Jonathan Dursi

mpi-tutorial. 1.5 day MPI tutorial for those with some C/Fortran knowledge.

poapy. A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

beyond-single-core-R. Short tour of parallel and foreach packages, and how to think about scaling data analyses

coarray-examples. Simple coarray examples for teaching

parallel-IO-tutorial. Half-day Parallel I/O tutorial for HPC - MPI-IO, HDF5, NetCDF

ML-for-scientists. Machine Learning for Scientists Tutorial

hadoop-for-hpcers-tutorial. Introduction to Hadoop for those from an HPC simulation background

mergevcf. Python package and routines for merging VCF files

Spark-Chapel-TF-UMich-2016. Slides and materials for workshop at University of Michigan MICDE

EuroMPI2016. Presentation for EuroMPI 2016

julia_v_chapel. Simple test cases comparing julia and chapel

glbio-jupyter-workshop. Instructions and files for #GLBIOCCBC16 Workshop 2, "Jupyter Notebooks for Performing and Sharing Bioinformatics Analyses"

make-for-reproducible-data-analysis. Shell

CHIUW2017. Keynote talk for CHIUW2017

rosalind_chapel. Rosalind exercises in chapel

data-model-parallelism. Repo for 2025 summer school

simple-squiggle-pseudomapper. Simple demonstration of using spatial indexes (here kd-trees) to approximately map nanopore squiggle reads

make_pattern_rules. Tutorial for using Makefile pattern rules

research-computing-teams. Website for the research computing teams newsletter

consensus_call_docker. Make PCAWG consensus calls given input VCFs

dask-sparse-mtx. A simple demonstration of using dask tasks to multiple sparse matrices stored in a file

scalable-analysis-R. A day-long tutorial on scalable data analysis in R

shell-for-scientists. An introduction to the command line and automation for researchers

intro-profiling-tools. Quick Introduction to some HPC profiling tools

opa_open_registered_controlled_ex. Python

dursi-blog. Content for blog

validation-pipeline. R

keycloak_ldap_local. Demo of using Keycloak to provide OAuth2/OIDC authentication using LDAP as a source of identities

IACS-SBU-2018. "HPC, Big Data, and Large Scale Genomics"

ga4gh_directory_singularity. First pass at a singularity version of the ga4gh server

alliance_oct24_nsight. Materials for NSight walkthrough for Alliance Federation Staff

simple-synthetic-somatic. Very simple synthetic somatic read/call generator for testing mechanics of pipelines

sga-annotate-docker. Docker file for sga annotation pipeline

mon_py_wrkshp. Jupyter Notebook