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assemblage

Tools for working with second gen assemblies, fasta sequences, etc

backend-update-center2

Update center backend

beast-plugin

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

biojava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

biojava-legacy

Legacy BioJava Code

biojava-sandbox

Experimentations with BioJava

biojs

A library of JavaScript components to represent biological data

biology-data

Data for bioinformatics tools, including input, parameters, and other files

biouno-mvn-repository

A Maven repository for BioUno plug-ins

biouno.github.io

BioUno web site

cantaloupe

High-performance dynamic IIIF image server in Java

cellprofiler-docker

clumpp-plugin

cmake_training

Examples showing how to use CMake

database-sparql-plugin

Adds SPARQL connectivity to the database plugin

distruct-plugin

Distruct plug-in for Jenkins

drmaa-java

Java implementation for DRMAA applications

drmaa-pbs

DRMAA PBS Java API, using command executions like qsub and qstat

drmaav2-mock

Reference implementation of the DRMAAv2 C Language Binding

dynamicparameter-plugin

Jenkins-CI plugin allowing dynamically generated build parameter default values

figshare-java-api

A Java API to interface with the FigShare API.

figshare-plugin

BioUno FigShare Plug-in

figtree-plugin

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.

geneticdifferentiation

Code snippets to calculate genetic differentiation in R. See posting at: XXXX

gridscale

Scala library for accessing various file, batch systems, job schedulers and grid middlewares.

iiif.io

IIIF Website, contexts, and source of specifications documents

image-gallery-plugin

Jenkins Plug-in for displaying galleries of images from a job workspace

jenkins-biouno-examples

Examples for Jenkins

jenkins-lsci

Jenkins for Life Science Continuous Integration

jenkins-scriptlets

Useful groovy scripts that can be used while using Jenkins-CI for workflow automation