AlphaFold 2 is here: what’s behind the structure prediction miracle
1–10 of 98 posts
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#2> Like most bioinformatics programs, AlphaFold 2 comes equipped with a “preprocessing pipeline”, which is the discipline’s lingo for “a Bash script that calls some other codes”.
Having Bioinformatics people requiring to stray a long way from their core competency to learn a scripting language from the 80's to write glue code seems... suboptimal. How many hours of expert time has been wasted figuring out how to split a string in bash?
Can us software people build a better tool to eliminate the need for this?
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#3> Like most bioinformatics programs, AlphaFold 2 comes equipped with a “preprocessing pipeline”, which is the discipline’s lingo for “a Bash script that calls some other codes”. Having Bioinformatics people requiring to stray a long way from their core competency to learn a scripting language from the 80's to write glue code seems... suboptimal. How many hours of expert time has been wasted figuring out how to split…
I think the tools already exist just that people are conservative with their choices.
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#4> Like most bioinformatics programs, AlphaFold 2 comes equipped with a “preprocessing pipeline”, which is the discipline’s lingo for “a Bash script that calls some other codes”. Having Bioinformatics people requiring to stray a long way from their core competency to learn a scripting language from the 80's to write glue code seems... suboptimal. How many hours of expert time has been wasted figuring out how to split…
I think the tools already exist just that people are conservative with their choices.
(Obligatory xkcd; you know the one)
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#5Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#6Earlier quoted context omitted.
(Obligatory xkcd; you know the one)
Not really?
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#7> Like most bioinformatics programs, AlphaFold 2 comes equipped with a “preprocessing pipeline”, which is the discipline’s lingo for “a Bash script that calls some other codes”. Having Bioinformatics people requiring to stray a long way from their core competency to learn a scripting language from the 80's to write glue code seems... suboptimal. How many hours of expert time has been wasted figuring out how to split…
Pretty much anyone that works with data has to clean their data, learning to use the tools to do that is important. Whether that's bash, perl, R, python, ... doesn't really matter that much. If they already know bash then bash is a good tool since they can now focus on their data instead of wasting time on learning a new tool to do the same thing.
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#8> Like most bioinformatics programs, AlphaFold 2 comes equipped with a “preprocessing pipeline”, which is the discipline’s lingo for “a Bash script that calls some other codes”. Having Bioinformatics people requiring to stray a long way from their core competency to learn a scripting language from the 80's to write glue code seems... suboptimal. How many hours of expert time has been wasted figuring out how to split…
It’s sad. Bio people really need friends in software to boost their research. Unfortunately they do a codeacademy python course for 5 min and try to get their projects going. Sometimes they succeed, sometimes they fail. But they don’t really have much time to dedicate to properly learn software dev and it’s not what they are into anyway, it’s a necessity.
I think we could create something like a GitHub of bio projects that need help and people assist with hopes of getting their names in a paper
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#9> Like most bioinformatics programs, AlphaFold 2 comes equipped with a “preprocessing pipeline”, which is the discipline’s lingo for “a Bash script that calls some other codes”. Having Bioinformatics people requiring to stray a long way from their core competency to learn a scripting language from the 80's to write glue code seems... suboptimal. How many hours of expert time has been wasted figuring out how to split…
I think the tools already exist just that people are conservative with their choices.
MLops is a pretty hot area right now. The industry is trying to figure out how to engineer these things in a robust way. It’s not ubiquitous at all yet. There are lots of tools that wrap K8s and help you train models, but trying in DataOps in a robust way…. I haven’t seen the definitive answer yet.
Seriously please tell me if you are founding this company so I can invest.
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#10> Like most bioinformatics programs, AlphaFold 2 comes equipped with a “preprocessing pipeline”, which is the discipline’s lingo for “a Bash script that calls some other codes”. Having Bioinformatics people requiring to stray a long way from their core competency to learn a scripting language from the 80's to write glue code seems... suboptimal. How many hours of expert time has been wasted figuring out how to split…
I think DeepMind went one step further and solved the entire problem for them. They don't even have to touch their keyboards anymore