Skip to content

Instantly share code, notes, and snippets.

Avatar
🎯
Focusing

Daniel Himmelstein dhimmel

🎯
Focusing
View GitHub Profile
@dhimmel
dhimmel / sciscore-manuscript-review.md
Last active May 4, 2020
Review of the "Rigor and Transparency Index" manuscript (https://doi.org/dkg6)
View sciscore-manuscript-review.md

Daniel Himmelstein's review of preprint v2

Review of version 2 of the following preprint:

Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods
Joe Menke, Martijn Roelandse, Burak Ozyurt, Maryann Martone, Anita Bandrowski
bioRxiv (2020-01-18) https://doi.org/dkg6
DOI: 10.1101/2020.01.15.908111

The study introduces an automated method called SciScore to detect whether an article's methods section mentions any of 15 categories, such as a consent statement or an organism. These metrics are combined to create a single score for each article called the "Rigor and Transparency Index". The authors applied the method to the PubMed Central Open Access subset with over 1 million articles to identify trends in the level of details provided by method sections.

@dhimmel
dhimmel / hetmech-query-node-pair.ipynb
Created Oct 23, 2018
Query relationship between the FTO gene and obesity using hetmech
View hetmech-query-node-pair.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@dhimmel
dhimmel / hetionet-v1.0-metaedge-xswap-stats.tsv
Last active Oct 2, 2018
Analytical derivation of the prior XSwap probability of a hetnet edge
View hetionet-v1.0-metaedge-xswap-stats.tsv
metaedge abbreviation n_edges n_connected_source_nodes n_connected_target_nodes n_source_wedges n_target_wedges n_wedges n_valid_xswaps
Anatomy–downregulates–Gene AdG 102240 36 15097 173440264 493897 173934161 5052523519
Anatomy–expresses–Gene AeG 526407 241 18094 2290279787 10749138 2301028925 136250872696
Anatomy–upregulates–Gene AuG 97848 36 15929 149352969 359661 149712630 4637353998
Compound–binds–Gene CbG 11571 1389 1689 104024 476540 580564 66357671
Compound–causes–Side Effect CcSE 138944 1071 5701 16998055 16764774 33762829 9618885267
Compound–downregulates–Gene CdG 21102 734 2880 1683615 291789 1975404 220661247
Compound–palliates–Disease CpD 390 221 50 326 2857 3183 72672
Compound–resembles–Compound CrC 12972 1281 1281 120047 120047 240094 83889812
Compound–treats–Disease CtD 755 387 77 1420 8070 9490 275145
@dhimmel
dhimmel / version-gh-pages.ipynb
Last active Feb 16, 2018
Convert Manubot gh-pages to use versioned directories
View version-gh-pages.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@dhimmel
dhimmel / Q5-other-responses.md
Last active Jan 4, 2018
Other responses from "What’s the primary reason you use Sci-Hub" survey question in https://doi.org/gbqq97
View Q5-other-responses.md

Questions

From In survey, most give thumbs-up to pirated papers by John Travis on 2016-05-06 in Science, question 5 was:

What’s the primary reason you use Sci-Hub or other pirated article repositories?

The possible answers were:

  1. I don’t have any access to the papers — 50.97% 5,046
  2. Convenience--It’s easier to use than the authentication systems provided by the publishers or my libraries — 16.90% 1,673
@dhimmel
dhimmel / bitcoin-random-outcomes.ipynb
Last active Jan 29, 2018
Using Bitcoin to randomly determine a future outcome involving untrusted parties
View bitcoin-random-outcomes.ipynb
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@dhimmel
dhimmel / GSEA-license.md
Last active Mar 11, 2017
GSEA/MSigDB License Agreement. Retrieved from http://software.broadinstitute.org/gsea/register.jsp?next=index.jsp on 2017-01-13
View GSEA-license.md

GSEA/MSigDB LICENSE AGREEMENT

MASSACHUSETTS INSTITUTE OF TECHNOLOGY SINGLE USER LICENSE AGREEMENT FOR INTERNAL RESEARCH PURPOSES ONLY

This Agreement is made between Massachusetts Institute of Technology with a principal address at 77 Massachusetts Avenue, Cambridge, MA 02139 ("MIT") and the subscriber above ("LICENSEE"), and is effective at the date the downloading is completed and proper registration/licensee subscriber information submitted ("EFFECTIVE DATE").

WHEREAS, LICENSEE desires to license the PROGRAM and/or DATABASE, as defined hereinafter, MIT wishes to have this PROGRAM and DATABASE utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14, and

View OpenCon2016_Logo_Verical_NoText.svg
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@dhimmel
dhimmel / CIBERSORT_license.md
Last active Mar 11, 2017
CIBERSORT License obtained in August 2016 from an unidentified trusted source.
View CIBERSORT_license.md

STANFORD NON-COMMERCIAL SOFTWARE LICENSE AGREEMENT

  1. THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY ("STANFORD") provides CIBERSORT software ("Program"), including any accompanying information, materials, or manuals, free of charge for non-commercial use only. By accepting, receiving, or using the Program, you ("RECIPIENT") agree to be bound by the terms of this agreement ("Agreement"). If you do not agree to the terms of this Agreement, then do not use the Program and promptly remove all copies of the program from your computer(s).
  2. RECIPIENT acknowledges that the Program is a research tool still in the development stage and that it is being supplied as is, without any accompanying services, support, or improvements from STANFORD. STANFORD makes no representations and extends no warranties of any kind, neither express nor implied.
  3. RECIPIENT shall not use the Program on behalf of any organization that is not a non-profit organization. RECIPIENT shall not use the Program for commercial
You can’t perform that action at this time.