leipzig / awesome-reproducible-research Goto Github PK

https://www.nature.com/articles/d41586-018-02108-9

https://github.com/psu-psychology/psy-511-reproducible-research-spring-2017
https://github.com/cbahlai/OSRR_course

https://github.com/terra-workflows/tetralogy-of-fallot/tree/master

let's get going with the non-case study papers of importance

https://gatesopenresearch.org/articles/4-17/v2

The Allotrope Data Format is a vendor, platform, and technique agnostic format adaptable for any laboratory technique to store the data, contextual metadata, and any ancillary files; a self-contained experiment. Class libraries provide the reusable software components to adapt existing applications or create new solutions that work with the ADF and taxonomies, and ensure the consistent adoption of the standards. The ADF Explorer is a free standalone, lightweight application provided for opening and viewing data stored in the data description, data cube, and data package within an ADF file.
​
The Allotrope Taxonomies and Ontologies form the basis of a controlled vocabulary and relationships for the contextual metadata needed to describe and execute a test or measurement and later interpret the data. Drawing from thought across member companies and the Allotrope Partner Network the standard language for describing the equipment, processes, materials, and results is being developed to cover a broad range of techniques and instruments, driven by real use cases, in an extensible design.
​
Allotrope Data Models provide a mechanism to define data structures (schemas, templates) that describe how to use the ontologies for a given purpose in a standardized (i.e. reproducible, predictable, verifiable) way.

https://nteract.io/

Thank you for the list! We included a text-mining based census of 1857 abstracts + 1520 full text articles discussing multi-omics, which included a look at deposition of data and software (in short we were not impressed with the adoption rates of Dryad/OSF/Zenodo, though this seems to be better with software repositories like GitHub/Bioconductor/PyPI or CRAN).

As it was not our prime focus, there may be false positives, so I describe it as a higher bound for repositories that were mentioned in papers rather than an accurate estimate though. I hope it may help someone who is looking at things like that in more detail.

Repository: https://github.com/krassowski/multi-omics-state-of-the-field.

Don't know if relevant/awesome enough for the list though.

https://osf.io/preprints/metaarxiv/2pczv/

https://zenodo.org/record/1194711
https://www.nature.com/articles/s41559-018-0488-4

It is not a journal, rather a database for empirical studies with information about methods, data and software used, availability of replication material and whether replications, corrections or retractions are known.

https://www.biorxiv.org/content/10.1101/614560v1

10.1371/journal.pone.0080278
case narrative
1

https://hrbopenresearch.org/articles/3-56/v2

https://qri.cloud/
hmmmm

• Delmont Metapangenomics
  • https://peerj.com/articles/4320/
  • http://merenlab.org/data/2018_Delmont_and_Eren_Metapangenomics/
  • https://figshare.com/projects/Data_for_Metapangenomics_by_Delmont_and_Eren_2018_/25231
• Jagadeesan Reconstructing african genome
  • https://www.nature.com/articles/s41588-017-0031-6.epdf
  • https://figshare.com/collections/Reconstructing_an_African_haploid_genome_from_the_18th_century/3940516

buck beware https://www.nature.com/articles/d41586-021-01824-z
bakker preregs https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000937
towse open psych https://link.springer.com/article/10.3758%2Fs13428-020-01486-1
goldacre CONSORT https://trialsjournal.biomedcentral.com/articles/10.1186/s13063-019-3173-2
serghiou openness https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001107

https://uwescience.github.io/neuroinformatics/2017/09/07/charter.html

https://www.nature.com/articles/s41591-020-01203-7

https://www.nature.com/news/preclinical-research-make-mouse-studies-work-1.14913

https://www.sciencedirect.com/science/article/abs/pii/S1364815220309452

hmm

https://blog.jetbrains.com/datalore/2020/12/17/we-downloaded-10-000-000-jupyter-notebooks-from-github-this-is-what-we-learned/

https://econjwatch.org/articles/replications-in-economics-a-progress-report

not going to add unless i can find a DOI. people need to get their shit together.

https://twitter.com/westwoodsam1/status/1385129877565804544?s=20

https://www.biorxiv.org/content/10.1101/2021.01.22.427844v1

https://github.com/pachterlab/CWGFLHGCCHAP_2021

this

https://doi.org/10.1162/99608f92.25982dcf

https://peerj.com/articles/3208/

_{Sent with GitHawk}

need to get my head around what is what

notebooks on steroids
codeocean
anaconda cloud
Google Cloud Datalab
Google Colaboratory
Gryd

workbenches
honestly, fuck workbenches

https://datproject.org/

data portals & repos
Synapse
data.world
figshare
Dryad
Repositive.io
kaggle
pachyderm
domino
protocols.io
datproject.org - a distributed filesharing system

development stacks
rsuite (WLOG solutions)

failure to replicate

https://jdblischak.github.io/workflowr/ - rmarkdown stack and bootstrap

http://openrefine.org/

https://royalsocietypublishing.org/doi/10.1098/rsos.201925

https://arxiv.org/abs/2011.01374

https://davidsoergel.com/posts/confirmation-depth-as-a-measure-of-reproducible-scientific-research

https://arxiv.org/pdf/2012.03554.pdf

reproducible builds are a set of software development practices that create an independently-verifiable path from source to binary code

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025290
a complete lab notebook:
http://journals.plos.org/plosone/article/file?type=supplementary&id=info:doi/10.1371/journal.pone.0025290.s001

10.1371/journal.pcbi.1008725
census
622 articles
computational biology

not sure what these guys are doing or if a polished course was finished
https://github.com/Reproducible-Science-Curriculum

10.1098/rsta.2020.0210
10.1098/rsta.2020.0069

https://101innovations.wordpress.com/

https://www.nature.com/articles/sdata2018158

https://arxiv.org/pdf/2107.03611.pdf

python src/doi2md.py --doi 10.1016/j.envsoft.2020.104873 --type study --field "Environmental Modelling" --size "7500 articles"

https://arxiv.org/abs/1708.04133
https://arxiv.org/abs/1709.06560

https://septentrio.uit.no/index.php/SCS/article/view/5601

https://github.com/mine-cetinkaya-rundel/2016-08-03-reproducible-undergrad-stats
https://github.com/mine-cetinkaya-rundel/dss_computing_bootcamp
https://github.com/Reproducible-Science-Curriculum/