Ask HN: What can I do to accelerate scientific research? • Hacker News Board

Re: Ask HN: What can I do to accelerate scientific research?

#51

Post by massung » Sat, Jun 15, 2019, 2:24 PM UTC

> What ideas do you have on how one can accelerate scientific research?

I work in genetics (as a software engineer).

If there was a major flaw in current scientific research (that involves software), it's that most labs care more about getting published than they do about the reproduce-ability and validation of their work. This means most of the software written in research is ad-hoc, write once, and often never looked at again. It was put together for the sole-purpose of producing some output that could be put in a paper and then lost to time.

A current "holy grail" of software in research would be to fix that: empower other labs to validate and reuse the software written and reproduce the work of other labs with different data sets. And it is actively being worked on in a couple places (that I know of, perhaps more):

* https://genepattern-notebook.org/

* https://app.terra.bio/

* https://software.broadinstitute.org/wdl/

Some of these are just about giving the community a common framework to use for their software (CWL, WDL, Jupyter), others are about data storage and making it easily accessible for others to use in the cloud for reproducing results.

If you want to have a impact, joining one of these groups would probably put you in a much closer position to doing that.

If you just wanted to work on something in your spare time that would be incredibly valuable, then might I suggest this:

It's amazing how much work is done in the scientific community using CSV/TSV files (usually gzipped). And most of that work is done via perl, sed, and awk. And often these are huge I'm working with a VCF file (TSV) right now that's 2 TB in size ZIPPED! It's crazy. Researchers often don't have the time, resources, or know-how to put together a simple Spark cluster and use it.

A command line tool that allowed someone to run SQL (or SQL-like) commands on a gzipped CSV file FAST would be invaluable. And if it could JOIN across CSV files ... wow!

Re: Ask HN: What can I do to accelerate scientific research?

#52

Post by mariushn » Sat, Jun 15, 2019, 2:41 PM UTC

biophysboy wrote: post #37

This is a pipe dream of mine, but I would love a Wikipedia of null results: nullpedia! Nobody publishes null results bc they’re not exciting, but I think a lot of NSF money would be saved if “failed” experiments were aggregated somewhere in a searchable way. There’s lot of questions. How to organize it? How to encourage participation? How to maximize usefulness while at the same time minimizing volunteer effort? How…

Good idea, and great challenges indeed. Taking this further, I'd call it experimenpedia, with experiments published as they are thought out. Be open for comments/review and showing related experiments before the actual experiment being done. This might prevent potential failures and let owners tweak the planned experiment before being actually done. Then do the experiment and publish the results, whatever they are.

I guess secrecy would actually win though, and nobody would use this?

Re: Ask HN: What can I do to accelerate scientific research?

#53

Post by mariushn » Sat, Jun 15, 2019, 2:44 PM UTC

claudius wrote: post #26

Provide funding for permanent positions. I'm currently in the last few months of my first postdoc in condensed matter physics (think superconductors, quantum computers etc.) but will move into industry next year for lack of perspectives towards a permanent position in a reasonable place. As far as I can tell, my research so far was not substandard and the software I wrote has enabled quite a few projects which otherw…

Excellent point. I cannot afford providing funding, but I can fund myself for 3 years to work on useful software.

> the software I wrote has enabled quite a few projects which otherwise would have not been possible or taken much longer

What's the common practice with such software? Is that published somewhere, open sourced? Or kept private in hopes of being monetized, with IP owned by the author/university?

Re: Ask HN: What can I do to accelerate scientific research?

#54

Post by abcxx99 » Sat, Jun 15, 2019, 2:47 PM UTC

mxcrossb wrote: post #30

abcxx99 wrote: post #4

Regarding the last point: try applying libraries like Quantum espresso [1] or CP2K [2] to real world problems and apply machine learning with the solutions they provide to a given problem. There's a tremendous amount of academic research being done in this direction but try and take these libraries and make them useful for real world applications. [1] https://github.com/QEF/q-e [2] https://github.com/cp2k/cp2k

As someone working in this field, I disagree. The state of these codes is that if you put garbage in, you get garbage out. Without a strong theoretical background, you’re generating junk. Of course, if he’s willing to spend several years developing his knowledge of the field, there is for sure room to help. If not in your suggested machine learning area, instead perhaps in improving the quality and usability of the c…

Of course you need to develop domain knowledge. But there's tremendous opportunity lying in these libraries, you just have to spend the time looking for it.

Re: Ask HN: What can I do to accelerate scientific research?

#55

Post by Glench » Sat, Jun 15, 2019, 2:47 PM UTC

I would go talk to scientists and try to understand deeply what they’re working on, how they do it, and what systems (social/technical/political) allow them to do it. I’ve done this a few times and it’s always illuminating and inspiring.

Re: Ask HN: What can I do to accelerate scientific research?

#56

Post by claudius » Sat, Jun 15, 2019, 2:50 PM UTC

mariushn wrote: post #53

claudius wrote: post #26

Provide funding for permanent positions. I'm currently in the last few months of my first postdoc in condensed matter physics (think superconductors, quantum computers etc.) but will move into industry next year for lack of perspectives towards a permanent position in a reasonable place. As far as I can tell, my research so far was not substandard and the software I wrote has enabled quite a few projects which otherw…

Excellent point. I cannot afford providing funding, but I can fund myself for 3 years to work on useful software. > the software I wrote has enabled quite a few projects which otherwise would have not been possible or taken much longer What's the common practice with such software? Is that published somewhere, open sourced? Or kept private in hopes of being monetized, with IP owned by the author/university?

At the moment it's "available within collaborations". My former supervisor has had some bad experiences with people using his open-sourced software without acknowledgement etc., which is of course not quite ideal if you actually want to build a career in academia for yourself. Monetisation is not really an option.

My toolkit is maybe a bit non-standard in that it has attracted a few external collaborators using it as well and I like to think I have taken better care of upholding coding standards, documentation etc.

Normally software in my field is kept within a group and dies after one or two PhD students have left.

Re: Ask HN: What can I do to accelerate scientific research?

#57

Post by mariushn » Sat, Jun 15, 2019, 2:50 PM UTC

massung wrote: post #51

> What ideas do you have on how one can accelerate scientific research? I work in genetics (as a software engineer). If there was a major flaw in current scientific research (that involves software), it's that most labs care more about getting published than they do about the reproduce-ability and validation of their work. This means most of the software written in research is ad-hoc, write once, and often never look…

Thanks so much, mussung, for your excellent practical feedback! Both alternatives that you listed are very tempting.

May I please ask you some followup questions? There's no email in your profile. My email is marius.andreiana@gmail.com

> A command line tool that allowed someone to run SQL (or SQL-like) commands on a gzipped CSV file FAST would be invaluable. And if it could JOIN across CSV files ... wow!

What prevents one importing each CSV in a postgres db as tables, creating indexes and then start running queries? Disk space availability? (My local drive is only 1TB)

Re: Ask HN: What can I do to accelerate scientific research?

#58

Post by mariushn » Sat, Jun 15, 2019, 2:53 PM UTC

thanatosmin wrote: post #21

mariushn wrote: post #15

Earlier quoted context omitted.

> I suggest talking to actual researchers and asking them what they really need, and give them that. Will start to do that, thanks! > No immediate financial return? I hope you can accept no financial return, period. That would be ok for the next 3 years.

I’d second this. Many labs, including ours, are happy to discuss challenges and opportunities with serious outside parties. If you emailed a few labs near you with a detailed explanation I’d expect you would get multiple responses.

Will do, thanks!

Re: Ask HN: What can I do to accelerate scientific research?

#59

Post by ims » Sat, Jun 15, 2019, 2:56 PM UTC

massung wrote: post #51

> What ideas do you have on how one can accelerate scientific research? I work in genetics (as a software engineer). If there was a major flaw in current scientific research (that involves software), it's that most labs care more about getting published than they do about the reproduce-ability and validation of their work. This means most of the software written in research is ad-hoc, write once, and often never look…

Is anyone using Athena on AWS for tasks like this? It goes without saying that the documentation is hit or miss, but SQL-ish queries of flat files on S3 (even gzipped) can be a nice way to get the same result without managing Spark instances.

Re: Ask HN: What can I do to accelerate scientific research?

#60

Post by mariushn » Sat, Jun 15, 2019, 3:03 PM UTC

UglyToad wrote: post #44

I saw this list linked yesterday from another HN article, might give some useful jumping off points: https://github.com/kakoni/awesome-healthcare One related thing I found from there was a list of projects for magnetic resonance imaging specifically: https://ismrm.github.io/mrhub/ I'd assume trying to contribute to those projects would hopefully give greater ROI than building a new thing (without a very specific idea…

Thanks!