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At least 1,243 records · Page 69

Axolotl: a scalable genomics library based on Apache Spark (Axolotl) v1.0.0

Axolotl is a Python library for scalable distributed genome and metagenome data analysis. Existing tools and systems that we rely on are struggling to keep up with the rapid explosion of genomic data. Compounding this issue, developing scalable solutions require a steep learning curve in parallel programming, which presents a barrier to academic researchers. While we do have scalable solutions for specific tasks, we lack comprehensive, end-to-end solutions. It's this gap in our toolkit that we aim to address with Axolotl. The Axolotl library is built for easy parallel processing, efficiently handling multiple tasks or large datasets simultaneously, and scaling up to meet the demands of extensive genomic data analysis.

Wang, Zhong↗

pnnl/pyraabe

Automated Raabe table generationPyRaabe is a Python package to automate Raabe table -- a graph representation of airway geometry -- generation from a triangulated surface of an airway geometry. With a single command, it extracts a centerline from an input 3D surface mesh and subsequently computes the relevant attributes for the Raabe table, including length, diameter, bifurcation angle, and gravity angle. These can be used to inform downstream models, such as the Multiple-Path Particle Dosimetry (MPPD) model.

Colby, Sean M.↗

IMMM-SFA/im3py

An IM3 template repository for Python projects that have time-steps

Vernon, Chris↗

ames-market/psst

Python version of the AMES Wholesale Power Market Test Bed; no GUI. Previously hosted by Iowa State University; PNNL has assumed hosting. AMES existed in a non-version controlled and inconsistent form. PNNL added price-sensitive loads for transactive systems, with various other bug fixes and features.

McDermott, Tom↗

pnnl/slim

Open source release of Python Systems Library which contains benchmark datasets, system emulators, and data loading codes.

Tuor, Aaron↗

pnnl/DeepDataProfiler

Python library for analyzing the internal structure of deep neural networks.

Praggastis, Brenda↗

HIPPO Software

HIPPO software is a Python implementation of the HIPPO technology. The HIPPO technology provides the computational and modeling capabilities for managing electricity market operations and for designing and prototyping future markets. The current software can solve the day-ahead unit commitment problem and perform simultaneous feasibility test. It can be used to handle industry scale electricity market.

Peng, Fan↗

pnnl/diet-parselantro

A data annotation tool that integrates with the python Jupyter notebook environment.

Central, PNNL Developer↗

NWQ-sim

NWQSim is a quantum circuit simulation environment developed at PNNL. It currently includes two major components: a state-vector simulator (SV-Sim) and a density matrix simulator (DM-Sim) and we may add more components, such as a Clifford simulator, in the future effort. NWQSim has two language interface: C/C++ and Python. It supports Q#/QDK frontend through QIR and QIR-runtime. It supports Qiskit and Cirq frontends through OpenQASM. NWQSim runs on several backends: Intel-CPU, Intel-Xeon-Phi, AMD-CPU, AMD-GPU, NVIDIA-GPU, and IBM-CPU. It supports three modes: (1) single processor, such as a single CPU (with and without AVX2 and AVX512 acceleration), a single NVIDIA GPU or a single AMD GPU; (2) single-node-multi-processors, such as multi-CPUs/Xeon-Phis, multi-NVIDA/AMD GPUs; (3) multi-nodes, such as a CPU cluster, a Xeon-Phi cluster (e.g., ANL Theta, NERSC Cori), an NVIDIA cluster (e.g., ORNL Summit, NERSC Perlmutter).

Li, Ang↗

y0-causal-inference/y0

❓y0 (pronounced "why not?") is for causal inference in Python: a software library intended to support the scientific discovery process.

Hoyt, Charles Tapley↗

JGCRI/stitches

Amalgamate existing climate data to create monthly climate variable fields. The STITCHES python library provides a user-friendly interface to top-down climate emulation.

Snyder, Abigail↗

pnnl/interflow

A Python package for organizing and calculating cross-sectoral interdependency flow values. The interflow package collects known resource flow values (e.g., water demand) between sectors provided by the user and calculates new sector flows for a secondary resource type (e.g., energy demand) based on provided resource intensity estimates, source sector fractions, and downstream sector discharge fractions.

Mongird, Kendall↗

pnnl/copper

Performance curve generator for building energy simulation. Copper is a tool in the form of Python package that can be used to generate metric specific performance curves for building energy simulations.

L., Jeremy↗

High-throughput electronic structure package

We introduce HTESP (High-Throughput Electronic Structure Package), an automated tool designed for high-throughput ab initio calculations. HTESP simplifies the entire workflow, including data extraction, input files generation, calculation submission, result collection, and plotting. The package is implemented in Python and Bash languages. In this paper, we provide detailed information about the package, its installation process and some illustrative examples to demonstrate its usage. Additionally, the package includes comprehensive online documentation on input parameters and tutorials to assist users.

Nepal, NirajK↗

ExaDigiT/RAPS

ExaDigiT is a framework for developing comprehensive digital twins of liquid-cooled supercomputers, which has three main modules: (1) a python-based Resource Allocator and Power Simulator (RAPS), (2) a Modelica-based Thermo-Fluidic cooling model, and (3) a C++-based augmented reality model built on Unreal Engine 5. RAPS either simulates workloads or replays historical workloads from system telemetry, and is able to predict dynamic energy consumption, as well as interact with the cooling model to predict cooling system behavior. Such a tool can be used together with reinforcement learning algorithms to provide an end-to-end optimization tool for data centers.

Brewer, Wesley [Oak Ridge National Laboratory (ORN↗

datacenterCoolingModel

ExaDigiT is a framework for developing comprehensive digital twins of liquid-cooled supercomputers, which has three main modules: (1) a python-based Resource Allocator and Power Simulator (RAPS), (2) a Modelica-based Thermo-Fluidic cooling model, and (3) a C++-based augmented reality model built on Unreal Engine 5. The Modelica-based cooling model is primarily built-on the open-source Transient Simulation Framework of Reconfigurable Models (TRANSFORM) library and the open-source autocsm library. The library follows the templating architecture developed in the TRANSFORM and the autocsm libraries. This tool can be easily extended to model other Frontier-like liquid cooled supercomputers.

Kumar, Vineet [Oak Ridge National Laboratory (ORNL↗

TwinMe4AD: WGAN-based Digital Twins for Anomaly Detection

SAND2024-08373O TwinMe4AD is a Python-based software tool designed for anomaly detection using digital twins that closely mimic real, wearable healthcare datasets. The tool is invaluable for scenarios where collecting data is either expensive or impractical, serving as a privacy-preserving solution. Sensitive information is protected by training deep learning models on synthetic data derived from real datasets. One of TwinMe4AD's key features is its anomaly detection capability, which is based on fourth-order moments of parameters. This versatile approach can be applied across a range of datasets, from univariate to multivariate, making it compatible with various types of data. It also generates synthetic twins using Wasserstein Generative Adversarial Networks (WGANs), allowing users to create a small cohort of a population similar to that of a village population. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Poorey, Kunal↗