AlphaFold 2 is here: what’s behind the structure prediction miracle
21–30 of 98 posts
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#22> 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…
> How many hours of expert time has been wasted figuring out how to split a string in bash?
Probably a good many more than would be needed to learn how to split a string in Python.
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#23https://github.com/deepmind/alphafold
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#24Thank you Google...thank you!
Why did they open source it? Wouldn’t this model be very valuable to the pharma industry?
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#25> 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…
There is a growing trend to include Docker (or Singularity, which is more compatible with HPC architectures common in bioinformatics) images alongside codes. In particular, AlphaFold 2 does provide a Dockerfile, and they even include a Python "launcher script" hiding all the details of running the code. Sadly, this is very uncommon in the community. In a bioinformatics meeting, the sentence "I spent X days setting up…
I work in power systems, and the situation is similar. Maybe worse because paper authors often come up with new computational techniques but don’t implement them in code (much less code with a dockerfile).
I look with much jealousy over at the computer science field where papers often include code, multiple versions under version control, automated tests, setup/docker scripts, and demonstration workflows and interfaces.
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#26Earlier quoted context omitted.
Bash is easier to explain and use than, eg, explaining ppl how to use Python subprocess Module Launch different apps, capture their output, etc. I find astonishing how bad Python is as a bash replacement. I often rather write an argument parser in bash than use Python if I have to invoke a bunch of commands.
Python is bad, but bash is worse as soon as you need any kind of logic. > explaining ppl how to use Python subprocess Module Launch different apps, capture their output There's no shame in using `os.system`.
Well, technically subprocess.check_call if you need to capture output.
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#27Thank you Google...thank you!
Why did they open source it? Wouldn’t this model be very valuable to the pharma industry?
It is written in the article. A few reasons could be pressure from the publishing magazine, emerging open source implementations of the same idea, and the fact that this is still far from easy to comercialize.
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#28To me the most interesting part of the article is the cometary on where basic research is going to happen in the future. The fear is that if it only happens in large companies, then the unbiased pool of experts society relies on will be smaller and less informed. Along with the issue of nobody being around for the slog of defining a field, setting up databases, competitions and standards. These are what allow well funded corporate labs to apply their skills and compute and blow a problem out of the water. The problem is, would they do the work to define an unknown problem in the first place?
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#29What are the big implications of being good at predicting protein structures?
Re: AlphaFold 2 is here: what’s behind the structure prediction miracle
#30Article at Nature: https://www.nature.com/articles/s41586-021-03819-2