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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.

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NASA NTRS2023

Evolutionary Flexibility and Rigidity in the Bacterial Methylerythritol Phosphate (Mep) Pathway

Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron–sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron–sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.

Bailey Marshall↗
NASA NTRSDate not supplied

Spaceflight Biospecimen and Data Sharing in Support of Science Discovery and Exploration

For decades, NASA and international partners have conducted biological experiments in space to understand effects of spaceflight and address potential hazards. To enable spaceflight back to the Moon, and then to Mars and beyond, it is imperative to further understand basic science and health risks associated with spaceflight, along with developing countermeasures. The sending of experiments and organisms into space is a costly endeavor. To maximize scientific return, sharing with the scientific community both space-flown biospecimens and data from completed experiments is essential. New fundamental, applied, and bioinformatic science insights can be gained from specimen and data sharing efforts. Data reuse enables spaceflight health risk modeling, analyzing adverse outcomes across spaceflight hazards, and deep space autonomous support for the flight medical officer. Space-flown biospecimens not required by mission Principal Investigators are regularly archived and made available for scientific request. The largest biorepository of these samples are found within NASA’s Institutional Scientific Collection at Ames Research Center (ISC-ARC), which stores over 32,000 specimens mostly from Shuttle and International Space Station (ISS) missions, but also some ground-based analog samples. The Ames Life Sciences Data Archive manages the ISC-ARC. Tissues are predominantly from mice and rats, though samples are also available from bacteria and quail. Only a handful of other similar collections exist worldwide. Rodent biospecimens exposed to simulated space radiation at Brookhaven National Laboratory are archived under the purview of NASA HRP Space Radiation Element. Microbial collection and analyses from 20 years of routine environmental monitoring of air, surfaces, and water systems of the ISS were performed to ensure a safe environment for astronauts. Samples from the ISC-ARC, space radiation and microbial collections are searchable and requestable through the NASA Life Sciences Data Archive (LSDA). Decades of planetary protection microbial isolates derived from spacecraft bioburden are archived in JPL’s microbial collection. Rodent biospecimens from spaceflight investigations conducted by the Japan Aerospace Exploration Agency (JAXA) are archived and available at the JAXA Biorepository at Tsukuba Space Center. The Russian Institute of Biomedical Problems also has a collection of animal, microbial, cellular, and fungi available for research from ground analog experiments. Several data repositories exist for scientists to utilize. The LSDA is the primary NASA source of life sciences research data and information. It contains decades of spaceflight and ground-analog research involving human, microbial, cellular, plant, and animal subjects. Data is collected from NASA-funded investigations through the Human Research Program and the Space Biology Program. The NASA Lifetime Surveillance of Astronaut Health collects and grants access to clinical and occupational health monitoring data from astronauts, with a list and description of data collected available for request through the LSDA. NASA GeneLab at ARC collects genomic, transcriptomic, proteomic, and metabolomic data from any species. It is a repository and platform for collaborative open-science bioinformatic approaches. JAXA is establishing an ‘omics-based repository in collaboration with the Tohoku Medical Megabank (ToMMo), called the JAXA-ToMMo Integrated Biobank for Space Life Science. Overall, the sharing of these biospecimen and data resources can assist researchers worldwide in understanding spaceflight effects on biology, along with enabling next generation data science applications for space exploration platforms. Websites: https://lsda.jsc.nasa.gov/ ; https://www.nasa.gov/ames/research/space-biosciences/isc-bsp ; https://www.nasa.gov/ames/research/space-biosciences/alsda

Ryan T. Scott↗
NASA NTRSDate not supplied

Elevating the Quality of Space Omics Sequencing Data: Innovations and Methodologies from NASA GeneLab Sample Processing Laboratory

NASA’s GeneLab, part of the NASA Open Science Data Repository, is a space-related database that hosts a diverse range of transcriptomics, proteomics, epigenomics and genomics data. The NASA GeneLab Sample Processing Laboratory (SPL) generates omics data from biological experiments conducted aboard the International Space Station, Space Shuttle and space related ground experiments, this omics data then hosted on the GeneLab repository. Samples generated such experiments pose numerous technical challenges such as small experimental sample size, variance in dissection times, limited tissue preservation methods, prolonged storage time, and more. GeneLab SPL team had developed specialized expertise in nucleic acid extraction, library preparation and sequencing of such biological samples via extensive training and years of experience. In order to ensure data accuracy and consistency across experiments, SPL has developed standardized protocols for each species and tissue type. These protocols in conjunction with quality control metrics and data standards are crucial in generating of high-quality data. SPL protocols and standards have been developed in collaboration with the scientific community and had been made publicly available on the GeneLab portal, guaranteeing comparability of datasets across spaceflight experiments. To ensure reliability of data generation, SPL leverages cutting-edge innovations in laboratory automation for sample processing. By leveraging these state-of-the-art platforms, SPL achieves high levels of data reproducibility while significantly minimizing sources of bias and variability, especially across experiments with large numbers of samples. Over the past few years, the space biology investigator community has accessed SPL-generated data from the Open Science Data Repository for a myriad of data re-analysis and re-use studies. We observe a trend that in-house SPL-generated data consistently outperforms outsourced sequencing data in terms of technical standards, quality control metrics, timeliness of data delivery, and sequencing and reagent efficiency. Superior data generation has and will continue to enable discoveries in disease, diagnostic tools, and the biological effects of long duration spaceflight.

GeneLab↗
NASA NTRSDate not supplied

Elevating the Quality of Space Omics Sequencing Data: Innovations and Methodologies from NASA GeneLab Sample Processing Laboratory

NASA’s GeneLab, part of the NASA Open Science Data Repository, is a space-related database that hosts a diverse range of transcriptomics, proteomics, epigenomics and genomics data. The NASA GeneLab Sample Processing Laboratory (SPL) generates omics data from biological experiments conducted aboard the International Space Station, Space Shuttle and space related ground experiments, this omics data then hosted on the GeneLab repository. Samples generated such experiments pose numerous technical challenges such as small experimental sample size, variance in dissection times, limited tissue preservation methods, prolonged storage time, and more. GeneLab SPL team had developed specialized expertise in nucleic acid extraction, library preparation and sequencing of such biological samples via extensive training and years of experience. In order to ensure data accuracy and consistency across experiments, SPL has developed standardized protocols for each species and tissue type. These protocols in conjunction with quality control metrics and data standards are crucial in generating of high-quality data. SPL protocols and standards have been developed in collaboration with the scientific community and had been made publicly available on the GeneLab portal, guaranteeing comparability of datasets across spaceflight experiments. To ensure reliability of data generation, SPL leverages cutting-edge innovations in laboratory automation for sample processing. By leveraging these state-of-the-art platforms, SPL achieves high levels of data reproducibility while significantly minimizing sources of bias and variability, especially across experiments with large numbers of samples. Over the past few years, the space biology investigator community has accessed SPL-generated data from the Open Science Data Repository for a myriad of data re-analysis and re-use studies. We observe a trend that in-house SPL-generated data consistently outperforms outsourced sequencing data in terms of technical standards, quality control metrics, timeliness of data delivery, and sequencing and reagent efficiency. Superior data generation has and will continue to enable discoveries in disease, diagnostic tools, and the biological effects of long duration spaceflight.

GeneLab↗
NASA NTRSDate not supplied

GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics dataand collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretationof the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLabhave begunand will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Samrawit Getachew Gebre↗
NASA NTRSDate not supplied

GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data, and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Samrawit Gebre↗
NASA NTRSDate not supplied

WEBINAR, May 6: New Discoveries Using GeneLab

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetry data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Sylvain V. Costes↗
NASA NTRS2019

Nasa GeneLab Computomics Reveal Horizontal Gene Transfer on International Space Station Environmental Metagenomes

Prokaryotic lifeforms can be observed to demonstrate many keen adaptive advantages, perhaps facilitated by a nature simplistic relative to divergent domains of life. In particular, decompartmentalized gene expression facilitates adaptation by allowing free exchange of genetic material, albeit at the cost of increased susceptibility to genetic damage. Thus, these lifeforms must compensate by embracing diverse investment strategies in an attempt to “brute force” the evolvability equation through precipitous genesis, lean metabolic efficiency, and sheer population. This prokaryotic archetype also enables symbiotic relationships with secondary mobile genetic elements known as plasmids, which have been shown to drive evolution on rapid temporal scales through processes such as conjugation and transformation. This study attempts to decipher whether these mechanisms of horizontal gene transfer (HGT) are major factors in determining prokaryote fitness within a unique isolated environment, the International Space Station (ISS). The ISS Microbial Tracking (MT) project has generated a wealth of data concerning the successive reigns of microbial genera that appear to thrive amidst harsh conditions for life. Despite relatively higher doses of ionizing radiation as compared to Earth, complications associated with microgravity, and the anti-microbial mélange deployed, microbial life still persists in this environment. The NASA GeneLab serves as a data repository and analysis platform to enable researchers to access space flight factor related data. With the use of GeneLab’s modern computational suites (computomics), phylogenetic and functional genomic investigations of HGT events were conducted on the data generated from the MT-1 project. The putative data concerning the plasmid population (plasmidome) of the ISS was algorithmically derived and compared to those of habitats with similar environmental dynamics- such as living quarters and hospitals- to investigate whether these HGT elements may play crucial role(s) in shaping the microbiome of this closed habitat that serves as the only inhabited structure in space.

Bense, Nicholas↗
NASA NTRSDate not supplied

NASA GeneLab: Open Science for Life in Space

NASA’s GeneLab helps scientists understand how the fundamental building blocks of life – DNA, RNA, proteins, and metabolites – change from exposure to the space environment including microgravity and cosmic radiation exposure. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data (collectively known as omics data) alongside essential metadata describing each spaceflight and space-relevant experiment. The open-access GeneLab repository currently consists of over 300 omics datasets generated by biological experiments, involving various model organisms, that are relevant to spaceflight. In order to maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab has started processing and analyzing these datasets to generate differential gene expression data and identify biological and physiological pathways that are dysregulated as a result of spaceflight. To aide GeneLab’s efforts to harmonize and democratize space-relevant omics data, over 130 scientists have joined one of four GeneLab Analysis Working Groups (Animal AWG, Plant AWG, Microbe AWG, Multi-Omics AWG) and together helped develop and adopted standard data analysis workflows for all data types available in GeneLab. Currently, the GeneLab Data System includes a data repository with federated search capability, an online controlled-access toolshed powered by "Galaxy" for users to process data with vetted standard workflows, a workspace for data sharing, a data submission portal, and the ability to browse and visualize transcriptomics processed data. The user interface was designed to be accessible to a broad variety of users, including high school and college students who can use it to learn about omics data analysis and space biology. The visualization portal enhances GeneLab’s ability to democratize omics data by removing the need for bioinformatics expertise to interpret transcriptomics data hosted on GeneLab. This presentation will provide an over-view of NASA’s GeneLab including how to navigate the GeneLab Data System and will conclude by providing resources for opportunities to work with GeneLab and NASA at large.

Amanda M Saravia-Butler↗
NASA NTRS2016

GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

The GeneLab project is a science initiative to maximize the scientific return of omics data collected from spaceflight and from ground simulations of microgravity and radiation experiments, supported by a data system for a public bioinformatics repository and collaborative analysis tools for these data. The mission of GeneLab is to maximize the utilization of the valuable biological research resources aboard the ISS by collecting genomic, transcriptomic, proteomic and metabolomic (so-called omics) data to enable the exploration of the molecular network responses of terrestrial biology to space environments using a systems biology approach. All GeneLab data are made available to a worldwide network of researchers through its open-access data system. GeneLab is currently being developed by NASA to support Open Science biomedical research in order to enable the human exploration of space and improve life on earth. Open access to Phase 1 of the GeneLab Data Systems (GLDS) was implemented in April 2015. Download volumes have grown steadily, mirroring the growth in curated space biology research data sets (61 as of June 2016), now exceeding 10 TB/month, with over 10,000 file downloads since the start of Phase 1. For the period April 2015 to May 2016, most frequently downloaded were data from studies of Mus musculus (39) followed closely by Arabidopsis thaliana (30), with the remaining downloads roughly equally split across 12 other organisms (each 10 of total downloads). GLDS Phase 2 is focusing on interoperability, supporting data federation, including integrated search capabilities, of GLDS-housed data sets with external data sources, such as gene expression data from NIHNCBIs Gene Expression Omnibus (GEO), proteomic data from EBIs PRIDE system, and metagenomic data from Argonne National Laboratory's MG-RAST. GEO and MG-RAST employ specifications for investigation metadata that are different from those used by the GLDS and PRIDE (e.g., ISA-Tab). The GLDS Phase 2 system will implement a Google-like, full-text search engine using a Service-Oriented Architecture by utilizing publicly available RESTful web services Application Programming Interfaces (e.g., GEO Entrez Programming Utilities) and a Common Metadata Model (CMM) in order to accommodate the different metadata formats between the heterogeneous bioinformatics databases. GLDS Phase 2 completion with fully implemented capabilities will be made available to the general public in September 2017.

Space Biology↗
NASA NTRS2020

GeneLab

GeneLab collects and enables analysis of spaceflight and ground-based spaceflight simulation genomic data, RNA and protein expression, and metabolic profiles. It interfaces with other existing databases containing spaceflight omic data. The 2011 National Research Council (NRC) Decadal Survey on NASA Life and Physical Sciences called for increased opportunities for multi-investigator spaceflight opportunities and greater use of genomic approaches to meet the needs of NASA researchers. To address these recommendations of the NRC Decadal Survey, the Space Life and Physical Sciences Research and Applications Division of NASA's Human Exploration and Operations Mission Directorate has initiated a transition to an Open Science architecture to increase research opportunities, and has developed the GeneLab Platform based on highly leveraged and integrated bioinformatics analytics. GeneLab is an interactive, open-access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Users can explore GeneLab datasets in the Data Repository, analyze data using the Analysis Platform, visualize high-order data and create collaborative projects using the Collaborative Workspace. Our primary goal is to maximize the utilization of the valuable biological research conducted aboard the International Space Station (ISS) by collecting genomic, transcriptomic, proteomic, and metabolomics data known as “omics”. By providing a portal linking processed data to flight parameters, GeneLab enables exploration of the molecular network responses of terrestrial biology to the space environment. This allows researchers to understand the complex responses of biological systems to the space environment. This technology development activity was transferred from the Human Exploration and Operations Mission Directorate to the Science Mission Directorate Division of Biological and Physical Sciences (BPS) in October 2020.

GeneLab↗
NASA NTRS2018

GeneLab: Omics Database for Spaceflight Experiments

Motivation - To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms. Results - The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated "omics" (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms. GLDS is supported by an integrated data system allowing federated search across several public bioinformatics repositories. Archived datasets can be queried using full-text search (e.g., keywords, Boolean and wildcards) and results can be sorted in multifactorial manner using assistive filters. GLDS also provides a collaborative platform built on GenomeSpace for sharing files and analyses with collaborators. It currently houses 172 datasets and supports standard guidelines for submission of datasets, MIAME (for microarray), ENCODE Consortium Guidelines (for RNA-seq) and MIAPE Guidelines (for proteomics).

omics↗
NASA NTRS2018

NASA's GeneLab: An Integrated Omics Data Commons and Workbench

GeneLab (http://genelab.nasa.gov) is a NASA initiative designed to accelerate “open science” biomedical research in support of the human exploration of space and the improvement of life on earth. The GeneLab Data Systems (GLDS) were developed to help investigators corroborate findings from “omics” (genomics, transcriptomics, proteomics, and metabolomics) assays and translate them into systems biology knowledge and, eventually, therapeutics, including countermeasures to support life in space. Phase I of the project (completed) emphasized developing key capabilities for submission, curation, storage, search, and retrieval of omics data from biomedical research in and of space environments. The development focus for Phase II (completed) was federated data search and retrieval of these kinds of data from other open-access repositories. The last phase of the project (in work) entails developing an omics analysis tool set, and a portal to visualize processed omics data, emphasizing integration with the data repository and search functions developed during the prior phases. The final product will be an open-access system where users can individually or collaboratively publish, search, integrate, analyze, and visualize omics data.

genome↗
NASA NTRS2018

NASA's GeneLab: An Integrated Omics Data Commons and Workbench

GeneLab (http://genelab.nasa.gov) is a NASA initiative designed to accelerate "open science" biomedical research in support of the human exploration of space and the improvement of life on earth. The GeneLab Data Systems (GLDS) were developed to help investigators corroborate findings from "omics" (genomics, transcriptomics, proteomics, and metabolomics) assays and translate them into systems biology knowledge and, eventually, therapeutics, including countermeasures to support life in space. Phase I of the project (completed) emphasized developing key capabilities for submission, curation, storage, search, and retrieval of omics data from biomedical research in and of space environments. The development focus for Phase II (completed) was federated data search and retrieval of these kinds of data from other open-access repositories. The last phase of the project (in work) entails developing an omics analysis tool set, and a portal to visualize processed omics data, emphasizing integration with the data repository and search functions developed during the prior phases. The final product will be an open-access system where users can individually or collaboratively publish, search, integrate, analyze, and visualize omics data.

genome↗
NASA NTRS2018

Steps Toward Improved Integration, Search, and Analysis of Heterogeneous Data in the Astrobiology Habitable Environments Database

The Astrobiology Habitable Environments Database (AHED) is a new data system being developed as a long-term, open-access repository for astrobiology data. AHED is intended to store user-contributed results from NASA or externally-funded research in astrobiology, and to encourage sharing and synergy within the astrobiology community. However, the interdisciplinary nature of astrobiology presents some specific challenges to data management, integration, and analysis within AHED. In some disciplines (e.g., genomics), open databases thrive because the contributed products are fairly uniform and standardized (e.g., sequence data). In astrobiology, each investigation produces a unique set of data products; this makes it difficult to search across different datasets to find similar data, or to combine results from separate investigations. With AHED, we are taking steps to ensure there is adequate metadata - both at the dataset and record levels - to facilitate search, integration, and analysis. At the dataset level, we are developing a new metadata standard for describing astrobiology datasets, with detailed information about content, funding source, and scientific relevance, along with a set of topical keywords for characterizing datasets. At the record level, we are encouraging users to provide more structured content and finer-grained metadata. In many user-contributed science data repositories, few restrictions are placed on the uploaded data format, and minimal or no record-level metadata is required; thus users are unburdened when it comes to data preparation. The tradeoff is that deep integration and search across datasets is almost impossible without standardized structures and metadata. Although AHED users are free to upload minimally-described datasets, they will be encouraged to use database authoring tools (supplied by the underlying platform - Open Data Repository's Data Publisher) plus a set of customizable astrobiology-specific templates to help structure their data and provide standardized metadata. In reward for their extra effort, AHED will be able to deliver enhanced search, discovery, and analysis capabilities.

astrobiology↗
NASA NTRSDate not supplied

Biological Data for Deep Space Mission Support

Increased biomedical risks and challenges associated with deep space missions (cis-Lunar, Mars transit, Mars surface) require new knowledge discovery and development of novel ecosystem and biomedical support capabilities. This paradigm shift supporting distant and long-duration missions requires biological data to be findable, accessible, interoperable, reusable (FAIR), and maximally open-access (i.e., there is a data governance continuum from closed to mediated to embargoed to open). The NASA “Open Science Data Repositories” (OSDR) aims to meet scientific, technical, and operational spaceflight needs, and offers the ability to upload, download, search, share, analyze, and visualize data across physiological, behavioral, ‘omics, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive (ALSDA), and NASA Biological Institutional Scientific Collection (NBISC). In the past year, ALSDA has undergone a transformation in its data collection, curation, and architecture methods. Standardizing non-genomic (phenotypic) datasets was, and will continue to be, a challenge because of their diverse nature (e.g., molecular, cellular, tissue, whole organism behavior; micro-computed tomography, intraocular pressure, fluorescence microscopy, western blot, ultrasonography; tabular, images, video). This year ALSDA, alongside GeneLab, introduced the Biological Data Management Environment (BDME) with the purpose to accept submission of data from space relevant experiments including spaceflight, radiation, simulated gravity, gravitropism, isolation and confinement, hostile closed environments and/or distance from Earth. In addition to bringing together omics, phenotypic, physiological, bioimaging, and behavioral data into one repository. By integrating with GeneLab a multi-project submission portal aims to reduce the burden on PIs submitting data and enabling the discovery of both omics and phenotypic data. The purpose of ALSDA is to collect, curate, and make all non-human space-relevant biological data maximally findable, accessible, interoperable, and reusable (FAIR). These scope of ALSDA data collected and submitted by PIs include study design metadata, subject metadata, assay metadata (parameters), raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). In 2021, a community of researchers rallied to form the ALSDA Analysis Working Group (AWG) and provided scientific consensus on dataset sample and assay metadata. The community and excitement around the ALSDA/OSDR system has already led to several data reuse studies, demonstrating value using machine learning (ML), knowledge graphs, and meta-analysis approaches.

space biology↗
NASA NTRSDate not supplied

Biological Data for Deep Space Mission Support

Increased biomedical risks and challenges associated with deep space missions (cis-Lunar, Mars transit, Mars surface) require new knowledge discovery and development of novel ecosystem and biomedical support capabilities. This paradigm shift supporting distant and long-duration missions requires biological data to be findable, accessible, interoperable, reusable (FAIR), and maximally open-access (i.e., there is a data governance continuum from closed to mediated to embargoed to open). The NASA “Open Science Data Repositories” (OSDR) aims to meet scientific, technical, and operational spaceflight needs, and offers the ability to upload, download, search, share, analyze, and visualize data across physiological, behavioral, ‘omics, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive (ALSDA), and NASA Biological Institutional Scientific Collection (NBISC). In the past year, ALSDA has undergone a transformation in its data collection, curation, and architecture methods. Standardizing non-genomic (phenotypic) datasets was, and will continue to be, a challenge because of their diverse nature (e.g., molecular, cellular, tissue, whole organism, behavior; micro-computed tomography, intraocular pressure, fluorescence microscopy, western blot, ultrasonography; tabular, images, video). This year ALSDA, alongside GeneLab, introduced the Biological Data Management Environment (BDME) with the purpose to accept submission of data from space relevant experiments including spaceflight, radiation, simulated gravity, gravitropism, isolation and confinement, hostile closed environments and/or distance from Earth. In addition to bringing together omics, phenotypic, physiological, bioimaging, and behavioral data into one repository. By integrating with GeneLab a multi-project submission portal aims to reduce the burden on PIs submitting data and enabling the discovery of both omics and phenotypic data. The purpose of ALSDA is to collect, curate, and make all non-human space-relevant biological data maximally findable, accessible, interoperable, and reusable (FAIR). These scope of ALSDA data collected and submitted by PIs include study design metadata, subject metadata, assay metadata (parameters), raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). In 2021, a community of researchers rallied to form the ALSDA Analysis Working Group (AWG) and provided scientific consensus on dataset sample and assay metadata. The community and excitement around the ALSDA/OSDR system has already led to several data reuse studies, demonstrating value using machine learning (ML), knowledge graphs, and meta-analysis approaches.

space biology↗
NASA NTRSDate not supplied

Enabling Open and Interoperable Science: Multi-Omics Data Processing Platform with NASA GeneLab Standardized Bioinformatics Workflows for Space and Earth Research

Multi-omics biological data continues to be generated at an astounding pace. Genomics, transcriptomics, metabolomics, and proteomics, or collectively known as multi-omics data, are used to assess biological functions, and provide invaluable insights into human, animal, plant, and environmental health both on Earth and in Space. Despite the abundance of these valuable data, the need for bioinformatics expertise, particularly as it relates to the niche filed of space biology, and a lack of accessible resources for processing these data limit their usefulness in deriving biological insights. The NASA Open Science Data Repository (OSDR) provides access to omics data from various spaceflight and analog studies. To enhance the accessibility and reusability of these data, GeneLab (part of OSDR) designs and implements standardized, community-driven, open-source bioinformatics workflows to transform raw omics data into standardized processed data. Currently, GeneLab-processed data from hundreds of space studies have been reused for meta-analyses. This has led to new insights and scientific publications that extend beyond the initial research, thereby enriching our understanding of molecular-scale biological responses to the space environment. To make these bioinformatics workflows open and accessible, GeneLab teamed up with DOE-funded initiatives, including the National Microbiome Data Collaborative (NMDC), to create the NASA EDGE [Empowering the Development of Genomics Expertise] Bioinformatics web-based platform. NASA EDGE utilizes shared compute resources to run the GeneLab standardized bioinformatics workflows, which eliminates the need for researchers to have their own high performance computing cluster. The web-based platform makes complicated biological analyses incredibly easy to perform, thus expanding the reach of these analyses to bioinformatics novices, students, and even citizen scientists enabling them to contribute to scientific discoveries and progress. The authors will demonstrate how the NASA EDGE platform can be used to process microbial omics data hosted on OSDR as well as user-generated omics datasets using GeneLab’s standard workflows.

Amanda M. Saravia-Butler↗