Software

The tools behind the research.

AI & machine learning

Neural networks · Agentic workflows

Modelling & inference

Stochastic models · Simulation-based inference

Programming & data

Python · R · C/C++ · SQL

Research computing

Linux · HPC · Docker

Web & visualisation

React · D3.js · Three.js

Open source

Software & contributions

software.index
$software list --all

Tools I develop8

ATLASOutbreak surveillance
PythonAgentic AIReact
EvoNNNeural inference
RPythonPyTorch
evesimEvolution simulation
RC++RcppSim
NetForgeContact networks
PythonSBMSim
HerdLinkNetwork exploration
ReactJSD3.jsViteSim
NetSpectraNetwork statistics
JSD3.jsTurf.js
EvoLabEvolution sandbox
JSSimPhylo
miniapePhylogenetic utilities
JSPhylo

Collaborative contributions3

treestatsTree statistics
RRcppPhylo
DDDDiversification
RRcppPhyloSim
DAISIEIsland biodiversity
RRcppPhyloSim
11 projects · open source & research software
Contact

Get in touch

Working on an interesting question in biology, networks or AI? Let’s connect.

tianjian.qin@wur.nl