Castedo Ellerman

Git repositories

• gitlab.com/castedo
• gitlab.com/ellerman
• gitlab.com/perm.pub
• github.com/castedo

Developed and still used by me

• cnest : simple scripts for personal (rootless) persistent parallel containers
• https://copyAId.it (text proofreading/copyediting utility using OpenAI GPT API)
• personal LLM agent harness
• jinjagen : short Python script using jinja2 to generate static websites
• JSOML : JSON semantics in XML file syntax
• git-prepr : git grafting scripts

Research Software

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

• msprime : population genetics simulator.
  Associated journal article: "Efficient ancestry and mutation simulation with msprime 1.0"
  Genetics. 2022 Mar; 220(3):iyab229.
  Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, et al
• tskit : tree sequence toolkit and Ancestral Recombination Graph (ARG) library.
  Associated journal article: "Population-scale ancestral recombination graphs with tskit 1.0"
  Nature Methods. 2026 Oct.
  Jeffery B, Wong Y, Thornton K, Tsambos G, Bisschop G, Deng Y, et al
• tskit containers

Novembre Lab (from lab "rotation", not as lab member)

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

Software no longer in use

Genetics

• genomology : Genomic genealogy library in R
• EPI511 minihapmap.py : upgrade to code of Advanced Population & Medical Genetics class

Lean proof assistant

• Notes on Lean : Notes on using Lean
• Using Vim 9 with Lean : Guide to using Vim 9 to write in Lean

Publishing technology experiment

• hidos : document successions library/utility
• epijats : automated typesetting, JATS XML rendering library/utility
• sshsig : SSHSIG format cryptographic signature verification library
• try.perm.pub (inactive)
• pilot.perm.pub (frozen)

Other

• unexceptional : helper functions for returning unexceptional Exception objects
• isomon : C/C++ library for ISO currency data