Questions tagged [reproducibility]

For questions about ensuring computational results are reproducible (e.g. how to best share the code for a calculation or whether particular hardware settings must also be specified.

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2 votes
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Deterministic SIR metapopulation model and coupling behavior

Context: I am trying to reproduce a figure from Keeling 2007 that illustrates time lags that can occur between the peaks (maximum) of the infected solutions for two subpopulations of a metapopulation ...
Jared Frazier's user avatar
2 votes
1 answer

Python bifurcation diagram of seasonally forced epidemiological models

TL:DR How can one implement a bifurcation diagram of a seasonally forced epidemiological model such as SEIR (susceptible, exposed, infected, recovered) in Python? I already know how to implement the ...
Jared Frazier's user avatar
5 votes
1 answer

Lab Notebooks for Computational Science

Many grants require an official record be kept of day-to-day research activities. For experimental research groups, this is often accomplished with a bound paper notebook in which the experimental ...
s47's user avatar
  • 151
5 votes
1 answer

How to record hardware and software info in Julia?

Watermark extension for Jupyter shows system and package information for reproducibility: ...
homocomputeris's user avatar
8 votes
1 answer

How reproducible are conda environments?

I am aiming at keeping my scientific studies and analyses reproducible: I am automating them as much as possible, I am sharing them, and I sharing them together with the execution environment(s) I've ...
Tim Tröndle's user avatar
13 votes
1 answer

What are the guidelines for conducting computational experiments?

Physics, biology, chemistry etc. have different sets of rules for making experiments: what events are considered relevant, how to avoid contamination of samples, how to create and fix a reproducing ...
homocomputeris's user avatar
6 votes
1 answer

How to compare runtimes of two algorithms in a reproducible way

I am solving one relatively simple problem with two different algorithm: one which uses brute force while the other is optimized. For a variety of reasons I actually cannot show the codes here but I ...
solalito's user avatar
  • 337
14 votes
4 answers

Any recommendations for unit-testing frameworks compatible with code/libraries that use MPI?

Usually, I write serial code, and when I do, I write unit tests with some xUnit-style testing framework (MATLAB xUnit, PyUnit/nose, or Google's C++ testing framework). Based on a cursory Google ...
Geoff Oxberry's user avatar
3 votes
3 answers

Reproducibility in molecular dynamics trajectories

Let's say I have two molecular dynamics (MD) simulators, A and B, which implement the following interface: $$ \left\{\vec{x}_i(t = 0), T_i, t \right\} \rightarrow \left\{\vec{x}_i(t), \vec{F}_i(t) \...
Max Hutchinson's user avatar
15 votes
1 answer

How to to easily reproduce published results in my own articles using my own code

I wrote a program/library which I used to obtain results in an article. (Here it is, but my question is general.) I have tests that I run regularly using ctest (it ...
Ondřej Čertík's user avatar
15 votes
4 answers

What would be the most helpful way to write code for a paper so that readers can clearly match the results to the code that generates them?

I'm writing a reproducible paper, and the paper has computational results that are generated by a Python script (a similar MATLAB script generates nearly identical results). I feel that the paper ...
Geoff Oxberry's user avatar
11 votes
5 answers

Increasing the archival longevity of code

Is there a published list of best practices to ensure longevity of code, with an eye towards reproducible scientific results? (e.g. open source, documentation practices, selecting dependencies, ...
cboettig's user avatar
  • 758
34 votes
8 answers

How do I make sure that the results of my simulations and the results in my paper are always in sync?

In one of my papers, I list some numerical results in addition to some figures. What I'd like to do is make sure that the numerical results in my paper always agree with the code. Right now, I just ...
Geoff Oxberry's user avatar
20 votes
5 answers

How to address numerical non-associativity for parallel reduction?

A parallel reduction assumes that the corresponding operation is associative. This assumption is violated for addition of floating point numbers. You might ask why I care about this. Well, it makes ...
Thomas Klimpel's user avatar
25 votes
5 answers

What material should I include with a journal article (or post online) in order to make my computational research reproducible?

Reproducibility has become more and more important in computational science research. (For instance, see this article by Roger Peng in Science; I'm aware of other such articles and web sites also.) ...
Geoff Oxberry's user avatar
19 votes
6 answers

What is the best way to do reproducible research if you need proprietary libraries?

Reproducible research in computation aims to make the code needed to generate the results in a computational paper available to other researchers so that they can run this code to reproduce the ...
Geoff Oxberry's user avatar