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Questions tagged [open-science]

Questions concerning "Open Science", or research done in full view of the public eye, with a focus on accessibly and reproducibility, including tools to enable such access.

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66 votes
8 answers
12k views

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

I have been working with my research group on a number of papers in a certain area of Computer Science. These papers have a certain portion which is theoretical (i.e. contains theorems, formalisms, ...
Grzegorczyk's user avatar
53 votes
8 answers
8k views

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

I'm a big believer in FOSS (Free Open Source Software), and a physics graduate student. I believe a lot of current researchers are not aware of free solutions to problems that are usually encountered ...
thosphor's user avatar
  • 2,143
49 votes
4 answers
7k views

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

I coded the methodology based on the paper "Free Water Elimination and Mapping from Diffusion MRI" and I am curious if I am legally bound to take permission from the authors or the journal in making ...
user57865's user avatar
  • 479
44 votes
6 answers
6k views

Should I write a paper on open-source software I've built?

I have been fairly active in the open-source software community with a few projects that have gotten some attention. However, my reputation in the academic/publications world is a little bit low and I'...
Luca Matteis's user avatar
  • 1,157
43 votes
7 answers
13k views

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

Say I have written code that performs a physics calculation. After this, I get a paper published based on the results of the code. In the interest of advancing the progress of science, I upload the ...
Tejas Shetty's user avatar
40 votes
4 answers
6k views

Getting a dump of arXiv metadata

Prompted by discussion in this post on Meta.MathOverflow.net I got interested in comparing usage of tags from MathOverflow to submissions in the respective disciplines of arXiv. (Vide a similar idea ...
Piotr Migdal's user avatar
  • 26.4k
32 votes
5 answers
4k views

Why don't publication venues systematically make the LaTeX source of papers available?

I wonder why most publication venues don't systematically make the LaTeX source for published papers available? (which implies systematically asking authors for the LaTex source) LaTex source are ...
Franck Dernoncourt's user avatar
30 votes
4 answers
5k views

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

Recently, we had a lecture about Reproducible research on of the slides was: Reproducibility: start from the same samples/data, use the same methods, get the same results. Replicability: ...
llrs's user avatar
  • 1,182
29 votes
5 answers
314 views

What criteria does a research project need to match to be called open science?

What kind of formal or non-written rules/requirements does our project need to match and follow so we can say that our project is open science? Is it only about research data which should be ...
kenorb's user avatar
  • 883
27 votes
2 answers
9k views

When can I safely use CC-BY license on arXiv?

On arXiv one can license a preprint on one of the following (see also a note on arXiv on licenses): arXiv.org perpetual, non-exclusive license to distribute this article (Minimal rights required by ...
Piotr Migdal's user avatar
  • 26.4k
24 votes
4 answers
510 views

What are the disadvantages of opening the source of your own science tools

I am currently finishing my PhD thesis and, as a great deal of the job was to create tools and protocoles, I am considering putting the different scripts I wrote on open source directories (such as ...
Wiliam's user avatar
  • 3,476
23 votes
4 answers
3k views

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

From what I heard, in German universities there is a push against foreign cloud applications such as Microsoft Office 365, Google G Suite, Github, and even Doodle. The DFN offers some alternatives, ...
Federico Poloni's user avatar
23 votes
2 answers
774 views

Why and how commonly are scientists concerned about open peer review?

Some years ago I published an article in a Copernicus Open Access Journal. They have a peer review process called Interactive Public Peer Review, i.e. the pre-print and the reviews are open access. ...
FuzzyLeapfrog's user avatar
22 votes
4 answers
2k views

How much effort do researchers take to publish their source code?

When publishing a paper, some researchers publish the source code used for the paper. Is there any research/study/survey/... that looked at how much effort do researchers take to publish their source ...
Franck Dernoncourt's user avatar
21 votes
4 answers
376 views

How to deal with sensitive individual data in open science?

I work with governmental register data, which includes sensitive information about individuals, and therefore cannot make datasets available to the public lest I risk violating the privacy of my ...
Kenji's user avatar
  • 2,717
20 votes
9 answers
5k views

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

I know, this is a bit of a broad question. But looking at the developments and having experienced a reasonable amount of pain with established publishers and their either complex, slow, or restrictive ...
mfg's user avatar
  • 1,471
20 votes
2 answers
312 views

How to protect scientific open research from being patented?

For instance, say a published paper demonstrated new possible invention or technology by analysing the data and publishing it publicly. Is there any way to protect such research or its data which can ...
kenorb's user avatar
  • 883
19 votes
4 answers
6k views

I want to opensource my code. Is it legal? Can I still publish?

I am a PhD (stipend) student at a Max Planck Institute (for a biological science) here in Germany. I came here to write software, but ended up spending practically all my time doing wet-lab work. As a ...
Wetlab Walter's user avatar
19 votes
2 answers
4k views

Reference on availability of source code used in computer science research articles?

I have several questions related to open-sourcing the source code used for a research article. Is there any research/study that addresses any of the following: What percentage of research articles ...
Franck Dernoncourt's user avatar
18 votes
2 answers
276 views

How can I protect open research from being plagiarised?

Since open research is about publishing data which are accessible to all, what kind of actions should I take to prevent open research from unauthorised copying or its data being plagiarised without ...
kenorb's user avatar
  • 883
17 votes
7 answers
4k views

An example of a researcher being 'scooped' as a result of working openly?

A reason that researchers sometimes give for not working in the open is the fear of having a publication 'scooped' by a competing researcher. Is there a clear, verifiable example where scooping has ...
tomp's user avatar
  • 437
17 votes
2 answers
1k views

I've reproduced a paper: where shall I share the code and findings?

The majority of papers don't share their code. However, I sometimes want to reproduce the results, and therefore re-code the experiments to try to reproduce the papers. Where shall I share the code, ...
Franck Dernoncourt's user avatar
15 votes
2 answers
676 views

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

I have just learnt about the details of this platform, located below: https://www.peerageofscience.org I am interested in trying out but none of my colleagues has experimented this platform. I am ...
Scientist's user avatar
  • 9,234
15 votes
2 answers
440 views

Are there any journals or conferences that take into account the availability of the source code when selecting the papers to publish?

Quite too many times I have read in a research article claiming that the source code will be made available, and, when I look for it, it turns out that the source code still hasn't been released. Are ...
Franck Dernoncourt's user avatar
15 votes
3 answers
411 views

Demand code and/or data as a condition of peer review?

It is still relatively uncommon for social scientists to share data or code as a part of the peer review process. I feel that this practice runs contrary to notions of replicability and ...
joemienko's user avatar
  • 251
14 votes
4 answers
2k views

Authors sharing accepted paper reviews

For transparency, I would like to share my accepted papers' anonymous peer reviews, if my coauthors unanimously agree. Some journals partner with websites such as openreview.net (which share reviews ...
nbonneel's user avatar
  • 243
14 votes
5 answers
2k views

Where to upload research data after article publication?

As the title says, I wish to publicly share a dataset used in one of my articles which has already been published (by MDPI, if that helps). I do not think the data is worthy of an article by itself, ...
Jakinduria's user avatar
14 votes
4 answers
260 views

Scientific hackathons or other intense voluntary bottom-up events

In programming there are many hackathons - intense voluntary one day-week events, where participants collaboratively attack problems. They may be proposed by a company, NGO, participants or a group; ...
Piotr Migdal's user avatar
  • 26.4k
12 votes
3 answers
2k views

Flair/Badge for arXiv paper?

This is borderline trivial, but in my attempt to publish my work in a public repository, I've found badges at the top of my README.md to be useful. For example, using Zenodo, I can create a badge that ...
Hooked's user avatar
  • 439
12 votes
5 answers
444 views

Are virtual machines good for reproducibility and open science?

Virtual machines (VMs) provide a way for scientists to package not only scientific software, but also data, external dependences, and even entire operating system configurations, facilitating a ...
Daniel Standage's user avatar
12 votes
2 answers
675 views

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

Recently my lab published a paper that uses a mouse line from another lab. Without going into too much detail since not everyone here is a Biologist, this other lab has a mouse with a reporter gene ...
Wetlab Walter's user avatar
11 votes
1 answer
825 views

Is there a Ronin alternative in Europe? How to be an independent scientist in the EU?

I am a senior postdoc in a theoretical/computational field and for various reasons I am quite tired of jumping from one postdoc to another (have to switch cities/continents every few years, and many ...
demitau's user avatar
  • 1,246
11 votes
3 answers
874 views

How should I share (cite) my datasets and R analysis/code files in my thesis?

I'm trying to follow some of the best practices of the "open science" movement. In my thesis, I've performed all of the analyses in R (a non-proprietary, open-source program for analyzing data), and ...
Tyler's user avatar
  • 211
10 votes
3 answers
188 views

Can open science project be performed/published by non-scientists?

In other words, can anybody publish an open science project, or does the author need to have some specific title or at least study the subject in order to receive some positive feedback from the ...
kenorb's user avatar
  • 883
10 votes
5 answers
361 views

Are there any proposals to make sharing code and data with publications a requirement?

Depending on the project, many researchers have to rewrite code and reproduce datasets from previous works in order to perform experimental evaluations. Although some dataset are understood to contain ...
Rubens's user avatar
  • 203
10 votes
4 answers
491 views

Risks of shifting to post-publication review

I've heard some compelling arguments from open science advocates for a system of reviewing scientific research outputs that focuses almost exclusively on post-publication peer review. The idea is that ...
Daniel Standage's user avatar
10 votes
2 answers
83 views

Are there any organisations which approve or manage open science projects?

Are there any organisations/foundations/hubs which manages/approve independent open science projects which are accepted and well recognised within mainstream scientific circles? For instance, what if ...
kenorb's user avatar
  • 883
10 votes
2 answers
524 views

Releasing one version of a Scientific Paper under an Open License

I am going to release a Technical Report that will be archived and made available online by the university's library. An abridged version of the work was accepted by a peer-reviewed conference and ...
clstaudt's user avatar
  • 1,003
9 votes
3 answers
2k views

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

I am a postdoc in mathematics. I like doing math, but I do not feel like I belong to a community, in the true sense of the word. My vision of mathematical research is that it should be a massive ...
anonymous cat's user avatar
9 votes
1 answer
526 views

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

I've recently read a curious article on machine learning where the author used a very interesting dataset, which would normally take thousands of man-hours to recreate. Now, assuming I would like to ...
user avatar
9 votes
2 answers
1k views

How would you decide to publish (or not) in F1000Research or other journals with alternative peer-review methods?

As pointed out by altmetrics, “Peer-review has served scholarship well, but is beginning to show its age. It is slow, encourages conventionality, and fails to hold reviewers accountable.” Not all ...
bbarker's user avatar
  • 269
9 votes
3 answers
860 views

What exactly would count as copyright infringement in a replication paper?

I have been following the review process of a replication journal In particular, it has an open review which can be seen. On a particular submission they are having a debate about whether copying ...
stochastic_random's user avatar
9 votes
3 answers
202 views

Using grants to make donations to institutions for using their resources/products?

In my academic area I constantly use free software/products such as Linux, Python, SageMath, Octave, Wikipedia, etc. I know that one can include software costs such as Matlab, Mathematica, Maple, ...
Roger's user avatar
  • 479
9 votes
1 answer
601 views

Good first-time study pre-registration website/service

For my PhD thesis in artificial intelligence, I am designing a human study where subjects interact with multiple versions of an algorithm and rate their experience. I like the idea of pre-registering ...
Martin Modrák's user avatar
8 votes
3 answers
1k views

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

I want to share both (1) programming codes and (2) datasets related to a research project. While I know some suitable platforms superficially, I cannot gauge their pros and cons in too much depth ...
anpami's user avatar
  • 8,744
8 votes
1 answer
285 views

How should I split my code and data between an open repository and the article's supplementary files?

I am working on a paper that involves some data and a piece of code to analyse the data. I want the results of the analysis to be reproducible and the code to be open. This concept of "reproducible ...
Gimelist's user avatar
  • 2,968
8 votes
1 answer
825 views

Why are some academic research datasets not available to people who only have freely available email addresses?

Why are some academic research datasets not available to people who only have freely available email addresses? For example, ImageNet is not available to people only have freely available email ...
Franck Dernoncourt's user avatar
8 votes
1 answer
174 views

What does "open" mean in science?

I understand that open science is based on open data, open access, open source, open methodology, etc. However, what does "open" exactly mean in context when we talk about "open science"?
kenorb's user avatar
  • 883
8 votes
2 answers
733 views

Pedagogical pros and cons of requiring undergraduate students to follow open/reproducible research practices?

I regularly teach an undergraduate course in which students are expected to complete projects that involve writing code. I also supervise undergraduates in other project and thesis work that involve ...
ff524's user avatar
  • 109k
7 votes
5 answers
5k views

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

Weeks ago I attended a lecture/seminar in NYU Shanghai, and I am not a student nor an alumnus of it. After the lecture I attempted to ask if I can have a copy of the slides because the content is so ...
Lzn's user avatar
  • 281