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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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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
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
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
3 votes
2 answers
558 views

Publish pre-research code on Github?

In preparation for future PhD work I came up with some ideas & protypes for software components that might later become scientifically relevant, both from a CS and application viewpoint. My ...
Victor Mataré's user avatar
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
3 votes
1 answer
72 views

Where to host lots of experiment data [duplicate]

We are a masters degree student group who have conducted a quite significant study which has pulled a lot of interest from the HCI/MI communities in CS. We have been encouraged to host all our data ...
Dennis's user avatar
  • 133
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
3 votes
0 answers
88 views

Is software packaging considered as a service duty? [closed]

I create from scratch and/or maintain software packages on behalf of the Debian GNU/(Linux|kFreeBSD) distribution; Debian serving as base for other apt-distributions as Ubuntu. Most of `my' packages ...
Spherical Triangle's user avatar
-1 votes
1 answer
978 views

open source programs for plotting? [closed]

Short version: Any suggestion on an Open-Source Software alternative to Grapher/Surfer/Origin/SigmaPlot? Details: This is not a shopping question. As a scientist I explore and plot data all the time. ...
terauser'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
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
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
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
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
4 votes
2 answers
187 views

Sharing data (not a data set) with a research paper

How to share data accompanying a research paper? I know there exist some places to share datasets, but sometimes I would like to share data that are not data set (e.g. experiment parameters, results, ...
Franck Dernoncourt's user avatar
1 vote
2 answers
361 views

Is there something like a "peer-review paper"?

Journals like CVPR (IEEE Conference on Computer Vision and Pattern Recognition) have a peer-reviewing process. Depending on the journal (or the publication published after a conference - is that also ...
Martin Thoma's user avatar
  • 1,268
2 votes
1 answer
74 views

Providing APIs instead of directly providing data sets

Several academic paper hosts such as PubMed and Cochrane give some machine readable access to their data by providing APIs, but do not directly provide the data sets. Is there any reason why they don'...
Franck Dernoncourt's user avatar
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
1 vote
1 answer
313 views

Advantages/disadvantages of bundling source code from separate, related papers?

Say that you have several papers, each with a set of experiments, in which the source code overlaps appreciably. If you wish to release the code for each paper, which is better: isolate the relevant ...
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
2 votes
1 answer
95 views

Concern about possible conflicts between research sharing policies

Funders, publishers, institutions and others are increasingly moving towards policies that are aimed at sharing research. The degree of openness — and other stipulations in those policies &...
Daniel Mietchen's user avatar
10 votes
4 answers
490 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
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
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
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
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
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
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
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
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
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
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
5 votes
2 answers
2k views

Does any university require students to release their source code in order to graduate?

I wonder whether there is any university that requires students to release their source code (or at least part of it) in order to obtain their PhD.
Franck Dernoncourt's user avatar
0 votes
2 answers
172 views

Multiple outlets publication

Perhaps, it's a naive question, but I'd like to have some clarification of my own thoughts on the subject. I'm curious about what is the rationale or need of 1) transferring copyright from authors of ...
Aleksandr Blekh's user avatar
5 votes
3 answers
237 views

Are there any academic data sets that force users to release any source code written to analyse them?

I am curious to know whether there exists any data set that forces users to publicly release any source code written to analyse it.
Franck Dernoncourt'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
2 votes
1 answer
120 views

Is it inappropriate to share journal article reviews?

I want to put the LaTeX source files for a paper that I just published up on GitHub (technically they are already there, but private). Is it inappropriate to include the (anonymous) reviews and my ...
petebachant'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
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
3 votes
0 answers
261 views

Reference on the time it takes for a source code used for a research article to be released

Is there any research/study/survey/... that looked at how much time it takes for the authors of a research article to release the source code? Ideally I'm looking for an approximation distribution. ...
Franck Dernoncourt's user avatar
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
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
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
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
0 votes
1 answer
3k views

Is there a proper format to cite open source software? [duplicate]

In my research I used a lot python libraries that I need to cite, I wonder if there is an accepted format for citing open-source software? Do I just put them together with all other references? Do I ...
Akavall's user avatar
  • 1,052
4 votes
4 answers
3k views

What software license allows me to have GPL for academic use and paid use by industry for my open-source project?

I have spend many years during my PhD developing a code base and decided to open-source the code when I finished. It's currently under GPL. The code is used by many different research group around the ...
boyfarrell's user avatar
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
2 votes
1 answer
85 views

Which licence choose for a new academic computing language?

Disclaimer: I am not sure this is the right place to ask the question, but since it is directly related to academic work, I though I'll give it a try. If it is not, please feel free to redirect ...
Wiliam's user avatar
  • 3,476
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
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