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

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

#81

Post by godelski »

My dream would be to have a place I could look at any paper (even if not on a campus internet connection), be able to look at raw data, code, and have a forum to facilitate discussions between researchers.

I know the first won't happen for awhile, but it is a dream (open science).

The second is direly needed but in some cases not practical. But I think there could be a lot to gain from just having a small portion of this. It could help verify results significantly. Also imagine if people could research things without having to have all the fancy instruments. Some of this already happens, but I think it is harder to find and not always easy to sort though. It isn't connected to papers and research. Just having a paper and a link to the data would be tremendous help.

Similarly code. I don't know a researcher that hasn't made an accidental bug in the code that changes results (some slight, some major). I think we need to get over that WE ALL write hacky code. Hacky code is better than a vague description in a paper because you don't have enough room to write an accurate description of your model. Science is supposed to be replicated! Even linking papers with a github account would be tremendous help. Some people don't want to share code, and I think this is a shame and anti-scientific (especially if you are using public money), but that's a rant on its own.

Researchers email one another all the time. Some of these discussions should be public. Papers leave a lot of gaps. An area researchers could add extra notes that couldn't be fit in a page limit, where collaboration can happen, or where people can just ask questions, would be great. Replicating results can be hard and we should be learning from one another's hurdles. That's the point of science after all, for to push the progress of humanity. Lack of ability to communicate should not be a gate.

Along with these things it would be nice to encourage putting up null results. Aside a paper I would love to know what challenges a researcher fought. That's where most of the work is. It is funny, we constantly talk about failure being 80-90% of research. Whole projects failing or just banging your head on the desk because you can't figure out why something isn't working. Let's open this up. Let's help one another. Let's talk about what went wrong and how we fixed things to get to our success. I can't think of anything that would help science more than this.

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

#82

Post by whatshisface »

GeorgeTirebiter wrote: post #76
whatshisface wrote: post #18

I have a request. Somebody needs to make matplotlib, but with a C API and lots of language bindings instead of only a python API. For example when I'm writing rust, my best option is to use a Python interop library that calls matplotlib...

Matplotlib is better than nothing, but... as I understand it, it was inspired by Matlab's plotting - and therefore is a bit quirky when translated to the Python paradigm. I use it tho. I think having a built-in web server via a visualization library that shows the graphs etc in a browser is 'optimal' -- because then, the whole crap of e.g. dealing with Tkinter to make your windows goes away. You achieve OS independen…

Locking it down to the web platform is IMO too restrictive - if it was instead a low-level library you could access it anywhere, including the browser (if you wrote the server on top of the library). Sometimes, you want to use GtK, for example if you want lightning quick startup times, or weird portability, or anything else like that.

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

#83

Post by prennert »

Build tools to make research more efficient and reproducible. The research community is a small market and has little money. Building tools is often not regarded as scientific activity and can lead to dead ends if publication is pursued.

So, if you do not have to rely on income anymore and want to contribute to science, build tools for the community. Or better, come up with a way to help scientists to build their own tools fast and efficiently.

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

#84

Post by godelski »

hannob wrote: post #78

Learning a lot how science actually works and how flawed it is I came to the conclusion that the biggest boost in scientific progress you could ever achieve is by eliminating science waste and doing more good science. There are a few tiny steps in the right direction, but it's frustratingly slow. Once you understand a phenomena like publication bias it's hard to swallow that there are still empirical studies publishe…

That is a very click-baity publication (yes, it happens). Title suggests this phenomena is independent of fields. Content talks about the high p value. Not every field uses this metric. So this publication is aimed pretty much at medicine.

While I think the p-value thing needs to be rethought, it is bold to claim "Most Published Research Findings Are False". Honestly it would be more accurate to say "Errors matter and we can't take findings at face value and ignore error bars". Which is pretty much something every self-respecting scientist should know in the first place.

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

#85

Post by godelski »

andreygrehov wrote: post #27
xwdv wrote: post #19

Earlier quoted context omitted.

> That would be ok for the next 3 years. No, I don’t mean no returns for three years, I mean no returns ever . You must go into this with both eyes open, don’t find yourself crippled later because you gave all your time and money away and have nothing to show for it.

What if he would sell models? A marketplace for trained models.

Some of this already happens. But you also have to realize that that is not in the spirit of science.

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

#86

Post by guzik »

Side note: I am the co-founder of Aidlab - a device and a platform that is widely used by biomedical scientists and students in their research (https://www.youtube.com/watch?v=wY0YPOKNk88)

In my free time I am working on my next project - an open-sourced platform where everyone can contribute to help fight death. The platform allows uploading anonymized, structured health records - publicly available. Why? Dying is a number #1 problem that should be solved together.

OP, if interested, drop me an email: jdomaszewicz (at) aidlab.com

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

#87

Post by bilifuduo »

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…

The Series of Unsurprising Results (SURE) Journal is starting to do this, but only for economics papers: https://blogs.canterbury.ac.nz/surejournal/

Vox recently ran a good profile on them and the importance of null results in general: https://www.vox.com/future-perfect/2019/5/17/18624812/public...

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

#88

Post by godelski »

tntn wrote: post #45
gvggf wrote: post #16

This will sound harsh, but it isn’t meant to be. Scientists code better then you do science. This is simply a consequence Of a weeding out mechanism for those that have no coding skills. The only ppl who get away with no coding skills are important professor with grad students to do the coding. This isn’t to say that our skills are great, but a generic programmers (I.e. CS majors) science abilities are approximately…

> Science needs models based on mechanistic understanding of the underlying phenomena. A model that merely predicts is useful for engineers, not scientists I'm not sure I agree. I'm aware of quite a bit of supercomputing time that is spent doing lattice QCD calculations (which apparently some scientists find useful), and though I'm no quantum physicist I'm pretty sure there is not much of a "mechanistic understanding…

I work with the DOE and was at ORNL before Summit was released (I got to play on Summit-dev). When making these models there is A LOT of exploration happening. There's a whole class of visualization techniques called "in situ" that visualize data as it comes off the press (memory is then dumped because there's neither enough storage space nor can we write to disk fast enough). I'll tell you that there will be a lot of restarting those simulations because the scientists need to explore the data as it is going on. Going in the wrong direction? Made a small mistake that causes cells explode? Realize you're not looking in the right region of interest? You restart the sim (thank god for restart files, right?). Exploration is one of the most important things in research and it is getting more and more difficult. I believe this is what the gp is after. Having these understandings helps you explore the data better. Creating these tools is hard work and takes a lot of collaboration too.

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

#89

Post by fghtr »

claudius wrote: post #56
mariushn wrote: post #53

Earlier quoted context omitted.

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…

This is a very sad state of affairs, therefore I would like to bring your attention to a petition towards open sourcing all scientific (and generally tax-paid) software:

https://publiccode.eu

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

#90

Post by mariushn »

guzik wrote: post #86

Side note: I am the co-founder of Aidlab - a device and a platform that is widely used by biomedical scientists and students in their research ( https://www.youtube.com/watch?v=wY0YPOKNk88 ) In my free time I am working on my next project - an open-sourced platform where everyone can contribute to help fight death. The platform allows uploading anonymized, structured health records - publicly available. Why? Dying is…

> The platform allows uploading anonymized, structured health records - publicly available.

Hi, I also started something similar, but there was no interest: https://juvmed.com/plan

Would you please share more details publicly about your plan?

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