111 votes
Accepted

Can I use a section of my thesis to "soap-box" about a meta-issue regarding research?

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 ...
xLeitix's user avatar
  • 135k
106 votes

Will a paper be retracted if a flaw in released software code invalidates its central idea?

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 ...
Buffy's user avatar
  • 365k
88 votes

What good is my paper if the code is not open source?

I think you have this all correct. The world would be a better place if all papers released all of the software that is used to generate the results shown in it. And that's not just a personal thought ...
Wolfgang Bangerth's user avatar
75 votes

I wrote the code based on a paper's methodology; are there any legal problems with making it open source?

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 ...
ff524's user avatar
  • 109k
35 votes

Will a paper be retracted if a flaw in released software code invalidates its central idea?

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 ...
Dan Romik's user avatar
  • 190k
32 votes
Accepted

(Why) Is post publication peer review (not) taking off?

Most papers that are published are uninteresting. The median paper has less than one reader not counting the authors and the reviewers. The current reviewing system relies on a network of ...
Alexander Woo's user avatar
22 votes
Accepted

Where to upload research data after article publication?

Have a look at Zenodo (https://zenodo.org/). It is free, gives you a DOI, and you can link your article with the data. It lets you upload 50 GB by default, but you can ask for more space if needed.
Rob's user avatar
  • 4,572
21 votes
Accepted

Is it always OK to ask for a copy of the lecturer's slides?

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 ...
Wolfgang Bangerth's user avatar
21 votes
Accepted

Authors sharing accepted paper reviews

Unless it is an explicit part of the reviewing process, or there is some rare overriding concern, you musn't publish the referee reports you've received. This is actually a rare situation where ...
Arno's user avatar
  • 44k
20 votes

Can I use a section of my thesis to "soap-box" about a meta-issue regarding research?

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 ...
Maarten Buis's user avatar
  • 43.7k
20 votes

Is there a contradiction between open access/science positions adopted at many universities and their reliance on Google services?

Its a totally seperate issue. Other than closed science = bad, large monopolistic tech company = bad, I not sure I see any connection. Open Science/Open Access is about publishing all your data and ...
Ian Sudbery's user avatar
  • 38.3k
17 votes

Getting a dump of arXiv metadata

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 https://export.arxiv.org/oai2 This will ...
miku's user avatar
  • 316
17 votes
Accepted

Has anyone here tried this alternative peer review platform 'Peerage of Science'?

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% ...
Janne Seppänen's user avatar
17 votes

What is the status of foreign cloud apps in German universities?

It not surprising that there is little good information on this issue available. As has already been written, this is all about the European data protection directive GDPR ("DSGVO" in German)...
DCTLib's user avatar
  • 15.1k
17 votes

(Why) Is post publication peer review (not) taking off?

In a sense, it has taken off; you just need to change your definitions: in mathematics, most papers get peer reviewed after they have appeared on the Arxiv and are available to the public. Results ...
Federico Poloni's user avatar
16 votes

Why are papers accepted even if they don't release code or data to allow reproducibility?

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 ...
Cape Code's user avatar
  • 27.1k
15 votes
Accepted

Is there any obligation for authors of a paper to provide the dataset used in their research, upon request?

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 ...
Fomite's user avatar
  • 52k
14 votes

What good is my paper if the code is not open source?

Check out this famous paper (in AI) by Google. It described an algorithm by which an AI can learn to play a game - in this case chess and shogi - by playing against itself only, and how such an AI can ...
Allure's user avatar
  • 128k
14 votes

What good is my paper if the code is not open source?

While I won’t comment on your particular case, I think it’s useful to consider science as a whole. You should realize that computer scientists are uniquely able to distribute an entire exact ...
Gilbert's user avatar
  • 241
13 votes

Will a paper be retracted if a flaw in released software code invalidates its central idea?

@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 ...
J Fabian Meier's user avatar
12 votes

Will a paper be retracted if a flaw in released software code invalidates its central idea?

Will this lead to retraction? With due respect - that is the wrong question. You've said that, in your scenario: correction of this logic flaw leads to invalidation of the central idea of the ...
einpoklum's user avatar
  • 39.1k
12 votes

What is the status of foreign cloud apps in German universities?

I am not aware of any official guideline to avoid using foreign cloud applications at German universities. However, I only know what is correct for my university. The federal system in Germany makes ...
Snijderfrey's user avatar
  • 8,961
12 votes
Accepted

Sharing research-related codes and datasets: Split them, or share them together on a single platform?

Each platform has its uses, so it's best to use both GitHub for your code and a scientific data archival repository, such as Zenodo, for your code and data. GitHub allows you to share your code in a ...
Diomidis Spinellis's user avatar
11 votes

Is it normal for things to be so cutthroat, and what to do about it?

Reality is very complicated. It is not one way or the other, often a mixture, and lots of judicious decision-making is required. Some environments are nicer than other, some people more trustworthy ...
Captain Emacs's user avatar
11 votes

Should I review differently when the review itself will be public?

In theory we should be as thoughtful and careful regardless. In practice I found that I paid more attention to correct spelling and formatting for reviews I knew were going to be available online. I ...
Maarten Buis's user avatar
  • 43.7k
11 votes
Accepted

What is the status of foreign cloud apps in German universities?

A bit more background: Teaching There is a parallel discussion happening about schools and their teaching tools during lockdown/school closures. (Both schools and universities in Germany are owned by ...
cbeleites unhappy with SX's user avatar
10 votes
Accepted

How do you validate a scientific paper that uses a non-public cell/animal line?

You've published the results in a prestigious journal. In most of those journals, that means you've promised to make those mice available to other researchers. For example, Nature says An inherent ...
iayork's user avatar
  • 13.4k
10 votes

Why are papers accepted even if they don't release code or data to allow reproducibility?

Sometimes reproducing results is as much work as producing them. If I give you my code, you not only have to check whether it gives the results I published, but also whether it is correct. Reading ...
Jan-Christoph Schlage-Puchta's user avatar
9 votes

Will a paper be retracted if a flaw in released software code invalidates its central idea?

Let me give you an answer that does not appeal to the grand ideals of science, like reproducibility and advancement. You are asking "what is in it for me", which I - as a person who spends most of my ...
nabla's user avatar
  • 13.4k
9 votes

What is the status of foreign cloud apps in German universities?

It's mostly about DSGVO (the Datenschutz-Grundverordnung). I don't know too much about it, but, if I understood correctly, it forbids that university staff stores data which affects their students on ...
Dirk's user avatar
  • 38.1k

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