Daniel Himmelstein dhimmel

## README.md

      
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              October 15, 2024 17:44
            
              
                MeSH topical descriptor network for cosmograph
              
          
    MeSH in Cosmograph

This gist includes the topical descriptor ontology from MeSH (Medical Subject Headings).
Here is a link that loads the data from this gist and prepopulates the cosmograph configuration
https://cosmograph.app/run/?data=https://gist.githubusercontent.com/dhimmel/c0333d85973285da981231f675dba3ec/raw/f725e8ce5b9095759ec41e4c6a51605f03d0cc38/cosmograph-mesh-edges.csv&meta=https://gist.githubusercontent.com/dhimmel/c0333d85973285da981231f675dba3ec/raw/f725e8ce5b9095759ec41e4c6a51605f03d0cc38/cosmograph-mesh-nodes.csv&gravity=0.24&repulsion=1&repulsionTheta=1.06&linkSpring=1&linkDistance=10&friction=0.85&renderLabels=true&renderHoveredLabel=true&renderLinks=true&linkArrows=true&nodeSizeScale=1&linkWidthScale=2&linkArrowsSizeScale=2&nodeSize=size-total%20links&nodeColor=color-mesh__ic__sanchez__scaled&nodeLabel=mesh_label&linkWidth=width-default&linkColor=color-default&
Screenshot

The visualization will look something like:

  
## openalex-metagraph.drawio
<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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

## ubuntu-quarter-screen-issue.md

      
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                dhimmel
                / ubuntu-quarter-screen-issue.md
            
            
              Created
              May 4, 2022 01:38
            
              
                Diagnosing the Ubuntu top left quarter display issue
              
          
    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


## disease-v2-review.md

      
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              March 2, 2022 02:26
            
              
                DISEASES v2 Review by Daniel Himmelstein
              
          
    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.

  
## benevolent-ai-metagraph-data-sources.drawio
<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">5Vxbd6q6Fv41HeOch3aEAF4eFail22CtdHXbN4oUowgeQBF+/ZnhouK9u9ius05vkpDMzMzLN5NJ6A0vzVYd35iPiTeynBuMRqsbXr7BmOPrGD5YTZzXwE9WY/t0lNdtKgY0sfJKlNcu6MgKSg1Dz3NCOi9Xmp7rWmZYqjN834vKzT48pzzq3LCtvYqBaTj7ta90FI6z2oaINvUPFrXHxcgcyu/MjKJxXhGMjZEXbVXxyg0v+Z4XZlezlWQ5THqFXLJ+90furhnzLTe8pANvL8YT7i/nXR74b7b+13zYS275nLcwLibs+eHYsz3XcLqeN4c67oZvT6wwjHPlGIvQg6pxOHPyuxkNa7QnyQ1reVXgLXzTOsEPV+jY8G0rPNEQi2sRgvFZ3swK/Rg6+pZjhHRZ5sTIjcBet9vICS5yUX1CbEJGd2k4i3ykG1xzgN/2O1zY7AJmH1KTzoEbzy3uwmDrBuseflHzl9Lp3GBp/8azZZghsL6nLCbzrvEOTldSiOFQ24VrE+Rv+VCxtBgzhtPKb8zoaMRotH0roInxntJDjGuPumEqLbF9I8pr5TIC1uqQx+WdN3a+rfbjNrevuZw6uhMF1MxI5aCRG+nFqs1pP7G5bAjf1spUb3GzTML7+AjA5nZtY83iPzcXsQovs1Y0/Jup6a7ZqOflYVqu4Vpelle5HtNCvFV4snwK02DWkNZV7rNfcMXD+hIbqKQvscDcgkSGEXmvjdJavm/

## tiga-review.md

      
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                dhimmel
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              Created
              December 1, 2020 17:53
            
              
                Review of TIGA (Target illumination GWAS analytics) preprint v1
              
          
    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:

  
## sciscore-manuscript-review.md

      
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              May 4, 2020 21:43
            
              
                Review of the "Rigor and Transparency Index" manuscript (https://doi.org/dkg6)
              
          
    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.

  
## hetmech-query-node-pair.ipynb

      
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              Created
              October 23, 2018 21:38
            
              
                Query relationship between the FTO gene and obesity using hetmech
              
          
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## 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

## version-gh-pages.ipynb

      
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              February 16, 2018 20:32
            
              
                Convert Manubot gh-pages to use versioned directories
              
          
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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