A paper a day

A Paper A Day May Week 1 0% 07 [[Zimpel 2020 Global Distribution Evolution|Zimpel et al (2020)...

Andrades valtuena et al. 2017 stone age plague

Andrades Valtuena et al. 2017 Stone Age Plague Field Value Title The Stone Age [[Plague...

Auspice

Auspice Summary Auspice is software that performs visualization of [[Phylogenetic phylogenies]]. Configu...

Bayesian evaluation of temporal signal

Bayesian Evaluation of Temporal Signal

Bioinformatics pipeline

Bioinformatics Pipeline Literature [[Snakemake]] [[nf-core/eager]]

Bison Mitochondria

Bison Mitochondria [[Bison Mitochondria]] started out as a single notes (like the others) but grew into its own folder of concepts. Peo...

Bootstrapping an existing tree

Bootstrapping an Existing Tree LSD Tree iqtree \ -s lsd.filter.aln \ -te lsd.filter.nwk \ -m K3Pu+F+I \ -b 10 \ -pre test \ ...

Bramanti 2021 assessing origins european

Bramanti 2021 Assessing Origins European Field Value Title Assessing the origins of the...

Calculate Geographic Rate

Calculate Geographic Rate km / subs / site km / year

Calculate p Value for Mugration

Calculate p Value for Mugration Given n states (i1, i2…,in) what is the probability of observing transition from state ij to ik by chanc...

Coefficient of variation

Coefficient of Variation Standard deviation of branch lengths divided by mean branch length.

Curate

Curate

Docx export with Manubot

Docx export with Manubot

Duchene 2020 bayesian evaluation temporal

Duchene 2020 Bayesian Evaluation Temporal Field Value Title [[Bayesian]] Evaluation of ...

Duchene et al. 2015 performance date Randomization test

Duchene et al. 2015 Performance Date-Randomization Test Field Value   Title The p...

Duchene et al. 2020 impact early public

Duchene et al. 2020 Impact Early Public Field Value Title The impact of early [[public ...

Eaton et al. 2021 plague phylogeography novel

Eaton et al. 2021 Plague Phylogeography Novel Field Value   Title [[Plague]] [[Ph...

Eroshenko et al. 2021 evolution circulation yersinia

Eroshenko et al. 2021 Evolution Circulation Yersinia Field Value Title [[Evolution]] an...

Extract pages from a pdf

Extract Pages from a PDF gs -sDEVICE=pdfwrite -dNOPAUSE -dBATCH -dFirstPage=2 -dLastPage=3 -sOutputFile=output.pdf input.pdf

Faria et al. 2018 genomic epidemiological monitoring

Faria et al. 2018 Genomic Epidemiological Monitoring Field Value Title Genomic and epid...

Figtree

Figtree Summary Figtree is software that performs visualization of phylogenetic trees. Command-Line figtree -graphic PDF test.nwk tes...

Fix 0.PE Clade in Auspice

Fix 0.PE Clade in Auspice

Fix Biopython Nexus Branch Lengths

Fix Biopython Nexus Branch Lengths Tasks task from "tasks" where contains(file.name, "Fix Biopython Nexus Branch Lengths") Existing ...

Footnote Shortcut

Footnote Shortcut Summary Footnote Shortcut that adds footnotes. Functions After installing and activating this plugin, you still hav...

Gamedev Constraints and New Beginnings - Demonlocke Devlog

Gamedev Constraints and New Beginnings - Demonlocke Devlog Field Value Title   ...

Geocode

Geocode Literature [[GeoPy]] [[Nominatim]] [[OpenStreetMap]]

Guellil et al. 2020 genomic historical synthesis

Guellil et al. 2020 Genomic Historical Synthesis Field Value Title A genomic and histor...

ImageMagick

ImageMagick Summary ImageMagick is software that converts image formats. Security Several formats requiring changing ImageMagick's se...

Integrated writing

Integrated Writing I have multiple different platforms that I write in. I would like to [[Integrated Writing Integr...

Isolation by distance

Isolation By Distance

Mapping the plague through natural language processing

Krauer 2021 Mapping Plague Natural Field Value Title Mapping the plague through natural...

Mvp

MVP [[MVP]] is a [[CSS]], shown at https://andybrewer.github.io/mvp/. [[@vimalkvn]] has a [[pandoc]] compatible version at https://gitla...

Mcmaster thesis pandoc template

McMaster Thesis Pandoc Template Setup [[McMaster]] Thesis Template Download the [[LaTeX]] thesis template from http://www.cas.mcmas...

Metadata

Metadata

Morelli et al. 2010 yersinia pestis genome

Morelli et al. 2010 Yersinia Pestis Genome Field Value Title Yersinia pestis genome seq...

Muller et al. 2017 structured coalescent its

Muller et al. 2017 Structured Coalescent Its | Field | Value | | ——- | ———————————————— | |...

NCBImeta

NCBImeta Summary [[NCBImeta]] is a command-line application that retrieves and organizes metadata from the [[National Ce...

National centre for biotechnology information

National Centre for Biotechnology Information

Nextstrain citations

Nextstrain Citations I want to be able to add and manage citations in [[Nextstrain]] and [[Auspice]]. I want to write [[Nextstrain ...

Nokogiri

Nokogiri Summary Nokogiri is a [[Ruby]] module for working with [[XML]] and [[HTML]]. Whenever I try to build [[Jekyll]] sites, I almo...

Obsidian Citations

Obsidian Citations Summary Obsidian Citations is a plugin that integrates citations with [[Zotero]]. Now open the Obsidian preferences...

Obsidian

Obsidian Tasks Pending table tags from "" where project=[[Obsidian]] and status!="done" Completed table tags from "" where project=...

Pdf export with manubot

PDF export with Manubot Manubot was developed by [@himmelstein2019OpenCollaborativeWriting]. A summary script was created at [[pa...

PDF export with wkhtmltopdf

[[PDF]] export with [[wkhtmltopdf]] Make sure regular [[PDF]] export works. # Convert Wikilinks ./pandoc/convert_wikilinks.py --inp...

PhD Dissertation

PhD Dissertation Projects [[NCBImeta]] [[Plague Phylodynamics and Phylogeography]] [[Plague Denmark]] Graph Filters: [[Projec...

Plague Genome Curation

Plague Genome Curation Literature Review [[Bioinformatics Pipeline]] [[Geocode]]

Plague Phylodynamics and Phylogeography

Plague Phylodynamics and Phylogeography Experiments [[Plague Genome Curation]] [[Plague Phylodynamics]] [[Plague Phylogeography]...

Plazzi et al. 2010 phylogenetic representativeness new

Plazzi et al. 2010 Phylogenetic Representativeness New Field Value Title Phylogenetic r...

Rasmussen et al. 2015 early divergent strains

Rasmussen et al. 2015 Early Divergent Strains Field Value Title Early divergent strains...

Read Krauer 2021 Paper

Read Krauer 2021 Paper [[Krauer 2021 Mapping Plague Natural]]

Sagulenko et al. 2018 treetime maximum Likelihood phylodynamic

Sagulenko et al. 2018 TreeTime Maximum-Likelihood Phylodynamic Field Value Title [[Tree...

Sed Fix Tree Files

Sed Fix Tree Files Tasks task from "tasks" where contains(file.name, "Sed Fix Tree Files") Code 100.00:20.70040[\[&date="-139.09...

Shi et al. 2010 using jackknife assess

Shi et al. 2010 Using Jackknife Assess Field Value Title shi2010UsingJackknifeAssess ...

Shortcuts Extender

Shortcuts Extender Summary Shortcuts Extender adds additional shortcuts to [[Obsidian]]. Functions Changing the Heading Level To c...

Snakemake

Snakemake Summary Snakemake is software that performs… tags: [[Tool]], #📝/🌱

Spyrou et al. 2018 analysis 3800 Year Old yersinia

Spyrou et al. 2018 Analysis 3800-Year-Old Yersinia Field Value Title Analysis of 3800-y...

Test homoplasy detection

Test Homoplasy Detection alignment: results/snippy_multi/all/snippy-core_chromosome.snps.filter1.aln tree: results/iqtree/all/iqtree-cor...

Test Miniconda on Windows

Test Miniconda on Windows Install [[Python Python 3.8]] [[conda miniconda]], not ...

Test Outlier Parameter in LSD

Test Outlier Parameter in LSD Tasks task from "tasks" where contains(file.name, "Test Outlier Parameter in LSD")

Test seraphim package

Test Seraphim Package Tasks task from "tasks" where contains(file.name, "Test Seraphim Package") setwd("C:/Users/ktmea/Projects/plagu...

Thesis Export LaTeX

Thesis Export LaTeX

Tidy Footnotes

Tidy Footnotes Summary Tidy Footnotes is a plugin that organizes footnotes. Functions Adds the command Tidy Footnotes. Whoops, here'...

Wagner et al. 2014 yersinia pestis plague

Wagner et al. 2014 Yersinia Pestis Plague Field Value Title Yersinia pestis and the Pla...

Write script to prepare spread3 input

Write Script to Prepare spreaD3 Input Tasks task from "tasks" where contains(file.name, "Write Script to Merge TimeTree and MCC") inp...

Xu et al. 2019 historical genomic data

Xu et al. 2019 Historical Genomic Data Field Value Title Historical and genomic data re...

Yersinia pestis

[[Yersinia pestis]] Phylogenetic Branches [[Branch]] [[Clade]] Subclade [[Branch 0]] ...

1000 Plagues in the Genomics Age

Literature

{{title}} Field Value Title   Year   Authors ...

Note

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{{title}} The [[{{title}}]] project is… Tasks table tags from "tasks" where project=[[{{title}}]]

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{{title}} Summary {{title}} is software that performs…

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{{title}} Field Value Title   Year   Channel ...

wkhtmltopdf

wkhtmltopdf Configure [[Ubuntu]] ```bash sudo vi /etc/apt/sources.list #add following line at the end of file deb http://security.u...

wkhtmltopdf

wkhtmltopdf Configure Ubuntu ```bash sudo vi /etc/apt/sources.list #add following line at the end of file deb http://security.ubunt...