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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What Journals include raw experimental data in publication

I was reading an article from Nature Immunology and found that the journal actually includes all the raw data for each figure. I found such practice very helpful, since we can re-analyze the raw data ...
3
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2answers
81 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 ...
48
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4answers
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 ...
3
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1answer
46 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 ...
21
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4answers
2k 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: ...
2
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0answers
65 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 ...
0
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1answer
109 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. ...
9
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1answer
313 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 ...
8
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2answers
177 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 ...
12
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2answers
469 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 ...
7
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1answer
150 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 ...
30
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5answers
3k 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 ...
3
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2answers
82 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, ...
1
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2answers
220 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 ...
2
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1answer
66 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'...
14
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2answers
311 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, ...
1
vote
1answer
74 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 ...
13
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3answers
265 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 ...
2
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1answer
85 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 &...
6
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4answers
200 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 ...
17
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4answers
4k 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 ...
7
votes
2answers
81 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"?
19
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2answers
76 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 ...
11
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5answers
48 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 ...
16
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7answers
416 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 ...
9
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3answers
32 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 ...
18
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2answers
48 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 ...
17
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2answers
97 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 ...
10
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2answers
51 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 ...
28
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6answers
107 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 ...
5
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2answers
552 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.
0
votes
2answers
132 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 ...
4
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2answers
144 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.
14
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4answers
1k 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 ...
2
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1answer
103 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 ...
27
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2answers
1k 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 ...
7
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1answer
135 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 ...
1
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1answer
194 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. ...
7
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2answers
334 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 ...
11
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1answer
1k 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 ...
2
votes
2answers
233 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 ...
10
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2answers
271 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 ...
0
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1answer
266 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 ...
3
votes
3answers
366 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 ...
9
votes
5answers
246 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 ...
2
votes
1answer
76 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 ...
7
votes
2answers
539 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 ...
32
votes
6answers
3k 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'...
2
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1answer
135 views

What are issues to consider when making your code for an experimental paradigm, which was conceived by someone else, publicly available?

General background In the cognitive sciences, it is often necessary to program/script experimental paradigms to conduct your studies. Basically, these programs present stimuli and collect responses, ...
17
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2answers
1k 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 ...