ljdursi/intro-profiling-tools

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Created over 10 years ago
Updated about 10 years ago

ljdursi/intro-profiling-tools

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Quick Introduction to some HPC profiling tools

mpi-tutorial

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

beyond-single-core-R

Short tour of parallel and foreach packages, and how to think about scaling data analyses

poapy

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

coarray-examples

Simple coarray examples for teaching

ML-for-scientists

Machine Learning for Scientists Tutorial

parallel-IO-tutorial

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

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"

Jupyter Notebook

rosalind_chapel

Rosalind exercises in chapel

make-for-reproducible-data-analysis

CHIUW2017

Keynote talk for CHIUW2017

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

dask-sparse-mtx

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

consensus_call_docker

Make PCAWG consensus calls given input VCFs

shell-for-scientists

An introduction to the command line and automation for researchers

scalable-analysis-R

A day-long tutorial on scalable data analysis in R

validation-pipeline

new-newsletter-page

Website for the research computing teams newsletter

opa_open_registered_controlled_ex

mon_py_wrkshp

Jupyter Notebook

IACS-SBU-2018

"HPC, Big Data, and Large Scale Genomics"

simple-synthetic-somatic

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

sga-annotate-docker

Docker file for sga annotation pipeline

dursi-blog

Content for blog

ga4gh_directory_singularity

First pass at a singularity version of the ga4gh server

keycloak_ldap_local

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