Readit NewsFeuilles_Mortes commented on I tried every todo app and ended up with a .txt file al3rez.com/todo-txt-journ... · Posted by u/al3rez
for doing laboratory work in my PhD, I've found no better app than OmniFocus. It's particularly valuable in its ability to create tasks via a templating system. This is crucial, for example, for managing 10+ genetic crosses at a time. Each cross takes weeks to move to the next step, but when that next step occurs, I need to be on top of the cross 2x / day. Juggling different crosses at different stages would be impossible for my brain without a system I can rely on. Other lab work follows similar workflows.
Instead of writing the counting tool he could have used the Multi-Point Tool in ImageJ [1] [2]. I used it just this morning for counting some embryos I collected.
[1] https://www.youtube.com/watch?v=BhFNiPsVRoM
[2] https://fiji.sc/
Feuilles_Mortes commented on Model Organisms Are Not Static asimov.press/p/model-orga... · Posted by u/mailyk
It's worth noting that we've found genetic differences between the N2 wild type strains used by different labs as well, so this is still a problem for C. elegans.
biology is hard
Feuilles_Mortes commented on Model Organisms Are Not Static asimov.press/p/model-orga... · Posted by u/mailyk
C. elegans is nice for this since you can freeze stocks in glycerol. Labs routinely go and thaw out the main wild-type reference stock if the lab stock has been around for too long.
Now I'm in a fly lab and no one's really figured a good way to freeze a fly stock down for long-term storage. So we're left to just accept some degree of background mutation and generally assume that it's not impacting our experiments too much...
I've been learning a lot about molecular biology recently, and am about to run some procedures related to plasmid isolation, gene cloning, and expression. Of note, the resources I've read, from AddGene, and The Bumbling Biochemist (excellent Youtube channel) emphasize sending your plasmids in for sequencing once complete, due to all the errors that can occur.
I am wondering if the plasmids the researchers here tested simply weren't sequenced. This wouldn't explain all classes of errors (like toxic protein production), but it may explain some. When you order from AddGene, they provide both the depositor's sequence results, if available, and their own results. The paper doesn't mention AddGene specifically; I'm curious how their plasmids compare to the ones tested.
Regarding toxic proteins: It seems like that would be a straightforward software addition to pass sequencing results through.
Before these companies like plasmidsaurus that do whole-plasmid sequencing for relatively cheap with nanopore, people generally only sequenced a region of interest using sanger sequencing. The rest of the plasmid was assumed to be mostly correct, as long as it grows on a bacterial resistance. As noted in the article, the rise of nanopore-based whole-plasmid sequencing has reduced a lot of these types of errors.
So uhm, can/should we start cutting these proviruses(?) out of our genomes? Unintended consequences?
Definitely not. Current estimates put viral DNA at about 8% of the human genome.
That's _amazing_.
I imagine this doesn't look impressive to anyone unfamiliar with the scene, but this was absolutely impossible with any of the older models. Though, I still want to know if it reliabily does this--so many other things are left to chance, if I need to also hit a one-in-ten chance of the composition being right, it still might not be very useful.
What was difficult about it?
Feuilles_Mortes commented on Ron Patrick's Street-Legal Jet Powered Volkswagen Beetle (2006) ronpatrickstuff.com/... · Posted by u/1317
This is wild, but I would strongly disagree on the aesthetic of it. In my opinion, he picked pretty much the worst possible car for this. Managed to make a jet-powered vehicle look... lame, somehow.
Imagine an El Camino or even an AMC Eagle with this contraption in the bed, how much cooler that would look? But really, how could you not use a Delorean as the base for this project??
I think it is much worse to create a special case that obscures the actual formatter being run and how it is being run (is ruff now preinstalled, or is it downloaded and cached in the same way as other tools?)