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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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31 views

back assign DOI to extant dataset

Would it be possible for researchers back-assign a DOI to an existing dataset they have rights to - where there is no permission to share it publically (privacy, organization proprietary, personnel to ...
0
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0answers
33 views

Seeking feedback on the Open Science MOOC [closed]

I'm not sure if this is 100% relevant to this site, but I figured many of you here would be able to help out. Recently, we launched the Open Science MOOC, as part of a community-driven initiative to ...
4
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3answers
160 views

Which journals make peer review history documents publicly available?

Nature Communications has had a policy since 2016 that authors are given the option to publish the peer review history of their paper. Are there other journals with the same initiative?
7
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5answers
526 views

Can you publish a paper Simply Implementing another Paper's Algorithm?

There was a highly cited paper published earlier this year in my field which introduced a highly theoretical, non trivial, algorithm that relied on extremely heavy theory. The algorithm was exact (...
4
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1answer
116 views

Reproducible science: do entities exist requiring Level 3 of TOP standards?

Quite many (if not most of) scientific articles, related to computational sciences, which I have seen, do not share both data and code leading to the figures. This may have of course good reasons ...
0
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2answers
78 views

Open university and admissions into a US Masters

Can a student with a bachelor's in engineering with very little chemistry take some courses in chemistry to get into a chemistry masters? How do US masters view courses taken from Open University, ...
2
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0answers
156 views

Is there a way to move a preprint from one service to another within the OSF system? [closed]

I have a project in Open Science Framework and a paper uploaded in the generic OSF preprint service, but now I want to change it to a more specialized preprint service within that system (MindRxiv in ...
6
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2answers
120 views

OpenStreetMaps in research publications: Is that possible?

In connection with Scholia (https://tools.wmflabs.org/scholia/), we are making OpenStreetMap plots online with the tiler from Wikimedia Foundation. When presented online OSM-derived maps are not a ...
5
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3answers
181 views

How to Store Incidental Information Gleaned in the Course of Conducting Research

I'm in the throes of writing my first substantial research paper in the field of Information Science. The topic looks promising and my advisor seems pleased with the work. Because of the nature of the ...
4
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1answer
120 views

Is there a “place” to deposit and, or publish reports produced in grad school?

I am looking for some kind of repository where I can "publish" my reports from grad school. I'd like to do this because it would be great if I could link those works with my ORCID and make them ...
3
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2answers
176 views

Innovative and free publication platform [closed]

I would like to create an open access journal / a platform that is free of charge for authors and readers. Ideally, I would like it to get away from the current norms: offer the possibility to publish ...
14
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2answers
389 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 ...
2
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1answer
221 views

How to add data availability statement in Physical Review Letters?

We have submitted our recent findings to PRL. As the second round of revision came through, we are almost confident that we will get published in PRL. Now we wanted to provide our algorithm as a ...
2
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0answers
90 views

How Reproducible should Data and Analysis Methodology Be?

My question might be a stretch given my lack of formal experience with writing and publishing research papers. But one thing I've noticed in my line of work and reading published papers is that the ...
9
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3answers
414 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 ...
8
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3answers
148 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, ...
7
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2answers
703 views

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

Some journals, such as many of the EGU Copernicus publications, publish the initial manuscript and the (anonymous) peer reviews and author replies along with the full manuscript. When reviewing for ...
53
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8answers
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 ...
5
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1answer
218 views

How much money do universities pay to access datasets?

Is there any research/study/survey that tried to quantify how much money universities / academic research labs pay to access data sets? For example, in the United States, many hospitals as well as ...
20
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2answers
461 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. ...
10
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3answers
1k 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 ...
7
votes
1answer
450 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 ...
3
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2answers
251 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 ...
49
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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
65 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 ...
25
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4answers
3k 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
77 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 ...
-1
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1answer
733 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
374 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 ...
11
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3answers
419 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
votes
2answers
524 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
votes
1answer
376 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
votes
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 ...
4
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2answers
116 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
vote
2answers
255 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
votes
1answer
71 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'...
16
votes
2answers
464 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
132 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 ...
15
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3answers
359 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
89 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 &...
7
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4answers
258 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 ...
19
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4answers
5k 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 ...
8
votes
1answer
143 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
118 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
233 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
2k 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
votes
3answers
59 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 ...
19
votes
2answers
148 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
152 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
61 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 ...