Pinned
A thread of #gget threads - all gget updates in chronological order
I will continue to add to this threadception as we post more updates. 🧵🧵
pachterlab.github.io/gget/
Laura Luebbert, PhD
1,000 posts
Laura Luebbert, PhD
@NeuroLuebbert
genetics, compbio & viruses · @FutureHouseSF @broadinstitute @Harvard · prev @Caltech · Author of gget (the software, not the coffee bar, unfortunately)
- After giving a talk at a conference recently, I received an email from an unfamiliar senior professor in the audience remarking that my “look has extremely improved over the years” from “nerdy lab mouse” to “a touch of upper class.” 1/4
- gget alphafold: Predict the 3D structure of a protein from its amino acid sequence using @DeepMind’s AlphaFold v2.0 from a Python or command-line environment in 3 lines of code. Runs on any laptop and requires only ~4 GB of disk space. Simply ‘pip install gget’ and:
00:00 - Replying to @NeuroLuebbertI am not sure if I am more appalled by the stalking or the fact that he felt comfortable putting this in writing. I have spent countless hours trying to convince male colleagues that sexism in science is still well and alive today, so I wanted to share this for awareness. 2/4
- Replying to @NeuroLuebbertI have received countless dismissive and objectifying comments like these throughout my career. If you’re a junior (or senior) female scientist experiencing discrimination and/or harassment, just know that it’s got nothing to do with you or your work and you’re not alone. 3/4
- Replying to @RogerSeheultI am not sure how this is relevant to this story?
- Replying to @NeuroLuebbertFull translation Note the use of the word "geil," which can be used as a synonym for "awesome" in an informal setting but literally means "horny." 4/4
- ”Imagine that DNA had a diameter of 1 m. Then the complex that copies the DNA would be the size of a @FedEx truck. It would be traveling at a speed of 500 km/h. It would be making a delivery on both sides of the street every ~10 cm. It would finish its journey in 40 min... 1/2
- I created a Colab tutorial that checks if a gene/transcript ID has an associated crystal structure, checks if related proteins with associated crystal structures are available, and then compares those to a de novo structure prediction: colab.research.google.com/github/pachter…
- Come find me and my giant poster at #ASHG2022 poster board 3211 tomorrow 3-5 pm! Let’s talk genomic reference databases and how to access them quickly and effortlessly. @GeneticsSociety
- Lior and I wrote a blog post about what it was like for me to find occurrences of duplicated (and seemingly manipulated) data as a first-year graduate student at @Caltech. I am speaking openly because I believe that we, as the scientific community, can do better.Replying to @lpachterIn a blog post, she tells the story of the reaction she received when she pointed this out to her (tenured) professor at the time, and to others. She was basically told not to waste her time: "a lot of the scientific literature has problems". liorpachter.wordpress.com/2024/07/02/the… 7/
- Can you spot the difference between these two BRCA2 protein sequences? They are 3,418 amino acids in length and only differ in a single amino acid. Yet, women expressing the mutant BRCA2 protein have a high likelihood of developing breast cancer. Why is that?
- We expanded kallisto to translated alignment (nucleotides <-> amino acids), and used it to detect novel viruses in RNA seq data. The single-cell resolution allowed us to determine whether the presence of these viruses affected host gene expression. 🧵 biorxiv.org/content/10.110…
- Replying to @JeremiahDJohnsThat highway would be considered walkable in California
