Obsidian Vault

Obsidian Vault

Katherine Eaton's Obsidian Vault

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    โฌœ/โœจ

  • 2021-03-23 Poinar Lab Meeting
  • Add outgroup to main project
  • Bison Metadata for Tyler
  • Building A Data Management Plan
  • Calculate pPCP1 Resequencing
  • Change column names to lowercase
  • Clade Dating Experiment
  • Collect results and figures
  • Construct new datasets
  • Create Multiple Alignments by Clade
  • Create new directories for snippy and iqtree
  • Create Prune Tree and Alignment
  • Create a placement dataset
  • Email BEAST Log to Emil
  • Email Sam About BEAST
  • Evaluate singleton sites
  • Execute Snakemake Rule Without Upstream
  • Extract SVG Using Puppeteer
  • File taxes
  • Fix france being in australia
  • Fix Obsidian Page Build Submodule
  • Integrate plague-phylogeography-paper as Submodule
  • Lab Meeting 2021-04-20
  • Learn dataview
  • Meet with ravneet
  • Meet with Hendrik
  • Plot Tip Uncertainty for 1.PRE
  • Read global tuberculosis paper
  • Remove the us lab strain
  • Review Kalamazoo Schedule
  • Run TreeTime Mugration
  • Send IBD Plots
  • Send Starting Tree to Australia
  • Separate Obsidian Repositories
  • Stabilize Pipeline CI
  • Test compute canada
  • Test Multiple MCMC Chains
  • Test outgroup pseudotuberculosis
  • Test polytomy option of iqtree
  • Test mvp CSS with notenote.link
  • Update Auspice Metadata
  • Verify dates
  • notenote.link

    • ๐Ÿ“/๐ŸŒฑ

  • A paper a day
  • Andrades valtuena et al. 2017 stone age plague
  • Auspice
  • Bayesian evaluation of temporal signal
  • Bioinformatics pipeline
  • Bison Mitochondria
  • Bootstrapping an existing tree
  • Bramanti 2021 assessing origins european
  • Coefficient of variation
  • Curate
  • Duchene 2020 bayesian evaluation temporal
  • Duchene et al. 2015 performance date Randomization test
  • Duchene et al. 2020 impact early public
  • Eaton et al. 2021 plague phylogeography novel
  • Eroshenko et al. 2021 evolution circulation yersinia
  • Extract pages from a pdf
  • Faria et al. 2018 genomic epidemiological monitoring
  • Figtree
  • Footnote Shortcut
  • Gamedev Constraints and New Beginnings - Demonlocke Devlog
  • Geocode
  • Guellil et al. 2020 genomic historical synthesis
  • ImageMagick
  • Integrated writing
  • Isolation by distance
  • Mapping the plague through natural language processing
  • Mvp
  • Makeover monday
  • Mcmaster thesis pandoc template
  • Metadata
  • Morelli et al. 2010 yersinia pestis genome
  • Muller et al. 2017 structured coalescent its
  • NCBImeta
  • National centre for biotechnology information
  • Nextstrain citations
  • Nokogiri
  • Obsidian Citations
  • Obsidian
  • PhD Dissertation
  • Plague Genome Curation
  • Plague Phylodynamics and Phylogeography
  • Plazzi et al. 2010 phylogenetic representativeness new
  • Rasmussen et al. 2015 early divergent strains
  • Sagulenko et al. 2018 treetime maximum Likelihood phylodynamic
  • Sed Fix Tree Files
  • Shi et al. 2010 using jackknife assess
  • Shortcuts Extender
  • Snakemake
  • Spyrou et al. 2018 analysis 3800 Year Old yersinia
  • Tidy Footnotes
  • Wagner et al. 2014 yersinia pestis plague
  • Xu et al. 2019 historical genomic data
  • Yersinia pestis
  • 1000 Plagues in the Genomics Age
  • Literature
  • Note
  • {}
  • {}
  • wkhtmltopdf
  • wkhtmltopdf

    • ๐Ÿ“ฅ/๐Ÿ“ฐ

  • Andrades valtuena et al. 2017 stone age plague
  • Anisimov et al. 2004 intraspecific diversity yersinia
  • Bramanti 2021 assessing origins european
  • Duchene 2020 bayesian evaluation temporal
  • Duchene et al. 2015 performance date Randomization test
  • Duchene et al. 2020 impact early public
  • Eaton et al. 2021 plague phylogeography novel
  • Eroshenko et al. 2021 evolution circulation yersinia
  • Faria et al. 2018 genomic epidemiological monitoring
  • Guellil et al. 2020 genomic historical synthesis
  • Kalkauskas et al. 2021 sampling bias model
  • Mapping the plague through natural language processing
  • Morelli et al. 2010 yersinia pestis genome
  • Muller et al. 2017 structured coalescent its
  • Plazzi et al. 2010 phylogenetic representativeness new
  • Rasmussen et al. 2015 early divergent strains
  • Sagulenko et al. 2018 treetime maximum Likelihood phylodynamic
  • Shi et al. 2010 using jackknife assess
  • Spyrou et al. 2018 analysis 3800 Year Old yersinia
  • Wagner et al. 2014 yersinia pestis plague
  • Xu et al. 2019 historical genomic data
  • Zimpel 2020 global distribution evolution
  • Literature

    • โฌœ/๐Ÿ“‹

  • Calculate Geographic Rate
  • Calculate p Value for Mugration
  • Docx export with Manubot
  • Fix 0.PE Clade in Auspice
  • Fix Biopython Nexus Branch Lengths
  • Makeover monday
  • Pdf export with manubot
  • PDF export with wkhtmltopdf
  • Read Krauer 2021 Paper
  • Test homoplasy detection
  • Test Miniconda on Windows
  • Test Outlier Parameter in LSD
  • Test seraphim package
  • Thesis Export LaTeX
  • Write script to prepare spread3 input
  • {}
  • {}
  • wkhtmltopdf

    • โฌœ/๐Ÿš‚

  • Call the nslsc
  • Chromosome resequencing experiment
  • Create tracelog pr for treetime
  • Schedule committee meeting
  • Troubleshoot node dates
  • Write draft

    • ๐Ÿ“/๐ŸŒฟ

  • Chromosome resequencing experiment
  • 1000 Plagues in the Genomics Era
  • Kalkauskas et al. 2021 sampling bias model
  • Phylogeography
  • SCDS Project Proposal (2019-2020)
  • Test github pages locally
  • Zimpel 2020 global distribution evolution
  • pandoc
  • {}

    • ๐Ÿ“ฅ/๐Ÿ“ฝ

  • Gamedev Constraints and New Beginnings - Demonlocke Devlog
  • {}

    • โฌœ/๐Ÿงจ

  • Kalamazoo 2021
  • Meet With Australia
  • Meet With Australia
  • Phylogeography Experiment
  • Plague Genome Curation
  • Plague Phylodynamics and Phylogeography Outline
  • Plan for BaseSpace Account
  • Read Bramanti 2021 Paper
  • {}