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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?

#101

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...

Probably not what you want to hear, but putting a matplotlib REST service inside of a container would be a pretty good start. Apps can talk over a local IP, the interface should be usable from curl.

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

#102
Come work with us at Plex Research. A huge problem our founder ran into while doing drug discovery research was that there's tons of data in the world, but no one is using it because it's all in thousands of different places. As a programming, it was crazy to me that even the most advanced organizations in industry (Novartis, Sanofi) or academia (Harvard, Stanford, ...) are still keeping many important datasets in Excel.

We're pulling together all of the world's biomedical research data, structuring it as a graph, and allowing research access all of it as easily as Google does the web:

https://www.plexresearch.com/products.html

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

#104

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…

You might be interested in OpenReview, which is doing something like this, mainly in the ML/AI academic community.

(Disclaimer: I’m one of the developers)

https://openreview.net

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

#105
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 prevent…

Two things that might be of use

1. SQLite can easily import multiple GB of CSV data, process it in memory, or persisted to disk, a great tool for analyzing datasets up to the low 10s of gigs.

2. XSV, https://github.com/BurntSushi/xsv

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

#106
The biggest problem scientists in academia face is that they can’t do actual research. They spend most of their time doing stuff that doesn’t matter. So probably the biggest leverage you have is to reduce the time they spend doing stuff that doesn’t matter.

The most effective way to do that is to establish an alternative form of institution that focuses only on research (and teaching if you like - teaching is not the problem). A tough challenge. One line of attack would be to contrast your costs with academia’s full economic coating model.

Failing that, here’s some things you can do:

- develop a paper reference system that actually works well. Mendeley is the best there is and it’s (IMO) rubbish. Poorly designed.

- build a typesetting system that’s an alternative to latex but is WYSIWYG. Particularly important outside of CS.

- build a free conference organising / review tool that works. EasyChair is popular and utter garbage.

- build tools to automate the grant writing process. A step by step system to create a grant proposal, tailored to each grant scheme. Yes, this would potentially damage the grant application process. But it doesn’t make any sense anyway, so at least this would free up a few years where academics could churn the required proposals out fast until you were somehow disallowed.

- provide free slide materials, examples, exercises for all the main CS etc topics. Some kind of “piece it together” kit so lecturers could save time making slides and other materials that tick boxes. Diagrams, for instance, would be very useful. Pseudocode too.

NB you probably won’t make any money.

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

#107

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...

Oh god yes how did I forget. Bury Matplotlib forever, please, someone, for the love of science.

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

#108
I work on a project called OpenReview (https://openreview.net) that aims to improve scientific peer review by encouraging transparency and research on the peer review process itself. Right now most of our activity is within the machine learning academic community, but we have plans to spread into other areas of computer science and more.

We’re looking for developers, if you’re interested: https://codeforscience.org/jobs?job=OpenReview-Developer

Let me know if you want to learn more and we can find a way to connect.

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

#109

The biggest problem scientists in academia face is that they can’t do actual research. They spend most of their time doing stuff that doesn’t matter. So probably the biggest leverage you have is to reduce the time they spend doing stuff that doesn’t matter. The most effective way to do that is to establish an alternative form of institution that focuses only on research (and teaching if you like - teaching is not the…

>develop a paper reference system that actually works well. Mendeley is the best there is and it’s (IMO) rubbish. Poorly designed.

Zotero works wonderfully for me. And it's open, which is a must.

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

#110

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...

Probably not what you want to hear, but putting a matplotlib REST service inside of a container would be a pretty good start. Apps can talk over a local IP, the interface should be usable from curl.

That's really close to how gnuplot is used.
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