Spencer Nystrom
@snystrom.com
Data science, genomics, software development. Formerly: Eukaryotic gene regulation, phage, graph genomes. On hiatus building distributed systems.
snystrom.com
snystrom.com
Tough to say without more details, but: provide an argument or an R option that allows users to enable the new behavior, but default to the old style while returning a warning that the old behavior will be deprecated in a later version. Later, alter the default before removing the old one.
November 17, 2025 at 4:50 AM
Tough to say without more details, but: provide an argument or an R option that allows users to enable the new behavior, but default to the old style while returning a warning that the old behavior will be deprecated in a later version. Later, alter the default before removing the old one.
Pick a time, I'll be there!
August 15, 2025 at 8:08 PM
Pick a time, I'll be there!
You can pry emacs from my cold dead fingers.
That being said, if you're not using this, you're missing out: github.com/kahole/edama...
That being said, if you're not using this, you're missing out: github.com/kahole/edama...
GitHub - kahole/edamagit: Magit for VSCode
Magit for VSCode. Contribute to kahole/edamagit development by creating an account on GitHub.
github.com
August 15, 2025 at 8:01 PM
You can pry emacs from my cold dead fingers.
That being said, if you're not using this, you're missing out: github.com/kahole/edama...
That being said, if you're not using this, you're missing out: github.com/kahole/edama...
I love eval(parse()) crimes.
I set the additional challenge that I wanted it to be a single string that got eval'd & only using base regex methods.
I set the additional challenge that I wanted it to be a single string that got eval'd & only using base regex methods.
December 3, 2024 at 8:13 PM
I love eval(parse()) crimes.
I set the additional challenge that I wanted it to be a single string that got eval'd & only using base regex methods.
I set the additional challenge that I wanted it to be a single string that got eval'd & only using base regex methods.
I was just messing with this. No code written, but my plan was:
`uv export --format requirements-txt`, sed away the versions, then `uv add -r requirements.txt`.
`uv export --format requirements-txt`, sed away the versions, then `uv add -r requirements.txt`.
December 3, 2024 at 3:59 AM
I was just messing with this. No code written, but my plan was:
`uv export --format requirements-txt`, sed away the versions, then `uv add -r requirements.txt`.
`uv export --format requirements-txt`, sed away the versions, then `uv add -r requirements.txt`.
But have you considered the career advantages of discovering a new -ome that only you uniquely have the magic touch to investigate
November 13, 2024 at 2:19 AM
But have you considered the career advantages of discovering a new -ome that only you uniquely have the magic touch to investigate
Funny enough, this exists here: bsky.app/profile/xblo...
March 25, 2024 at 2:17 PM
Funny enough, this exists here: bsky.app/profile/xblo...
If I'm paying for software, I want the method to be great, yes, but what we really *want* to be buying is stability and maintenance so we can focus on our core products.
September 29, 2023 at 6:39 PM
If I'm paying for software, I want the method to be great, yes, but what we really *want* to be buying is stability and maintenance so we can focus on our core products.
It was really disappointing. Ultimately came down to: inflexible legal / payment agreements (in one case wanting a several year commitment & full payment up front), and there's no guarantee the project won't die anyway due to funding lapses, etc. in which case we lose access, so becomes too risky.
September 29, 2023 at 6:37 PM
It was really disappointing. Ultimately came down to: inflexible legal / payment agreements (in one case wanting a several year commitment & full payment up front), and there's no guarantee the project won't die anyway due to funding lapses, etc. in which case we lose access, so becomes too risky.
Been on the purchasing side a time or two and we just decided to give up rather than deal with the headache.
September 29, 2023 at 5:16 PM
Been on the purchasing side a time or two and we just decided to give up rather than deal with the headache.
Could also run something like mFOLD but I'm not fully convinced that translates to efficacy, but at the very least might indicate which ones are easier/harder to clone.
September 26, 2023 at 6:29 PM
Could also run something like mFOLD but I'm not fully convinced that translates to efficacy, but at the very least might indicate which ones are easier/harder to clone.
At that point I'd dip into genetic variants. More consistent seq across population == better? Avoid runs of same nt, prefer terminal GC clamp (or other platform-specific discriminators)?
I usually make a matrix of these scores & minimize (can weight or not)
No clue about the alt-nt pairing algo.
I usually make a matrix of these scores & minimize (can weight or not)
No clue about the alt-nt pairing algo.
September 26, 2023 at 6:15 PM
At that point I'd dip into genetic variants. More consistent seq across population == better? Avoid runs of same nt, prefer terminal GC clamp (or other platform-specific discriminators)?
I usually make a matrix of these scores & minimize (can weight or not)
No clue about the alt-nt pairing algo.
I usually make a matrix of these scores & minimize (can weight or not)
No clue about the alt-nt pairing algo.
If the list is small, order em all?
September 26, 2023 at 4:41 PM
If the list is small, order em all?
(Where k is the length of your construct)
September 26, 2023 at 4:41 PM
(Where k is the length of your construct)
For ASOs I'm not as sure (other considerations there for alt-nt's for stability, etc), but for RNAi, it can be hard to predict what works best. If you have a fusion or something you can try spanning the boundary.
I like to grab all kmers in ROI & subset to unique ones vs the masked genome.
I like to grab all kmers in ROI & subset to unique ones vs the masked genome.
September 26, 2023 at 4:40 PM
For ASOs I'm not as sure (other considerations there for alt-nt's for stability, etc), but for RNAi, it can be hard to predict what works best. If you have a fusion or something you can try spanning the boundary.
I like to grab all kmers in ROI & subset to unique ones vs the masked genome.
I like to grab all kmers in ROI & subset to unique ones vs the masked genome.
We are now well beyond my realm of expertise!
September 26, 2023 at 4:26 PM
We are now well beyond my realm of expertise!
I guess it depends most on your delivery vehicle. Nusinersen works so well (in part) cause you can just inject directly into the spine. Not sure your cancer type of interest, but I think that is key here if the end goal is 'quickest to patient'. If you have to go through the liver, 🤷♀️
September 26, 2023 at 3:25 PM
I guess it depends most on your delivery vehicle. Nusinersen works so well (in part) cause you can just inject directly into the spine. Not sure your cancer type of interest, but I think that is key here if the end goal is 'quickest to patient'. If you have to go through the liver, 🤷♀️
Ok but Fiesta Grill is at least an 11/10, I'd hardly call that low standards.
September 25, 2023 at 3:50 PM
Ok but Fiesta Grill is at least an 11/10, I'd hardly call that low standards.
Are you more interested in knockdown, or specifically using ASOs to do the knockdown? Admittedly not familiar with implementing ASOs in the lab, but shRNAs are pretty easy to design & test a lot of.
September 25, 2023 at 10:46 AM
Are you more interested in knockdown, or specifically using ASOs to do the knockdown? Admittedly not familiar with implementing ASOs in the lab, but shRNAs are pretty easy to design & test a lot of.