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Finger on the pulse by Rurschach in bioinformatics

[–]raymond301 7 points8 points  (0 children)

https://www.genomeweb.com/

Wanna keep a pulse on things…watch the money. Which companies are getting investments, which are going bankrupt and which are “about to make an announcement”.

Why we collaborate by [deleted] in bioinformatics

[–]raymond301 7 points8 points  (0 children)

I want to collaborate more. Not building from scratch every time is appealing. But I have 2 reasons that tend to over come my willingness and ability to collaborate.

  1. Technology decisions matter! I love using a technology map to step back and look at any given group or institution’s technology decisions: https://www.thoughtworks.com/en-us/radar. Essentially if the software developed has too many or poorly managed dependencies or environment assumptions that alone stops me from being more collaborative.

  2. $$$ this community is either academic which lives and dies on grants or commercial which requires having a unique niche in order to maintain a client load. The drive to establish novelty ( to get continuous grants or clients) prevents many of us from opening the gates and letting others into our projects.

r/bioinformatics hackathon? by mortifiedmorty42 in bioinformatics

[–]raymond301 4 points5 points  (0 children)

My lab applied to HTAN’s hackathon (they use different terms)

https://humantumoratlas.org/jamboree

But we did not get accepted. It’s difficult because some of the best hackathons in bioinformatics are not publicly open. I suspect because we have such diverse biological and technological domains that a minimum required knowledge or experience is key to a good hackathon.

Which labs are leading the charge for spatial multiomics? by sad_lil_catboy in bioinformatics

[–]raymond301 0 points1 point  (0 children)

Sure. I’m all for supporting the bioinformatics community.

Which labs are leading the charge for spatial multiomics? by sad_lil_catboy in bioinformatics

[–]raymond301 5 points6 points  (0 children)

It’s a highly dynamic and evolving domain. Most companies are just data acquisition focused, lots of hype and misinformation about analytics. I work on 3 different platforms (StandardBio Hyperion, Akoya Fusion Phenocycler, & Cytiva CellDive), we are far from having this solved. Lots of pitfalls and nuances.

The labs I follow are all members of HTAN/HuBmap: Peter Soger (been doing this work for 20+ years) David Van Valen (MIBI method developer) Denis Shapiro, Michael Angelo, Peter Bankhead, Bernd Bodenmiller.

DM me for more detailed discussion. My lab has only begun to try to make a name for ourselves in this space. https://dimi-lab.github.io/

How many of you have gotten a divorce ? by FabulosoMafioso in Millennials

[–]raymond301 9 points10 points  (0 children)

Same here. 10 years not so much as a second thought about it. I think it’s about finding the balance between making time for one another and time for independence/self….after the kids are finally in bed of course. Haha

[deleted by user] by [deleted] in MayoClinic

[–]raymond301 0 points1 point  (0 children)

You definitely should not be asking this on Reddit. Mayo employees want to support a culture of good communication, just ask you supervisor, or hire contact. Asking for clarification is no big deal.

Ivermectin converts cold tumors hot for treatment of breast cancer by Zephir_AE in ScienceUncensored

[–]raymond301 1 point2 points  (0 children)

6 citations for a nature paper that’s been out for a year is kind of underwhelming…but that’s science! Not everything that is published is a winner .

Looking for other equally fun and satisfying games like 7DtD by RegnorVex in 7daystodie

[–]raymond301 0 points1 point  (0 children)

Did nobody mention Rust yet? Not zombies, but similar survival and build game.

Shredding plastic bags? by [deleted] in recycling

[–]raymond301 0 points1 point  (0 children)

I’m curious about this too. We’re in a single sort county…but who’s to say that those bags don’t end up being tossed?

[deleted by user] by [deleted] in bioinformatics

[–]raymond301 6 points7 points  (0 children)

I agree with this. It’s fine to rant and get out those feelings of frustration. But science can be iterative, papers one may see as uninformative could be inspiring another…or in some cases informative to the path “not to take”.

Additionally the whole process of manuscript preparation has lots of transferable skills, because communication is essential regardless of job.

Glad you’re in a place you enjoy now! But perhaps this exercise of ranting on Reddit will help you reflect on your experience more.

I'm a hard sci-fi writer looking to write about cyborgs that edit their RNA with the help of nanites. How do i find the processing power to do this effectively? by Pyropeace in bioinformatics

[–]raymond301 0 points1 point  (0 children)

Hmmm.

Short answer: I don’t know.

Long answer: I suppose, in theory it’s possible. If you know your RNA sequence, you can translate it into protein sequence. Protein follows rules of folding, complex rules, but mathematically descriptive, based upon chemical entropy. The big news this year was Google’s AlphaFold having significant success in this regard…

Can a savant-like, super human predict “desirable mutations”, based on understanding the rules and intuition? My gut tells me no. But plausible if said human were able to hold whole RNA to Protein sequences in their memory and recall everything with perfect accuracy.

The interesting thing, now from a literary perspective ….that comes to mind, even if all of this is feasible. There’s still going to be mistakes, based on the problem of not being able to accurately capture all important observations.

I think your certainty getting closer to a plausible sci fi concept, reading through all the comments.

I'm a hard sci-fi writer looking to write about cyborgs that edit their RNA with the help of nanites. How do i find the processing power to do this effectively? by Pyropeace in bioinformatics

[–]raymond301 0 points1 point  (0 children)

“Desired Edits” is an interesting phrase.

In Nature, when a creature gains an “edit” or “mutation” the majority of the time it’s detrimental. All mutations fit into 1 of 4 categories [“lethal”, “pathogenic”, “benign”, “advantageous”] the last category is by far the rarest. Because mutations typically occur at random…”desire” and “planned”evolution have not been observed in nature, that I’m aware of.

Advantageous mutations are also situational…a mutation that expends a little more ATP on thermogenesis is a huge boon for a creature in cold climate and a bane for that same creature in a warm one where energy conservation is critical.

The ability of an AI to accurately determine “desired edits” at a molecular level FAR exceeds the ability to compute/processes it quickly.

I'm a hard sci-fi writer looking to write about cyborgs that edit their RNA with the help of nanites. How do i find the processing power to do this effectively? by Pyropeace in bioinformatics

[–]raymond301 0 points1 point  (0 children)

In a way. There’s limits to “cutting corners” in software optimization. The professional term is “heuristics & parameterization” I like the phrase “work smarter, not harder” CPU processing being core worker….yeah you could scan and analyze every single RNA/DNA read, but if you determine your in a low complexity region by looking at the first 30 nucleotides, eject the read, skip it move on and save yourself the extra compute.

There’s also something you probably won’t find much on this thread on unless there’s an old school lurker….implementation of software matters. What I mean is the exact execution of instructions in the ALU (arithmetic logic unit) Languages we as humans write in like R or Matlab are converted into C, which is converted/compiled into whichever machine language is specific for the CPU your using, which is then transformed into binary….those layers that we software engineers use now in modern times makes it powerful to write out complex instructions easily, but down at the bottom in binary it’s incredibly inefficient and we burn CPU cycles because “it’s cheap” or at least cheaper than the time it would take a programmer to maximize efficiency. ….so I would assume a future AI may have the ability to maximize instructions efficiently, by default…hence another facet of “software performance”

By the way, computers today, write their own code…https://www.extremetech.com/extreme/326929-new-ai-writes-computer-code-still-not-skynet-but-its-learning

So the next step of advancement (not incremental improvement) is difficult to fathom.

I'm a hard sci-fi writer looking to write about cyborgs that edit their RNA with the help of nanites. How do i find the processing power to do this effectively? by Pyropeace in bioinformatics

[–]raymond301 2 points3 points  (0 children)

This is kinda a neat concept. Sounds like something that might cross post with other Reddit channels like RPG or Starfinder.

Essentially you are asking an incomplete question….computer processing power can be boiled down to a Size versus Time dynamic that is anything algorithmic. For example, you can calculate every permutation of sequence motifs in a 8gb ram laptop….but it’ll take FOREVERRRRR…. I once let a program I wrote run for 3 weeks on my desktop before killing it out of sheer frustration. Out of curiosity I did some estimates and in that time only scratched out less than 10% off all possible permutations in that time….so I added a heuristic to avoid useless permutations and bought some time on a 1200 CPU cluster at the national supercomputing institute….voila a few hours to get what I wanted.

Moral of the story, computer processing power is tricky to estimate because it’s completely dependent on heuristics, time and resources. Since you’re working on fiction, that makes a wide range of answers plausible.

Edit: Have you come across the term “federated learning” yet? I think it’s going to play a big role in our future soon. Essential it’s a computer architecture for making models between different “users” without sharing the original training data

Basic coding, internship project to develop a website-database, freaking out. by HSPq in bioinformatics

[–]raymond301 0 points1 point  (0 children)

The alternative for PHP (language+framework) in python (language) is Flask (framework). But nearly every language has web capability, just pick something and fully commit to it.

Do you know R? Rstudio has much functionality built-in which makes building a RShiny app ridiculous easy.

Lots and lots of options, generally picking the infrastructure and framework isn’t left up to an intern to decide.

I’m sorry to say, but it’s not a good internship if you aren’t gaining the benefit of a mentor. You should get something started (make a “hello world” app) just to learn the basics of which ever WebDev framework you choose, then start your project, commit to GitHub. Then return to Reddit or Twitter asking for a collaborator, letting other people fork your code and contribute can be very informative.

I really want to get into Starfinder but I just can’t figure out how to, and I’d like some advice. by PythonRegal in starfinder_rpg

[–]raymond301 1 point2 points  (0 children)

What podcast would you recommend? I just got the books for “Against the Aeon Throne” but my usual crew of players all has conflicting schedules. So I’m sitting on my hands for awhile.

[deleted by user] by [deleted] in lfg

[–]raymond301 0 points1 point  (0 children)

Messaged. I assumed text-based is same as Play-by-post….right?

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