111

I think this is a fairly bad idea, for the following reasons: It's largely shouting in the woods. Let's face it, while you may feel that your thesis is the only piece of work that's "truly yours", it will likely also be the least-read piece of your career. More to the point, your (presumed) target audience (young physicists in other departments) are very ...


107

If the main idea in the paper has been invalidated by the correction in the code, you would do well to try to retract the paper yourself. This is just a point of professional ethics. It also protects you in a way from future claims if people don't examine everything thoroughly. The journal may not be able to actually retract the paper, but might be able to ...


75

You are not required to get permission to implement an idea you have read about in a paper, or to make it open source. The paper is protected by copyright, but this only protects the text and images in the paper (the expression of the idea), not the idea itself. The copyright on the paper does not prevent you from creating your own realization of the idea ...


35

Will there be any positive gain thanks to the publishing of the code to me? Publishing the code is necessary to make the calculation reproducible and the results verifiable. If I were the referee of your paper I would likely insist that you publish the code. So the “positive gain” would be that your paper will not be rejected outright. It will also help ...


34

I had faced this exact situations a few years ago. I had developed an open source project, which went pretty popular and started being used by many corporations across the globe. Since, I was looking for strengthening my presence in academia, I planned to write a paper on it and sent to a decent journal. The result was rejection with a plethora of useful ...


31

I suspect that this is a solution in search of a problem. Most likely journals aren't making LaTeX versions of papers available because they don't see a demand for such a service from the side of the readers; this would take effort to implement and maintain; and some authors would object to the idea of making it easier for others to reuse (read: plagiarize) ...


28

I'm the main developer of several open-source libraries, one published and one under review, so I can give you a pretty up-to-date overview on open-source in the machine learning community. This may differ for your field, but probably not much. Whether or not your university will allow you to open-source and/or publish depends entirely on them. Based on my ...


24

I think your question is actually about why publishers don't make the LaTeX source of papers available to readers rather than why publishers don't accept submissions in LaTeX form. You might want to clarify your question. Some publishers prefer to accept PDF versions of paper for review, but then ask for LaTeX source code after the paper has been ...


23

My main confusion was not realizing that The Open Archives Initiative Protocol for Metadata Harvesting is a separate protocol, not a subset of arXiv API. In this case, the relevant queries are ListIdentifiers (10k items per query) and ListRecords (1k items per query). To get just identifiers we need to write: http://export.arxiv.org/oai2?verb=...


21

Here's a relevant study on computer science systems research that addresses your first question, "What percentage of research articles are provided with their source code?". The study is described in a tech report: "Measuring Reproducibility in Computer Systems Research." Christian Collberg, Todd Proebsting, Gina Moraila, Akash Shankaran, Zuoming Shi, ...


21

It is always appropriate to ask. But some people are unwilling to share their slides for a variety of reasons (none of which I think are particularly good, for basically the reasons you mention in your quote). So you may or may not get the slides, but it is certainly ok to request them!


20

The purpose of a thesis is to show that you can do independent research. Your advisor and your committee members will read your thesis to see if you achieved that goal. Anything in the thesis that does not help them determine that, wastes their time (not too much, as they will probably just skip it, but still it risks annoying people whom you don't want to ...


19

Yes, you should. But on the other hand, do not necessarily assume it will be accepted easily. Some advices: Your best bet is a demo track in a CS conference (as Peter suggested). For CS demo apps maximum number of pages is usually four, so use them wisely. Check all major CS conferences (VLDB, SIGMOD, EDBT and those focusing on Linked Data - RDF). Check ...


18

This isn't a peer-reviewed article, but nonetheless it's worth linking to because it specifically addresses your question, albeit as an n=1 case: Bruna, E. 2014 THE OPPORTUNITY COST OF MY #OPENSCIENCE WAS 36 HOURS + $690 In this blog post, a biologist Emilio Bruna states it took about 25 hours of his time to appropriately document his code (associated with ...


17

Your license is not the GPL if you add additional restrictions, and your restrictions may turn out to be incompatible with the GPL in subtle ways. Consult an IP attorney. Fortunately for you, even if your code is GPL, many companies might not want to use it because they might worry about it infecting their product. So, you might be able to charge them for a ...


17

Legally speaking, any disclosure of an invention prevents it from being patented: it counts as prior art. Disclosure includes not only publication but also public demonstrations, as well as sales (except possibly when subject to a non-disclosure agreement). This is part of the novelty requirement of patentability. There is an exception: in some countries, ...


17

There are multiple answers to your question. Academic publishing assumes good faith. At least in the circles where the majority of people are genuinely interested in the advancement of science. This is the only viable mode of sharing scientific information between adults, although it sometimes fail as we all know it. Publishing should firstly serve the ...


17

Peerage of Science received 102 submissions in 2017. Some submissions get zero reviews, but those that are reviewed have a decent chance of getting publishing offers from participating journals: 60% received at least one publishing offer, some got 4 or 5 offers. The other submissions - probably - got negative reviews and then of course do not attract ...


16

Some disadvantages could be: People may expect you to maintain the code. If you don't maintain it, the code may be rendered useless at some point. You might feel forced to document the code. This is actually an advantage, but many people would not realise that ;) You might have to work on cleaning up the code. Exactly the same point as above applies, if you ...


16

Shameless plug: I wrote a generic OAI harvesting tool, that will harvest Arxiv just fine. It's called metha and consists of a few commands: $ metha-sync http://export.arxiv.org/oai2 This will download all data up to the last full day (it will take a couple of days). The XML API responses are compressed and placed under ~/.metha directory. Metha will use ...


16

The Kuiper belt object Haumea was perhaps discovered by a second group through looking at observation logs - it was very controversial. The controversy has a wikipedia article


15

Great question! Unfortunately, I think there are not going to be great answers. Three ideas have come up in my discussions with users of registry data: Describe data access procedures completely: Be as transparent as you possibly can be about how you acquired the data, how others can acquire them, and what the policies and costs associated with acquisition ...


15

Inherently? No. While it might be good for science generally, they're under no obligation to do so. That being said, some funding agencies require data be made available as a condition of their support, and some journals require it as a condition of publication. Absent that though, there's no obligation to do so.


14

Yes, of course anyone can publish an open science project. As many of us in the scientific community wish would happen, the project should be judged on merit, not who initiated it, where they studied, or what their background or education is. These principles are enshrined in the San Francisco Declaration on Research Assessment (DORA), which have been ...


14

Use a license. Different open science journals/repositories/etc. allow you to license your publication(s)/data/etc. Some allow you to choose a license; others do not. Others may have different repositories. For example, arXiv gives submitters a licensing choice: arXiv does not ask that copyright be transferred. However, we require sufficient rights to ...


13

@Buffy is certainly right that Science itself gains a lot if people publish their code. Papers without code (the norm in many scientific areas) are hard to reproduce or build upon. But you ask what you gain from this, or if it might harm your career. First of all, it is unlikely that somebody finds a major flaw in your program and it is even more unlikely ...


12

I found a service that can create custom badges: shields.io. Using the arXiv background color (Firebrick #B31B1B) I was able to create a badge that looked more or less "official". An example of their template and my specific use case: http://img.shields.io/badge/<SUBJECT>-<STATUS>-<COLOR>.svg http://img.shields.io/badge/math.CO-arXiv%...


12

The Journals: Generally, open sourcing a code should not be an obstacle for publication. To the contrary: there is a movement to make as much academic code as possible open - see for example GitXiv. The only problem I see is that open sourcing the code prior to publication may impact the anonymity of blind review. I have however read and authored multiple CS ...


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