Dane Deemer

Computational Biologist at Purdue University. Big tennis and Detroit Lions fan.

[Dane Deemer @TurboDogPurdue]

@bradylabs @ATinyGreenCell MongoDB is a mix of structure/no structure for a database core (my go to). It’s also super easy to setup once you learn the basics. SQLite is serverless and the most popular DBMS, so that’s a great option too. Depends on how big your database is going to be. #MongoDB #sqlite

[A. Murat Eren (Meren) @merenbey]

Additional restrictions in the free version of Slack makes the #anvio community question whether we need a more appropriate solution.

If you are an anvi'o user, or simply interested in this discussion, please read this blog post and help us: https://t.co/xBi9ctAWtf

[Dane Deemer @TurboDogPurdue]

As long as you expel only to the first stop you’re still accurate. What disturbs me more is people pipetting with their pointer finger on the plunger

[Ola Bartolik @OBartolik]

I learned that some scientists go to the second plunger on a micropipette to suck up extra solution to negate the small amount of solution that is stuck in the pipette tip when they expel, but doesn't that mess with the accuracy of the micropipette? I feel deeply disturbed

[Dane Deemer @TurboDogPurdue]

https://t.co/32S8aFmShg Great tool for visualization and project management. They hooked me up with a free 10-person subscription for University use #miro #Turbodog #projectmanagement Highly recommend!

[Dane Deemer @TurboDogPurdue]

MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads https://t.co/iQfQXJBTEM

[ASM @ASMicrobiology]

Microplastics have created a new niche for microbes—the plastisphere. In this new #mSystems study, researchers conducted a microcosm experiment with 2 different microplastic & soils types to decipher mechanisms shaping the soil plastisphere microbiota. https://t.co/DqStzW8XgC

[Dr Ashwana Fricker (she/her) @tinycosmical]

Ran out of purification kits, so tried the "freeze n squeeze" method for my digests I saw here to great success! Don't know where original credit is due, but thanks @ATinyGreenCell (where I originally saw it mentioned). Twitter is a magical place...

[Dane Deemer @TurboDogPurdue]

@LukeThompson @bielleogy For example a way to snowball data from multiple analyses and relate them to one another, or keep them in an object so you’re not chasing files around?

[Dane Deemer @TurboDogPurdue]

@LukeThompson @bielleogy Interesting design and enjoy the paper. I work a lot with #snakemake and have lots of intertwined pipelines similar to this, where you can modularly piece a few together and automate/hide tedious code as needed. Have you given much thought to reducing the flat file output?

[Dane Deemer @TurboDogPurdue]

This is The Turbodog.

[Dane Deemer @TurboDogPurdue]

#Turbodog

[Dane Deemer @TurboDogPurdue]

Esp when you want to throw a bunch of data in and clean it later.
#snakemake #MongoDB

[Dane Deemer @TurboDogPurdue]

Curious about lab data archiving (esp with ebbs and flows of students) SOPs given all the great #sql and esp #NoSQL db options. Anyone using #MongoDB as a document preserver when personnel leave? Can’t convince myself of a better tool #dataengineering #Turbodog

[Dane Deemer @TurboDogPurdue]

@bielleogy Nice gel! Middle ladder position makes me uncomfortable

[Dane Deemer @TurboDogPurdue]

@gregcaporaso @theoreticalfun Those pi kits are pretty rad and can be used for so many things

[Dane Deemer @TurboDogPurdue]

@AmyDWillis I like seeing people using #snakemake; I’m always advocating for it and surprised how many people haven’t used it. Especially nice to wrap around #anvio functionality

[Dane Deemer @TurboDogPurdue]

@PatSchloss The exception is when excel helpfully turns gene names into dates, and you’re reporting on the significance of Oct-17 in your metabolic pathway analysis

[Dane Deemer @TurboDogPurdue]

VIM > Nano

[Dane Deemer @TurboDogPurdue]

hello world