Obsidian Vault
Katherine Eaton's Obsidian Vault
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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...
Coefficient of variation
Coefficient of Variation Standard deviation of branch lengths divided by mean branch length.
Curate
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 Β 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 Β 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...
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 Β ...
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...
Makeover monday
Makeover Monday [Makeover Monday A weekly social data project](https://www.makeovermonday.co.uk/)
Mcmaster thesis pandoc template
McMaster Thesis Pandoc Template Setup [[McMaster]] Thesis Template Download the [[LaTeX]] thesis template from http://www.cas.mcmas...
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 | | ββ- | ββββββββββββββββ | |...
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=...
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...
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 performsβ¦ tags: [[Tool]], #π/π±
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...
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...
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]] ...
Literature
{{title}} Field Value Title Β Year Β Authors ...
Note
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{{title}} Summary {{title}} is software that performsβ¦
{{title}} Field Value Title Β Year Β 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 Configure Ubuntu ```bash sudo vi /etc/apt/sources.list #add following line at the end of file deb http://security.ubunt...
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