4.57
CH09-28 1.4
CH10-01 1.29
CH10-08 1.83
CH10-11 0.99

Full Google Sheet for this project:

from Sam’s Notebook