Information for comment at Ubuntu uses only the top left quarter of the screen
Output from lsb_release -a:
No LSB modules are available.
Distributor ID: Pop
Description: Pop!_OS 22.04 LTS
Release: 22.04
Codename: jammy
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| """ | |
| This file contains python functions for automatically retreiving DOI metadata | |
| and creating bibtex references. `get_bibtex_entry(doi)` creates a bibtex entry | |
| for a DOI. It fixes a Data Cite author name parsing issue. Short DOIs are used | |
| for bibtex citation keys. | |
| Created by Daniel Himmelstein and released under CC0 1.0. | |
| """ | |
| import urllib.request |
dhimmel
/ benevolent-ai-metagraph-data-sources.drawio
Last active
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
/ 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
/ weighted-r2.R
Last active
September 5, 2022 06:03
Computing the R-squared of a linear regression model with weighted observations in R
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| # Compare four methods for computing the R-squared (R2, coefficient of determination) | |
| # with wieghted observations for a linear regression model in R. | |
| # This work was written by Daniel Himmelstein (@dhimmel) with guidance | |
| # from Alex Pankov (@a-pankov). It is released as CC0 (public domain). | |
| get_r2_cor <- function(y, y_pred, w) { | |
| # Calculate R2 using the correlation coefficient method | |
| xy = cbind(y, y_pred) | |
| return(boot::corr(d=xy, w=w) ^ 2) | |
| } |
dhimmel
/ ubuntu-quarter-screen-issue.md
Created
May 4, 2022 01:38
Diagnosing the Ubuntu top left quarter display issue
dhimmel
/ disease-v2-review.md
Last active
March 2, 2022 02:26
DISEASES v2 Review by Daniel Himmelstein
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
/ tiga-review.md
Created
December 1, 2020 17:53
Review of TIGA (Target illumination GWAS analytics) preprint v1
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)
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.
We designed a hetnet for drug repurposing that contains 50 thousand nodes (of 10 labels) and 3 million relationships (of 27 types). And we’ve chosen neo4j for handling network storage and interaction.
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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