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bodkan/README.md

> whoami

I did my PhD in ancient DNA genomics at the Max Planck Institute for Evolutionary Anthropology in Leipzig where I studied the evolutionary histories of anatomically modern humans, Neanderthals, and Denisovans (but also extinct elephants!).

I'm currently working at the GLOBE Institute at the University of Copenhagen where I'm building new tools for spatial data analysis and population genomics simulations. The underlying themes of my work are reproducibility and design of intuitive user-programmable interfaces to complex computational methods: I enjoy building tools that help experts work on novel questions more efficiently while lowering the barrier of entry to novice users.


The most recent outcome of my work is an R package slendr (CRAN), which provides a framework for building programmable population genetic simulations on real geographic landscapes, as well as for simulation of traditional non-spatial population genetic models, entirely in R. You can read more about slendr in this paper.

I'm also the developer of admixr (CRAN), an R package for automated, reproducible analyses using the ADMIXTOOLS software. This package has already been used in several dozen of publications and has thousands of users, many of which have had little to no experience with data analysis and programming.


If you would like to get in touch, send me an email at contact@bodkan.net.

You can also find me on Twitter @dr_bodkan.

Pinned

  1. slendr Public

    Population genetic simulations in R 🌍

    R 31 2

  2. admixr Public

    An R package for reproducible and automated ADMIXTOOLS analyses

    R 21 8

  3. 🎄 Advent of Code 2021 in R 🎄

    R 2

  4. popgen2022 Public

    Lecture notes and materials on popgen simulations

    HTML 6 3

  5. Source code and Jupyter notebooks for the paper: "The limits of long-term selection against Neandertal introgression"

    HTML 4

  6. bam-caller Public

    A simple Python CLI program for calling pseudo-haploid genotypes from BAM files

    Python 1 1

2,231 contributions in the last year

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Mon Wed Fri
Activity overview
Contributed to bodkan/slendr, bodkan/adventofcode2021, bodkan/admixr and 16 other repositories

Contribution activity

September 2022

Created a pull request in bodkan/slendr that received 2 comments

Make serialization of slendr models to disk optional (for faster msprime coalescent runs)

This is is an attempt to implement #97. Skipping serialization to disk makes it possible to call our msprime back-end Python code directly, without…

+749 −537 2 comments
3 contributions in private repositories Sep 15 – Sep 16

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