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Ask HN: Should I publish my research code?

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Re: Ask HN: Should I publish my research code?

#231

Post by goodpoint »

skrebbel wrote: post #163
goodpoint wrote: post #101

Earlier quoted context omitted.

This is not what licenses are for!! They are not statements about the quality of your work or anything similar. Use standard and well understood licenses e.g. GPL for code and CC for documentation. The world does not need more license fragmentation.

This has explicit usage limitations that matter in science land, which is very much the kind of thing that belongs in a license. Eg: You are permitted to use the Program to validate scientific claims submitted for peer review, under the condition that You keep modifications to the Program confidential until those claims have been published. Moreover, sure, lots of the license is text that isn't common in legal docume…

> clearly communicate intent

Again, this is not how a license work. You can express your intents, ideas and desires in a README file and in many other ways.

The license is nothing more than a contract that provides rights to the recipient under certain conditions. Standing up in court is its real power and only purpose.

That's why we should prefer licenses that stood up in court and have been written by lawyers rather than developers or scientists.

Re: Ask HN: Should I publish my research code?

#232

Post by bumby »

UncleOxidant wrote: post #212
bumby wrote: post #176

Earlier quoted context omitted.

What are your thoughts on including pseudocode within the paper directly? It seems to clear up some of the ambiguities while adding brevity since it doesn't provide the somewhat frivolous details of implementation. I think it also limits some of the potential stylistic critiques.

It's not a bad idea to include pseudocode, but my pet peeve is that there's really no standard for pseudocode. I tend to write pseudocode that looks like python. I did that in an internal paper for a group I worked in a few years back and the manager of the group made me change it to look more like C (complete with for loops as: for(i=0; i<x; i++) which made no sense to me).

Oh, haha, then disregard my intuition that it would help avoid stylistic critiques :-)

Re: Ask HN: Should I publish my research code?

#233

Post by mataug »

My take on this is that some code is 10X better than no code.

There have been times when I've had to abandon incorporating an idea presented in a research paper because the paper doesn't have enough information for me to implement it in code. I could've made a lot of progress with some proof of concept code, even if it wasn't clean.

Re: Ask HN: Should I publish my research code?

#234

Post by gmiller123456 »

anon_123g987 wrote: post #108
guy-brush wrote: post #56

In my view and personal experience, the pros outweigh the cons: * You increase the impact of your work and as a consequence also might get more citations. * It's the right thing to do for open and reproducible research. * You can get feedback and improve the method. * You are still the expert on your own code. That someone picks it up, implements an idea that you also had and publishes before you is unlikely. * I nev…

> It's the right thing to do for open and reproducible research. Everybody here talks about how publishing code helps (or even makes possible) reproducibility, but this is not true, on the contrary, it hinders it. Reproducing the results does not mean running the same code as the author and plotting the same figures as in the paper. This is trivial and good for nothing. Reproduction is other researchers independently…

"Reproducing results" in a scientific context doesn't mean taking the original author's data and going through the same process. It usually means taking different data and going through the same process. Having code on hand to put new data through the same process makes that a lot easier.

Re: Ask HN: Should I publish my research code?

#235

Post by larrydag »

Here's a good example. The Fisher's iris flower data was released with his work in a 1936 paper. It was used as an example of his discriminate analysis. This data set has been repeatedly used over and over to show examples of cluster analysis and segmentation. Many statistics teachers use it in their curriculum. You never know where the research could lead to growth and development in a field.

https://en.wikipedia.org/wiki/Iris_flower_data_set

Re: Ask HN: Should I publish my research code?

#236

Post by tpoacher »

> The paper itself is enough to reproduce all the results.

Unlikely. Following the algorithm from scratch may produce "similar" results, but not "reproduce", bugs and all. The only thing that can do that is your code.

Plus, typically, when you set out to reproduce a paper from only the algorithmic description, it's typically not until you're 2 or 3 weeks into coding that you realise the original paper made many assumptions in the code that were not explicitly stated in the paper.

> However, the implementation can easily take two months of work to get it right.

An even more important reason why you should release your code.

> In my field many scientists tend to not publish the code nor the data.

A regrettable state of affairs indeed.

> They would mostly write a note that code and data are available upon request.

I have personally come across many cases where this promise could no longer be honoured by the time of the request. Publish the code.

> I can see the pros of publishing the code as it's obviously better for open science and it makes the manuscript more solid and easier for anyone trying to replicate the work.

It is also increasingly a requirement for funding bodies

But on the other hand it's substantially more work to clean and organize the code for publishing

> Then don't. Release it under the CRAPL, stating as much. It is still better than nothing.

> it will increase the surface for nitpicking and criticism (e.g. coding style, etc).

If you were an entrepreneur hoping to peddle snake oil and not get found out, then I would see your point. But you're a scientist, you're supposed to welcome such criticism and opportunities for improvement. If anything, you might even get collaborations / more publications on the basis of improving on that code.

> Besides, many scientists look at code as a competitive advantage so in this case publishing the code will be removing the competitive advantage.

I would sincerely not feel very comfortable calling such people "scientists".

Re: Ask HN: Should I publish my research code?

#238

Post by actually_a_dog »

paulluuk wrote: post #137
LandR wrote: post #98

Earlier quoted context omitted.

> "Generally, academic software is stapled together on a tight deadline; an expert user has to coerce it into running; and it's not pretty code. Academic code is about 'proof of concept.'" What do you know, it turns out the professional software developers I work with are actually scientists and academics!!

They don't call it "Computer Science" for nothing ;)

Maybe a little OT, but, I'd rather it be called "computing science." Computers are just the tool. I believe it was Dijkstra who famously objected to it being called "computer science," because they don't call astronomy "telescope science," or something to that effect.

Re: Ask HN: Should I publish my research code?

#239

Post by cycomanic »

As a fellow scientist I would say go for it. I know people who had a vast amount of citations (>2000) for a paper accompanying a code/program release that they made at an opportune moment (they released a code for designing/analysing photonic crystals just when the field was taking off).

Now in the vast majority of cases you will only get a couple of people looking at your code (my experience so far), but still I think it's worth it. The question is, clean up the code or not. Ideally you would, because it increases the chance of someone using it by a lot. On the other hand with the realities of academic work, this is largely underappreciated.

So I recommend to find a balance, clean up enough so it is reasonably straight forward to run the code. Write a good readme that points to the paper and gives the appropriate citation.

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