iiinova — where your digital self keeps evolving

Greg Fedewa @science.ninja · 28/07/2026

You can export to PowerPoint! It will take some trial and error to get it perfectly though

Greg Fedewa @science.ninja · 24/07/2026

Maybe reach out to @thecrashcourse.bsky.social ? They are a nonprofit that makes high quality courses free to the public

000

Greg Fedewa @science.ninja · 22/06/2026

Having to go on LinkedIn is one of the worst parts of job hunting right now.

010

Greg Fedewa @science.ninja · 19/05/2026

This is a good example of why it's important to include a pronunciation guide for software names even if you think it's obvious.

020

Greg Fedewa @science.ninja · 07/04/2026

I don't think you have to feed them any bugs if you don't want. All of my plants from Cal Carnivores do just fine with the random fly, or you can give them a drop of fertilizer

010

Greg Fedewa @science.ninja · 18/03/2026

I think there is, but if you were looking at something like cancer progression, I'd be a little shocked if glasses were related. For sleep, maybe birth order, or birth month. It might be on path but i would be shocked if it had an effect as big as other things.

100

Greg Fedewa @science.ninja · 18/03/2026

How silly is too silly? Sleeping position, glasses. More silly: even/odd address, car color

101

Greg Fedewa @science.ninja · 05/03/2026

Have you tried Typora? It's my default if I just want to write some notes without having any bloat.

000

Greg Fedewa @science.ninja · 03/02/2026

It might not be a perfect solution for you, but I just finished a project where I used an R kernel and .ipynb notebooks specifically because it then had inline outputs. Worked really well in Position.

110

Greg Fedewa @science.ninja · 29/01/2026

I always have to tell myself, the debrief and documentation are part of the task and need to be scheduled as part of it.

010

Greg Fedewa @science.ninja · 18/01/2026

All of them and turn it into a mole?

010

Greg Fedewa @science.ninja · 08/01/2026

I know, right? And they didn't even want to interview me, either.

010

Greg Fedewa @science.ninja · 05/01/2026

If you want it for a group, you could self host Vikjuna, an open source project management app. If it is just for you, Emacs Org-mode is also an option. It can be as feature rich or lite as you want. The main downside is the lack of mobile apps, though.

000

Greg Fedewa @science.ninja · 16/12/2025

Python's pathlib has been around since 2012 and I can't believe that every other language hasn't implemented the same idea. It is one of Python's best features.

000

Greg Fedewa @science.ninja · 26/11/2025

I would still suggest Quarto, since it is just a superset of markdown. You don't have to render. When I run code on a server, I usually use Posit/VSCode's remote connect to the server and then run the code cells and have the outputs right there. I also like ipynb, but it depends on the language

000

Greg Fedewa @science.ninja · 26/11/2025

What features do you need? My personal preference right now is just Quarto and then render it into whatever format you want.

120

Greg Fedewa @science.ninja · 11/11/2025

I've been looking for these myself. It isn't a single study, but some of the Zymo standards have been sequenced with all three.

000

Greg Fedewa @science.ninja · 07/11/2025

So glad that a feature I've wanted, and then worked on, is finally out! Run all the bin QC tools now!

021

Reposted by Greg Fedewa

Ryan Hernandez @rdhernand.bsky.social · 24/10/2025

🚨PhD opportunity at the intersection of computation & biology! 🖥️🧬🧪 Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science. 📢 Info session: 11/6 @ 1 PM PT bmi.ucsf.edu/admissions Learn more👇

Join our virtual info session on Nov 6, 2025, at 1 PM PT!

Explore cutting-edge research in computational biology!
Learn how we train future scientific leaders!
Get answers to your questions about our program!
Meet current students and faculty!
Find out what makes a successful application!

https://bmi.ucsf.edu/admissions

153

Greg Fedewa @science.ninja · 24/10/2025

I am not an expert on TagSeq, but I have debugged a lot of sequencing before. Can you say what species it is (is the genome just repetitive)? Did you remember to deduplicate the reads based on UMIs?

100

Greg Fedewa @science.ninja · 20/10/2025

Getting your ears pierced this weekend won't help dispel them

000

Greg Fedewa @science.ninja · 17/10/2025

"I think we should have the Mobius parade. It will never stop, never start. It always was and will always be."

000

Greg Fedewa @science.ninja · 16/10/2025

I still say "Turn down your radio" to people around me.

020

Greg Fedewa @science.ninja · 30/09/2025

How does everyone keep track of where they left off when reading #QuartoPub book websites? Is there an Quarto or browser extension ? I have a browser bookmark to the main page, but (ideally) I would want some button i click to go to my "bookmarked" page.

010

Greg Fedewa @science.ninja · 29/09/2025

I don't understand what you mean, published articles and data should all have DOI numbers that will act as a permanent hyperlink. Books and physical things could be links to a photo attached. If someone is citing a work that can never be verified it probably isn't a good source for a college paper.

050

Greg Fedewa @science.ninja · 29/09/2025

Have you thought about requiring all sources to have hyperlinks? You shouldn't need to track anything down if the student already did

140

Greg Fedewa @science.ninja · 29/09/2025

One hundred thousand people shouting "arr" preventing you from finishing your opener, The Captains Wife's Lament.

020

Greg Fedewa @science.ninja · 16/09/2025

Just a random guess, but 0.008==1/125 . Are these based on some 125 question survey?

000

Greg Fedewa @science.ninja · 11/09/2025

On point 1a, are they saying they won't require a data sharing plan? That would be such a huge step backward.

000

Greg Fedewa @science.ninja · 11/09/2025

It might only be a small step in the right direction, but did you see @fraserlab.com recent post about trying to fix preprint reviews (they found out the authors weren't being notified) ?

010

Greg Fedewa @science.ninja · 27/08/2025

Does anyone know of non-profits, consortiums, labs, or groups that focus on genome sequencing rare/endangered plants? I can't seem to find anything, but it seems like this should exist. I am only finding groups that sequenced a single rare species or two. 🌱🧪 #plantsky #academicsky

030

Greg Fedewa @science.ninja · 16/08/2025

That sounds like an awesome postdoc.

010

Greg Fedewa @science.ninja · 05/08/2025

Verified résumés could be interesting, but I think the problem is LLMs are being used by real people, but they allow people to tailor and apply to every job they can find. I really dislike take homes as they favor people without families/outside responsibilities.

000

Greg Fedewa @science.ninja · 02/08/2025

I have heard this (and that a lot of them look like they are written by an LLM) from a few people, but haven't seen much news on it. If it really is just a flood of some people spamming every job opening, I wonder how that will force the whole process to change.

100

Greg Fedewa @science.ninja · 26/07/2025

I am pretty sure the same thing is happening in industry too. It's brutal out here right now.

030

Greg Fedewa @science.ninja · 21/07/2025

This is a weird question, but what is the link to purchase your Cornell Notes vault? Everything seems to point to your website having one, but I can't find a link anywhere.

000

Greg Fedewa @science.ninja · 01/07/2025

This is interesting because the literature has quite a few cases of saying that at least a few fungal species have a genome that can rearrange given a new environment. Things like Starships moving 100kb chunks and such.

120

Greg Fedewa @science.ninja · 27/06/2025

Not sure why I didn't guess that. I guess I need to rewatch your lectures to refresh.

000

Greg Fedewa @science.ninja · 27/06/2025

Is there something you recommend for learning the correct way?

110

Greg Fedewa @science.ninja · 25/06/2025

Now where is the @quarto.org plugin for that?

010

Greg Fedewa @science.ninja · 19/06/2025

Are the raw reads available? I've got some microbe genomics project ideas and it would be awesome to test them on some bugs sequenced multiple ways.

110

Greg Fedewa @science.ninja · 18/06/2025

It's wild to me how horrible it still is to apply for a job. Do you really need to know the exact date I started my last job? Your site needs me to manually enter my full resume even after I just uploaded it? Your screener looked for Pandas instead of pandas?

000

Reposted by Greg Fedewa

Greg Fedewa @science.ninja · 06/06/2025

My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.

062

Greg Fedewa @science.ninja · 06/06/2025

062

Greg Fedewa @science.ninja · 31/05/2025

It is great to have that and will work for most people. I just prefer containers to conda after having too many dependency conflict situations with conda. But now I'm wondering if there is an automatic way to build containers from conda yamls. Biocontainers sort of does it, but it isn't local.

000

Greg Fedewa @science.ninja · 30/05/2025

Having all that is already pretty great. The other thing I would suggest is to have a dockerfile and/or apptainer definition file. Being able to containerize stuff makes it so much easier to run on hpc and cloud services.

110

Greg Fedewa @science.ninja · 30/05/2025

I wish feedback was more common on preprints, but I suggested it mostly because it's available sooner. I might be unusual, but in choosing a software I usually care more about the repo/comparisons to others than seeing it in a big journal.

120