Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “github”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein–protein interactions

Abstract Summary Batch yeast two-hybrid (Y2H) assays, leveraged with next-generation sequencing, have afforded successful innovations for the analysis of protein–protein interactions. NGPINT is a Conda-based software designed to process the millions of raw sequencing reads resulting from Y2H–next-generation interaction screens. Over time, increasing compatibility and dependency issues have prevented clean NGPINT installation and operation. A system-wide update was essential to continue effective use with its companion software, Y2H-SCORES. We present NGPINT V3, a containerized implementation built with both Singularity and Docker, allowing accessibility across virtually any operating system and computing environment. Availability and implementation This update includes streamlined dependencies and container images hosted on Sylabs (https://cloud.sylabs.io/library/schuyler/ngpint/ngpint) and Dockerhub (https://hub.docker.com/r/schuylerds/ngpint), facilitating easier adoption and integration into high-throughput and cloud-computing workflows. Full instructions and software can be also found in the GitHub repository https://github.com/Wiselab2/NGPINT_V3 and Zenodo https://doi.org/10.5281/zenodo.15256036.

Biochemistry & Molecular Biology↗
DOE OSTI2025

A change language for ontologies and knowledge graphs

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language (https://github.com/INCATools/kgcl), a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable Controlled Natural Language (CNL). This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of “apply patch” and “diff” commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders—e.g. ontology edits can be specified by commands like “add synonym ‘arm’ to ‘forelimb’” or “move ‘Parkinson disease’ under ‘neurodegenerative disease’.” We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its CNL, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

Maximum a posteriori Ly α estimator (MAPLE): band power and covariance estimation of the 3D Ly α forest power spectrum

We present a novel maximum a posteriori estimator to jointly estimate band powers and the covariance of the three-dimensional power spectrum (P3D) of Ly $\alpha$ forest flux fluctuations, called MAPLE. Our Wiener-filter based algorithm reconstructs a window-deconvolved P3D in the presence of complex survey geometries typical for Ly $\alpha$ surveys that are sparsely sampled transverse to and densely sampled along the line of sight. We demonstrate our method on idealized Gaussian random fields with two selection functions: (i) a sparse sampling of 30 background sources per square degree designed to emulate the current Dark Energy Spectroscopic Instrument; (ii) a dense sampling of 900 background sources per square degree emulating the upcoming Prime Focus Spectrograph Galaxy Evolution Survey. Our proof-of-principle shows promise, especially since the algorithm can be extended to marginalize jointly over nuisance parameters and contaminants, i.e. offsets introduced by continuum fitting. Our code is implemented in JAX and is publicly available on GitHub.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Neural network-based model of galaxy power spectrum: fast full-shape galaxy power spectrum analysis

ABSTRACT We present a neural network-based emulator for the galaxy redshift-space power spectrum that enables several orders of magnitude acceleration in the galaxy clustering parameter inference, while preserving 3$\sigma$ accuracy better than 0.5 per cent up to $k_{\mathrm{max}}$ = 0.25 $\, h\text{Mpc}^{-1}$ within Lambda-cold dark matter ($\Lambda$CDM) and around 0.5 per cent $w_0$–$w_a$CDM. Our surrogate model only emulates the galaxy bias-invariant terms of one-loop perturbation theory predictions, these terms are then combined analytically with galaxy bias terms, counter-terms, and stochastic terms in order to obtain the non-linear redshift-space galaxy power spectrum. This allows us to avoid any galaxy bias prescription in the training of the emulator, which makes it more flexible. Moreover, we include the redshift $z \in [0,1.4]$ in the training which further avoids the need for re-training the emulator. We showcase the performance of the emulator in recovering the cosmological parameters of $\Lambda$CDM by analysing the suite of 25 AbacusSummit simulations that mimic the Dark Energy Spectroscopic Instrument luminous red galaxies at $z=0.5$ and 0.8, together as the emission line galaxies at $z=0.8$. We obtain similar performance in all cases, demonstrating the reliability of the emulator for any galaxy sample at any redshift in $0 \lt z \lt 1.4$. We will make our emulator public at github repository.

Trusov, Svyatoslav (ORCID:0000000224146720)↗
DOE OSTI2021

ECO: the Evidence and Conclusion Ontology, an update for 2022

The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows tracking of annotation provenance, establishment of quality control measures, and evidence-based data mining. ECO is in use by dozens of data repositories and resources with both specific and general areas of focus. ECO is continually being expanded and enhanced in response to user requests as well as our aim to adhere to community best-practices for ontology development. The ECO support team engages in multiple collaborations with other ontologies and annotating groups. Here we report on recent updates to the ECO ontology itself as well as associated resources that are available through this project. ECO project products are freely available for download from the project website (https://evidenceontology.org/) and GitHub (https://github.com/evidenceontology/evidenceontology). ECO is released into the public domain under a CC0 1.0 Universal license.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies

Abstract BioPortal (https://bioportal.bioontology.org) is the world’s most comprehensive repository of biomedical ontologies. It provides infrastructure for finding, sharing, searching, and utilizing biomedical ontologies. Launched in 2005, BioPortal now includes 1549 ontologies (1182 of them public). Its open, freely accessible website enables anyone (i) to browse the ontology library, (ii) to search for terms across ontologies, (iii) to browse mappings between terms, (iv) to see popularity ratings and recommendations on which ontologies are most relevant to their use cases, (v) to annotate text with ontology terms, (vi) to submit an ontology, and (vii) to request ontology changes. The library of ontologies can be accessed programmatically via a REST application programming interface (API). Recent enhancements include a BioPortal knowledge graph that integrates knowledge from multiple ontologies; a unified data model for interoperability with other knowledge sources; ontology popularity ratings and recommendations for relevant ontologies; and the ability to request ontology changes via a simple user interface that automatically converts user change requests to GitHub Pull Requests that specify the edits that will be made to the ontology upon approval.

Vendetti, Jennifer↗
DOE OSTI2022

Deblurring galaxy images with Tikhonov regularization on magnitude domain

Abstract We propose a regularization-based deblurring method that works efficiently for galaxy images. The spatial resolution of a ground-based telescope is generally limited by seeing conditions and is much worse than space-based telescopes. This circumstance has generated considerable research interest in the restoration of spatial resolution. Since image deblurring is a typical inverse problem and often ill-posed, solutions tend to be unstable. To obtain a stable solution, much research has adopted regularization-based methods for image deblurring, but the regularization term is not necessarily appropriate for galaxy images. Although galaxies have an exponential or Sérsic profile, the conventional regularization assumes the image profiles to behave linearly in space. The significant deviation between the assumption and real situations leads to blurring of the images and smoothing out the detailed structures. Clearly, regularization on logarithmic domain, i.e., magnitude domain, should provide a more appropriate assumption, which we explore in this study. We formulate a problem of deblurring galaxy images by an objective function with a Tikhonov regularization term on a magnitude domain. We introduce an iterative algorithm minimizing the objective function with a primal–dual splitting method. We investigate the feasibility of the proposed method using simulation and observation images. In the simulation, we blur galaxy images with a realistic point spread function and add both Gaussian and Poisson noise. For the evaluation with the observed images, we use galaxy images taken by the Subaru HSC-SSP. Both of these evaluations show that our method successfully recovers the spatial resolution of the deblurred images and significantly outperforms the conventional methods. The code is publicly available from the GitHub 〈https://github.com/kzmurata-astro/PSFdeconv_amag〉.

Murata, Kazumi↗
DOE OSTI2024

Measuring stomatal and guard cell metrics for plant physiology and growth using StoManager1

Abstract Automated guard cell detection and measurement are vital for understanding plant physiological performance and ecological functioning in global water and carbon cycles. Most current methods for measuring guard cells and stomata are laborious, time-consuming, prone to bias, and limited in scale. We developed StoManager1, a high-throughput tool utilizing geometrical, mathematical algorithms, and convolutional neural networks to automatically detect, count, and measure over 30 guard cell and stomatal metrics, including guard cell and stomatal area, length, width, stomatal aperture area/guard cell area, orientation, stomatal evenness, divergence, and aggregation index. Combined with leaf functional traits, some of these StoManager1-measured guard cell and stomatal metrics explained 90% and 82% of tree biomass and intrinsic water use efficiency (iWUE) variances in hardwoods, making them substantial factors in leaf physiology and tree growth. StoManager1 demonstrated exceptional precision and recall (mAP@0.5 over 0.96), effectively capturing diverse stomatal properties across over 100 species. StoManager1 facilitates the automation of measuring leaf stomatal and guard cells, enabling broader exploration of stomatal control in plant growth and adaptation to environmental stress and climate change. This has implications for global gross primary productivity (GPP) modeling and estimation, as integrating stomatal metrics can enhance predictions of plant growth and resource usage worldwide. Easily accessible open-source code and standalone Windows executable applications are available on a GitHub repository (https://github.com/JiaxinWang123/StoManager1) and Zenodo (https://doi.org/10.5281/zenodo.7686022).

Wang, Jiaxin (ORCID:0000000348085085)↗
DOE OSTI2024

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement integrating all three data types was made by the recently released GeneMark-ETP. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS, and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under an assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperforms BRAKER1 and BRAKER2. The average transcript-level F1-score is increased by about 20 percentage points on average, whereas the difference is most pronounced for species with large and complex genomes. BRAKER3 also outperforms other existing tools, MAKER2, Funannotate, and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Microscopic constraints for the equation of state and structure of neutron stars: A Bayesian model mixing framework

Bayesian model mixing (BMM) is a statistical technique that can combine constraints from different regions of an input space in a principled way. Here we extend our BMM framework for the equation of state (EOS) of strongly interacting matter from symmetric nuclear matter to asymmetric matter, specifically focusing on zero-temperature, charge-neutral, 𝛽-equilibrated matter. We use Gaussian processes (GPs) to infer constraints on the neutron-star matter EOS at intermediate densities from two different microscopic theories: chiral effective-field theory (𝜒⁢EFT) at baryon densities around nuclear saturation, 𝑛 𝐵 ∼ 𝑛 0 , and perturbative QCD at asymptotically high baryon densities, 𝑛 𝐵 ⩾ 20⁢𝑛 0 . The uncertainties of the 𝜒⁢EFT and pQCD EOSs are obtained using the BUQEYE truncation error model. We demonstrate the flexibility of our framework through the use of two categories of GP kernels: conventional stationary kernels and a nonstationary changepoint kernel. We use the latter to explore potential constraints on the dense matter EOS by including exogenous data representing theory predictions and heavy-ion collision measurements at densities ⩾ 2⁢𝑛 0 . We also use our EOSs to obtain neutron-star mass-radius relations and their uncertainties. Finally, our framework, whose implementation will be available through a GitHub repository, provides a prior distribution for the EOS that can be used in large-scale neutron-star inference frameworks.

Bayesian methods↗
DOE OSTI2021

BeeSwarm: Enabling Parallel Scaling Performance Measurement in Continuous Integration for HPC Applications

Testing is one of the most important steps in software development–it ensures the quality of software. Continuous Integration (CI) is a widely used testing standard that can report software quality to the developer in a timely manner during development progress. Performance, especially scalability, is another key factor for High Performance Computing (HPC) applications. There are many existing profiling and performance tools for HPC applications, but none of these are integrated into CI tools. In this work, we propose BeeSwarm, an HPC container based parallel scaling performance system that can be easily applied to the current CI test environments. BeeSwarm is mainly designed for HPC application developers who need to monitor how their applications can scale on different compute resources. We demonstrate BeeSwarm using a multi-physics HPC application with Travis CI, GitLab CI and GitHub Actions while using ChameleonCloud and Google Compute Engine as the compute backends. Finally, our results show that BeeSwarm can be used for scalability and performance testing of HPC applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

How R Developers explain their Package Choice: A Survey

Background: Contemporary software development relies heavily on reusing already implemented functionality, usually in the form of packages. Aims: We aim to shed light on developers' preferences when selecting packages in R language. Method: To do that, we create and administer a survey to over 1000 developers who have added one of two common dataframe enhancement libraries in R to their projects: data.table or tidyr. We design a questionnaire using the Social Contagion Theory (SCT) following prior work on technology adoption and ensure that key dimensions affecting developer choice are considered. Results: Of the 1085 developers we contacted, 803 completed the survey asking them to prioritize various factors known to affect developer perceptions of package quality and to provide their background. Most developers self-identified as data scientists with two to five years of work experience. We found significant differences between the preferences of developers who chose data.table and tidyr. Surprisingly, package reputation based on easy-to-see measures, such as the number of stars on GitHub, was not an important factor for either group. Conclusions: Our findings demonstrate the inherently social nature of package adoption. They can help design future studies on how different populations of developers make decisions on which software packages to use in their projects. Finally, package developers and maintainers can benefit by better understanding the prime concerns of the users of their packages.

Malviya Thakur, Addi↗
DOE OSTI2020

STEPS: A Portable Numerical Simulation Toolkit for Electrical Power System Dynamic Studies

Numerical simulation is the key technique for large scale power system analysis. Redistribution of global renewable power via international interconnections requires new simulation tools to study the interconnected systems with different nominal frequencies as a whole. In this paper we introduce an open source simulation toolkit for electrical power systems (STEPS) which is hosted at Github. Its kernel is coded in C++ with major functions of power flow and electro-mechanical dynamic simulation. Flexible options are provided and configurable to improve power flow solution and dynamic simulation. Common devices and models are supported in STEPS for AC/DC hybrid system studies. Studies of interconnected systems with different nominal frequencies is supported in STEPS for research of international interconnection. Application program interfaces are provided and wrapped with Python to enable high-level interfaces for general applications. STEPS is thread safe and parallel computation is supported in both kernel and script levels to accelerate simulation. It is portable and works on Windows and GNU/Linux platforms. Cases from small to large scale systems are thoroughly tested to validate the toolkit with commercial packages as benchmarks.

42 ENGINEERING↗
DOE OSTI2021

Generative Patch Priors for Practical Compressive Image Recovery

In this work, we propose the generative patch prior (GPP) that defines a generative prior for compressive image recovery, based on patch-manifold models. Unlike learned, image-level priors that are restricted to the range space of a pre-trained generator, GPP can recover a wide variety of natural images using a pre-trained patch generator. Additionally, GPP retains the benefits of generative priors like high reconstruction quality at extremely low sensing rates, while also being much more generally applicable. We show that GPP outperforms several unsupervised and supervised techniques on three different sensing models – linear compressive sensing with known, and unknown calibration settings, and the non-linear phase retrieval problem. Finally, we propose an alternating optimization strategy using GPP for joint calibration-and-reconstruction which performs favorably against several baselines on a real world, uncalibrated compressive sensing dataset. The code and models for GPP are available on github.

compressed sensing↗
DOE OSTI2025

Automating Traffic Microsimulation from SYNCHRO UTDF to SUMO

Modern transportation research relies on seamlessly integrating traffic signal data with robust network representation and simulation tools. This study presents utdf2gmns, an open-source Python tool that automates conversion of the Universal Traffic Data Format, including network representation, signalized intersections, and turning volumes into the General Modeling Network Specification (GMNS) Standard. The resulting GMNS-compliant network can be converted for microsimulation in SUMO. By automatically extracting intersection control parameters and aligning them with GMNS conventions, utdf2gmns minimizes manual preprocessing and data loss. utdf2gmns also integrates with the Sigma-X engine to extract and visualize key traffic control metrics, such as phasing diagrams, turning volumes, volume-tocapacity ratios, and control delays. This streamlined workflow enables efficient scenario testing, accurate model building, and consistent data management. Validated through case studies, utdf2gmns reliably models complex urban corridors, promoting reproducibility and standardization. Documentation is available on GitHub and PyPI, supporting easy integration and community engagement.

Luo, Roy [ORNL] (ORCID:0009000312909983)↗
DOE OSTI2022

The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fire in the Amazon region

1. LiDAR data are being increasingly used to provide a detailed characterization of the vertical profile of forests. This characterization enables the generation of new insights on the influence of environmental drivers and anthropogenic disturbances on forest structure as well as on how forest structure influences important ecosystem functions and services. Unfortunately, extracting information from LiDAR data in a way that enables the spatial visualization of forest structure, as well as its temporal changes, is challenging due to the high dimensionality of these data. 2. In this study, we show how the Latent Dirichlet Allocation model applied to LiDAR data (LidarLDA) can be used to identify forest structural types and how the relative abundance of these forest types changes throughout the landscape. The code to fit this model is made available through the open-source r package LidarLDA in github. We illustrate the use of LidarLDA both with simulated data and data from a large-scale fire experiment in the Brazilian Amazon region. 3. Using simulated data, we demonstrate that LidarLDA accurately identifies the number of forest types as well as their spatial distribution and absorptance probabilities. For the empirical data, we found that LidarLDA detects both landscape-level patterns in forest structure as well as the strong interacting effect of fire and forest fragmentation on forest structure based on the experimental fire plots. More specifically, LidarLDA reveals that proximity to forest edge exacerbates the impact of fires, and that burned forests remain structurally different from unburned areas for at least 7 years, even when burned only once. Importantly, LidarLDA generates insights on the 3D structure of forest that cannot be obtained using more standard approaches that just focus on top-of-the-canopy information (e.g. canopy height models based on LiDAR data). 4. By enabling the mapping of forest structure and its temporal changes, we believe that LidarLDA will be of broad utility to the ecological research community.

54 ENVIRONMENTAL SCIENCES↗