Obsidian Vault

2021-03-23 Poinar Lab Meeting

Plague-Phylogeography Novel Synthesis and Geospatial Analysis Katherine Eaton Poinar Lab Meeting...

2021 03 23 scratch

Meeting: Poinar Lab Cool ideas from lab members go here :) [[Emil Karpinski]] and [[Zachery...

2021 03 27 scratch

2021-03-27 Scratch Plotly might be a good candidate for drawing maps: https://plotly.com/pyth...

2021 03 28 scratch

2021-03-28 Scratch [[Plague Phylodynamics and Phylogeography]] I woke up with a few questions to...

2021 03 29 scratch

2021-03-29 Scratch Email I've discovered I'll need to do COVID awareness training befor...

2021 03 30 scratch

2021-03-30 Scratch Today I'm going to continue working on [[Sampling Bias Experiment]] in pr...

2021 04 03 scratch

2021-04-03 Scratch I'm reading the [[TimeTree]] paper and getting some ideas. I should re...

2021 04 04 scratch

2021-04-04 Scratch Marginal Distribution I want to be able to plot the marginal probabi...

2021 04 26

📆 2021-04-26 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 04 27

📆 2021-04-27 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 04 28

📆 2021-04-28 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 04 30

📆 2021-04-30 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 05 03

📆 2021-05-03 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 05 04

📆 2021-05-04 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 05 05

📆 2021-05-05 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 05 06

📆 2021-05-06 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

2021 05 07

📆 2021-05-07 Before planning a day, reflect on the [[PhD Timeline]]. Does what you [[want to do]...

A paper a day

A Paper A Day May Week 1 0% 07 [[Zimpel 2020 Global Di...

Add outgroup to main project

Add Outgroup to Main Project

Analyze first beast1 run

Analyze First BEAST1 Run Tasks task from "tasks" where contains(file.name, "Anal...

Ancient dna

Ancient DNA

Ancient

Andrades valtuena et al. 2017 stone age plague

Andrades Valtuena et al. 2017 Stone Age Plague Field Value ...

Anisimov et al. 2004 intraspecific diversity yersinia

Anisimov et al. 2004 Intraspecific Diversity Yersinia Field Value ...

Auspice

Auspice Summary Auspice is software that performs visualization of [[Phylogeneti...

Beast

BEAST BEAST1 Inputs Tree What kind of [[Nexus]] format does [[BEAST#BEAST1|BEAST1]] need? ...

Bayesian evaluation of temporal signal

Bayesian Evaluation of Temporal Signal

Bioinformatics pipeline

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

Bison Metadata for Tyler

Bison Metadata for Tyler Create [[NCBImeta Paper]] database ncbimeta/NCBImeta --config co...

Bison Mitochondria

Bison Mitochondria [[Bison Mitochondria]] started out as a single notes (like the others) but gr...

Bootstrapping an existing tree

Bootstrapping an Existing Tree LSD Tree iqtree \ -s lsd.filter.aln \ -te lsd.filter.nwk \ ...

Bos et al. 2016 eighteenth century yersinia

Bos et al. 2016 Eighteenth Century Yersinia Field Value ...

Bramanti 2021 assessing origins european

Bramanti 2021 Assessing Origins European Field Value ...

Branch 1

Branch 1 tags: [[Yersinia pestis]]

Bryan jenks

Bryan Jenks tags: [[People]]

Build a new timetree

Build a New TimeTree Sub Tasks task from "tasks" where contains(file.name, "Build...

Building A Data Management Plan

Building A Data Management Plan Workshop Link Presenter: [[Isaac Pratt]] Notes The institut...

Calculate bait concentration for enrichment

Calculate Bait Concentration for Enrichment

Calculate chromosome resequencing

Calculate Chromosome Resequencing D24: 15M D62: 5M D72: 5M R21: 15M

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...

Calculate pPCP1 Resequencing

Calculate pPCP1 Resequencing target-coverage-perc: 80% target-coverage-bp: 7,690 bp target-dep...

Call the nslsc

Call the NSLSC 1 888 815-4514 ![[Confirm My Enrolment.png]]

Change column names to lowercase

Change Column Names to Lowercase metadata.py config.py parse_tree.py clock_model.py m...

Chromosome resequencing experiment

Chromosome Resequencing Experiment Field Value Projec...

Clade Dating Experiment

Clade Dating Experiment Problem The estimates of [[Clade clade]] [[MRCA]] ...

Clade

Clade [[Yersinia pestis]]

Clock model

Clock Strict Clock Relaxed Clock tags: #📝/🌱

Coefficient of variation

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

Collect results and figures

Collect Results and Figures

Construct new datasets

Construct New Datasets I've been struggling with this task for a few reasons. Alignment ...

Continuous phylogeography with beast

Continuous Phylogeography with BEAST BEAST2 My current problem is numerical instability, in tha...

Continuous

Continuous Continuous traits in [[Phylogeography phylogeography]]. ...

Coupledmcmc

CoupledMCMC tags: #📝/🌱

Create Multiple Alignments by Clade

Create Multiple Alignments by Clade Tasks Clades [[0.ANT]] [[0.PE]] [[0.PRE]] [[1.ANT...

Create new directories for snippy and iqtree

Create New Directories for Snippy and IQTREE I want to have better organization of the output fo...

Create Prune Tree and Alignment

Create Prune Tree and Alignment Prune Prune IQTREE and Alignment, No Outgroup snakemak...

Create tracelog pr for treetime

Create Tracelog PR for Treetime Handle filename of tracelog in wrappers. Test task from &...

Create a placement dataset

Create a Placement Dataset I should create a placement dataset that helps do more refined testin...

Cui et al. 2013 historical variations mutation

Cui et al. 2013 Historical Variations Mutation Field Value ...

Curate

Dellicour 2020 phylodynamic workflow rapidly

Dellicour 2020 Phylodynamic Workflow Rapidly Field Value ...

Discrete

Discrete Discrete traits in [[Phylogeography phylogeography]]. ...

Docx export with Manubot

Duchene 2020 bayesian evaluation temporal

Duchene 2020 Bayesian Evaluation Temporal Field Value ...

Duchene et al. 2015 performance date Randomization test

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

Duchene et al. 2019 inferring infectious disease

Duchene et al. 2019 Inferring Infectious Disease Field Value ...

Duchene et al. 2020 impact early public

Duchene et al. 2020 Impact Early Public Field Value T...

Edi keyword automation

EDI Keyword Automation Field Value Project [[ED...

Eaton et al. 2021 plague phylogeography novel

Eaton et al. 2021 Plague Phylogeography Novel Field Value ...

Email BEAST Log to Emil

Email BEAST Log to Emil Tasks task from "tasks" where contains(file.name, "Email...

Email Sam About BEAST

Email Sam About BEAST Tasks task from "tasks" where contains(file.name, "Email S...

Emergence

Emergence tags: #📝/🌱

Emil karpinski

Emil Karpinski Role: PhD Student Project: [[Megafauna]] tags: [[People]]

Environment

Eroshenko et al. 2021 evolution circulation yersinia

Eroshenko et al. 2021 Evolution Circulation Yersinia Field Value ...

Evaluate singleton sites

Evaluate Singleton Sites Literature In the context of multiple sequence alignment and phylog...

Execute Snakemake Rule Without Upstream

Execute Snakemake Rule Without Upstream Problem I am analyzing [[Plague Phylodyn...

Extract pages from a pdf

Extract Pages from a PDF gs -sDEVICE=pdfwrite -dNOPAUSE -dBATCH -dFirstPage=2 -dLastPage=3 -sOut...

Extract SVG Using Puppeteer

Extract SVG Using Puppeteer Workflow The full workflow is documented in this comment. Notes ...

Faria et al. 2018 genomic epidemiological monitoring

Faria et al. 2018 Genomic Epidemiological Monitoring Field Value ...

Figtree

Figtree Summary Figtree is software that performs visualization of phylogenetic trees. Command...

File taxes

File Taxes

Filter constant sites in script

Filter Constant Sites in Script Tasks task from "tasks" where contains(file.name, &qu...

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 france being in australia

Fix France Being in Australia There is a problem in mapping

Fix Obsidian Page Build Submodule

Foci

Foci Concepts [[Plague]] [[Persistence]] [[Europe]] [[Caucasus]] [[Eurasia]]

Footnote Shortcut

Footnote Shortcut Summary Footnote Shortcut that adds footnotes. Functions After installing a...

Gamedev Constraints and New Beginnings - Demonlocke Devlog

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

Genome

Geocode

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

Geographic origin

Geographic Origin

Geographic

Geospatial

Github

GitHub Fork # Sync to remote git remote add upstream <original:repo> git fetch up...

Guellil et al. 2020 genomic historical synthesis

Guellil et al. 2020 Genomic Historical Synthesis Field Value ...

Hendrik poinar

Hendrik Poinar Field Information Role Instituti...

ImageMagick

ImageMagick Summary ImageMagick is software that converts image formats. Security Several for...

Integrate plague-phylogeography-paper as Submodule

Integrate plague-phylogeography-paper as Submodule Tasks Add submodule cd phd/ git submodu...

Integrated writing

Integrated Writing I have multiple different platforms that I write in. I would l...

Interdisciplinary

Isolation by distance

Isolation By Distance

Jesper boldsen

Jesper Boldsen Role: Collaborator Project: [[Plague Denmark]] tags: [[People]]

Jessica hider

Jessica Hider Role: Project: tags: [[People]]

Julia gamble

Julia Gamble Role: Collaborator Project: [[Plague Denmark]] tags: [[People]]

1000 Plagues in the Genomics Era

When used within a multi-disciplinary approach, genetic evidence provides an intriguing window in...

Kalamazoo 2021

Kalamazoo 2021 [[2021-05-10 May 10]] - [[2021-05-15 May 15]] 2021 ...

Kalkauskas et al. 2021 sampling bias model

Kalkauskas et al. 2021 Sampling Bias Model Field Value ...

Kanban

Kanban Boards Overdue table project as Project,type as Type,due as Due from "" where d...

Katherine eaton

Katherine Eaton Field Information Role Institut...

Mapping the plague through natural language processing

Krauer 2021 Mapping Plague Natural Field Value Title ...

Lnba

Late Neolithic Bronze Age

Lab Meeting 2021-04-20

Lab Meeting 2021-04-20 Meeting Link Meeting Notes Updates There may be a vaccination plan ...

Learn dataview

Learn Dataview File Information table file, tags from "" where file.name="Yersin...

Leo featherstone

Leo Featherstone Field Information Role Institu...

Mvp

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

Majander et al. 2020 ancient bacterial genomes

Majander et al. 2020 Ancient Bacterial Genomes Field Value ...

Makeover monday

Makeover Monday [Makeover Monday A weekly social data project](https://www....

Marie Helene b hardy

Marie-Helene B Hardy Role: PhD Student Project: [[Plague York Barbican]] tags: [[People]]

Mcmaster thesis pandoc template

McMaster Thesis Pandoc Template Setup [[McMaster]] Thesis Template Download the [[LaTeX]] t...

Meet With Australia

Meet With Australia 2021-05-13 1800 EST / 0800 AEST Meeting Link \pagebreak Meet With Aust...

Meet With Australia

Meet With Australia [[2021-05-13]] 1800 EST / 0800 AEST Meeting Link \pagebreak Meet With ...

Meet with emil

Meet With Emil [[Dellicour 2020 Phylodynamic Workflow Rapidly Dellicour et ...

Meet with ravneet

Meet With Ravneet Mention the keep-singletons filtering script change. [[Calculate Chromoso...

Meet with Hendrik

Meet with Hendrik [[2021-05-04]] Meeting Link Notes Present the working draft Nextstrain N...

Metadata

Monica green

Monica Green Field Information Role Institution...

Morelli et al. 2010 yersinia pestis genome

Morelli et al. 2010 Yersinia Pestis Genome Field Value ...

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 o...

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 [[Au...

Nokogiri

Nokogiri Summary Nokogiri is a [[Ruby]] module for working with [[XML]] and [[HTML]]. Whenever...

Obsidian Citations

Obsidian Citations Summary Obsidian Citations is a plugin that integrates citations with [[Zote...

Obsidian

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

Over Represented

Over-Represented

Pdf export with manubot

PDF export with Manubot Manubot was developed by [@himmelstein2019OpenCollaborativeWriting]...

PDF export with wkhtmltopdf

[[PDF]] export with [[wkhtmltopdf]] Make sure regular [[PDF]] export works. # Convert Wikil...

PhD Dissertation

PhD Dissertation Projects [[NCBImeta]] [[Plague Phylodynamics and Phylogeography]] [[Pla...

Phylogenetic

Phylogeography Experiment

Phylogeography Experiment Field Value Project [...

Phylogeography

Phylogeography Summary This page explores [[Phylogeography]], particularly the [...

Plague denmark

Plague Denmark [[Plague Denmark]] started out as a single notes (like the others) but grew into ...

Plague Genome Curation

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

Plague Phylodynamics and Phylogeography Outline

Plague Phylodynamics and Phylogeography Outline Concepts [[Plague]] [[Yersinia pestis]] ...

Plague Phylodynamics and Phylogeography

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

Plague

Plague Disease caused by the bacterium [[Yersinia pestis]].

Plan for BaseSpace Account

Plan for BaseSpace Account Emails Hi Everyone, Following up from lab meeting, our Basespa...

Plazzi et al. 2010 phylogenetic representativeness new

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

Plot Tip Uncertainty for 1.PRE

Rasmussen et al. 2015 early divergent strains

Rasmussen et al. 2015 Early Divergent Strains Field Value ...

Ravneet sidhu

Ravneet Sidhu Role: Collaborator Project: [[Plague Denmark]] tags: [[People]]

Read Bramanti 2021 Paper

Read Bramanti 2021 Paper [[Bramanti 2021 Assessing Origins European]]

Read global tuberculosis paper

Read Global Tuberculosis Paper [[Zimpel 2020 Global Distribution Evolution]]

Read Krauer 2021 Paper

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

Reintroduction

Remove the us lab strain

Remove the US Lab Strain

Resampling

Resampling Bootstrap Jacknife Leave One Out Randomization tags: #📝/🌱

Review Kalamazoo Schedule

Richard neher

Richard Neher Field Information Role Institutio...

Run TreeTime Mugration

Run TreeTime Mugration Tasks task from "tasks" where contains(file.name, "Run Tr...

Samea3713715

SAMEA3713715 tags: [[Sample]]

Samn00715800

SAMN00715800 This is strain 8291, the [[East Smithfield]] sample from the [[Black Death]]. ta...

SCDS Project Proposal (2019-2020)

Project Overview Background When used within a multi-disciplinary approach, genetic evidence pr...

Sabin 2020 seventeenth Century mycobacterium tuberculosis

Sabin 2020 Seventeenth-Century Mycobacterium Tuberculosis Field Value ...

Sagulenko et al. 2018 treetime maximum Likelihood phylodynamic

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

Sampling bias experiment

Sampling Bias Experiment Field Value Project [[...

Sampling bias

Sampling Bias Here I'm working on the concept of [[Sampling Bias]] from [[Rasmussen et al. 2...

Schedule committee meeting

Schedule Committee Meeting

Sebastian duchene

Sebastian Duchene Role: Collaborator Project: [[Plague Phylodynamics and Phylogeography]] tag...

Sed Fix Tree Files

Sed Fix Tree Files Tasks task from "tasks" where contains(file.name, "Sed Fix Tr...

Send IBD Plots

Send IBD Plots repo commit https://github.com/ktmeato...

Send Starting Tree to Australia

Send Starting Tree to Australia Tasks Send them a IQTREE that's in genetic distance (reduce...

Separate Obsidian Repositories

Separate Obsidian Repositories Rename [[obsidian-vaults]] to [[obsidian-public]]. Create a ...

Sequence Free

Sequence-Free

Shi et al. 2010 using jackknife assess

Shi et al. 2010 Using Jackknife Assess Field Value Ti...

Shortcuts Extender

Shortcuts Extender Summary Shortcuts Extender adds additional shortcuts to [[Obsidian]]. Funct...

Snakemake

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

Spread

Spread Related Notes [[Spread]]

Spyrou et al. 2016 historical pestis genomes

Spyrou et al. 2016 Historical Pestis Genomes Field Value ...

Spyrou et al. 2018 analysis 3800 Year Old yersinia

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

Stabilize Pipeline CI

Substitution rate

Substitution Rate

Test compute canada

Test Compute Canada Install ssh keaton@graham.computecanada.ca cd /scratch/keaton ...

Test github pages locally

Test [[Github Pages]] Locally Github Pages is an easy way to create and host your own [[static s...

Test homoplasy detection

Test Homoplasy Detection alignment: results/snippy_multi/all/snippy-core_chromosome.snps.filter1...

Test lsd2 in iqtree

Test [[LSD2]] in IQTREE cut -f 1,4 ../metadata/all/metadata.tsv | tail -n+2 | sed 's/\[\|\]...

Test Miniconda on Windows

Test Miniconda on Windows Install [[Python Python 3...

Test Multiple MCMC Chains

Test Multiple MCMC Chains Tasks task from "tasks" where contains(file.name, "Tes...

Test outgroup pseudotuberculosis

Test Outgroup Pseudotuberculosis Strain Accession Status ...

Test Outlier Parameter in LSD

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

Test polytomy option of iqtree

Test Polytomy Option of IQTREE

Test seraphim package

Test Seraphim Package Tasks task from "tasks" where contains(file.name, "Test Se...

Test mvp CSS with notenote.link

Thesis Export LaTeX

Tidy Footnotes

Tidy Footnotes Summary Tidy Footnotes is a plugin that organizes footnotes. Functions Adds th...

Timetree

Timetree A time-scaled phylogeny, where branch lengths are years and units are substitutions/sit...

Transmission

Tree prior

Tree Prior Yule Birth Death Coalescent Constant Population Size Skyline tags: #📝/🌱

Troubleshoot node dates

Troubleshoot Node Dates Provide info on application specifics.

Under Represented

Under-represented

Update Auspice Metadata

Update Auspice Metadata Catch where province doesn't exist and coordinates are bad. Add...

Verify dates

Verify Dates seq_name date_width date_central 1/precision ...

Wagner et al. 2014 yersinia pestis plague

Wagner et al. 2014 Yersinia Pestis Plague Field Value ...

Winter 2021 writing bootcamp

Winter 2021 Writing Bootcamp Zoom Link Tasks task from "tasks" where contains(file.n...

Write draft

Write Draft

Write script to prepare spread3 input

Write Script to Prepare spreaD3 Input Tasks task from "tasks" where contains(file.nam...

Xu et al. 2019 historical genomic data

Xu et al. 2019 Historical Genomic Data Field Value Ti...

Yellow fever virus

Yellow Fever Virus tags: [[Organism]]

Yersinia pestis

[[Yersinia pestis]] Phylogenetic Branches [[Branch]] [[Clade]] Subcl...

Zachery dickson

Zachery Dickson Role: PhD Student Project: [[Sepsis]] tags: [[People]]

Zhgenti et al. 2015 genome assemblies 11

Zhgenti et al. 2015 Genome Assemblies 11 Field Value ...

Zimpel 2020 global distribution evolution

Zimpel 2020 Global Distribution Evolution Field Value ...

notenote.link

notenote.link Notes [[Markdown]] files with no [[YAML]] frontmatter don't get built into...

pandoc

pandoc Summary [[pandoc]] converts text files into different formats. I'm hoping to use it ...

Example PDF