Questions tagged [reproducible-research]

Questions related to research in which data and/or code is made publicly available so that others may verify the findings and build upon them.

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2
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1answer
98 views

What can be done (by the community as a whole) to make it easy (for persons other than the authors) to reproduce numerical results in a paper?

For example see reproduced papers repository. I am restricting the scope to theory papers that have some results obtained through numerical techniques. The fields may be as diverse as physics, ...
39
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4answers
10k views

Requesting raw data from previously published research

I am working on a mathematical model to help explain some experimental results and generate new hypotheses. Unfortunately, I have neither the resources nor interest to gather experimental data, but in ...
1
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2answers
43 views

Reproducible, open, transparent, ethical Research when confronted to (patient) data anonymization : is it at all possible in practice?

A lot of Hype goes in reproducible, open and transparency for data analysis theses days in some fields mores that other. The code is to be share as well as the dataset. How to achieve this in a ...
5
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3answers
223 views

Is it acceptable practice to make the source code of a re-implemented paper available online

It is the usual practice that researchers re-implement others' work for the purpose of comparison or result verification. If for instance researcher A re-implements researcher B's paper and improves ...
-1
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1answer
82 views

History behind reproducible research tools and literate programming [closed]

Reproducibility was talked about by Robert Boyle in 17th century. Literate Programming was invented in 1984 by Donald Knuth. Reproducible Research tools like R markdown were invented recently. My ...
60
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6answers
12k views

How to proceed when the baseline (state-of-the-art) published results claim much better performance than I can reproduce?

I am graduate student, to finish my degree I need to build methods outperform what is already there. An issue that I came across with, is that two papers reported way (I mean more than 20%) more than ...
4
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2answers
185 views

How to deal with non-reproducible research?

For context, I am a PhD student in bioinformatics, working partly in development of new statistical models and partly in applying models to data. I recently came across a paper which describes an ...
1
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1answer
203 views

How do we test in academia, if a research area is a money burning machine or non/pseudo-scientific?

In the recent decades more and more meta studies were undertaken on the reproducibilty rate of distinct research areas like psychology, biomedicine... The results are probably shocking to most ...
3
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1answer
158 views

What are the advantages of writing a thesis with rMarkdown? [closed]

I think the question is self-explanatory but to add a bit of a background, I'll be starting my M.Sc. research quite soon and I want to create and maintain a workflow that allows me to devote my time ...
33
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4answers
20k views

Can I request the code behind a research paper from the author?

I am in the field of computer science. It is often the case when I am reading a paper I start to wonder, "Wow stunning results, however, I would like to prove that." or "How exactly did he get these ...
27
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5answers
4k views

What to do when the claims in a paper are proven to be wrong?

What can be done to correct an error that might be hiding a certain author's sole purpose of publishing a paper, no matter the soundness of their method? In a nutshell, the particular case that ...
-1
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1answer
112 views

Are most real-world (engineering) problems about scale? [closed]

As an engineering post-graduate student a few years back, and now an engineer working in industry, I have often had this realization very strongly - that most problems we "adults" work on are about "...
3
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2answers
109 views

Is it worth posting reproducibility studies

As an undergraduate interested in Academia, is it worth posting your reproducibility study of a paper on arXiv and linking to it on Google scholar? Is it useful to future graduate schools? ...
3
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2answers
252 views

Incentives for independent researchers to work on reproducible research

For the sake of high-quality science diffusion, there is no doubt that reproducible research is a good practice as it helps to demonstrate the robustness of the proposed methods and boosts the ...
6
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2answers
247 views

Is it beneficial for a student to publish their research code and data?

There are at least four benefits of releasing the code and data produced during a thesis or research project (citing textually this laboratory): Allows to reproduce figures in the revisions of a ...
6
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2answers
290 views

Am I responsible for not reproducibility of collaborators’ result?

Recently, I have ran into some issues about reproducibility of some of my research results which are obtained by our collaborators from different university. In fact, in our current repository there ...
4
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1answer
121 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 ...
10
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2answers
3k views

What is the difference between repeatability, replicability and reproducibility?

I have seen many instances where authors used the term "reproducibility" and "replicability" interchangeably in the social and behavioural sciences. Sometimes, they distinguish between the "...
-2
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2answers
227 views

How to become a reliable researcher? [closed]

I am a biology student with major interest in neuroscience and molecular biology. It's my first year at university. What should I do if I want to be a reliable researcher in biological sciences, ...
8
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2answers
191 views

Reproducing work of others - name them as conflicts of interest?

We are currently reproducing several papers in a specific sub-field of computer science under different experimental conditions. When we submit the paper, we will be required to declare people who may ...
18
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3answers
650 views

Do we know what proportion of scientific reproducibility issues are fraud-related?

A few days ago there was an article on the LSE blog about scientific reproducibility which made little sense to me until I realised they were equating 'low reproducibility' with 'scientific fraud': ...
9
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3answers
557 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 ...
2
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3answers
157 views

Finding reproducible articles

My idea is learning new methods/fields by reproducing someone else results, and I would like to pick nice/good papers to learn from. If we define reproducibility as starting from the same samples/data,...
4
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1answer
340 views

Where can I find examples of research misconduct reports?

I am writing a report documenting evidence for research misconduct. The report is to be submitted to the ethics board of a university. Are there publicly available examples of such reports? Not the ...
4
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2answers
258 views

Reproducible and exact calculations vs. approximate and slightly random results in experiment

When experiments are performed and reported in an academic article, I learned that reproducibility is important. I am implementing a system where I stand between the choices to use GPU acceleration to ...
84
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12answers
12k views

Is it ethical to use proprietary (closed-source) software for scientific computation?

I have data from an ordinary scientific experiment. Now, in order to analyse the data, the most convenient way for me is to use some proprietary, closed-source software. Is it ethical to use such ...
4
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1answer
307 views

What is the best philosophy and practice to use smartphones for academic life? [closed]

I am doing research in theoretical physics, and have learned that smartphones can bring in a lot of distractions to your life if you want to focus on your research and study. Like facebook, twitter ...
5
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1answer
150 views

Ask the author of a paper for suggestions of where to publish replication results

I based my thesis on a published paper and ask its original author if he was interested in seeing the results. After approaching him (with your help provided: How to address an author showing ...
57
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7answers
3k views

Popular proprietary program or obscure open source substitute for reproducible research?

For a long time, I had been using open source software for my work to boost "reproducible research". I believed that if I made my codes open source and the softwares to run those codes in were open ...
6
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2answers
248 views

How to address an author showing replicated results from his paper?

I have replicated a method of interpolation recently proposed by certain author, and I want to tell him that I have done so. I suppose the author is interested in knowing that students are engaged ...
0
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1answer
160 views

How much should we trust that the approach described in a paper solves the problem that it addresses as well as it claims to?

To be honest, I'm not sure how exactly to word my question in order not to cause any miss-understanding. During my literature review sometimes I encounter with researches which propose an approach ...
63
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5answers
8k views

Why not make students reproduce work?

Typically, PhD theses are expected to have novel results. As science advances, it is becoming increasingly difficult to accumulate enough knowledge to begin a project that pushes the boundaries. ...
28
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8answers
4k views

Who is supposed to repeat experiments?

A follow up to this question. There is an issue in science with experiments not being repeated. I asked if PhDs can be done on repeating experiments and the answer is kind of mixed. Most PhDs aren't ...
15
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3answers
1k views

Can you do a PhD solely on repeating experiments of others?

In here, they say there is a problem with results not being replicated. I know a PhD is supposed to be "original" research. But could you do a PhD solely on replicating the results of others? ...
2
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1answer
68 views

Do measurement protocols belong anywhere in the scientific publications?

My research as a starting PhD student currently consists of reproducing and building upon the experiments carried out by other research groups 5--10 years ago. To this end, I have developed a number ...
9
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2answers
600 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 ...
27
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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: ...
15
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4answers
2k views

How does a PhD student go about doing a meta analysis of a research question?

I just thought that I would put this question out here because I am currently working on a meta analysis of a particular research question in my field (HCI/information science). Moreover, this ...
1
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1answer
91 views

How to identify studies that should be replicated?

In psychology voting on which studies should be replicated is established on a website. The ReplicationWiki (that I founded) offers a voting option for studies in economics and related fields, but it ...
36
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3answers
3k views

How to get the data to reproduce a published result?

I'm studying published journal articles on my topic, and I'd like to reproduce their analysis. How can I get a copy of their dataset and enough specifications to reproduce their numerical results? ...
12
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2answers
578 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 ...
18
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5answers
4k views

Can I trust a paper that hides implementation details?

In Computer Science, sometimes we're assigned to reproduce the results presented by a paper that already have been published. In many cases (most of them) the code is not available, making the task ...
6
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3answers
153 views

Are there any experiment reproducibility databases?

Quite often when I read a medical research article I wonder whether other researchers tried to reproduce the experiment. I could go through the list of papers that cite the article but I find this ...
16
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2answers
493 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, ...
3
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2answers
187 views

How can we perpetuate reproducibility?

Two years ago, Roger Peng discussed in his blog the ramifications of requiring reproducibility for the first producers of research objects, but not for reusers. He then proposed What I think a good ...
11
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5answers
281 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 ...
5
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2answers
1k views

When replicating results, what should I do when the author didn't use the method the paper said they did?

I am replicating a model to report on how well it does on a new evaluation metric I am proposing. The method/hyperparameters of the model are given in a paper about it, where it breaks all benchmarks ...
16
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6answers
966 views

Licence that converts to GPL after publication but is copyrighted prior to publication

I would like to post an repository on github that includes data and analysis code in R. The analysis and data forms part of a journal article submission. I'm happy for people to view the code and data ...
5
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4answers
522 views

Ethical considerations in publishing raw data

Apart from taking measures to maintain confidentiality, do I need my ethical approval to specify permission to publish raw data along with my study? I'm trying to facilitate reproducibility in my ...
16
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3answers
2k views

Open Source Software and Reproducibility in Computer Science

As a PhD researcher in computer science, my scientific results often take the form of algorithms, which in turn come with implementations. I am convinced that releasing these implementations under an ...