Information for comment at Ubuntu uses only the top left quarter of the screen
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Distributor ID: Pop
Description: Pop!_OS 22.04 LTS
Release: 22.04
Codename: jammy
dhimmel
/ openalex-metagraph.drawio
Last active
October 14, 2022 14:33
Open Alex Metagraph source for https://app.diagrams.net/
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| <mxfile host="Electron" modified="2022-01-11T22:24:44.620Z" agent="5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) draw.io/16.1.2 Chrome/96.0.4664.55 Electron/16.0.5 Safari/537.36" etag="3d_x8ajHgV-OkkuHk2Cl" version="16.1.2" type="device"><diagram id="CRBQrBPZslJF9kaArlf7" name="Page-1">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 |
dhimmel
/ ubuntu-quarter-screen-issue.md
Created
May 4, 2022 01:38
Diagnosing the Ubuntu top left quarter display issue
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dhimmel
/ disease-v2-review.md
Last active
March 2, 2022 02:26
DISEASES v2 Review by Daniel Himmelstein
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DISEASES 2.0 Review
Reference
DISEASES 2.0: a weekly updated database of disease–gene associations from text mining and data integration
Dhouha Grissa, Alexander Junge, Tudor I Oprea, Lars Juhl Jensen
bioRxiv (2021-12-09) https://doi.org/gn3fj4
DOI: 10.1101/2021.12.07.471296
The webapp and latest downloads are available at . Version 1 is described in the 2015 publication.
dhimmel
/ benevolent-ai-metagraph-data-sources.drawio
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August 14, 2023 14:59
Metagraph of the Benevolant AI knowledge graph from Paliwal et al 2020
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| <mxfile host="app.diagrams.net" modified="2021-06-08T17:05:33.560Z" agent="5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/90.0.4430.85 Safari/537.36" etag="oN2ExXKtZoTKyfjxyag6" version="14.7.6" type="device"><diagram id="CpBVq6cUYyMfxSufbEmF" name="Page-1">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 |
dhimmel
/ tiga-review.md
Created
December 1, 2020 17:53
Review of TIGA (Target illumination GWAS analytics) preprint v1
View tiga-review.md
Review of TIGA Preprint v1 by Daniel Himmelstein on 2020-12-01
Resources
TIGA: Target illumination GWAS analytics
Jeremy J. Yang, Dhouha Grissa, Christophe G. Lambert, Cristian G. Bologa, Stephen L. Mathias, Anna Waller, David J. Wild, Lars Juhl Jensen, Tudor I. Oprea
bioRxiv (2020-11-12) https://www.biorxiv.org/content/10.1101/2020.11.11.378596v1
DOI: 10.1101/2020.11.11.378596
Related links:
dhimmel
/ sciscore-manuscript-review.md
Last active
May 4, 2020 21:43
Review of the "Rigor and Transparency Index" manuscript (https://doi.org/dkg6)
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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
/ hetmech-query-node-pair.ipynb
Created
October 23, 2018 21:38
Query relationship between the FTO gene and obesity using hetmech
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dhimmel
/ hetionet-v1.0-metaedge-xswap-stats.tsv
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October 2, 2018 15:38
Analytical derivation of the prior XSwap probability of a hetnet edge
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| 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
/ version-gh-pages.ipynb
Last active
February 16, 2018 20:32
Convert Manubot gh-pages to use versioned directories
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dhimmel
/ Q5-other-responses.md
Last active
January 4, 2018 01:41
Other responses from "What’s the primary reason you use Sci-Hub" survey question in https://doi.org/gbqq97
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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:
- I don’t have any access to the papers — 50.97% 5,046
- Convenience--It’s easier to use than the authentication systems provided by the publishers or my libraries — 16.90% 1,673
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