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DOE OSTI2022

Toward designing effective exascale scientific computing workflows: experiences and best practices

Many fields within scientific computing have embraced advances in big-data analysis and machine learning, which often requires the deployment of large, distributed and complicated workflows that may combine training neural networks, performing simulations, running inference, and performing database queries and data analysis in asynchronous, parallel and pipelined execution frameworks. Such a shift has brought into focus the need for scalable, efficient workflow management solutions with reproducibility, error and provenance handling, traceability, and checkpoint-restart capabilities, among other needs. Here, we discuss challenges and best-practices for deploying exascale-generation computational science workflows on resources at the Oak Ridge Leadership Computing Facility (OLCF). We present our experiences with large-scale deployment of distributed workflows on the Summit supercomputer, including for bioinformatics and computational biophysics, materials science, and deep learning model optimization. We also present problems and solutions created by working within a Python-centric software base on traditional HPC systems, and discuss steps that will be required before the convergence of HPC, AI, and data science can be fully realized. Our results point to a wealth of exciting new possibilities for harnessing this convergence to tackle new scientific challenges.

Coletti, Mark↗

DOE OSTI2023

A Joint Roman Space Telescope and Rubin Observatory Synthetic Wide-Field Imaging Survey

We present and validate 20 deg(2) of overlapping synthetic imaging surveys representing the full depth of the Nancy Grace Roman Space Telescope High-Latitude Imaging Survey (HLIS) and 5 yr of observations of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). The two synthetic surveys are summarized, with reference to the existing 300 deg(2) of LSST simulated imaging produced as part of Dark Energy Science Collaboration (DESC) Data Challenge 2 (DC2). Both synthetic surveys observe the same simulated DESC DC2 universe. For the synthetic Roman survey, we simulate for the first time fully chromatic images along with the detailed physics of the Sensor Chip Assemblies derived from lab measurements using the flight detectors. The simulated imaging and resulting pixel-level measurements of photometric properties of objects span a wavelength range of similar to 0.3-2.0 mu m. We also describe updates to the Roman simulation pipeline, changes in how astrophysical objects are simulated relative to the original DC2 simulations, and the resulting simulated Roman data products. We use these simulations to explore the relative fraction of unrecognized blends in LSST images, finding that 20-30 per cent of objects identified in LSST images with i-band magnitudes brighter than 25 can be identified as multiple objects in Roman images. These simulations provide a unique testing ground for the development and validation of joint pixel-level analysis techniques of ground- and space-based imaging data sets in the second half of the 2020s - in particular the case of joint Roman-LSST analyses.

gravitational lensing↗

NASA NTRSDate not supplied

Beyond Fair: Engagement, Data Usability, and Open Community Productivity through the NASA Open Science Data Repository

The FAIR principle (findable, accessible, interoperable, and reusable) governs the storage and sharing of NASA space biology and health data[1]. These guiding principles maximize reuse of data and the reproducibility of scientific findings. The NASA Open Science Data Repository (OSDR; an expansion of NASA GeneLab) was built on the FAIR principles and houses over 500 studies and close to 1000 datasets from decades of space life sciences experiments. OSDR embodies the FAIR principles through data governance that includes mediated, embargoed, and fully open access data. The FAIR data governance principles were recently proposed to be expanded to encompass a FAIREST framework for assessing research data repositories (FAIR + Engagement, Social connections, and Trust)[2]. FAIREST emphasizes the importance of data repositories engaging with the scientific community and gaining the trust of researchers regarding data quality. Trust also refers to the TRUST principles developed for assessment of digital repositories: Transparency, Responsibility, User Focus, Sustainability, Technology[3]. We present the “Open Science for Life in Space” Analysis Working Groups (AWGs) as evidence regarding the power of engagement, social connections, and trust which has enhanced OSDR’s capabilities and productivity. AWG members engage in two main activities. One, members provide feedback on OSDR scientific standards for data ingestion, curation, and reuse (study, subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability). Two, AWG members collaborate to mine-reuse OSDR data to conduct scientific analysis. With nearly 800 active members, the AWGs have resulted in 32 publications re-using OSDR data and contributed many papers in two major special issues in Cell (2020) and Nature (2024). AWGs also serve as networking groups, facilitate social connections between researchers at all levels of experience, and also have a social online ‘Forum’ used to keep members informed on projects and opportunities. This community-centric, productive, and trustworthy data culture has resulted in a broader effect with international space agencies, academics, and the commercial space sector wanting to submit their data to OSDR. Ten studies of Inspiration 4 data were recently publicly released by OSDR, as were some JAXA human data. Coming up soon in OSDR are data submissions from the European Space Agency, Virgin Galactic PIs, and SpaceX Polaris Dawn. A major benefit of OSDR is the array of standardized and uniformly formatted data (which was developed through AWG member consensus), from which visualization tools, analysis tools, and machine learning models can be built or trained. This talk will cover the Multi-Study Visualization Tool, the Environmental Data Application, RadLab, and a UCSF-NSF funded knowledge graph biomedical health discovery tool ‘SPOKE’ currently being integrated with OSDR. OSDR also provides training programs in bioinformatics and machine learning to improve the scientific community’s awareness of data availability and to boost their ability to perform data analysis. The increasing engagement of the scientific community and the public with technologies powered by artificial intelligence (AI) heightens the need for data analysis to be transparent. The AI for Life in Space initiative leverages the data products provided in OSDR to train AI models, with an emphasis on explainable and trustworthy AI, which would not be possible without FAIR data and metadata. Overall, here we will demonstrate the importance for NASA life sciences data repositories to adhere to the FAIREST framework, by providing examples and success stories from different aspects of OSDR.

data↗

NASA NTRSDate not supplied

The NASA Open Science Data Repository: Biomedical Fair Data, Analysis Tools, User Communities, Publications, and Discoveries for Deep Space Missions

Increased biomedical risks and challenges associated with deep space missions require new knowledge discovery, new health countermeasures, and development of novel ecosystems, life support, crop production, and biomedical support capabilities. To meet NASA’s Moon to Mars strategic program goals for Human and Biological Sciences, findable, accessible, interoperable, reusable (FAIR), and maximally open-access data is going to be required to enable humanity to thrive in deep space. Indeed, this cornerstone perspective on FAIR and maximally open access data was also recommended in the recent 2023-2032 Decadal Survey from the National Academies of Sciences, Engineering, and Medicine. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database, and meets various scientific, technical, and operational spaceflight needs. It offers public users and submitters the ability to upload, download, search, share, analyze, and visualize data across ‘omics, physiological, phenotypic, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive, and the NASA Biological Institutional Scientific Collection. OSDR has >455 studies with datasets from model organisms and non-NASA human astronauts. There are ~12 datasets from the Inspiration 4 (I4) mission, spanning metagenomics, comprehensive metabolic panels, clonal hematopoiesis, spatial transcriptomics, proteomics, and cytokine panels. In the interest of data privacy, two I4 datasets have raw FASTQ and FASTA files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) which was developed based on industry norms. OSDR also recently began a collaboration with the European Space Agency (ESA) to scientifically curate and make available >200 terabytes of human and model organism space-relevant data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics assay data types, and ~50 physiological-phenotypic-imaging assay data types, spanning ultrasonography, micro-computed tomography, histology, morphometric photography, rebound tonometry, gait analysis, optical coherence tomography, novel object recognition, flow cytometry, and immunohistochemistry. A suite of analysis tools are available for OSDR users including: 1) an Environmental Data Application to compare radiation, CO2, relative humidity, temperature, and other telemetry across missions and subjects, 2) the RadLab database, a collaboration between NASA, ESA, the German and Italian Space Agencies, and the Bulgarian Academy of Sciences, which compiles radiation measurements relevant to human spaceflight and provides tools for accessing and manipulating the data, and 3) a Multi-study visualization tool which enables users to look across and combine GeneLab’s omics datasets across different experiments and missions. There are ~600 volunteer OSDR Analysis Working Group (AWG) members who: 1) provide feedback on scientific standards for reuse (subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability), and 2) collaborate to mine-reuse OSDR data conducting scientific analysis. OSDR has enabled 60 publications as of September 2023, many directly from AWG collaborations most notably the Cell Press package in 2020. Lastly, there are at least 15 articles which mine OSDR data part of a package of ~50 articles across Nature Portfolio with research stemming from I4, the Japan Aerospace Exploration Agency, NASA Space Biology, and the NASA Human Research Program.

space biology↗

NASA NTRSDate not supplied

NASA Open Science Data Repository: Biomedical FAIR Data, Analysis Tools, User Communities, and Discoveries for Deep Space Missions

open access↗

DOE OSTI2021

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein–ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient’s genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes

Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. In conclusion, we demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.

60 APPLIED LIFE SCIENCES↗

NASA NTRSDate not supplied

Diversity and Inclusion in Spacecraft Science Teams: What Do We Know and What Can We Do About It?

Introduction: Not only does the planetary science community lack diversity [1-3], the subset of the community that participates on spacecraft science team is even less diverse than the community as a whole [1, 4]. Results of 2020 Workforce Survey: Previous studies of the diversity of members of spacecraft science teams made incorrect assumptions about the nature of the data before collecting the data. Those analyses assumed a binary gender and ignored the existence of planetary scientists who are neither men nor women [4-6]. We present here results where demographic data was collected without assumptions; each individual surveyed supplied their own answers to demographic questions. The April 2020 survey of Planetary Scientists, which was conducted by the Statistical Research Center of the American Institute of Physics (AIP) and funded by the American Astronomical Society (AAS)’s Division of Planetary Science (DPS) asked participants their gender with 4 possible responses: Woman, Man, Another identify (please specify if you wish), and Prefer not to answer. 32% of respondents chose Woman, 67% chose Man and 1% chose Another gender identity [1]. The survey also asked demographic questions on race, ethnicity, LGBTQ+ identity, and disability. For a full list of questions, see https://dps.aas.org/sites/dps.aas.org/files/reports/2020/survey2020_questionnaire.pdf. In addition to demographic questions, the 2020 Workforce survey asked how many times respondents had been involved in Mission proposals as a Principal Investigator (PI) and, separately, as a Co-Investigator (CoI) [1]. Answers to questions about mission involvement were correlated with answers to demographic questions and the results show that members of historically underrepresented groups (non-white scientists, women, members of the LGBTQ+ community, and disabled scientists) were less likely to be involved in spacecraft mission proposals than were members of historically overrepresented groups [1]. The figures below show the correlated responses for four different axes of underrepresentation [1]. Note that while the figure on gender shows only Women and Men (due to the small percentage of folks answering “Another gender”), non-binary respondents are included in the LGBTQ+ community figure. Conclusion: Being part of a spacecraft science team is a goal for many planetary scientists. With it comes brand new data, more stable funding, and a sense of awe and exploration. It can lead to a cascade of opportunities from conference and public presentations, to membership in subsequent mission teams, and prestige in the community [4]. As a result, participation in spacecraft teams can be used a measure of success within the field. From the survey results, we see that members of historically excluded groups, even after they have overcome barriers to participating in the field, are still experiencing barriers to success within the field itself. Why?: The diminishing percentage of members of underrepresented groups as a career progresses has been referred to as a “leaky pipeline”. However, this fails to adequately capture the experiences of the members of these underrepresented groups as it implies a passive process. In order to capture the active processes (bias, discrimination, harassment, and other exclusionary behaviors) that contribute to low retention in the workforce, the term “Hostile Obstacle Course” is more useful [7,8]. It is these processes that need to be addressed in order to retain valued members of our community. Moving Forward: In order to broaden participation in planetary science, particularly mission science teams, we need to address conditions that create hostile workplace climates. What can mission teams and other groups do to address these conditions? First, each group/team needs to evaluate their own members to determine what specific barriers exist in their own interactions. One tool to accomplish this would be an anonymous survey designed to understand how team members feel about working within the group. Working with professionals who know how to create and analyze such surveys (often called “climate surveys” when applied to University students, for example) would ensure that the survey meets its goals and does not make assumptions that counter the meaningfulness of the results. Such professionals in EDIA (Equity, Diversity, Inclusion, and Accessibility) and workplace culture can make suggestions for policy changes that would eliminate hostile workplace conditions. Policy changes that are often suggested include instituting professional EDIA training for the team and/or for team leadership, instituting and following a code of conduct [9], including more interactive group activities in group meetings, etc. Training and information on EDIA is available for all members of the planetary science community. The first place to look would be in your University or Institution’s EDIA or human resources offices. Bystander Intervention is often offered as part of other meetings [10]. A newer offering is a Workshop on EDIA for Leaders in Planetary Science led by Julie Rathbun (first author of this abstract) and JA Grier (https://edialps.psi.edu/). This 3-day workshop gives participants the tools they need to enact positive change in their personal and professional spheres. The first workshop was help in November 2022 and another workshop will take place in the late spring 2023 with exact dates to be announced soon.

J. A. Rathbun↗

DOE OSTI2023

Design, execution, and interpretation of plant RNA-seq analyses

Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences. We discuss the importance of experimental design in RNA-seq, including considerations for sampling and replication, to avoid pitfalls and wasted resources. Approaches for processing RNA-seq data include quality control and counting features, and we describe common approaches and variations. Though differential gene expression analysis is the most common analysis of RNA-seq data, we review multiple methods for assessing gene expression, including detecting allele-specific gene expression and building co-expression networks. With the production of more RNA-seq data, strategies for integrating these data into genetic mapping pipelines is of increased interest. Finally, special considerations for RNA-seq analysis and interpretation in plants are needed, due to the high genome complexity common across plants. By incorporating informed decisions throughout an RNA-seq experiment, we can increase the knowledge gained.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

LLMs for Mfg.—On the State of Large Language Models and Applications to Manufacturing

Additive Manufacturing (AM), referred to as 3D printing, has emerged as a key pillar of Industry 4.0 enabling layer-by-layer fabrication of intricate geometries from CAD models. In parallel, Large Language Models (LLMs), deep learning models for natural language generation trained on vast text corpora, have demonstrated unprecedented capabilities in understanding and generating human-like text. The convergence of these trends opens new opportunities at the intersection of AM and AI/ML, where LLMs can assist engineers and researchers in design, manufacture planning, and knowledge discovery. Recent academic work has begun to explore LLM applications in AM and adjacent fields, such as material science, mechanical engineering, and design for additive manufacturing. This exploration ranges from intelligent process planning to domain-specific knowledge retrieval. This survey provides a comprehensive review of current developments, focusing on peer-reviewed literature contributions that apply, adapt, and advance LLMs in general and domain-specific domains. We analyze state-of-the-art (SOTA) techniques, such as fine-tuning foundational models for specific domains, retrieval-augmented generation (RAG) pipelines, knowledge graph integration, and delve into the architectures and evaluation methods employed. The goal of this survey is to inform researchers and practitioners of the current capabilities and limitations of LLMs in general and in domain-specific applications, and to outline how these models are being tailored to meet the requirements of these applications.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Atacama Cosmology Telescope: High-resolution component-separated maps across one third of the sky

Observations of the millimeter sky contain valuable information on a number of signals, including the blackbody cosmic microwave background (CMB), Galactic emissions, and the Compton-y distortion due to the thermal Sunyaev-Zel’dovich (tSZ) effect. Extracting new insight into cosmological and astrophysical questions often requires combining multiwavelength observations to spectrally isolate one component. Here, in this work, we present a new arc-minute-resolution Compton-y map, which traces out the line-of-sight-integrated electron pressure, as well as maps of the CMB in intensity and E-mode polarization, across a third of the sky (around 13,000 deg 2 ). We produce these through a joint analysis of data from the Atacama Cosmology Telescope (ACT) data release 4 and 6 at frequencies of roughly 93, 148, and 225 GHz, together with data from the Planck satellite at frequencies between 30 and 545 GHz. We present detailed verification of an internal linear combination pipeline implemented in a needlet frame that allows us to efficiently suppress Galactic contamination and account for spatial variations in the ACT instrument noise. These maps provide a significant advance, in noise levels and resolution, over the existing Planck component-separated maps and will enable a host of science goals including studies of cluster and galaxy astrophysics, inferences of the cosmic velocity field, primordial non-Gaussianity searches, and gravitational lensing reconstruction of the CMB.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2000

Air, Ocean and Climate Monitoring Enhancing Undergraduate Training in the Physical, Environmental and Computer Sciences

Faculty in the Department of Physical, Environmental and Computer Sciences strongly believe in the concept that undergraduate research and research-related activities must be integrated into the fabric of our undergraduate Science and Technology curricula. High level skills, such as problem solving, reasoning, collaboration and the ability to engage in research, are learned for advanced study in graduate school or for competing for well paying positions in the scientific community. One goal of our academic programs is to have a pipeline of research activities from high school to four year college, to graduate school, based on the GISS Institute on Climate and Planets model.

Hope, W. W.↗

DOE OSTI2024

Using AI for Wave-front Estimation with the Rubin Observatory Active Optics System

Abstract The Vera C. Rubin Observatory will, over a period of 10 yr, repeatedly survey the southern sky. To ensure that images generated by Rubin meet the quality requirements for precision science, the observatory will use an active-optics system (AOS) to correct for alignment and mirror surface perturbations introduced by gravity and temperature gradients in the optical system. To accomplish this, Rubin will use out-of-focus images from sensors located at the edge of the focal plane to learn and correct for perturbations to the wave front. We have designed and integrated a deep-learning (DL) model for wave-front estimation into the AOS pipeline. In this paper, we compare the performance of this DL approach to Rubin’s baseline algorithm when applied to images from two different simulations of the Rubin optical system. We show the DL approach is faster and more accurate, achieving the atmospheric error floor both for high-quality images and low-quality images with heavy blending and vignetting. Compared to the baseline algorithm, the DL model is 40× faster, the median error 2× better under ideal conditions, 5× better in the presence of vignetting by the Rubin camera, and 14× better in the presence of blending in crowded fields. In addition, the DL model surpasses the required optical quality in simulations of the AOS closed loop. This system promises to increase the survey area useful for precision science by up to 8%. We discuss how this system might be deployed when commissioning and operating Rubin.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2016

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We believe this is an important step towards seamless process deployment in heterogeneous environments that will enhance community access to NASA data and tools in a scalable way, promote software reuse, and improve reproducibility of scientific results.

earth exchange↗

DOE OSTI2023

Comparison of open‐source three‐dimensional reconstruction pipelines for maize‐root phenotyping

Abstract Understanding three‐dimensional (3D) root traits is essential to improve water uptake, increase nitrogen capture, and raise carbon sequestration from the atmosphere. However, quantifying 3D root traits by reconstructing 3D root models for deeper field‐grown roots remains a challenge due to the unknown tradeoff between 3D root‐model quality and 3D root‐trait accuracy. Therefore, we performed two computational experiments. We first compared the 3D model quality generated by five state‐of‐the‐art open‐source 3D model reconstruction pipelines on 12 contrasting genotypes of field‐grown maize roots. These pipelines included COLMAP, COLMAP+PMVS (Patch‐based Multi‐View Stereo), VisualSFM, Meshroom, and OpenMVG+MVE (Multi‐View Environment). The COLMAP pipeline achieved the best performance regarding 3D model quality versus computational time and image number needed. In the second test, we compared the accuracy of 3D root‐trait measurement generated by the Digital Imaging of Root Traits 3D pipeline (DIRT/3D) using COLMAP‐based 3D reconstruction with our current DIRT/3D pipeline that uses a VisualSFM‐based 3D reconstruction on the same dataset of 12 genotypes, with 5–10 replicates per genotype. The results revealed that (1) the average number of images needed to build a denser 3D model was reduced from 3000 to 3600 (DIRT/3D [VisualSFM‐based 3D reconstruction]) to around 360 for computational test 1, and around 600 for computational test 2 (DIRT/3D [COLMAP‐based 3D reconstruction]); (2) denser 3D models helped improve the accuracy of the 3D root‐trait measurement; (3) reducing the number of images can help resolve data storage problems. The updated DIRT/3D (COLMAP‐based 3D reconstruction) pipeline enables quicker image collection without compromising the accuracy of 3D root‐trait measurements.

09 BIOMASS FUELS↗

DOE OSTI2024

ULTRA-effective labeling of tandem repeats in genomic sequence

In the age of long read sequencing, genomics researchers now have access to accurate repetitive DNA sequence (including satellites) that, due to the limitations of short read-sequencing, could previously be observed only as unmappable fragments. Tools that annotate repetitive sequence are now more important than ever, so that we can better understand newly uncovered repetitive sequences, and also so that we can mitigate errors in bioinformatic software caused by those repetitive sequences. To that end, we introduce the 1.0 release of our tool for identifying and annotating locally repetitive sequence, ULTRA Locates Tandemly Repetitive Areas (ULTRA). ULTRA is fast enough to use as part of an efficient annotation pipeline, produces state-of-the-art reliable coverage of repetitive regions containing many mutations, and provides interpretable statistics and labels for repetitive regions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Accelerating polyketide synthase engineering for high TRY production of biofuels and bioproducts (CRADA Final Report)

Polyketide synthase (PKS) enzymes have a modular, deterministic logic that holds the potential to act as a flexible chemical factory for the biological production of a huge diversity of valuable small molecule compounds. However, engineering a custom PKS to produce a specific desired product currently requires years of trial and error, for reasons that remain poorly understood. In this project, we have developed a rapid, high throughput, Design-Build-Test-Learn (DBTL) cycle for polyketide synthases (PKSs) and demonstrate its utility for production of materials precursors. The objectives are 1) to develop a rapid, high-throughput (HT) DBTL cycle for PKSs that will enable production of a large number of unnatural, organic molecules on demand at high titer, rate, and yield (TRY); 2) to demonstrate the utility of the PKS DBTL cycle to produce three molecules: one commodity chemical (caprolactam or valerolactam) and two novel materials precursors (caprolactam or valerolactam derivatives); and 3) to demonstrate the utility of the PKS DBTL cycle to increase the TRY of one molecule (caprolactam or valerolactam). In this project, we have successfully demonstrated our high throughput PKS DBTL pipeline, and have biologically produced valerolactam and several other novel nylon monomers.

09 BIOMASS FUELS↗