Trang Le
#math graduate. Postdoc fellow with Jason Moore.
Some slides borrowed from https://slides.com/dhimmel/force2018
Manubot
system for writing papers via GitHub
Daniel Himmelstein
Motivation
- The Deep Review
- review article on deep learning in precision medicine
- 27 authors from 20 different institutions
Nice properties
- transparent & reproducible
- immediate & permissionless
- versioned & automated
- collaborative
- open & free of charge
tpot-ds-ms
Modify the ms source
Continuous integration
Continuous deployment
Pull requests for ms collab
Citation
This is a sentence with 5 citations [
@doi:10.1038/nbt.3780;
@pmid:29424689;
@pmcid:PMC5938574;
@arxiv:1407.3561;
@url:https://greenelab.github.io/meta-review/
].
References
-
Reproducibility of computational workflows is automated using continuous analysis
Brett K Beaulieu-Jones, Casey S Greene
Nature Biotechnology (2017-03-13) https://doi.org/f9ttx6
DOI: 10.1038/nbt.3780 · PMID: 28288103 · PMCID: PMC6103790
-
Sci-Hub provides access to nearly all scholarly literature.
Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
eLife (2018-03-01) https://www.ncbi.nlm.nih.gov/pubmed/29424689
DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410
-
Opportunities and obstacles for deep learning in biology and medicine
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman, … Casey S. Greene
Journal of the Royal Society Interface (2018-04) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938574/
DOI: 10.1098/rsif.2017.0387 · PMID: 29618526 · PMCID: PMC5938574
-
IPFS - Content Addressed, Versioned, P2P File System
Juan Benet
arXiv (2014-07-14) https://arxiv.org/abs/1407.3561v1
-
Open collaborative writing with Manubot
Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
(2018-08-03) https://greenelab.github.io/meta-review/
This is a sentence with 5 citations [1,2,3,4,5].
Get started
- PSB 2019 special session
- tiny.cc/manubot
Manubot
By Trang Le
Manubot
Presentation on 2018-11-12 for the Moore Lab's Lunch&Learn.
