rescience/submissions

ReScience C submissions

The ReScience Journal

ReScience is a platinum open-access peer-reviewed journal that targets computational research and encourages the explicit replication of already published research promoting new and open-source implementations in order to ensure the original research is reproducible. To achieve such a goal, the whole editing chain is radically different from any other traditional scientific journal. ReScience lives on github where each new implementation is made available together with the comments, explanations and tests. Each submission takes the form of a pull request that is publicly reviewed and tested in order to guarantee any researcher can re-use it. If you ever replicated a computational result from the literature, ReScience is the perfect place to publish this new implementation. Reproducible Science is Good. Replicated Science is better.

The Editorial Board

Note: This repository contains the first volumes of ReScience. Articles were submitted as pull requests to ReScience-submissions, which were merged upon acceptance with a reference added to this repository. The new ReScience C workflow is a bit different and based on two new repositories: one for submissions and another one containing the accepted articles. The entry point for ReScience remains its Web site.

Archives

• Volume 4 - Issue 1
• Volume 3 - Issue 1
• Volume 2 - Issue 1
• Volume 1 - Issue 1

submissions's Issues

[Re] The Wisconsin Card Sorting Test: an implementation of Dehaene and Changeux Neuronal Network Model

Original article: Dehaene, S., & Changeux, J. P. (1991). The Wisconsin Card Sorting Test: Theoretical analysis and modeling in a neuronal network. Cerebral cortex, 1(1), 62-79.

PDF URL: https://github.com/PaulineBock/WCSTDehaeneChangeux/blob/master/ReScience_Dehaene.pdf
Metadata URL: https://github.com/PaulineBock/WCSTDehaeneChangeux/blob/master/Metadata.yaml
Code URL: https://github.com/PaulineBock/WCSTDehaeneChangeux

Scientific domain: Computational Neuroscience
Programming language: Python
Suggested editor:

10 year reproducibility challenge: reproduction of J. Chem. Phys. 112, 4417 (2000)

article.pdf

Original article: Gottfried and McBane, J. Chem. Phys. 112, 4417 (2000)

PDF URL: https://github.com/ReScience/submissions/files/3882888/article.pdf
Metadata URL: https://github.com/ReScience/submissions/files/3888185/metadata.zip
Code URL: https://github.com/mcbaneg/tenyears-submission (also: http://faculty.gvsu.edu/mcbaneg/virial6-resciencec.zip)

Scientific domain: Chemical Physics
Programming language: Fortran
Suggested editor:

Reproducibility Report of "Variational Sparse Coding"

Original article: Variational Sparse Coding (https://openreview.net/forum?id=SkeJ6iR9Km)

PDF URL: https://github.com/reproducibility-challenge/iclr_2019/blob/master/papers/FrazadaTigre-SkeJ6iR9Km/ReScience_submission.pdf
Metadata URL: https://github.com/reproducibility-challenge/iclr_2019/blob/master/papers/FrazadaTigre-SkeJ6iR9Km/metadata-draft.yaml
Code URL: https://zenodo.org/record/2657330#.XMzD46YpBSM

Scientific domain: Machine Learning
Programming language: Python
Suggested editor: ICLR Reproducibility Challenge Editors

Corresponding Author: @Alfo5123
Challenge PR: reproducibility-challenge/iclr_2019#146

ICLR Reproducibility Challenge, 2019

[Re] A Reservoir Computing Model of Reward-Modulated Motor Learning and Automaticity

Original article: A Reservoir Computing Model of Reward-Modulated Motor Learning and Automaticity

PDF URL: https://github.com/rsankar9/Reimplementation-SUPERTREX/blob/main/ReScience_submission/article.pdf
Metadata URL: https://github.com/rsankar9/Reimplementation-SUPERTREX/blob/main/ReScience_submission/metadata.yaml
Code URL: https://github.com/rsankar9/Reimplementation-SUPERTREX/tree/main/Code

Scientific domain: Computational Neuroscience
Programming language: Python, MATLAB
Suggested editor:

Ten Years Challenge: [Rp] Typographical features for scene text recognition

Original article: Weinman, J. J. (2010, August). Typographical features for scene text recognition. In 2010 20th International Conference on Pattern Recognition (pp. 3987-3990). IEEE. DOI:10.1109/ICPR.2010.970

PDF URL: http://www.cs.grinnell.edu/~weinman/tmp/rescience/rescience20_submitted.pdf
Metadata URL: http://www.cs.grinnell.edu/~weinman/tmp/rescience/metadata.yaml
Code URL:

• Archive: DOI:11084/23333
• Temporary: http://www.cs.grinnell.edu/~weinman/tmp/rescience/ (+ README)

Scientific domain: Pattern Recognition (Machine Learning)
Programming language: CUDA, Matlab, Java, C
Suggested editor: Thomas Arildsen, Lorena Barba, Georgios Detorakis

The code archive DOI is being processed. It may not appear for 48–72 hours.

Some of the LaTeX output/layout seems a bit wonky. If anyone would like to make behind-the-scenes suggestions, they may view the source at overleaf

Original comment/submission

[Re] Deep Convolution Neural Network and Autoencoders-Based Unsupervised Feature Learning of EEG Signals

Original article:
T. Wen and Z. Zhang, "Deep Convolution Neural Network and Autoencoders-Based Unsupervised Feature Learning of EEG Signals," in IEEE Access, vol. 6, pp. 25399-25410, 2018.

PDF URL: https://github.com/bruAristimunha/Re-Deep-Convolution-Neural-Network-and-Autoencoders-Based-Unsupervised-Feature-Learning-of-EEG/blob/master/article/article.pdf
Metadata URL: https://github.com/bruAristimunha/Re-Deep-Convolution-Neural-Network-and-Autoencoders-Based-Unsupervised-Feature-Learning-of-EEG/blob/master/article/metadata.yaml
Code URL: https://github.com/bruAristimunha/Re-Deep-Convolution-Neural-Network-and-Autoencoders-Based-Unsupervised-Feature-Learning-of-EEG

Scientific domain: Neuroscience, EEG, Computational Neuroscience
Programming language: Python
Suggested editor:
@rougier , @ogrisel , @qihongl ,
@rth , @rgutzen , @emmanuelle , @jpgard

Ten Years Reproducibility Challenge: paper number #22

Original article: Barnett AG, Dobson AJ, For the WHO MONICA Project (2004) Estimating trends and seasonality in coronary heart disease. Statist Med 23:3505-3523. DOI: 10.1002/sim.1927

PDF URL: https://github.com/agbarnett/tenyears/raw/master/article/article.pdf
Metadata URL: https://github.com/agbarnett/tenyears/raw/master/article/metadata.yaml
Code URL: https://github.com/agbarnett/tenyears

Scientific domain: Epidemiology
Programming language: SAS
Suggested editor:

Ten years challenge: fermions at unitarity

Original article: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.96.160402
Preprint, ungated: https://arxiv.org/abs/cond-mat/0602224

PDF URL: https://github.com/ev-br/unitarity_repro/blob/repro_unitarity/article.pdf
Metadata URL: https://github.com/ev-br/unitarity_repro/blob/repro_unitarity/metadata.yaml
Code URL: https://github.com/ev-br/10yr_repro_challenge_35/releases/tag/v1.1

Scientific domain: Physics
Programming language: Fortran / Python
Suggested editor:

This is paper 36 in ReScience/ten-years#1

Ten Years Reproducibility Challenge: Drivers of Evapotranspiration from Boreal Wildfires

Original article: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2486.2008.01776.x

PDF URL: https://github.com/bpbond/ten-years-paper33/blob/master/article/paper33-report.pdf
Metadata URL: https://github.com/bpbond/ten-years-paper33/blob/master/article/metadata.yaml
Code URL: https://github.com/bpbond/ten-years-paper33

Scientific domain: Earth Sciences/Ecology
Programming language: R
Suggested editor:

[Re] Mathematical analysis of depolarization block mediated by slow inactivation of fast sodium channels in midbrain dopamine neurons.

Original article: https://www.ncbi.nlm.nih.gov/pubmed/25185810

PDF URL: https://github.com/mupsh/ReScience_Qian_2014/blob/master/article/article.pdf
Metadata URL: https://github.com/mupsh/ReScience_Qian_2014/blob/master/article/metadata.yaml
Code URL: https://github.com/mupsh/ReScience_Qian_2014

Scientific domain: Computational Neuroscience
Programming language: Python
Suggested editor: Benoit Girard, Tiziano Zito

[RE] Effective Program Debloating via Reinforcement Learning

Original article: Effective Program Debloating via Reinforcement Learning

PDF URL: https://gitlab.com/onepoint/recherche-et-developpement/optimus/chisel-replication/-/blob/master/Replication_CHISEL.pdf
Metadata URL: https://gitlab.com/onepoint/recherche-et-developpement/optimus/chisel-replication/-/blob/master/metadata.yaml
Code URL: https://gitlab.com/onepoint/recherche-et-developpement/optimus/chisel-replication/-/tree/master

Scientific domain: Program Debloating and Machine Learning
Programming language: Python
Suggested editor: Visual Studio Code or VIM

[Re] Assortative matching and search

Dear Editors,

I would like to request a review for the following replication.

Original articles:

• Shimer, R., and Smith, L. (2000). Assortative matching and search. Econometrica, 68(2), 343–369. http://doi.org/10.1111/1468-0262.00112
• Smith, L. (2006). The Marriage Model with Search Frictions. J. Political Econ., 114(6), 1124–1144. https://doi.org/10.1086/510440

PDF URL: https://github.com/fgeoffroy/-Re-Assortative-matching-and-search/blob/main/article/article.pdf
Metadata URL: https://github.com/fgeoffroy/-Re-Assortative-matching-and-search/blob/main/article/metadata.yaml
Code URL: https://github.com/fgeoffroy/-Re-Assortative-matching-and-search

Scientific domain: Game theory
Programming language: Python
Suggested editor:

[Rp] Structural flexibility in proteins: impact of the crystal environment

Original article: Hinsen, K (2008) Structural flexibility in proteins: impact of the crystal environment. Bioinformatics 24:521. (Open Access version)

PDF URL: https://github.com/khinsen/rescience-ten-year-challenge-paper-3/raw/master/article/article.pdf
Metadata URL: https://github.com/khinsen/rescience-ten-year-challenge-paper-3/raw/master/article/metadata.yaml
Code URL: https://github.com/khinsen/rescience-ten-year-challenge-paper-3/

Scientific domain: Biophysics
Programming language: Python
Suggested editor: @delsuc

[Re] A Neurodynamical Model for Working Memory

Original article: A Neurodynamical Model for Working Memory

PDF URL: [Re] A Neurodynamical Model for Working Memory
Metadata URL: Metadata.yaml
Code URL: Code repository

Scientific domain: Computational Neuroscience
Programming language: Python
Suggested editor:

10 year challenge: Eglen and Wong (2008)

Original article: https://arxiv.org/abs/1208.0986 (postprint of 2008 paper)

PDF URL: https://github.com/sje30/rescience-hor/blob/master/template-master/article2.pdf
Metadata URL: https://github.com/sje30/rescience-hor/blob/master/template-master/metadata.yaml
Code URL: https://github.com/sje30/rescience-hor/

Scientific domain: Computational Neuroscience
Programming language: R
Suggested editor: Timothée Poisot or Karthik Ram or Etienne Roesch

Eliminating the Variability of Cross-Validation Results with LIBLINEAR due to Randomization and Parallelization

Title: Eliminating the Variability of Cross-Validation Results with
LIBLINEAR due to Randomization and Parallelization
Title: Eliminating the Variability of Cross-Validation Results for Some Randomized and Parallelized Learning Algorithms

PDF URL: https://github.com/sukhoy/RSC_paper/raw/master/article.pdf
Metadata URL: https://github.com/sukhoy/RSC_paper/blob/master/metadata.yaml
Suggested editor: Konrad Hinsen, Nicolas P. Rougier

Cover letter PDF: https://github.com/sukhoy/RSC_paper/raw/master/Cover_Letter.pdf

Ten-year challenge: Reproduction of An allosteric model of calmodulin [PNAS 105(31), 10768 (2008)]

Original article: M.I. Stefan, S.J. Edelstein, N. Le Novère (2008). An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. PNAS 105(31), 10768.

PDF URL: https://github.com/MelanieIStefan/calmodulin_reproduction/blob/master/ReScience_Calmodulin.pdf
Metadata URL:
Code URL: https://github.com/MelanieIStefan/calmodulin_reproduction

Scientific domain: Systems neuroscience
Programming language: SBML, R
Suggested editor: This is part of the 10-year challenge, so should be handled by the challenge organisers

Ten-year Reproduciblity Challenge: Fluctuation Domains

Original article: Carl Boettiger, Jonathan Dushoff, Joshua S Weitz (2010). Fluctuation domains in adaptive evolution, Theoretical Population Biology 77 (1) 6-13. doi:10.1016/j.tpb.2009.10.003.

PDF URL: https://github.com/cboettig/fluctuationDomains/blob/rescience/rescience/article.pdf
Metadata URL: https://github.com/cboettig/fluctuationDomains/blob/rescience/rescience/metadata.yaml
Code URL: https://github.com/cboettig/fluctuationDomains/releases/tag/rescience

Scientific domain: Ecology & Evolution
Programming language: C, R
Suggested editor:

[Re] Context-Dependent Encoding of Fear and Extinction Memories in a Large-Scale Network Model of the Basal Amygdala

Original article: Vlachos, I., Herry, C., Lüthi, A., Aertsen, A., & Kumar, A. "Context-dependent encoding of fear and extinction memories in a large-scale network model of the basal amygdala". PLoS Comput Biol, v. 7, n. 3, p. e1001104, 2011.

PDF URL: https://github.com/tawantayron/RE-Fear-and-extinction-in-a-BA-net-model/blob/master/article.pdf
Metadata URL: https://github.com/tawantayron/RE-Fear-and-extinction-in-a-BA-net-model/blob/master/metadata.yaml
Code URL: https://github.com/tawantayron/RE-Fear-and-extinction-in-a-BA-net-model

Scientific domain: Computational Neuroscience
Programming language: Python and Brian 2
Suggested editor: @benoit-girard
Suggested reviewer: @mstimberg @heplesser @rgutzen @TiinaManninen

Ten Years Reproducibility Challenge: Identifying essential genes by mutagenesis

Original article: Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Broman KW, Bishai WR (2003) A post-genomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Proc Natl Acad Sci USA 100:7213-7218 doi:10.1073/pnas.1231432100

PDF URL: https://kbroman.org/Paper_ReScience2020/article/article.pdf
Metadata URL: https://github.com/kbroman/Paper_ReScience2020/blob/master/article/metadata.yaml
Code URL: https://github.com/kbroman/Paper_ReScience2020

Scientific domain: Genetics
Programming language: R
Suggested editor: @karthik

Reproducibility Report of "Meta learning with differentiable closed-form solvers"

Original article: : Meta-learning with differentiable closed-form solvers (https://openreview.net/pdf?id=HyxnZh0ct7)

PDF URL: https://github.com/reproducibility-challenge/iclr_2019/blob/master/papers/LCAX-HyxnZh0ct7/LCAX_camera_ready.pdf
Metadata URL: https://github.com/reproducibility-challenge/iclr_2019/blob/master/papers/LCAX-HyxnZh0ct7/ReScience_src/metadata-draft.yaml
Code URL: https://zenodo.org/record/2662494#.XMzE-aYpBSM

Scientific domain: Machine Learning
Programming language: Python
Suggested editor: ICLR Reproducibility Challenge Editors

Corresponding Author: @ArnoutDevos
Challenge PR: reproducibility-challenge/iclr_2019#150

ICLR Reproducibility Challenge, 2019

Reproducibility Report of "Learning Neural PDE Solvers with Convergence Guarantees"

Original article: Learning Neural PDE Solvers with Convergence Guarantees (https://openreview.net/forum?id=rklaWn0qK7)

PDF URL: https://github.com/reproducibility-challenge/iclr_2019/blob/master/papers/zoidberg-rklaWn0qK7/zoidberg_camera_ready.pdf
Metadata URL: https://github.com/reproducibility-challenge/iclr_2019/blob/master/papers/zoidberg-rklaWn0qK7/rescience_report/metadata-draft.yaml
Code URL: https://zenodo.org/record/2660730

Scientific domain: Machine Learning
Programming language: Python
Suggested editor: ICLR Reproducibility Challenge Editors

Corresponding Author: @francescobardi
Challenge PR: reproducibility-challenge/iclr_2019#136

ICLR Reproducibility Challenge, 2019

[Re] Chaos in a Three-Species Food Chain

Original article: Hastings, A., & Powell, T. (1991). Chaos in a Three-Species Food Chain. Ecology, 72(3), 896–903. https://doi.org/10.2307/1940591

PDF URL: https://github.com/BIO6032/2019_replication_HastingsPowell_1991/blob/master/article/article.pdf
Metadata URL: https://github.com/BIO6032/2019_replication_HastingsPowell_1991/blob/master/article/metadata.yaml
Code URL: https://github.com/BIO6032/2019_replication_HastingsPowell_1991/

Scientific domain: Ecology
Programming language: Julia
Suggested editor: @karthik @delsuc

Tagging co-author @tpoisot

[Rp] Loupe

Original article: N. P. Rougier. “LOUPE.” In: Tremplin Micro 19 (Mar. 1988), pp. 60–61

PDF: https://github.com/rougier/TYRC-apple/blob/master/article/article.pdf
Metadata: https://github.com/rougier/TYRC-apple/blob/master/article/metadata.yaml
Code: https://github.com/rougier/TYRC-apple

Scientific domain: None
Programming language: Applesoft basic 😄
Suggested editor: @khinsen
Suggested reviewer: @BrunoLevy

[¬Rp] Stokes drag on conglomerates of spheres

Original article: B. Cichocki, K. Hinsen, Stokes drag on conglomerates of spheres, Phys. Fluids 7:286 (1995)

PDF URL: https://github.com/khinsen/rescience-ten-year-challenge-paper-4/raw/master/article/article.pdf
Metadata URL: https://github.com/khinsen/rescience-ten-year-challenge-paper-4/raw/master/article/metadata.yaml
Code URL: https://github.com/khinsen/rescience-ten-year-challenge-paper-4/

Scientific domain: Fluid dynamics
Programming language: Fortran 77
Suggested editor:

Since this is a failed reproduction attempt, no results are presented, meaning that editors and reviewers do not need to be familiar with the application domain .

10 year challenge: Davison, Feng and Brown (2003)

Original article: https://doi.org/10.1152/jn.00623.2002

PDF URL: https://github.com/apdavison/bulbnet-reproduction/blob/master/reproducibility_challenge_2020/article.pdf
Metadata URL: https://github.com/apdavison/bulbnet-reproduction/blob/master/reproducibility_challenge_2020/metadata.yaml
Code URL: https://github.com/apdavison/bulbnet-reproduction

Scientific domain: Computational Neuroscience
Programming language: Hoc
Suggested editor: Tiziano Zito or Georgios Detorakis or Etienne Roesch

Note that this is paper #5 in ReScience/ten-years#1

Reproduction of a comparison between operant and classical conditioning of identical stimuli in tethered Drosophila

Original article:
Brembs B and Heisenberg M (2000): The Operant and the Classical in Conditioned Orientation of Drosophila melanogaster at the Flight Simulator. Learn Mem. 7(2): 104–115. doi: 10.1101/lm.7.2.104
PDF URL original article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311324/pdf/x2.pdf
PDF URL submitted article:
https://github.com/brembs/DFS_reproduction/blob/master/article.pdf
Metadata URL:
https://github.com/brembs/DFS_reproduction/blob/master/DFSreproduction.yaml
Code URL:
https://github.com/brembs/DFS_reproduction/tree/master/evaluation_code

Scientific domain:
Neurobiology
Programming language:
Turbo Pascal, R, C++
Suggested editor:

[Rp] Gifa V.4: A complete package for NMR data set processing

Original article: [Rp] Gifa V.4: A complete package for NMR data set processing

PDF URL: https://github.com/delsuc/Gifa/blob/master/article/article.pdf
Metadata URL: https://github.com/delsuc/Gifa/blob/master/article/metadata.yaml
Code URL: https://github.com/delsuc/Gifa/blob/master/code

Scientific domain: NMR, data processing
Programming language: Fortran77, C, Gifa macro
Suggested editor: Pierre de Buyl, Konrad Hinsen, Thomas Arildsen, Georgios Detorakis

ReScience challenge: resurrecting a 30-year-old Turbo Pascal program for generating Maucha ionic diagrams

Original article:
Silberbauer, M.J. and King, J.M., 1991. Geographical Trends in the Water Chemistry of Wetlands in the South-Western Cape Province, South Africa. Southern African Journal of Aquatic Sciences, 17 (1/2), 82–88.
PDF URL:
Silberbauer-2020.pdf
Metadata URL:
http://www.riv.co.za/wv/data/Silberbauer-2020.yaml
Code URL:
https://archive.softwareheritage.org/browse/origin/https://github.com/MikeSilberbauer/maucha-ionic-diagram.git/
Scientific domain:
Aquatic Science
Programming language:
Turbo Pascal
Suggested editor:

Ten years reproducibility challenge: paper #9

Original article: M. Danelutto, R. Di Cosmo, X. Leroy, and S. Pelagatti. “Parallel Functional Programming with Skeletons: the OCamlP3L experiment.” In: ACM Workshop on ML and its applications. ACM. Baltimore, United States, Sept. 1998. https://hal.archives-ouvertes.fr/hal-01499962v1

PDF URL: https://gitlab.inria.fr/dicosmo/ocamlp3l-rescience/-/blob/master/article.pdf
Metadata URL: https://gitlab.inria.fr/dicosmo/ocamlp3l-rescience/-/blob/master/metadata.yaml
Code URL: https://archive.softwareheritage.org/swh:1:rev:2db189928c94d62a3b4757b3eec68f0a4d4113f0;origin=https://gitorious.org/ocamlp3l/ocamlp3l_cvs.git/

Scientific domain: Parallel programming, HPC
Programming language: OCaml
Suggested editor:

[Re] [Ten Year Challenge] Oscillating chemical reactions and phase separation simulated by molecular dynamics

Original article: https://aip.scitation.org/doi/abs/10.1063/1.475237

@article{Geisshirt:1997,
  author  = {Kenneth Geisshirt and Eigil L. Praestgaard and Soren Toxvaerd},
  title   = {Oscillating chemical reactions and phase separation simulated by molecular dynamics},
  journal = {Journal of Chemical Physics},
  volume  = {107},
  number  = {22},
  pages   = {9406--9412},
  year    = {1997}
}

PDF URL: https://github.com/kneth/rescience-ten-year-challenge-paper/blob/master/article.pdf
Metadata URL: https://github.com/kneth/rescience-ten-year-challenge-paper/blob/master/metadata.yaml
Code URL: https://github.com/kneth/MDreac/tree/master/oldsrc

Scientific domain: non-equilibrium thermodynamics, chemical kinetics
Programming language: Fortran-77
Suggested editor:

[Re] Measures for investigating the contextual modulation of information transmission.

Original article:
Smyth, D., Phillips, W. A. and Kay, J.(1996) 'Measures for investigating the contextual modulation of information transmission', Network: Computation in Neural Systems, 7:2,307 — 316

PDF URL:
https://github.com/sepehrmn/mahmoudian-2020-rescience/blob/master/article/Reproduction_of_Smyth_et_al__1996.pdf

Metadata URL:
https://github.com/sepehrmn/mahmoudian-2020-rescience/blob/master/article/metadata.yaml

Code URL:
https://github.com/sepehrmn/mahmoudian-2020-rescience/tree/master/code

Scientific domain: Computational Neuroscience

Programming language: Python

Suggested editor:

[Re] Modeling Insect Phenology Using Ordinal Regression and Continuation Ratio Models

Original articles:

• B. Dennis, W.P. Kemp,and R.C. Beckwith (1986): "Stochastic Model of Insect Phenology: Estimation and Testing." Environmental Entomology 15(3):540–546. https://doi.org/10.1093/ee/15.3.540
• S.G. Candy (1991): "Modeling Insect Phenology Using Ordinal Regression and Continuation Ratio Models." Environmental Entomology 20(1):190–195. https://doi.org/10.1093/ee/20.1.190

PDF URL: https://github.com/pboesu/replication_candy_1991/blob/master/article/article.pdf
Metadata URL: https://github.com/pboesu/replication_candy_1991/blob/master/article/metadata.yaml
Code URL: https://github.com/pboesu/replication_candy_1991

Scientific domain: Ecology
Programming language: R
Suggested editor: @karthik @tpoisot

Editor (@tpoisot) checklist

• Reviewer 1
  • assigned @juniperlsimonis
  • returned
• Reviewer 2
  • assigned @aammd
  • returned

[Re] [Ten Year Challenge] Volume computation for polytopes: Vingt ans après

Original article:
B. Büeler, A. Enge, and K. Fukuda.
Exact Volume Computation for Polytopes: A Practical Study.
In: Polytopes — Combinatorics and Computation.
Ed. by G. Kalai and G. M. Ziegler.
Vol. 29. DMV Seminar.
Basel: Birkhäuser Verlag,
2000,
pp. 131–154

PDF URL:
https://gitlab.inria.fr/enge/revinci/-/blob/master/article/revinci.pdf

Metadata URL:
https://gitlab.inria.fr/enge/revinci/-/blob/master/article/metadata.yaml

Code URL:
https://gitlab.inria.fr/enge/revinci/-/tree/master/code

Data URL:
https://gitlab.inria.fr/enge/revinci/-/tree/master/data

Scientific domain:
Discrete Mathematics

Programming language:
C

Suggested editor:
None of the editors seems to be from this field; potential reviewers from the current list are Markus Pfeiffer, Dmitrii Pasechnik and Bruno Levy, with whom I have no conflict of interest.

Review Request: C. de la Torre-Ortiz and A. Nioche

Dear ReScience editors,

I request a review for the following replication:

Original article: https://doi.org/10.3389/fncom.2015.00149

PDF URL: https://github.com/c-torre/replication-recanatesi-2015/blob/master/re-neural-network-model-of-memory-retrieval.pdf
Metadata URL: https://github.com/c-torre/replication-recanatesi-2015/blob/master/metadata.tex
Code URL: https://github.com/c-torre/replication-recanatesi-2015/

Scientific domain: Computational Neuroscience
Programming language: Python
Suggested editor: @oliviaguest

[Re] The principal components of natural images

Original article: The Principal Components of Natural Images by Hancock et al (1991),
http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=044DFF560FC2E801B579C2F23D268B44?doi=10.1.1.41.192&rep=rep1&type=pdf*

PDF URL: https://github.com/IainDaviesMaths/Hancock-Rescience-Paper/blob/master/article.pdf
Metadata URL: https://github.com/IainDaviesMaths/Hancock-Rescience-Paper/blob/master/metadata.yaml
Code URL: https://github.com/IainDaviesMaths/Reproduction-Hancock

Scientific domain: Computational Neuroscience
Programming language: Julia
Suggested editor: -

[Re] Faster Teaching via POMDP Planning (partial replication)

Original article: Faster Teaching via POMDP Planning by Rafferty et. al (2016) , https://www.onlinelibrary.wiley.com/doi/full/10.1111/cogs.12290

PDF URL: https://github.com/luksurious/faster-teaching/blob/master/replication-paper.pdf
Metadata URL: https://github.com/luksurious/faster-teaching/blob/master/metadata.yaml
Code URL: https://github.com/luksurious/faster-teaching

Scientific domain: Cognitive Science
Programming language: Python
Suggested editor: -

(Sorry, I had first put the wrong link to the paper, it is now working well)

ICLR Reproducibility Challenge Editorial

Title: ICLR Reproducibility Challenge 2019
PDF URL: https://github.com/koustuvsinha/iclr19_rc_editorial/blob/master/article.pdf
Metadata URL: https://github.com/koustuvsinha/iclr19_rc_editorial/blob/master/metadata.yaml
Suggested editor: Nicolas Rougier, Konrad Hinsen

Ten years reproducibility challenge: paper #41

Original article: Storage Tradeoffs in a Collaborative Backup Service for Mobile Devices_(2006)

PDF URL: article.submitted.pdf
Metadata URL: metadata.yaml
Code URL: https://gitlab.inria.fr/lcourtes-phd/edcc-2006-redone

Scientific domain: Fault tolerance, Software engineering
Programming language: C, Scheme
Suggested editor:

[Re] Process Aware Stealthy Attack Detection on Industrial Control Systems.

Original article: Wissam Aoudi, Mikel Iturbe, and Magnus Almgren. 2018. Truth Will Out:
Departure-Based Process-Level Detection of Stealthy Attacks on Control
Systems. In 2018 ACM SIGSAC Conference on Computer and Communications
Security (CCS ’18), October 15–19, 2018, Toronto, ON, Canada. ACM, New
York, NY, USA, 15 pages. https://doi.org/10.1145/3243734.3243781

PDF URL: https://github.com/rahulrajpl/PyPASAD/blob/master/Rescience%20Submission/article.pdf
Metadata URL: https://github.com/rahulrajpl/PyPASAD/blob/master/Rescience%20Submission/metadata.yaml
Code URL: https://github.com/rahulrajpl/PyPASAD

Scientific domain: Cybersecurity for Critical Infrastructure
Programming language: Python
Suggested editor:

Reproducibility Report of "h-detach: Modifying the LSTM gradient towards better optimization"

Original article: h-detach: Modifying the LSTM Gradient Towards Better Optimization (https://openreview.net/pdf?id=ryf7ioRqFX)

PDF URL: https://github.com/reproducibility-challenge/iclr_2019/blob/master/papers/TeamYakataka-ryf7ioRqFX/TeamYakataka_camera_ready.pdf
Metadata URL:
Code URL: https://zenodo.org/record/2657361#.XMq6eEPhXCI

Scientific domain: Machine Learning
Programming language: Python
Suggested editor: ICLR Reproducibility Challenge Editors

Corresponding Author: @dido1998
Challenge PR: reproducibility-challenge/iclr_2019#148

ICLR Reproducibility Challenge, 2019

Reproduction of Step width enhancement in a pulse-driven Josephson junction

Original article: S. Maggi, Step width enhancement in a pulse-driven Josephson junction, Journal of Applied Physics vol. 79, no. 10, pp. 7860--7863 (1996), doi: 10.1063/1.362395.

PDF URL: https://github.com/sabinomaggi/ten-years-challenge-pulsed-drive/blob/submission/article/article.pdf
Metadata URL: https://github.com/sabinomaggi/ten-years-challenge-pulsed-drive/blob/submission/article/metadata.yaml
Code URL: https://github.com/sabinomaggi/ten-years-challenge-pulsed-drive/tree/submission/code

Scientific domain: Physics
Programming language: Fortran/Visual Basic
Suggested editor:

[Re] Reproduction of the normal and pathological dynamics in the basal ganglia-thalamo-cortical network

Original article: Leblois A, Boraud T, Meissner W, Bergmann H, Hansel D. Competition
between feedback loops underlies normal and pathological dynamics in the
basal ganglia. J Neurosci 26: 3567–3583, 2006.

PDF URL: https://github.com/aleblois/BGdynamics2006/blob/master/ReScience_C__BGdynamics2006.pdf
Metadata URL: https://github.com/aleblois/BGdynamics2006/blob/master/metadata.tex
Code URL: https://github.com/aleblois/BGdynamics2006
yaml file: https://github.com/aleblois/BGdynamics2006/blob/master/metadata.yaml

Scientific domain: Neuroscience
Programming language: C and Matlab
Suggested editor: Etienne Roesch, Tiziano Zito, Benoît Girard, Nicolas Rougier

Reproducibility of 'Poincaré dodecahedral space parameter estimates'

Original article: Roukema, B. F., Z. Buliński, and N. E. Gaudin, 2008, Poincaré dodecahedral space parameter estimates, Astronomy and Astrophysics, 492, 657 arXiv:0807.4260, https://ui.adsabs.harvard.edu/abs/2008A&A...492..657R

PDF URL: https://codeberg.org/boud/RBG08/raw/branch/master/Roukema_ReSciC2020.pdf
Metadata URL: https://codeberg.org/boud/RBG08/src/branch/master/metadata.yaml
Code URL: https://codeberg.org/boud/0807.4260 (and swh)

Scientific domain: Astronomy (Cosmology)
Programming language: C + Fortran 77
Suggested editor: Based on fortran + C + scientific field per the official profiles, @pdebuyl would seem to be the most appropriate

This is Paper number 12 at ReScience/ten-years#1.

Ten-year reproducibility challenge: friction coefficients of mixed globular/chain molecules (1995)

Original article:
Charles H. Robert. "Estimating friction coefficients of mixed globular/chain molecules, such as protein/DNA complexes." Biophys. J. 69 (Sept. 1995), pp. 840–848
https://doi.org/10.1016/S0006-3495(95)79957-X

PDF URL:
revised MS
https://github.com/charlestonchas/rehydro-rescience-submit/blob/master/tex/article.pdf

Metadata URL:
https://github.com/charlestonchas/rehydro-rescience-submit/blob/master/tex/metadata.yaml

Code URL:
[https://zenodo.org/record/3878075](version 1.0.2 https://zenodo.org/record/3878075)

Scientific domain:
Structural Biology, Hydrodynamics

Programming language:
Mathematica

Suggested editor:
Konrad Hinsen

[Re] Ten years challenge: Velho and Legrand (2009) - Accuracy Study and Improvement of Network Simulation in the SimGrid Framework

Original article: https://dl.acm.org/doi/10.4108/ICST.SIMUTOOLS2009.5592 or https://hal.inria.fr/inria-00361031/file/simutools09.pdf

@inproceedings{velho:inria-00361031,
  TITLE = {{Accuracy Study and Improvement of Network Simulation in the SimGrid Framework}},
  AUTHOR = {Velho, Pedro and Legrand, Arnaud},
  URL = {https://hal.inria.fr/inria-00361031},
  BOOKTITLE = {{SIMUTools'09, 2nd International Conference on Simulation Tools and Techniques}},
  ADDRESS = {Rome, Italy},
  YEAR = {2009},
  MONTH = Mar,
  PDF = {https://hal.inria.fr/inria-00361031/file/simutools09.pdf},
  HAL_ID = {inria-00361031},
  HAL_VERSION = {v1},
}

PDF URL: https://github.com/alegrand/reproducibility-challenge
Metadata URL: https://hal.inria.fr/inria-00361031/
Code URL: https://github.com/alegrand/reproducibility-challenge

Scientific domain: Computer Science
Programming language: C/C++
Suggested editor: @khinsen or @rougier

[Re] A Multi-Functional Synthetic Gene Network

Original article: A Multi-Functional Synthetic Gene Network: A Frequency Multiplier, Oscillator and Switch

PDF URL: [Re] A Multi-Functional Synthetic Gene Network
Metadata URL: metadata.yaml
Code URL: GitHub repository

Scientific domain: Biological Computing / Synthetic Biology
Programming language: Octave
Suggested editor: C. Titus Brown, Konrad Hinsen

[Re] Hippocampal Phase-Amplitude Coupling unearthed again

This is a submission to the Ten Years Reproducibility Challenge.

Original article: Hentschke, H., Perkins, M.G., Pearce, R.A., & Banks, M.I. (2007) Muscarinic blockade weakens interaction of gamma with theta rhythms in mouse hippocampus. Eur.J.Neurosci., 26, 1642–1656.

PDF URL: https://github.com/hhentschke/ReScience_10yrReproChallenge/blob/master/paper/article.pdf
Metadata URL: https://github.com/hhentschke/ReScience_10yrReproChallenge/blob/master/paper/metadata.yaml
Code URL: https://github.com/hhentschke/ReScience_10yrReproChallenge

Scientific domain: Neuroscience
Programming language: Matlab
Suggested editor: Thomas Arildsen

Reproduction of ODP-PIV from the 1998 “Particle Image Velocimetry with Optical Flow” paper

Original article: Quénot, Georges & Pakleza, Jaroslaw & Kowalewski, Tomasz. (1998). Particle Image Velocimetry with Optical Flow. Experiments in Fluids. Volume 25, Issue 3, pp 177–189. 10.1007/s003480050222.

PDF URL: http://mrim.imag.fr/georges.quenot/rescience/jeif98/ReScience_C_ODP_PIV.pdf
Metadata URL: http://mrim.imag.fr/georges.quenot/rescience/jeif98/metadata.yaml
Code URL: https://github.com/quenot/opflow/tree/master/jeif98

Scientific domain: Image Processing
Programming language: ANSI C
Suggested editor:

Reproduction in Computational Mechanics

Original article: Olivier Pantalé, Parallelization of an object-oriented FEM dynamics code: influence of the strategies on the Speedup. (2005) Advances in Engineering Software, 36 (6). 361-373.

Paper n°38 for the 10 years reproduciblity challenge.

PDF URL: article.pdf
Code URL: https://github.com/pantale/ReDynELA

Scientific domain: Computational Mechanics
Programming language: C++ and C
Suggested editor: