diff --git a/docs/_variables.yml b/docs/_variables.yml
new file mode 100644
index 00000000..9ee32a89
--- /dev/null
+++ b/docs/_variables.yml
@@ -0,0 +1,6 @@
+exercises:
+ simulation:
+ baseurl: https://percyfal.github.io/pgip-jlite/lab
+ howto: exercises/simulation/index.html#sec-exercise-simulation-howto
+ coalescent: exercises/simulation/index.html#sec-exercise-simulation-coalescent
+ msprime: exercises/simulation/index.html#sec-exercise-simulation-msprime
diff --git a/docs/about.qmd b/docs/about.qmd
index 3ce2201c..2f7e8c87 100644
--- a/docs/about.qmd
+++ b/docs/about.qmd
@@ -32,6 +32,14 @@ format:
[Jason Hill](https://nbis.se/about/staff/jason-hill)
:::
+::: {.organisers-child}
+
+
+
+[André Soares](https://nbis.se/about/staff/andre-soares)
+
+:::
+
:::
## Venue
diff --git a/docs/assets/profile/andre-soares.png b/docs/assets/profile/andre-soares.png
new file mode 100644
index 00000000..55843635
Binary files /dev/null and b/docs/assets/profile/andre-soares.png differ
diff --git a/docs/exercises/index.qmd b/docs/exercises/index.qmd
index fa4b8fde..4fb7dcc0 100644
--- a/docs/exercises/index.qmd
+++ b/docs/exercises/index.qmd
@@ -5,10 +5,10 @@ description: "List of all exercises"
listing:
type: grid
grid-columns: 4
- fields: [image, title, subtitle, author]
+ fields: [title, subtitle, author]
sort: false
contents:
- - test/test.ipynb
+ - simulation/index.qmd
date: ""
toc: false
sidebar: false
diff --git a/docs/exercises/simulation/index.qmd b/docs/exercises/simulation/index.qmd
new file mode 100644
index 00000000..ddc8d57b
--- /dev/null
+++ b/docs/exercises/simulation/index.qmd
@@ -0,0 +1,31 @@
+---
+title: "Introduction to simulation"
+author:
+ - "Per Unneberg"
+format: html
+---
+
+::: {.callout-note}
+
+{{< meta date >}}: The simulation exercises are currently hosted at
+[{{< var exercises.simulation.baseurl >}}/index.html]({{< var
+exercises.simulation.baseurl >}}/index.html). The repository will
+shortly be moved to the NBIS github organization.
+
+:::
+
+## Instructions {#sec-exercise-simulation-howto}
+
+Start by going through the [HOWTO]({{< var
+exercises.simulation.baseurl >}}?path=HOWTO.ipynb)
+
+## 1. Introduction to the coalescent {#sec-exercise-simulation-coalescent}
+
+Work through the [introduction to the coalescent]({{< var
+exercises.simulation.baseurl >}}?path=coalescent.ipynb) workbook.
+
+## 2. Introduction to msprime {#sec-exercise-simulation-msprime}
+
+Work through the [introduction to msprime]({{< var
+exercises.simulation.baseurl >}}?path=simulation_with_msprime.ipynb)
+workbook.
diff --git a/docs/program.qmd b/docs/program.qmd
index a5e1896c..98c536d4 100644
--- a/docs/program.qmd
+++ b/docs/program.qmd
@@ -3,22 +3,79 @@ title: "Program"
toc: false
date: ""
sidebar: false
+engine: knitr
format:
html:
number-sections: false
---
-Course program:
+The aim of this workshop is to provide an introduction to commonly
+used methods in population genomics. As the focus of the course is on
+hands-on work, the topics have been designed to cover the fundamental
+analyses that are common in many population genomics studies. The
+course consists of lectures and exercises, with a focus on the
+practical aspects of analyses. Whereas lectures introduce some
+background theory, their primary aim is to set the stage for
+accompanying exercises.
-- introduction to the coalescent and simulations
-- variant calling and variant filtering
-- describing genetic diversity
-- population structure and admixture
-- selection scans
+## Covered topics
+
+- Foundations of population genetics
+- Introduction to simulation and the coalescent
+- Basics of variant calling
+- Variant filtering and sequence masks
+- Characterization and intepretation of DNA sequence variation
+- Calculation and interpretation of summary statistics from variation
+ data
+- Investigating population structure with admixture modelling and
+ principal component analyses
+- Demographic modelling using sequentially Markovian coalescent models and linkage disequlibrium
+- Selection scans
+
+## Learning objectives
+
+Upon completion of this course, you will be able to:
+
+- describe the different forces of evolution and how they influence
+ genetic variation
+- understand and interpret genealogical trees and how they relate to
+ genetic variation data
+- describe the basics of the coalescent
+- perform simple coalescent simulations with msprime
+- run simple SLiM forward simulation models
+- describe and run the steps of a variant calling pipeline, including
+ quality control of raw reads, read mapping, and variant calling
+- know how and when to filter raw variant calls using manual coverage
+ filters
+- describe and calculate nucleotide diversity from variation data
+- analyze population structure with admixture modelling and
+ dimensionality reduction methods
+- perform demographic modelling with sequential Markovian coalescent
+ models
+- describe methods that identify regions undergoing adaptation and
+ selection
+- run selection scans, score identified regions and interpret findings
+ in the context of genome annotations
+
+## Requirements
+
+- Basic knowledge in R or Python
+- Basic knowledge of variant calling, or the equivalent of NBIS course
+ "Introduction to Bioinformatics using NGS data"
+- Basic knowledge of population genetics
+- Basic understanding of frequentist statistics
+- A computer
+
+Desirable:
+
+- Experience with analysis of NGS and other omic data
## Preparation
-### Readings
+### Suggested readings
+
+Although not required, it is recommended to briefly go through the
+following papers (in particular @fuller_PopulationGeneticsCoral_2020):
- @fuller_PopulationGeneticsCoral_2020
- @johri_RecommendationsImprovingStatistical_2022
@@ -34,3 +91,83 @@ the exercises. You can apply for an account
Look at , in particular
for information on how to connect to and work on uppmax.
+
+### Software installation
+
+::: {.callout-important}
+
+Instructions will be updated when a full list of required programs are
+available.
+
+:::
+
+In case there are issues with UPPMAX we ask you to prepare a local
+backup compute environment on your computer. We will use the
+[conda](https://docs.conda.io/en/latest/) package manager to install
+necessary requirements from the package repositories
+[bioconda](https://bioconda.github.io/) and
+[conda-forge](https://conda-forge.org/).
+
+#### 1. Install conda
+
+To start using conda, follow the [quick command line install
+instructions](https://docs.conda.io/en/latest/miniconda.html#quick-command-line-install)
+to install the minimal conda installer
+[miniconda](https://docs.conda.io/en/latest/miniconda.html).
+
+#### 2. Configure conda
+
+Configure conda to access the package repositories (see also [bioconda
+usage](https://bioconda.github.io/#usage)). This will modify your
+`~/.condarc` file:
+
+```{bash}
+#| label: conda-configuration
+#| echo: true
+#| eval: false
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda config --set channel_priority strict
+```
+
+::: {.callout-important}
+
+Please note that the order of these commands is important!
+
+:::
+
+#### 3. Create an isolated course environment
+
+It is suggested you create and change to a isolated environment `pgip`
+dedicated to the course:
+
+```{bash }
+#| label: create-conda-pgip
+#| echo: true
+#| eval: false
+conda create -n pgip python=3.10 r-base
+conda activate pgip
+```
+
+To deactivate an environment you issue the command `conda deactivate`.
+
+#### 4. Install packages
+
+You can install packages as follows (remember to activate `pgip`!):
+
+```{bash }
+#| label: conda-install-packages
+#| echo: true
+#| eval: false
+conda install bcftools angsd mosdepth
+```
+
+::: {.callout-tip}
+
+If installation is slow, you can try the
+[mamba](https://mamba.readthedocs.io/en/latest/mamba-installation.html) installer.
+
+:::
+
+
diff --git a/docs/schedule.qmd b/docs/schedule.qmd
index 72765cc4..ef917ca5 100644
--- a/docs/schedule.qmd
+++ b/docs/schedule.qmd
@@ -1,7 +1,6 @@
---
title: "Schedule"
toc: false
-date: ""
sidebar: false
format:
html:
@@ -16,7 +15,7 @@ format:
-[**2023-08-23: Note that the schedule is tentative and subject to change!**]{.largest}
+[**{{< meta date >}}: Note that the schedule is tentative and subject to change!**]{.largest}
@@ -24,56 +23,59 @@ format:
::: {.contents-table .column-body-outset}
-| Topic | Time | Author | Links |
-|------------------------------------------|-------------|------------|----------------------------------------------------------------------------------------------------------|
-| [**6-Nov-2023 (Mon)**]{.highlight} | | | |
-| Coffee and welcome | 08:30-09:00 | | |
-| Introduction to PGIP | 09:00-09:30 | JH, NO, PU | |
-| Population genomics in practice | 09:30-10:00 | PU | [Slides](slides/pgip/index.html) |
-| Coffee break | 10:00-10:30 | | |
-| Population genetics foundations | 10:30-12:00 | PU | [Slides](slides/foundations/index.html) |
-| Lunch | 12:00-13:00 | | |
-| Introduction to simulation | 13:00-15:00 | PU | [Slides](slides/simulation/index.html), [Exercise](https://percyfal.github.io/pgip-jlite/lab/index.html) |
-| Coffee break | 15:00-15:30 | | |
-| Introduction to simulation | 15:30-17:00 | PU | [Slides](slides/simulation/index.html), [Exercise](https://percyfal.github.io/pgip-jlite/lab/index.html) |
-| [**7-Nov-2023 (Tue)**]{.highlight} | | | |
-| Recap day 1 | 09:00-09:30 | PU | |
-| Variant calling and filtering | 09:30-10:00 | PU | Slides, Exercise |
-| Coffee break | 10:00-10:30 | | |
-| Variant calling and filtering, continued | 10:30-12:00 | PU | Slides, Exercise |
-| Lunch | 12:00-13:00 | | |
-| Genetic diversity | 13:00-15:00 | PU | Slides, Exercise |
-| Coffee break | 15:00-15:30 | | |
-| TBA | 15:30-17:00 | | |
-| [**8-Nov-2023 (Wed)**]{.highlight} | | | |
-| Recap day 2 | 09:00-09:30 | PU | |
-| PCA | 09:30-10:00 | | |
-| Coffee break | 10:00-10:30 | | |
-| Fst | 10:30-12:00 | | |
-| Lunch | 12:00-13:00 | | |
-| Admixture | 13:00-15:00 | | |
-| Coffee break | 15:00-15:30 | | |
-| f-statistics | 15:30-17:00 | | |
-| | | | |
-| [**9-Nov-2023 (Thu)**]{.highlight} | | | |
-| Recap day 3 | 09:00-09:30 | | |
-| Demography | 09:30-10:00 | | |
-| Coffee break | 10:00-10:30 | | |
-| Demography and psmc | 10:30-12:00 | | |
-| Lunch | 12:00-13:00 | | |
-| Selection | 13:00-15:00 | | |
-| Coffee break | 15:00-15:30 | | |
-| Selection | 15:30-17:00 | | |
-| | | | |
-| [**10-Nov-2023 (Fri)**]{.highlight} | | | |
-| Recap | 09:00-10:00 | JH, NO, PU | |
-| Coffee break | 10:00-10:30 | | |
-| Guest lecture | 10:30-11:30 | | |
-| Recap continued | 11:30-12:00 | JH, NO, PU | |
-| Lunch | 12:00-13:00 | | |
-| Guest lecture | 13:00-14:00 | | |
-| Recap continued | 14:00-15:00 | JH, NO, PU | |
-| Project discussion | 15:00-17:00 | | |
+| Topic | Time | Author | Links |
+|------------------------------------------|-------------|----------------|---------------------------------------------------------|
+| [**6-Nov-2023 (Mon)**]{.highlight} | | | |
+| Coffee and welcome | 08:30-09:00 | | |
+| Introduction to PGIP | 09:00-09:30 | AS, JH, NO, PU | |
+| Population genomics in practice | 09:30-10:00 | PU | [Slides](slides/pgip/index.html) |
+| Coffee break | 10:00-10:30 | | |
+| Population genetics foundations | 10:30-12:00 | PU | [Slides](slides/foundations/index.html) |
+| Lunch | 12:00-13:00 | | |
+| Introduction to the coalescent | 13:00-15:00 | PU | [Slides](slides/simulation/index.html) |
+| | | | [Instructions]({{< var exercises.simulation.howto >}}) |
+| | | | [Exercise]({{< var exercises.simulation.coalescent >}}) |
+| Coffee break | 15:00-15:30 | | |
+| Introduction to msprime | 15:30-17:00 | PU | [Slides](slides/simulation/index.html) |
+| | | | [Exercise]({{< var exercises.simulation.msprime >}}) |
+| [**7-Nov-2023 (Tue)**]{.highlight} | | | |
+| Recap day 1 | 09:00-09:30 | PU | |
+| Variant calling and filtering | 09:30-10:00 | PU | Slides, Exercise |
+| Coffee break | 10:00-10:30 | | |
+| Variant calling and filtering, continued | 10:30-12:00 | PU | Slides, Exercise |
+| Lunch | 12:00-13:00 | | |
+| Genetic diversity | 13:00-15:00 | PU | Slides, Exercise |
+| Coffee break | 15:00-15:30 | | |
+| TBA | 15:30-17:00 | | |
+| [**8-Nov-2023 (Wed)**]{.highlight} | | | |
+| Recap day 2 | 09:00-09:30 | PU | |
+| PCA | 09:30-10:00 | | |
+| Coffee break | 10:00-10:30 | | |
+| Fst | 10:30-12:00 | | |
+| Lunch | 12:00-13:00 | | |
+| Admixture | 13:00-15:00 | | |
+| Coffee break | 15:00-15:30 | | |
+| f-statistics | 15:30-17:00 | | |
+| | | | |
+| [**9-Nov-2023 (Thu)**]{.highlight} | | | |
+| Recap day 3 | 09:00-09:30 | | |
+| Demography | 09:30-10:00 | | |
+| Coffee break | 10:00-10:30 | | |
+| Demography and psmc | 10:30-12:00 | | |
+| Lunch | 12:00-13:00 | | |
+| Selection | 13:00-15:00 | | |
+| Coffee break | 15:00-15:30 | | |
+| Selection | 15:30-17:00 | | |
+| | | | |
+| [**10-Nov-2023 (Fri)**]{.highlight} | | | |
+| Recap | 09:00-10:00 | JH, NO, PU | |
+| Coffee break | 10:00-10:30 | | |
+| Guest lecture | 10:30-11:30 | | |
+| Recap continued | 11:30-12:00 | JH, NO, PU | |
+| Lunch | 12:00-13:00 | | |
+| Guest lecture | 13:00-14:00 | | |
+| Recap continued | 14:00-15:00 | JH, NO, PU | |
+| Project discussion | 15:00-17:00 | | |
:::
diff --git a/docs/slides/foundations/index.qmd b/docs/slides/foundations/index.qmd
index 9dfc395e..73a20302 100644
--- a/docs/slides/foundations/index.qmd
+++ b/docs/slides/foundations/index.qmd
@@ -1199,7 +1199,7 @@ followed by success). This is the [geometric
distribution](https://en.wikipedia.org/wiki/Geometric_distribution)
$Ge(p)$, with parameter $p=\frac{1}{2N}$, and expected value
$\frac{1}{p}={2N}$. That is, the **expected time for two chromosomes
-to find a common ancester (i.e., coalesce) is $2N$ generations**.
+to find a common ancestor (i.e., coalesce) is $2N$ generations**.
:::
diff --git a/docs/slides/index.qmd b/docs/slides/index.qmd
index cb2337ac..90777d0c 100644
--- a/docs/slides/index.qmd
+++ b/docs/slides/index.qmd
@@ -5,12 +5,12 @@ description: "List of all presentations"
listing:
type: grid
grid-columns: 4
- fields: [image, title, subtitle, author]
+ fields: [title, subtitle, author]
sort: false
contents:
- - introduction/index.qmd
- pgip/index.qmd
- foundations/index.qmd
+ - simultation/index.qmd
date: ""
toc: false
sidebar: false