24 Matching Annotations
  1. Last 7 days
  2. Oct 2021
    1. The analysis that I present is applicable to all branches of science whose models are based on continuous mathematics, such as algebraic, differential, or integral equations.

      I wonder if this could be applied also to the problem of reproducibility in the context of journalism and/or (h)ac(k)tivism. My approch has been to use relatively simple and self-contained connected infrastructures/tools and maybe pair them with functional package managers. The approach here could be complementary to it (still it's to early in the text to say)

  3. May 2021
  4. Mar 2021
    1. An example app is an application that is designed to reproduce a bug or demonstrate an issue.
    2. Before a bug can be fixed, it has to be understood and reproduced. For every issue, a maintainer gets, they have to decipher what was supposed to happen and then spend minutes or hours piecing together their reproduction. Usually, they can’t get it right, so they have to ask for clarification. This back-and-forth process takes lots of energy and wastes everyone’s time. Instead, it’s better to provide an example app from the beginning. At the end of the day, would you rather maintainers spend their time making example apps or fixing issues?
  5. Feb 2021
  6. Jan 2021
    1. Also as an aside, your REPL is far, far too complicated. You've got a much better chance of us being able to see your issue and fix it if you boil it down to just the minimum required code in order to reproduce the issue.
  7. Nov 2020
    1. Now that Rails has a dependency on Webpack, it then has a dependency on Node.js and Yarn, surprise! Which means we also need to ensure the versions used for those binaries are specific.
  8. Oct 2020
    1. Omitted details change everything here. There won't be circular dependency because unused import is skipped. Consider providing stackoverflow.com/help/mcve .
  9. Sep 2020
    1. If you can't understand where it's coming from in the stack traces, please post screenshots or create reproducing sandboxes and we'll try to help. Most of these are probably coming from a few libraries, so the most productive thing to do is to reduce these cases and then file issues with those libraries.
  10. Jun 2020
  11. Feb 2020
  12. Jul 2018
    1. We used the program STRUCTURE v2.3.4 [16]

      Cited reference is open access and describes the method

    2. NA extractions were attempted for all taxa for which recent and sufficient tissues were available. Of the samples that were successfully extracted, at least two individuals for each taxon were included when available. This yielded 44 Malagasy Canarium accessions, to which we added an additional four Southeast Asian Canarium species to serve as outgroups. Genomic libraries were prepared for genotyping-by-sequencing (GBS) following the protocol described by Escudero et al. [14], but with the addition of a size selection step. After restriction digestion, fragment sizes were visualized on an Agilent 2100 Bioanalyzer and selected in the range of 300–800 bp using a Pippin Prep system. The final library containing 48 barcoded individuals was sequenced on two lanes of an Illumina HiSeq 2500 at Yale University’s Center for Genome Analysis to generate 75 bp single-end reads.

      Protocol not fully open. Based on closed access paper. Extension to method is clearly described.

    3. Fully reproducible code is available in the form of jupyter notebooks (https://jupyter.org) with instructions to install all necessary software, download sequence data, assemble it, and run genomic analyses (https://github.com/dereneaton/Canarium-GBS) (DOI 10.5281/zenodo.1273357). For all genomic analyses in this study we used the ipyrad Python API and the ipyrad-analysis toolkit (https://github.com/dereneaton/ipyrad) which provides a set of wrappers around common genomic analysis tools to run highly parallelized analyses using simple Python scripts.

      Well-described dry lab notebooks with open code, and Python analysis toolkit is open source.

  13. May 2018
    1. En total, se analizaron los datos de 18.662 estudiantes de pregrado en el período 1530 y de 18.989 en el período 1610.

      ¿Estos datos podrían estar disponibles como datos anonimizados, para hacer otro tipo de inferencias estadísticas o hallazgos?

  14. Apr 2016
  15. Dec 2015
    1. Similarly, in science there exists substantial expertise making brilliant connectionsbetween concepts, but it is being conveyed in silos of English prose known as journalarticles. Every scientific journal article has a methods section, but it is almost impossibleto read a methods section and subsequently repeat the experiment—the English languageis inadequate to precisely and concisely convey what is being done.

      This issue of reproducible science is starting to be tackled but I do believe formal methods and abstractions would go along way to making sure we adhere these ideas. It is a bit like writing a program with global state vs a functionally defined program, but even worse, since you may forget to write down one little thing you did to the global state.