Discover tgvaughan/sicm Open Source project

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Created about 8 years ago
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tgvaughan

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Unofficial HTML version of Sussman and Wisdom's "Structure and Interpretation of Classical Mechanics"

PirateScope

wxPython oscilloscope client for dangerousprototypes.com's Bus Pirate.

Python

icytree

Browser-based utility for phylogenetic tree visualisation.

JavaScript

MultiTypeTree

BEAST 2 package which provides support for multi-type trees: phylogenetic trees on structured populations.

Java

MASTER

A versatile simulation engine for stochastic population dynamics models.

Java

bacter

Bacterial phylogenetics in BEAST 2.

Java

feast

Tasty additions to BEAST 2

Java

BDMM-Prime

Multi-type birth-death-sampling modelling for BEAST 2.

Java

BuildRoster

Employee roster generator.

Python

TimeTrees.jl

Phylogenetic tree type for julia

Julia

JsonBrowse

Basic graphical JSON object heirarchy browser

Java

remaster

High-fidelity stochastic tree simulation for BEAST 2.

Java

bioinf702_lectures

Lecture slides for bioinf702

HTML

BayesianMCMCLectures

Lectures I gave for a Bayesian statistics minicourse at the University of Hohenheim.

JavaScript

dvtm

Fork of dvtm (http://www.brain-dump.org/projects/dvtm) that provides simple runtime configuration of key bindings and other basic options via an ini-like config file.

EpiInf

BEAST 2 package for performing inference on epidemiological parameters using the exact likelihood.

Jupyter Notebook

h5shell

Command shell interface for HDF5 scientific data files.

Python

talks

Repository for my web-based talks

HTML

HamiltonianTreeDynamics

Rough visualisation of classical mechanics in tree space

Processing

PhotoDist

Estimate distances from stereo photo pairs.

Java

mEpiLabWorkshop

One day BEAST 2 workshop delivered to mEpiLab

JavaScript

pitchfork

Bayesian phylogenetic inference under models supporting explicit polytomies.

Java

HK_2018_Slides

Lecture for C3BI workshop in HK, 2018

JavaScript

ModelSelection

BEAST 2 code for simple model selection.

Java

R0-manuscript-materials

Supplemental files and data for the manuscript "Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data".

beast.m4

Some basic m4 macros for BEAST 2 XMLs

HK_2018_MiniProject

Instructions and data for student mini-project at the 2018 C3BI course on molecular phylogenetics.

Python

BSLoader

Easily load R scripts provided by BEAST 2 packages.

icylog

Browser-based BEAST log file analyzer.

JavaScript

TransmissionChainAnalyses

Scripts needed to reproduce phylodynamic analyses from Nadeau et al. 2021.

ceskykrumlov2018_lectures

Talks presented at the 2018 Workshop on Population and Speciation Genomics, Cesky Krumlov

JavaScript

tgvaughan/sicm

tgvaughan

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