Advancing Space Radiation Biology with Big Data, Open Science, Standards, and ML
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Sylvain V. Costes↗
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Open Science for Life in Space: Data Sharing and Tools for Knowledge Discovery
The next era in human space exploration is rapidly approaching and will require the use of countermeasures to deep space health hazards. The development of countermeasures (or, the re-purposing of existing agents) will be highly dependent on our understanding of basic biological responses to space stressors (e.g. ionizing radiation, altered gravitational fields, altered day-night cycles, confinement, isolation, hostile-closed environments, distance-duration from Earth, exposure to celestial regolith, etc.). The fast-growing array of space biological data, which in the past was simply archived after minimal analysis, holds great potential if it can be reorganized and formatted for Open Science. Organizing the data for such analysis is a challenge because of its diverse nature (molecular, cellular, tissue, imaging, whole organism and behavior). We will discuss here several strategies that NASA’s Biological and Physical Science Division has put in place to maximize the return on investment for spaceflight bioscience data. Open Science, as a scientific philosophy, is the concept that the more people who have access to the data, the more knowledge will be gained from it. This guiding principle led NASA to develop GeneLab in 2015. GeneLab houses spaceflight and relevant ground-based multi-omics data, and has grown to ~400 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, rodent, small animal, and microbial space experiments. GeneLab provides users with various tools for data analysis and a visualization portal that allows users to interact with gene expression data from space-related ‘omics experiments. Open Science is also about building scientific communities, and with this spirit in mind, GeneLab has spawned several Analysis Working Groups (AWGs), comprised of more than 200 volunteer scientists. The AWGs initially provided feedback on the processing pipeline and metadata ‘omics standards for GeneLab. Over the last few years, they have become a community-driven science enterprise, engaging in large meta-analysis of GeneLab datasets, resulting in 10 publications (beyond the originally submitted research). Overall, the Open Science nature of GeneLab has resulted in a high degree of data re-use, resulting in 38 additional publications derived from the original 67 publication over the past four years. The enormous success and knowledge gained from GeneLab has led to a collection of sister NASA “Open Science Data Repositories (OSDR)” and research support groups. These include the NASA Ames Life Sciences Data Archive (ALSDA), the NASA Biological Institutional Scientific Collection (NBISC), and the Biospecimen Sharing Program (BSP). All are adopting the GeneLab data architecture system to maximize open-access, find-ability, accessibility, interoperability, and reusability (FAIR). ALSDA collects and curates phenotypic-physiological bioimaging-behavioral data from space and space-relevant non-human experiments, oftentimes coming from the same omics-associated experimental datasets found in GeneLab. Since 2021, a community of ~100 researchers have rallied around ALSDA, to provide feedback in a new ALSDA AWG focused on phenotypic-physiological investigation-sample-assay metadata standards (e.g., Micro-Computed Tomography, Light/Fluorescence Microscopy, Western Blot, Flow Cytometry, Novel Object Recognition, Elevated Plus Maze, etc. of ~50 assays collected). These standards are part of a new single point-of-entry data submission portal for all non-human Space Biology and Human Research Program principal investigators, to submit, curate, and share their research data. With open-access space biological data now collected and curated together with rich metadata, and with the potential for linkage to “big data” from the international biological and medical communities (NIH, EBI, etc.), the artificial intelligence and machine learning (AI/ML) era has started for Space Biology. Several other talks will cover these topics in this conference.
life sciences↗
Open Science for Life in Space: Data Sharing and Tools for Knowledge Discovery
The next era in human space exploration is rapidly approaching and will require the use of countermeasures to deep space health hazards. The development of countermeasures (or, there-purposing of existing agents) will be highly dependent on our understanding of basic biological responses to space stressors (e.g. ionizing radiation, altered gravitational fields, altered day-night cycles, confinement, isolation, hostile-closed environments, distance-duration from Earth, exposure to celestial regolith, etc.). The fast-growing array of space biological data, which in the past was simply archived after minimal analysis, holds great potential if it can be reorganized and formatted for Open Science. Organizing the data for such analysis is a challenge because of its diverse nature (molecular, cellular, tissue, imaging, whole organism and behavior). We will discuss here several strategies that NASA's Biological and Physical Science Division has put in place to maximize the return on investment for spaceflight bioscience data. Open Science, as a scientific philosophy, is the concept that the more people who have access to the data, the more knowledge will be gained from it. This guiding principle led NASA to develop GeneLab in 2015. GeneLab houses spaceflight and relevant ground-based multi-omics data, and has grown to ~400 transcriptomatic, proteomic, metabolomic and epigenomic datasets from plant, rodent, small animal, and microbial space experiments. GeneLab provides users with various tools for data analysis and a visualization portal that allows users to interact with gene expression data from space-related 'omics experiments. Open Science is also about building scientific communities, and with this spirit in mind, GeneLab has spawned several Analysis Working Groups (AWGs), comprised of more than 200 volunteer scientists. The AWGs initially provided feedback on the processing pipeline and metadata 'omics standards for GeneLab. Over the last few years, they have become a community-driven science enterprise, engaging in large meta-analysis of GeneLab datasets, resulting in 10 publications (beyond the originally submitted research). Overall, the Open Science nature of GeneLab has resulted in a high degree of data-use, resulting in 40 enabled publications by open data. The enormous success and knowledge gained from GeneLab has led to a collection of sister NASA "Open Science Data Repositories (OSDR)" and research support groups. These include the NASA Ames Life Sciences Data Archive (ALSDA), the NASA Biological Institutional Scientific Collection (NBISC), and the Biospecimen Sharing Program (BSP). All are adopting the GeneLab data architecture system to maximize open-access, find-ability, accessibility, interoperability, and reusability (FAIR). ALSDA collects and curates phenotypic-physiological bioimaging-behavioral data from space and space-relevant non-human experiments, oftentimes coming from the same omics-associated experimental datasets found in GeneLab. Since 2021, a community of ~100 researchers have rallied around ALSDA, to provide feedback in a new ALSDA AWG focused on phenotypic-physiological investigation-sample-assay metadata standards (e.g., Micro-Computed Tomography, Light/Flourescence Microscopy, Western Blot, Flow Cytometry, Novel Object Recognition, Elevated Plus Maze, etc. of ~50 assays collected). These standards are part of a new single point-of-entry data submission portal for all non-human Space Biology and Human Research Program principal investigators, to submit, curate, and share their research data. With open-access space biological data now collected and curated together with rich metadata, and with the potential for linkage to "big data" from the international biological and medical communities (NIH, EBI, etc.), the artificial intelligence and machine learning (AI/ML) era has started for Space Biology.
omics↗
Dawn: A Simulation Model for Evaluating Costs and Tradeoffs of Big Data Science Architectures
No abstract available
climate↗
Space-to-Ground Interactions While Conducting Scientific Fieldwork Under Mars Mission Constraints
The Biologic Analog Science Associated with Lava Terrains (BASALT) project is a 4-year program dedicated to iteratively designing, implementing, and evaluating concepts of operations (ConOps) and supporting capabilities to enable and enhance scientific exploration for future human Mars missions. BASALT incorporates three field deployments during which real (non-simulated) biological and geochemical field science is conducted at two high-fidelity Mars analog locations under simulated Mars mission conditions, including communication de-lays and data transmission limitations. BASALT’s primary science objective is to investigate how the redox conditions of altered basaltic environments affect the development of microbial communities in these Mars-relevant settings. Field sites include the active East Rift Zone on the Big Island of Hawaii, reminiscent of early Mars when basaltic volcanism and interaction with water were widespread, and the dormant eastern Snake River Plain in Idaho, similar to present-day Mars where basaltic volcanism is rare and most evidence for volcano-driven hydrothermal activity is relict. BASALT’s primary science operations objective is to investigate exploration ConOps and capabilities that facilitate scientific return during human-robotic exploration under Mars mission constraints. Each field deployment consists of ten extravehicular activities (EVAs) on the volcanic flows in which two extravehicular and two intravehicular (IV) crew-members conduct the science while communicating across time delay and under bandwidth constraints with an Earth-based Mission Support Center (MSC) comprised of expert scientists and operators. Communication latencies of 5 and 15-minute one-way light time and low (0.512 Mb/s uplink, 1.54 Mb/s down-link) and high (5.0 Mb/s uplink, 10.0 Mb/s downlink) bandwidth conditions are being evaluated. EVA crewmembers communicate with the MSC via voice and text messaging and provide scientific instrument data, still imagery, video streams, and GPS tracking information. The MSC reviews this data across delay and provides recommendations for presampling and sampling tasks. The scientists used dynamic leaderboards (priority rank-ing lists), to track and rank candidate samples relative to one another and against the science objectives for the current EVA and the overall mission. Updates to the dynamic leaderboards are relayed regularly to the IV crewmembers to provide scientific feedback from Earth and to help minimize crew idle time (time spent waiting for Earth input during which no productive tasks are performed). EVA timelines are strategically designed to enable continuous (delayed) feedback from an Earth-based science team while simultaneously minimizing crew idle time. Such timelines are operationally advantageous, reducing transport costs by eliminating the need for crews to return to the same locations on multiple EVAs while still providing opportunities for recommendations from science experts on Earth, and scientifically advantageous by minimizing the potential for cross-contamination across sites. This paper will highlight the space-to-ground interaction results from the three BASALT field deployments, including planned versus actual EVA time-line data, ground assimilation times (the amount of time available to the MSC to provide input to the crew), and idle time. Furthermore, we describe how these results vary under the different communication latency and bandwidth conditions. Together, these data will provide a basis for guiding and prioritizing capability development for future human exploration missions.
Beaton, Kara H.↗
Intra-EVA Space-to-Ground Interactions when Conducting Scientific Fieldwork Under Simulated Mars Mission Constraints
The Biologic Analog Science Associated with Lava Terrains (BASALT) project is a four-year program dedicated to iteratively designing, implementing, and evaluating concepts of operations (ConOps) and supporting capabilities to enable and enhance scientific exploration for future human Mars missions. The BASALT project has incorporated three field deployments during which real (non-simulated) biological and geochemical field science have been conducted at two high-fidelity Mars analog locations under simulated Mars mission conditions, including communication delays and data transmission limitations. BASALT's primary Science objective has been to extract basaltic samples for the purpose of investigating how microbial communities and habitability correlate with the physical and geochemical characteristics of chemically altered basalt environments. Field sites include the active East Rift Zone on the Big Island of Hawai'i, reminiscent of early Mars when basaltic volcanism and interaction with water were widespread, and the dormant eastern Snake River Plain in Idaho, similar to present-day Mars where basaltic volcanism is rare and most evidence for volcano-driven hydrothermal activity is relict. BASALT's primary Science Operations objective has been to investigate exploration ConOps and capabilities that facilitate scientific return during human-robotic exploration under Mars mission constraints. Each field deployment has consisted of ten extravehicular activities (EVAs) on the volcanic flows in which crews of two extravehicular and two intravehicular crewmembers conducted the field science while communicating across time delay and under bandwidth constraints with an Earth-based Mission Support Center (MSC) comprised of expert scientists and operators. Communication latencies of 5 and 15 min one-way light time and low (0.512 Mb/s uplink, 1.54 Mb/s downlink) and high (5.0 Mb/s uplink, 10.0 Mb/s downlink) bandwidth conditions were evaluated. EVA crewmembers communicated with the MSC via voice and text messaging. They also provided scientific instrument data, still imagery, video streams from chest-mounted cameras, GPS location tracking information. The MSC monitored and reviewed incoming data from the field across delay and provided recommendations for pre-sampling and sampling tasks based on their collective expertise. The scientists used dynamic priority ranking lists, referred to as dynamic leaderboards, to track and rank candidate samples relative to one another and against the science objectives for the current EVA and the overall mission. Updates to the dynamic leaderboards throughout the EVA were relayed regularly to the IV crewmembers. The use of these leaderboards enabled the crew to track the dynamic nature of the MSC recommendations and helped minimize crew idle time (defined as time spent waiting for input from Earth during which no other productive tasks are being performed). EVA timelines were strategically designed to enable continuous (delayed) feedback from an Earth-based Science Team while simultaneously minimizing crew idle time. Such timelines are operationally advantageous, reducing transport costs by eliminating the need for crews to return to the same locations on multiple EVAs while still providing opportunities for recommendations from science experts on Earth, and scientifically advantageous by minimizing the potential for cross-contamination across sites. This paper will highlight the space-to-ground interaction results from the three BASALT field deployments, including planned versus actual EVA timeline data, ground assimilation times (defined as the amount of time available to the MSC to provide input to the crew), and idle time. Furthermore, we describe how these results vary under the different communication latency and bandwidth conditions. Together, these data will provide a basis for guiding and prioritizing capability development for future human exploration missions.
Beaton, Kara H.↗
2015 Space Radiation Standing Review Panel
The 2015 Space Radiation Standing Review Panel (from here on referred to as the SRP) met for a site visit in Houston, TX on December 8 - 9, 2015. The SRP met with representatives from the Space Radiation Element and members of the Human Research Program (HRP) to review the updated research plan for the Risk of Radiation Carcinogenesis Cancer Risk. The SRP also reviewed the newly revised Evidence Reports for the Risk of Acute Radiation Syndromes Due to Solar Particle Events (SPEs) (Acute Risk), the Risk of Acute (In-flight) and Late Central Nervous System Effects from Radiation Exposure (CNS Risk), and the Risk of Cardiovascular Disease and Other Degenerative Tissue Effects from Radiation (Degen Risk), as well as a status update on these Risks. The SRP would like to commend Dr. Simonsen, Dr. Huff, Dr. Nelson, and Dr. Patel for their detailed presentations. The Space Radiation Element did a great job presenting a very large volume of material. The SRP considers it to be a strong program that is well-organized, well-coordinated and generates valuable data. The SRP commended the tissue sharing protocols, working groups, systems biology analysis, and standardization of models. In several of the discussed areas the SRP suggested improvements of the research plans in the future. These include the following: It is important that the team has expanded efforts examining immunology and inflammation as important components of the space radiation biological response. This is an overarching and important focus that is likely to apply to all aspects of the program including acute, CVD, CNS, cancer and others. Given that the area of immunology/inflammation is highly complex (and especially so as it relates to radiation), it warrants the expansion of investigators expertise in immunology and inflammation to work with the individual research projects and also the NASA Specialized Center of Research (NSCORs). Historical data on radiation injury to be entered into the Watson “big data” study must be used with caution. The general scientific issues of reproducibility, details of experimental methods and data analysis from preclinical and basic research laboratories have been raised broadly over the last few years (not specific to this work) and indicate that caution must be applied in the ways these data are used. This pertains to preclinical data and also to phase 3 clinical trials in radiation oncology and medical oncology. Of course, appropriate use and analysis of these “big-data” sets also offer the potential of pinpointing limitations and extracting remaining useful information. Emphasis should be placed on the latter possibility. A key target is risk reduction from radiation exposure. Progress of the entire space program, now moving towards the Mars mission, requires timely answers to key components of human risk, which are known to be complex. Periodic review of progress should be conducted with additional resources directed into achieving critical milestones. Turning the long red bars to yellow and green (or for some risks such as CNS possibly to grey) must be high priority. That such progress will require new science and not engineering means that it should be viewed in a knowledge-based light. The technology-based aspects of engineering issues are certainly as important, however, science and knowledge-based problems are solved in a different way than engineering. Timelines for engineering are more predictable, while for science, progress can be methodical with occasional major incremental findings that can rapidly change the rate of progress. As opportunities for rapid incremental changes arise, periodic enhancement of investment is strongly recommended to enable such new knowledge to be quickly and efficiently exploited. Collaborations and linkages with National Institute of Allergy and Infectious Diseases (NIAID), the Biomedical Advanced Research and Development Authority (BARDA) and the Department of Defense (DoD) are in place and more are encouraged, where possible, with the radiation injury and medical countermeasure studies. This could include utilizing some of their animal model testing contracts to facilitate obtaining results using common platforms. Such approach will facilitate the comparison of results among laboratories, and will facilitate and accelerate the development of medical countermeasures. It is particularly noteworthy that the NASA Space Radiation Element is reaching out to the Multidisciplinary European Low Dose Initiative (MELODI) platform coordinating low dose radiation risk research, and to other international agencies that are studying low dose radiation effects in an effort to fill the void generated by the cancelation of the Department of Energy (DOE) low dose radiation program. While NASA is working actively with NIAID and BARDA to integrate their relevant findings of radiation mitigator investigations to NASA programs, the committee notes its disappointment that the United States currently lacks a dedicated low dose radiation program with clear mechanistic orientation and aimed at the quantification and mitigation of human radiation risk on Earth. This void gives to the NASA Space Radiation Program Element special societal value, but also makes its overall design more challenging.
Steinberg, Susan↗
FAIRness and Usability for Open-Access Omics Data Systems
Omics data sharing is especially crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the "FAIRness" of NASA's GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. 14 metrics. The range of Pass ratings was 29-79% of the 14 metrics, Partial Pass 0-21%, and Fail 7-50%. The range of overall FAIRness scores was 5-12 (out of 14). The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. We propose two new principles that Big Data systems, in particular, should consider for increasing data accessibility. We relate our experiences implementing semantic integration of omics data from several systems for the federated querying and retrieval functions of the GLDS, given the shortcomings in data interoperability of these systems.
Berrios, Daniel C.↗
FAIRness and Usability for Open-access Omics Data Systems
Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the "FAIRness" of NASA's GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility.
Berrios, Daniel C.↗
FAIRness and Usability for Open-access Omics Data Systems
Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the “FAIRness” of NASA’s GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility.
Berrios, Daniel C.↗
Federated Giovanni: A Distributed Web Service for Analysis and Visualization of Remote Sensing Data
The Geospatial Interactive Online Visualization and Analysis Interface (Giovanni) is a popular tool for users of the Goddard Earth Sciences Data and Information Services Center (GES DISC) and has been in use for over a decade. It provides a wide variety of algorithms and visualizations to explore large remote sensing datasets without having to download the data and without having to write readers and visualizers for it. Giovanni is now being extended to enable its capabilities at other data centers within the Earth Observing System Data and Information System (EOSDIS). This Federated Giovanni will allow four other data centers to add and maintain their data within Giovanni on behalf of their user community. Those data centers are the Physical Oceanography Distributed Active Archive Center (PO.DAAC), MODIS Adaptive Processing System (MODAPS), Ocean Biology Processing Group (OBPG), and Land Processes Distributed Active Archive Center (LP DAAC). Three tiers are supported: Tier 1 (GES DISC-hosted) gives the remote data center a data management interface to add and maintain data, which are provided through the Giovanni instance at the GES DISC. Tier 2 packages Giovanni up as a virtual machine for distribution to and deployment by the other data centers. Data variables are shared among data centers by sharing documents from the Solr database that underpins Giovanni's data management capabilities. However, each data center maintains their own instance of Giovanni, exposing the variables of most interest to their user community. Tier 3 is a Shared Source model, in which the data centers cooperate to extend the infrastructure by contributing source code.
Giovanni↗
Disruptive Technologies and Their Putative Impacts Upon Society and Aerospace- Entering The Virtual Age
Developments in technology over the recent decades have been extraordinary. They include the IT, bio, nano, and now quantum and energetics technology arenas and their many combinatorial interactions and impacts. In the main, these are at the frontiers of the small and in a combinational, synergistic feeding frenzy with each other. They fall under the broad category of Disruptive Technologies and have greatly altered society. The outlook for the runout of these and other technology developments augers mid-term to later alterations in components of the human existence theorem, including the requirement to work for our living and our physiological makeup and longevity (Ref 1). The IT revolution began in the 1950s with the development of solid-state electronics. The biologics revolution began later in the 1960s and 1970s with DNA and genomics, and the nano revolution in the 1990s with self-forming nano systems and carbon nanotubes. Quantum technology is now developing rapidly, aided by enabling nano systems, and the energetics revolution is providing ever more efficient and less expensive renewable energy sources. The IT revolution has produced improvements of an astounding eleven orders of magnitude in computing speed since the late 1950s. As we shift from silicon to biological, optical, nano, molecular, and atomic computing, improvements of some 4 orders of magnitude are evidently possible from either optical or DNA computing [Refs 2and 3], then there are combinatorials. Then there is quantum computing, under development worldwide for an increasing number of applications and proffering phenomenal capabilities. The current fastest computers are considerably beyond human brain speed. Machine intelligence is developing well after decades of inadequate machine capability, now no longer the case, and a detour into expert systems. Researchers in machine intelligence are now pursuing deep learning approaches using neural nets, which are proving to be extremely useful. Some believe the frontier of potential human-level machine intelligence may be found in biomimetics and brain-emulation approaches. There is even a possibility of “emergence”—i.e., when the machine intelligence is complex enough that it “wakes up,” as when human intelligence emerged via evolution during the million-plus years of the hunter-gatherer epoch [ Ref 4]. In fact, some posit that human intelligence can be improved upon and is only a cul-de-sac of what is conceivable. The IT revolution has produced massive changes in human society and economics—from the Internet, enabling the rapid expansion of knowledgeability (and even what is knowable), to an increasingly pervasive trend of “tele-everything.” The extraordinary compilation, storage, and availability of truly massive amounts of information could, when combined with AI and under the mantra of “big data,” greatly improve many of our technical and commercial processes and their content including elucidating new heuristic governing laws.
Dennis M. Bushnell↗