Discover ncsa/CytologyML Open Source project by NCSA (@ncsa)

NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.

NEAT

bhr-site

Blackhole Router Site

A simple Python/Mesa model of COVID-19 contagion and possible measures

COVID19-mesa

No elephant flows - flow shunting for Arista switches using EOS API

dumbno

bro-doctor

Variant Calling Pipeline in Cromwell/WDL

MayomicsVC

bro-clickhouse

Backend implementation for running MLFlow projects on Slurm

mlflow-slurm

The aggregate job launcher of single-core or single-node applications on HPC sites

bro-simple-scan

Zeek

Scheduler

Fortran

http-logger

http request logger for sinkhole purposes

xcat-tools

Useful tools for xCAT

Create Certificates from IngressRoutes

traefik-certmanager

Open Authorization for MyProxy

oa4mp

bro-interface-setup

BHR Block manager that uses ExaBGP

bhr-client-exabgp

bro-is-darknet

Zeek

bhr-client

Client for the BHR site

bro-cluster-in-a-box-setup

Helm charts for software developed at NCSA (as well as some dependencies)

charts

Smarty

bhr-bro

Bro integration for the BHR toolset

nagios-plugins

Nagios plugins

Application of two different DeepONet models in multi-physics additive manufacturing applications.

AM_DeepONet

Isolated, Scalable, & Lightweight Environment for Training

islet

Parallel Synchronization For Locally Mounted File Systems

psync

AmeriFlux Pipeline Repository

ameriflux-pipeline

Scripts and code for the LCI Workshop series

lci-scripts

NCSA-Genomics_MLCC

Deep autoencoder for unsupervized multi-label cancer classification.

A novel DeepONet architecture that is specifically designed for generating predictions on different 3D geometries discretized by different number of mesh nodes.

Swift-T-Variant-Calling

Swift

GeomDeepONet

Don't Repeat Yourself Machine Learning: A Machine Learning library to reduce code duplication, and automate testing.

DRYML

sans-holiday-hack-2016

SANS Holiday Hack 2016

Sentieon_DNASeq_Benchmarking

Benchmarking scripts

NCSA Hydro System Documentation

hydro_documentation

Rotate bro logs atomically and serially

bro-atomic-rotate

Parfu tar-like MPI tool for creating or extracting directory tree archives. Devel-branch version (0.5.1) is tar-compatible; earlier versions are not.

parfu_archive_tool

C++

swsuite

Bro plugin that provides a ZeroMQ log writer.

bro-zeromq-writer

C++

ncsa-shib-idp

Shibboleth Identity Provider (IdP) 4 for NCSA built on InCommon's Trusted Access Platform Docker Container

CSS

security-lib

A general repository of code security and building secure applications

Puppet module to install SpectrumScale (GPFS) on a node, add it to a GPFS cluster, and, optionally, mount some filesets.

puppet-spectrumscale

Scripts to benchmark computational performance of GATK3.8 and GATK4

react-template

JavaScript

GATK_Benchmarking

Terraform and other scripts to start kubernetes cluster on radiant.

GenomicsCortextVarNextflow

Nextflow

radiant-cluster

HCL

CPRHD_WNV_USA_SWMM

Storm Water Management Model - Green Infrastructure

Update work done on the swsuite by the Fall2022 CIP interns

radiant-cluster-template

HCL

-swsuite-CIP-UpdatesV2

control-repo

pylut

hpc-conda-envs

Conda environmental files for HPC clusters

Lua

Polyglot

Node.js library for Clowder

clowderjs

JavaScript

phyloflow

Phylogenic tree computation and packaging with Docker, WDL

An open source scientific workflow system that simplifies the integration of data and modeling tools to support research and enable cross disciplinary integration to produce targeted outputs that address particular engineering and educational needs.

datawolf

the QDL programming language

qdl

Home for Lab Dragon - A new costumizable and powerful electronic lab notebook

lab-dragon

NCSA Common Puppet Profiles - configure standard monitoring of host

dns-infra-check

puppet-profile_monitoring

NCSA Common Puppet Profiles - configure NCSA Service backups

puppet-profile_backup

NCSA Common Puppet Profiles - configure auditing functionality

puppet-profile_audit

Deploy a new puppet master service.

puppet_deployment

Puppet module to install and configure the MySQL orchestrator

puppet-mysql_orchestrator

General Roofline Evaluation Gadget

GREG

puppet-profile_system_auth

NCSA Common Puppet Profiles - configure standard system authentication

Sends notifications when Slurm compute nodes are down.

sinfo_mon

CustomImageBuilder

TGI_RAILS_Documentation

NCSA Common Puppet Profiles - configure the stats of SELinux

puppet-profile_selinux

Tools for security using Java 8

crypto-java8

NCSA Common Puppet Profiles - basic puppet master setup

puppet-profile_puppet_master

sdaiakeys

A Globus Online test workflow to use with Jenkins. The workflow verifies basic endpoint functionality.

jenkins-globus-online-workflow

NCSA Common Puppet Profiles - install configure Lustre client

puppet-profile_lustre_client

Custom version of the Open OnDemand Jupyter Lab app.

OOD-JupyterLab

HTML

syswipe

Scrub disks and factory reset a server when it is decommissioned.

Setup and manage a database to use for Puppet External Node Classifier

puppetserver-enc

Puppet Module to install and configure OpenAFS

puppet-openafs

The SDAIA project provides a secure, fast, and decentralized model for disseminating threat intelligence data.

Delta-OOD-JupyterLab

HTML

sdaia

issues

Want to join the NCSA Organization? Have a question for the team? Ask here.

puppet-profile_allow_ssh_from_bastion

myproxy fork - work in progress

pcapblackout

myproxy

dumbno-client-go

datacarousel

Data Carousel for HDF5 Data Archived in AWS Glacier

Blue Waters New User Training

bw-new-user-training

HTML

puppet-profile_timezone

Puppet profile for configuring time-zone

Command Line Interface to JIRA

jiracmdline

Puppet module for configuring Slurm workload manager

puppet-slurm

AttackTagger

NCSA Common Puppet Profiles - basic firewall config

puppet-profile_firewall

Genomics_MGC_VariantCalling_Nextflow

archi_tools

CPRHD_SES

Schedule events in Outlook 365

outlook-scheduler

bhr-source-bhr

NCSA Common Puppet Profiles - configure rsyslog client or relay for NCSA

100

puppet-profile_rsyslog