Bernie Pope

berp. An implementation of Python 3

language-python. A parser for Python 2.x and 3.x written in Haskell

blip. A bytecode compiler for Python 3

ministg. Ministg is an interpreter for a high-level, small-step, operational semantics for the STG machine.

js-turtle. Turtle graphics in Javascript using HTML5 canvas

haskell-mpi. MPI bindings for Haskell

rubra. Infrastructure code to support DNA pipeline

methpat. A program for summarising CpG methylation patterns

haskell-linux-perf. Haskell library for reading perf.data files from the linux performance events tool.

python_cheat_sheet_notebook. Python cheat sheet notebook

favr. Filtering and Annotation of Variants that are Rare

lfg. A lagged fibonacci generator in Haskell

pbs2slurm. Tool for converting PBS/Torque scripts into SLURM scripts

rover. Read overlap variant caller.

varlap. A tool aimed at quality control of DNA variants arising from sequencing alignments. It reports a suite of statistics about variants relating to their local alignment context in BAM files.

gurita. A convenient and expressive tool for data analytics and plotting on the command line

haskell-sprng. Haskell binding to the SPRNG library

annokey. Annotation of gene lists with keyword hits from the NCBI gene database

crpipe. Bioinformatics pipeline based on Ruffus

ngs-pipeline. Next generation sequencing pipeline

cwl_explorer. Interactive visualisation of CWL workflows

mpi-article-monad-reader. Article about the Haskell MPI bindings for the Monad.Reader magazine

HiTIME. High-resolution Twin-Ion Metabolic Extraction

banzai. Python

scala-fungraph. Functional graphics in Scala

language-python-test. Code for testing the language-python library

pyray. Ray tracer in Python

vimrc. My vimrc file

classify_sequencer. Try to detect DNA sequencing platform from read IDs

md5_pipeline. A pipeline for running md5 checksums over many files in parallel

saveSvgAsPng. HTML

binary_search_tree. Simple unbalanced binary search tree in Python

pseudofinder. Find processed pseudogenes in DNA sequencing data using input structural variants

snvly. Snvly is a tool aimed at quality control of DNA variants arising from sequencing alignments. It reports a suite of statistics about variants relating to their local alignment context in BAM files.

lynch_gatk. GATK variant calling pipeline for Suspected Lynch Syndrome project

coglabweb. Website for the Colorectal Oncogenomics Group

pipeline_base. Infrastructure for bioinformatics pipelines based on Ruffus

vcbsig. Website for the Victorian Cancer Bioinformatics Special Interest Group

python_rainfall_ipython. IPython example using rainfall data

twin_ion_pipeline. A pipeline for detecting twin ion signals in LCMS data

hiplex-primer. Python

bamcover. Plot graphs of read coverage for BAM files

asteroids. A clone of the asteroids game using the Pygame library

jobscript_generator. An interactive webpage for generating job scripts for the SLURM scheduler

undr_rover. Unmapped primer directed ROVER

HiTIME-CPP. Detection of twin-ion signals in Liquid chromatography-mass spectrometry (LCMS) data.

make-pbs-script. Automate the creation of simple PBS scripts, using a question and answer dialog