Castedo 21stC Publishing
- https://copyAId.it (text proofreading/copyediting utility using OpenAI GPT API)
- https://try.perm.pub (Your citable, living documents. Anywhere and forever.)
- hidos : document successions library/utility
- epijats : automated typesetting, JATS XML rendering library/utility
- sshsig : SSHSIG format cryptographic signature verification library
Development Tools
- Notes on Lean : Notes on using Lean
- Using Vim 9 with Lean : Guide to using Vim 9 to write in Lean
- cnest : simple scripts for personal (rootless) persistent parallel containers
- unexceptional : helper functions for returning unexceptional Exception objects
- git-prepr : git grafting scripts
- jinjagen : short Python script using jinja2 to generate static websites
- JSOML : JSON semantics in XML file syntax
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 (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
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