Castedo Ellerman

Research software

Tree sequence community (github.com/tskit-dev)

• msprime : population genetics simulator
  Journal article: Baumdicker, Franz et al. "Efficient ancestry and mutation simulation with msprime 1.0." Genetics, March 2022; doi:10.1093/genetics/iyab229
• tskit : the tree sequence toolkit
• tskit containers

Novembre Lab (github.com/NovembreLab)

• montecarloop : caching and analysis of estimates from Monte Carlo simulations
• spatial-sfs : spatial distribution of rare deleterious alleles

Advanced Population & Medical Genetics class

• EPI511 minihapmap.py : upgrade to code used in Alkes Price's EPI511 course at Harvard

Other

• genomology : Genomic genealogy library in R

21stC publishing

Software

• basecast : authoring tool generating JATS XML baseprints, HTML previews and PDF files from LaTeX and/or markdown source files
• epijats : JATS XML rendering library/utility
• hidos : digitial successions library/utility
• copyAIdit : OpenAI GPT text copyediting/proofreading utility

Infrastructure

• popgen.es
• Baseprints
• Why try Digital Succession Identifiers
• DSI technical specification
• perm.pub pilot project

Development tools

• JSOML : JSON semantics in XML file syntax
• cnest : simple scripts for personal (rootless) persistent parallel containers
• git-prepr : git grafting scripts
• jinjagen : short Python script using jinja2 to generate static websites

More

• gitlab.com/castedo
• github.com/castedo