Declaration of participation

[rougier]

This thread collects declaration of participation to the Ten Years Reproducibility Challenge. You can add your own declaration by adding the article your target with possibly a link to an open access version of the PDF.

Declared number of participants: 35 Number of targeted papers: 43 Oldest targeted paper: 28 years old (@MikeSilberbauer)

[rougier]

Paper number: 1 Reference: Rougier, N.P. and Vitay, J. 2006. Emergence of Attention within a Neural Population. Neural Networks 19, 5, 573–581. DOI:10.1016/j.neunet.2005.04.004

Article age: 13 years old Open access version (optional): PDF Confidence in success (optional): low (not sure to have the sources anymore)

[aleblois]

Paper number: 2 Reference: Leblois A, Boraud T, Meissner W, Bergman H, Hansel D (2006) Competition between feedback loops underlies normal and pathological dynamics in the basal-ganglia. J. Neurosci. 26: 3567-83. DOI:10.1523/JNEUROSCI.5050-05.2006

Article age: 13 years old Open access version (optional): PDF Confidence in success (optional): high ;)

[khinsen]

Paper number: 3 Reference: Hinsen, K (2008) Structural flexibility in proteins: impact of the crystal environment. Bioinformatics 24:521. DOI:10.1093/bioinformatics/btm625

Article age: 12 years (the publication date is December 2007) Open access version: PDF Confidence in success: high (but not without effort)

Comment: this is my first paper for which all source code has been published

See this repository for progress on the reproduction attempt.

[khinsen]

Paper number: 4 Reference: Cichocki B, Hinsen K (1995) Stokes drag on conglomerates of spheres. Phys. Fluids 7:286. DOI:10.1063/1.868626

Article age: 24 years Open access version: none (but see this summary prepared for the reproduction attempt) Confidence in success: low (not sure I can find all the code)

See this repository for progress on the reproduction attempt.

[apdavison]

Paper number: 5 Reference: Davison A.P., Feng J. and Brown D. (2003) Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. Journal of Neurophysiology 90: 1921–1935 doi:10.1152/jn.00623.2002

Article age: 16 years Open access version: the PDF can be freely downloaded from the publisher site, but is not under an open licence. Confidence in success: high

[sje30]

Paper number: 6 Reference: Stephen Eglen, Alistair Bray & Jim Stone (1997) Unsupervised discovery of invariances, Network: Computation in Neural Systems volume 8, issue 4 DOI:10.1088/0954-898X_8_4_006 Article age: 22 years Open access version: / Confidence in success: low

Paper number: 7 Reference: Stephen J. Eglen and James C.T. Wong (2008) Spatial constraints underlying the retinal mosaics of two types of horizontal cells in cat and macaque, Visual Neuroscience, volume 25, issue 2 DOI:10.1017/S0952523808080176 Article age: 11 years Open access version: PDF Confidence in success: high

[cboettig]

I'd be interested in attempting this for the following paper: https://doi.org/10.1016/j.tpb.2009.10.003 if it is acceptable -- I guess it depends on the definition of 'published date'. The final accepted version of the paper was published online by the journal on 18 October 2009 (as you can see at that DOI under "show more"), but the print version did not appear until February 2010, a month after your cutoff. As some journals only have online versions to begin with, it seems reasonable to use the date of online publication rather than print publication, but please let me know either way. Details here:

Paper number: 8 Reference: 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 Article age: 10 years Open access version: arxiv:1004.4233 Confidence in success: moderate

[rdicosmo]

Paper Number: 9 Reference: Marco Danelutto, Roberto Di Cosmo, Xavier Leroy, and Susanna Pelagatti. Parallel functional programming with skeletons: the OCamlP3L experiment. In Proceedings ACM workshop on ML and its applications. Cornell University, 1998. Article age: 20 years Open Access version: http://xavierleroy.org/publi/ocamlp3l-mlws.pdf Confidence in success: moderate Comment: Incredible but true, I cannot seem to find an online version of this paper, except for the locally archived copy on Xavier's publications webpage and mine. Making a note here to deposit it on an open access repository when I start working on this :-)

[jrfaller]

Paper Number: 10 Reference: Jean-Rémy Falleri, Marianne Huchard, Mathieu Lafourcade, Clémentine Nebut: Metamodel Matching for Automatic Model Transformation Generation. MoDELS 2008: 326-340 Article age: 12 years Open Access version: https://hal-lirmm.ccsd.cnrs.fr/lirmm-00322879/ Confidence in success: moderate Comment: This one of my first papers, so the sentimental value is high :). However, the code has been through a lot since it was hosted on Google Code, so the first challenge will be to retrieve the latest version. Additionnally, I had much less knowledge on software construction tools at the time, therefore this should be fun!

[delsuc]

Paper Number: 11 Reference: Dominique Tramesel, Vincent Catherinot, Marc-André Delsuc Modeling of NMR processing, toward efficient unattended processing of NMR experiments doi: 10.1016/j.jmr.2007.05.023 Article age: 12 years Open Access version: http://www.delsuc.net/pdf/2007-Journal%20of%20Magnetic%20Resonance-Tramesel.pdf Confidence in success: low Comment: This program is piling up some FORTRAN77 code linked to Java and controlled by python scripts using jython (a flavor of python running inside the Java machine) ! Additionally, all FORTRAN codes are purely 32bits. If this is too difficult, I intend falling back on the pure FORTRAN code, published in 1996 (so one year short to Konrad one) which could actually be easier. Reference: Jean-Luc Pons, Thérèse E. Malliavin, Marc A. Delsuc Gifa V. 4: A complete package for NMR data set processing. doi: 10.1007/BF00228146

April 2020: I finally decided to go for the alternative goal - and successfully reproduced the 1996 paper - this was Much simpler. You find it here.

[broukema]

Paper Number: 12 Reference: Roukema, B. F.; Buliński, Z.; Gaudin, N. E. Poincaré dodecahedral space parameter estimates Astronomy and Astrophysics, 2008, 492, 657-673 ADS: https://ui.adsabs.harvard.edu/abs/2008A%26A...492..657R DOI: 10.1051/0004-6361:200810685 Article age: 11 years Open Access version: https://arXiv.org/abs/0807.4260 (green open access) Confidence in success: high Dates of archiving: Web.archive.org has archived at least the two URLs which are listed in the Comments: field of ArXiv:0807.4260:

• https://web.archive.org/web/20110810143023/http://cosmo.torun.pl/GPLdownload/dodec/
• https://web.archive.org/web/20110810142735/http://cosmo.torun.pl/GPLdownload/MCMC/ These URLs have been publicly accessible since around the date of publishing the article, and the software is free-licensed.

[brembs]

Paper Number: 13 Reference: Brembs, B., & Heisenberg, M. (2000). The operant and the classical in conditioned orientation of Drosophila melanogaster at the flight simulator. Learning & memory (Cold Spring Harbor, N.Y.), 7(2), 104–115. Article age: 19 years Open Access Version: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311324/ Confidence in success: high Comment: I will take the old raw data and reproduce the performance indices in the paper. I still have the raw data and the evaluation software (C++) ought to work as it did back then.

[kbroman]

Paper Number: 14 Reference: 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 Article age: 16 years Confidence in success: moderate Comment: I'm happy with my reproduction, which is at https://github.com/kbroman/Paper_ReScience2020; now to write the paper.

[ivanov]

Would you consider the reproducibility of a poster? I've got this one from the GPU Tech Conference 2009.

Paper Number: 15 Reference: Ivanov P. (2009) Estimating the Entropy of Natural Scenes from Nearest Neighbors using CUDA. GPU Technology Conference. San Jose, CA. Poster age: 10 years Confidence in success: moderate Comment:

Perhaps of interest to the journal was that this poster itself was a novel computational approach (GPU computing) replication of Chandler D.M., Field D.J. (2007) Estimates of the information content and dimensionality of natural scenes from proximity distributions. Journal of the Optical Society of America A.

The extra challenge is that it was done using CUDA 1.0 or 1.1 language from NVidia using GPUs of that time, which have long been replaced with newer versions, including newer hardware. So this will be a test of the portability of the then experimental numerical techniques to modern hardware and software.

[sabinomaggi]

Paper Number: 16 Reference: Sabino Maggi, Step width enhancement in a pulse‐driven Josephson junction, Journal of Applied Physics 79, 7860 (1996). DOI: 10.1063/1.362395 Article age: 23 years Confidence in success: moderate to low

[hhentschke]

Paper number: 17 Reference: 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. DOI: https://doi.org/10.1111/j.1460-9568.2007.05779.x Article age: 12 years Confidence in success: high for reproducing the figures from saved precomputed data, moderate for crunching the raw data

This was the first in a series of studies on rodent hippocampal rhythms (electrical activity of that part of the brain involved in memory formation and navigation), so I was granted ample time back then as a postdoc to develop maintainable, better-than-ephemeral code. The project made me befriend the concept of surrogate data and a panoply of crosscorrelational and spectral analysis methods, which had been both satisfactory and challenging in terms of computational efficiency (never mind that these days the methodological approach would be different). Curious to see whether the maintainability strategy pans out. All written in Matlab.

[yarikoptic]

Paper number: 18 Reference: Hanke M (@mih), Halchenko YO (@yarikoptic), Sederberg PB (@psederberg), Olivetti E, Fründ I, Rieger JW, Herrmann CS, Haxby JV (@JamesVHaxby), Hanson SJ and Pollmann S (2009). PyMVPA: a unifying approach to the analysis of neuroscientific data. Front. Neuroinform. 3:3. doi: 10.3389/neuro.11.003.2009 Article age: 10 years Open access version: PDF Confidence in success: medium to high (main code IIRC should be available, environment - rebuildable, all of the data - need to be found)

[kneth]

Paper number: 19 Reference: Geisshirt, K. (@kneth), Praestgaard, E. and Toxvaerd, S. Oscillating chemical reactions and phase separation simulated by molecular dynamics. Journal of Chemical Physics, volume 107, no. 22, pp. 9406-9412 (1997). DOI: https://doi.org/10.1063/1.475237 Article age: 22 years Open access version: Confidence in success: medium to high (source code is available at https://github.com/kneth/MDreac)

The paper is from my Ph.D. studies, and I haven't done much academic research since.

[arnodelorme]

Paper number: 20 Reference: Delorme, A., Westerfield, M., Makeig, S. (2007) Medial prefrontal theta bursts precede rapid motor responses during visual selective attention. Journal of Neuroscience, 27(44):11949-59. Article age: 12 years Open access version: https://www.ncbi.nlm.nih.gov/pubmed/17978035 Confidence in success: relatively high

All the figures in this paper were created using custom EEGLAB scripts. EEGLAB strives for backward compatibility. I expect I will be able to run my script with minimal changes, and will document the necessary changes in the article.

[MikeSilberbauer]

Paper number: 21 Reference: 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. DOI: https://doi.org/10.1080/10183469.1991.9631315 Article age: 28 years Open access version: The above article at is not open access, but the following article refers to the same data visualisation method, and is open access: Day, J.A. and King, J.M., 1995. Geographical patterns, and their origins, in the dominance of major ions in South African rivers. South African Journal of Science, 91, 299–306. URL https://hdl.handle.net/10520/AJA00382353_6757 Confidence in success: If the Turbo Pascal program runs in DOSbox, quite high.

The Maucha ionic diagrams of water chemistry in these two papers were generated in Turbo Pascal. The mapping process involved printing the symbols, cutting them out and gluing them onto a map (the true cut-and-paste).

Ironically, running pre-2009 versions of the Maucha diagram software that plotted the symbols directly onto a digital map would present greater difficulties: for example, the oldest ran in Esri's Arc Macro Language under Arc/Info on a Sun Unix server.

Postscript: The Maucha procedure lives on in a version coded in R, which has been available since 2011 (e.g. Silberbauer, M., 2011. "Multivariate" Point Data Visualisation - Geographical Information Systems Developments to Aid in Water Quality Management. In: S. Geertman, W. Reinhardt, and F. Toppen, eds. The 14th AGILE International Conference on Geographic Information Science: Advancing Geoinformation Science for a Changing World. Utrecht, the Netherlands: AGILE. https://agile-online.org/index.php/conference/proceedings/proceedings-2011)

[agbarnett]

Paper number: 22 Reference: Barnett, A. G., Dobson, A. J. and For the WHO MONICA (monitoring trends and determinants in cardiovascular disease) Project (2004), Estimating trends and seasonality in coronary heart disease. Statist. Med., 23: 3505-3523. doi:10.1002/sim.1927 Article age: 15 years Open access version: Not available Confidence in success: Good, I think the data is on a CD somewhere and may also be publicly available via the MONICA website. The code is probably gone after moving jobs.

[rougier]

Paper number: 23 Reference: N.Rougier (1988), Loupe, Tremplin Micro, 19: 60-61 Article age: 31 years Open access version: Scan at archives.org Confidence in success: This is my very first code published in a (non scientific) journal running on Apple IIe (and applesoft). It is not meant to be a real entry for the challenge but I'm confident I'll manage to run it since there is a lot of resources around Apple II and from my memory, the language never changed (think Python!) such that any emulator will do. I even discovered that you can now emulate it online (through MAME). Alos, I've an Apple 2e in my office, I might try to have it run on the old machine, just for fun.

[quenot]

Paper number: 24 Reference: Quénot, Georges & Pakleza, Jaroslaw & Kowalewski, Tomasz. (1998). Particle Image Velocimetry with Optical Flow. Experiments in Fluids. Volume 25, Issue 3, pp 177–189. DOI: 10.1007/s003480050222. Article age: 21 years. Open access version: author version. Confidence in success: high, already partially reproduced, ANSI C code with no dependency. Repository: work in progress. Comment: first use of Optical Flow for Particle Image Velocimetry (248 citations).

[ghost]

Paper number: 25 Reference: Benno Büeler, Andreas Enge and Komei Fukuda: Exact Volume Computation for Polytopes: A Practical Study. In Gil Kalai and Günter M. Ziegler (editors): Polytopes — Combinatorics and Computation, DMV Seminar vol. 29. Birkhäuser Verlag, Basel 2000, pp. 131–154. Article age: 19 years Open access version: author version Confidence in success: high, ANSI C code with a simple Makefile and some C library dependencies Comment: This is my first scientific article, it will be fun to have a look at it again.

[BrunoLevy]

Paper numbers: 26, 27, 28, 29,30,31 References: 2001: Constrained Texture Mapping, SIGGRAPH 2001: https://members.loria.fr/Bruno.Levy/papers/constrainedtex_SIGGRAPH_2001.pdf 2002: Least Squares Conformal Maps, SIGGRAPH 2002: https://members.loria.fr/Bruno.Levy/papers/LSCM_SIGGRAPH_2002.pdf 2004: ABF++: Fast Angle-Based Flattening, ACM Trans. Graphics https://hal.inria.fr/inria-00105689 2006: Periodic Global Parameterization, ACM Trans. Graphics https://hal.archives-ouvertes.fr/inria-00104853/ 2006: Laplacian Eigenfunctions, Shape Modeling Intl https://members.loria.fr/Bruno.Levy/papers/Laplacian_SMI_2006.pdf 2009: On centroidal Voronoi Diagrams, ACM Trans Graphics https://hal.archives-ouvertes.fr/inria-00547936/ Article ages: 18,17,15,13,13,10 years Confidence in success: why are you asking ? You trust me, right ? Comment: The integrality of my published work starting back to Y2K has code in working condition. I take the challenge, but with 6 articles, else it is too easy ! Links: 20Y of research code in the following repositories: Graphite: http://alice.loria.fr/software/graphite/doc/html/ Geogram: http://alice.loria.fr/software/geogram/doc/html/index.html

[mcbaneg]

Paper number: 32 Reference: J. Gottfried and George C. McBane, "Interaction second virial coefficients from a recent H$_2$--CO potential energy surface", J. Chem. Phys. 112(9), 4417 (2000) Article age: 19 years Open access version: https://scholarworks.gvsu.edu/chm_articles/13 Confidence in success: high, took about an hour last Friday

[bpbond]

Paper number: 33 Reference: Bond-Lamberty, Peckham, Gower, and Ewers (2009). Effects of fire on regional evapotranspiration in the central Canadian boreal forest, Global Change Biology 15(5):1242-1254, 10.1111/j.1365-2486.2008.01776.x. Article age: 10 years old Open access version: ? Confidence in success: fairly high (have R code; it's fairly simple; have archived output from 2009)

[kyleniemeyer]

Paper number: 34 Reference: Niemeyer, Sung, and Raju (2010). Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis, Combustion and Flame 157(9): 1760–1770. https://doi.org/10.1016/j.combustflame.2009.12.022

Article age: 10 years old Open access version: arXiv:1607.05079 [physics.chem-ph] Confidence in success: medium to high (I have an updated version of the code, some version control going back to 2012, and possibly an archive of the original version)

[ev-br]

Paper number: 36 Reference: Evgeni Burovski, Nikolay Prokof’ev, Boris Svistunov, and Matthias Troyer Phys. Rev. Lett. 96, 160402 (2006). https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.96.160402 Open Access version: https://arxiv.org/abs/cond-mat/0602224

Article age: 14 years Confidence in success: moderately high. The computational code is plain Fortran 90 with only external dependencies being BLAS/LAPACK, and it was at the time developed/tested/run on several systems (MS Visual Fortran on Win 2000, Intel Fortran on Operton Beowulf cluster under CentOS, native Cray X1E system/compilers). (A what we then considered a demo version of the code is available online at http://mcwa.csi.cuny.edu/umass/fermions/fermi.html and differs from the original code only in adding some comments). The main challenge will be in reproducing the data analysis / plotting part, which was done (IIRC) in Origin under Windows 2000. So this will have to be redone with some other tool. Or I manage to find the original Origin project files and find a free reader.

One caveat is that I probably will only be able to reproduce a subset of simulations, for the full set is prohibitively costly CPU time wise.

[5reddman]

I won't participate out of respect to my deceased chemistry professor (the field practically died with him) but at least I can tell you why reading about this challenge in NATURE amused me to no end.

I'm from a different generation of programmers. I learned programming on a TI-58 (pocket calculator, the languange was factually assembler, 240 program steps maximum!). For 30 years or so I was the computer expert of our workgroup, doing all work with the good old INVEIX proggie from Berkeley, which is an abomination by todays quality standards (the undocumented control parameter field, good god, and the overload of warnings which you should happily ignore). It's written in FORTRAN, worked already splendidly, warnings or not, about 10-20 years before my time (just needed a bit of adaption to the local machines here), and also runs without problems on the free FORCE compiler on my PC (but gcc probably will have a heart attack seeing the code :-).

So, the only thing I would need for reproducing any of my (main) papers would be browsing the 4000 lines of code and find which are the device numbers of the IO parameter files, and this trouble is only because my chemistry account was deleted, otherwise all I would have to do is specify the input files (still saved on my PC) and type "go". Papers with help programs or those with DFT calculations (damned if I knew what I did :-) are possibly exempt.

A few years ago I took up a Computer Science studium here in Hamburg just for teh luz and now know exactly what you are talking about. Good grief, the kiddies' first touch is JAVA! They will NEVER learn to program like old wizard me :-) And good luck trying to get THAT to work 40 years later! (I admit I wrote this overlong comment merely because I love dissing JAVA :-)

[khinsen]

@5reddman Thanks for this first declaration of non-participation! I must admit that I can't follow your reasoning: in my opinion, showing that your old work is still reproducible would be a way to honor your deceased professor's work! Moreover, if your expectations are proven correct in practice, that would provide useful guidance to future scientists in choosing technology.

[pbnjay]

Paper number: 37 Reference: Erich J. Baker, Jeremy J. Jay, Vivek M. Philip, Yun Zhang, Zuopan Li, Roumyana Kirova, Michael A. Langston, Elissa J. Chesler. (2009) Ontological discovery environment: A system for integrating gene–phenotype associations. Genomics 94 (6), 377-387 https://doi.org/10.1016/j.ygeno.2009.08.016 Open Access version: https://www.sciencedirect.com/science/article/pii/S0888754309002067

Article age: 11 years Confidence in success: high. I have version-controlled source code, and data used for the analysis was mostly publicly available supplementary files from open access publications. I might not have been AS GOOD at provenance tracking back then, but I was at least aware of it and made some attempts.

I started working through it today and was live-tweeting the process... :) https://twitter.com/thepbnjay/status/1223243703956860935

[pantale]

Paper number: 38 Reference: 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.

Article age: 15 years old Official URL: http://dx.doi.org/10.1016/j.advengsoft.2005.01.003 Open access version: https://oatao.univ-toulouse.fr/5378/

Confidence in success: medium to high, as I have an updated version of the code with a lot of new features, but I want to re-run the old version that has been used to produce the related paper. I think that the code will re-run but the results in terms of parallelization-speedups will not be the same since the openMP library that has been used and the computer architecture have evolved a lot during the last past 15 years.

[alegrand]

Paper number: 39 Reference: Pedro Velho and Arnaud Legrand, Accuracy Study and Improvement of Network Simulation in the SimGrid Framework. (2009) SIMUTools'09, 2nd International Conference on Simulation Tools and Techniques, Mar 2009, Rome, Italy.

Article age: 10 years old Open access version: https://hal.inria.fr/inria-00361031

Confidence in success: medium to high. This is a simulation only article. It compares two simulation methods of network communications (packet level vs. flow based) and relies on two simulators (SimGrid and GTNetS). Interestingly, this article is already a reproduction from the work of US colleagues. At that time, although we had access to their code and most of their protocol, we had failed reproducing the same numerical values (although overall results were similar), which was very frustrating for both them and us. This motivated us to improve our methodology so let's hope I'll succeed. :smiley:

[charlestonchas]

Paper number: 40

Reference: Charles H. Robert (1995) "Estimating Friction Coefficients of Mixed Globular/Chain Molecules, such as Protein/DNAComplexes" Biophysical Journal 69, 840-848.

Article age: 25 years (in 2020) Open access version: (coming soon)

Confidence in success: Pretty high. The code is written in Mathematica notebooks. I kept the originals, which are converted and read by the more recent version of Mathematica I still use. I've also modified the code at various points in the years since (mainly the 3D macromolecular modelling functions).

[civodul]

Paper number: 41

Reference: Ludovic Courtès, Marc-Olivier Killijian, and David Powell, "Storage Tradeoffs in a Collaborative Backup Service for Mobile Devices", Proceedings of the Sixth European Dependable Computing Conference (EDCC 6), 2006.

Article age: 14 years old Open access version: https://hal.inria.fr/hal-00187069/en

Confidence in success: Medium. The article contains results involving a non-trivial software stack that won't work as-is today. The scripts and data sets used to produce the results need to be salvaged from an old version-control repository that should be on an old hard disk...

[a-kharechko]

Paper number: 42

Reference: Kharechko, A., Shawe-Taylor, J., Herbrich, R. and Graepel, T. (2004) Text Categorization via Ellipsoid Separation. PASCAL Workshop on Learning Methods for Text Understanding and Mining, Grenoble, France, 26 - 29 Jan 2004.

Article age: 16 years Open access version: https://eprints.soton.ac.uk/263412/

Confidence in success: Moderately high. The code was written in MatLab and calls SDPT3 package whose version which was used that time is no longer supported by the most recent releases of MatLab, yet the package has been maintained (i.e. revised and updated). Moreover, MatLab itself has evolved since then, so the code may need to be adapted to its new syntax.

[weinman]

Paper number: 43

Reference: Weinman, J. (Aug. 2010). Typographical Features for Scene Text Recognition. In Proc. IAPR Intl. Conference on Pattern Recognition (ICPR), pp. 3987--3990.

Article age: 10 years

Open access version: http://www.cs.grinnell.edu/~weinman/pubs/weinman10typographical.pdf

Confidence in successs: Moderate. The experiments use a deep chain of processing across multiple libraries and environments (C, CUDA, Matlab, Java). Although the code (and "glue" scripts) is all available to me, versions of libraries and languages were not always recorded. To link against/run within modern versions requires some tweaks. Preliminary results indicate repeatability, if not precisely reproducibility.

[MelanieIStefan]

Paper number: 44

Reference:

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):10768-73.

Article age: 12 years

Open access version: https://www.pnas.org/content/105/31/10768

Confidence in success: OK. The model was written in SBML and the code was deposited to BioModels Database at the time of publication. In theory, it should be as simple as downloading the SBML from BioModels Database and running it in an appropriate simulator.

[sje30]

Paper number: 6 Reference: Stephen Eglen, Alistair Bray & Jim Stone (1997) Unsupervised discovery of invariances, Network: Computation in Neural Systems volume 8, issue 4 DOI:10.1088/0954-898X_8_4_006 Article age: 22 years Open access version: / Confidence in success: low

Paper number: 7 Reference: Stephen J. Eglen and James C.T. Wong (2008) Spatial constraints underlying the retinal mosaics of two types of horizontal cells in cat and macaque, Visual Neuroscience, volume 25, issue 2 DOI:10.1017/S0952523808080176 Article age: 11 years Open access version: PDF Confidence in success: high

I've been able to replicate #7 but habe not yet been able to write a short paper. Am I too late? Would need a fwe hours to summarise what I needed to do (but as hoped, it passed!)

https://github.com/sje30/rescience-hor

[khinsen]

It's still April 30th until midnight. We didn't actually specify a time zone, so we'll be generous and accept any time zone of our little planet ;-)

[sje30]

made it ! https://github.com/ReScience/submissions/issues/34

[BrunoLevy]

On my side, could not made it ...

Get the software: check

Make it run: check

Reproduce all the results: check

Find time to write the article: FAIL

-- Bruno

On 4/30/20 1:04 PM, Stephen Eglen wrote:

made it ! ReScience/submissions#34 https://github.com/ReScience/submissions/issues/34

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ReScience/ten-years/issues/1#issuecomment-621764714, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEUTN3PCNZXNVBCV4KGZLSTRPFLNPANCNFSM4I7JWQBA.

[sje30]

@BrunoLevy -- I was in your position ujntil 24 hours ago; started writing the paper last night. You still have a few hours (but grab the master-template/ folder from rescience first to help you write the report... I made the mistake of doing that after finishing the report!)

[sje30]

It's still April 30th until midnight. We didn't actually specify a time zone, so we'll be generous and accept any time zone of our little planet ;-)

Is there a timezone GMT-200 ?!?

[MelanieIStefan]

Hi same boat here, writing it up as we speak. Plenty of time! (cough)

[khinsen]

@BrunoLevy So your problem is not reproducibility, but producibility? That sounds like a great theme for another challenge ;-)

@sje30 It's a pity the Earth is round, which makes time modulo 24h. Maybe the Flat Earth society can propose something more convenient ;-)

BTW, this got me interested in actual time zones. It looks like the most favorable one is GMT-11. In the other direction, it seems to go up to GMT+14, which I find mildly surprising.

[pbnjay]

I'm not going to make it with paper 37. I'm almost caught up on all my deadlines after transitioning to online instruction, but this had to take a back seat. Good luck everyone!

[alegrand]

Hi there, I've just uploaded a submission but I have to confess I'm still working on it. As several others, I have obtained successful replication results some months ago but never had the time to write it up. I started writing only yesterday after reading your messages and I'm about 2/3 done so it should be completely done in a few hours, almost the AOE deadline... ;) I hope the organizers will forgive me.

Best,

Arnaud

[bpbond]

I, too, did the reproducibility work, wrote up the results in an Rmarkdown report posted in #11 , and then ran out of time in April to get it all finished and submitted. Apologies!