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Open Science for Plants in Space: Data Sharing, Standards, and Informatics for Reuse and Knowledge Discovery

Upcoming deep space missions will rely on plants for crew and ecosystem health. Open access space biology data enables scientists to examine the biological responses of plants to ionizing radiation, altered gravity, low atmospheric pressure, elevated CO2, altered photoperiods and many other abiotic stressors. Open Science is the practice of making research available to all, while respecting diverse cultures, and fostering collaborations with equity. 2023 is the ‘Year of Open Science’, and NASA has a 5-year Transform to Open Science (TOPS) initiative designed to rapidly transform the agency toward an inclusive culture of open science. NASA’s Open Science Data Repository (OSDR) within NASA’s Biological and Physical Sciences Division provides access to data from space-relevant biological experiments. OSDR combines two databases, GeneLab and Ames Life Sciences Data Archive (ALSDA) to maximize access to standardized ‘omics (e.g., transcriptomics, proteomics) and phenotypic data (e.g., microscopy, biomass), respectively. GeneLab started in 2014 with the creation of the first space-relevant FAIR (Findable, Accessible, Interoperable, Reusable) biological ‘omics repository, providing detailed metadata on investigation, sample, and assay levels. The addition of ALSDA to OSDR expands plant data analysis capabilities across both phenotypic and ‘omics data. Today, OSDR hosts 62+ plant datasets and has enabled 58 peer-reviewed publications. Most of these publications were collaboration efforts under the OSDR Analysis Working Groups (AWGs). AWGs provide great opportunities for investigators to collaborate and set new standards for space-relevant data and metadata. The AWGs welcome any ASPB members interested in contributing plant expertise for space biology, and to serve as subject matter experts as we establish the framework for modern plant data archiving. Investigators are invited to submit their space-relevant plant datasets to OSDR and visit the site to learn about the tools OSDR has to offer (osdr.nasa.gov/bio).

FAIR

Open Science for Plants in Space: Data Sharing, Standards, and Informatics for Reuse and Knowledge Discovery

Upcoming deep space missions will rely on plants for crew and ecosystem health. Open access space biology data enables scientists to examine the biological responses of plants to ionizing radiation, altered gravity, low atmospheric pressure, elevated CO2, altered photoperiods and many other abiotic stressors. Open Science is the practice of making research available to all, while respecting diverse cultures, to foster collaborations with equity. NASA has declared 2023 as the ‘Year of Open Science’ and created a 5-year Transform to Open Science (TOPS) initiative designed to rapidly transform the agency toward an inclusive culture of open science. NASA’s Open Science Data Repository (OSDR) within the Biological and Physical Sciences Division provides access to data from space-relevant biological experiments. OSDR combines two databases, GeneLab and Ames Life Sciences Data Archive (ALSDA) to maximize access to standardized ‘omics (e.g., transcriptomics, proteomics) and phenotypic data (e.g., microscopy, biomass), respectively. GeneLab started in 2014 with the creation of the first space-relevant FAIR (Findable, Accessible, Interoperable, Reusable) biological ‘omics repository, providing detailed metadata on investigation, sample, and assay levels. The addition of ALSDA to OSDR expands plant data analysis capabilities across both phenotypic and ‘omics data. Today, OSDR hosts 62+ plant datasets and has enabled 58 peer-reviewed publications. Most of these publications were collaboration efforts under the OSDR Analysis Working Groups (AWGs). AWGs provide great opportunities for investigators to collaborate with community members and set new standards for space-relevant data and metadata. The AWGs welcome any ASGSR members interested in contributing plant expertise for space biology, and to serve as subject matter experts as we establish the framework for modern plant data archiving. Investigators are encouraged to submit their space-relevant plant datasets to OSDR and visit the site to learn about the tools OSDR has to offer (osdr.nasa.gov/bio).

FAIR

Open Science for Plants in Space: Data Sharing, Standards, and Informatics for Reuse and Knowledge Discovery

Upcoming deep space missions rely on plants and crops for crew and ecosystem health. Access to space plant data enables scientists to gain a deeper understanding of biological responses to ionizing radiation, altered gravity, low atmospheric pressure, elevated CO2, and altered photoperiods. Open Science is the practice of making research available to all, while respecting diverse cultures, fostering collaborations with equity. 2023 is the ‘Year of Open Science’, and NASA has a 5-year Transform to Open Science (TOPS) mission designed to rapidly transform the agency toward an inclusive culture of open science. NASA’s Open Science Data Repository (OSDR) developed by NASA’s Biological and Physical Sciences Division provides access to data from space-relevant biological experiments. OSDR combines two databases, GeneLab and Ames Life Sciences Data Archive (ALSDA) to maximize access to standardized ‘omics (e.g., transcriptomics, proteomics) and phenotypic data (e.g., microscopy, biomass), respectively. OSDR started in 2014 with the creation of the first space-relevant FAIR (Findable, Accessible, Interoperable, Reusable) biological ‘omics repository (GeneLab), providing detailed metadata on investigation, sample, and assay levels. Today, GeneLab hosts 62 plant datasets which have led to 5 published peer-reviewed meta-analysis publications. Most of these publications were collaboration efforts under the OSDR Analysis Working Groups (AWGs). AWGs provide great opportunities for investigators to collaborate and set new standards for space-relevant data and metadata. The AWGs are welcoming any ASPB members interested in providing plant expertise for space biology. The addition of ALSDA to OSDR is also expanding analysis capability beyond ‘omics. Now is the time to get involved as a Subject Matter Expert as we establish the framework for modern plant data archiving through the AWGs. Investigators are invited to submit their space-relevant plant datasets to OSDR and visit the site to learn about the tools OSDR has to offer (osdr.nasa.gov/bio).

FAIR

Accelerating Space Life Sciences: Successes and Challenges of Biospecimen and Data Sharing

NASA's current human space flight research is directed towards enabling human space exploration beyond Low Earth Orbit (LEO). To that end, NASA Space Flight Payload Projects; Rodent Research, Cell Science, and Microbial Labs, flown on the International Space Station (ISS), benefit the global life sciences and commercial space communities. Verified data sets, science results, peer-reviewed publications, and returned biospecimens, collected and analyzed for flight and ground investigations, are all part of the knowledge base collected by NASA's Human Exploration and Operations Mission Directorate's Space Life and Physical Sciences Research and Applications (SLPSRA) Division, specifically the Human Research and Space Biology Programs. These data and biospecimens are made available through the public Life Sciences Data Archive (LSDA) website to promote basic discovery, pre-clinical and clinical science.The NASA Institutional Scientific Collection (ISC), stores flight and ground biospecimens from Space Shuttle and ISS programs. These specimens are curated and managed by the Ames Life Sciences Data Archive (ALSDA), an internal node of NASA's LSDA. The ISC stores over 30,000 specimens from experiments dating from 1984 to present. Currently available specimens include tissues from the circulatory, digestive, endocrine, excretory, integumentary, muscular, neurosensory, reproductive, respiratory and skeletal systems.NASA's biospecimen collection represents a unique and limited resource of unique spaceflight payload and ground control research subjects. These specimens are harvested according to well established SOPs that maintain their quality and integrity. Once the primary scientific objectives have been met, the remaining specimens are made available to provide secondary opportunities for complementary studies or new investigations to broaden research without large expenditures of time or resources. Website: https://lsda.jsc.nasa.gov/

Scott, Ryan T.

Data sharing helps avoid “smoking gun” claims of topological milestones

Manipulating the topology of electronic bands can realize new states of matter, with possible implications for information technology. A central question is how to tell whether a topological regime has been achieved. Experiments are often guided by a prediction of a distinct and self-explanatory signal called “the smoking gun.” However, in micrometer- or nanometer-scale specimens, phenomenology can mimic the anticipated behavior without containing the exotic states. We show limited data that are consistent with the presence of four topological phenomena; by considering additional data, we identified the most likely origins of the observed patterns as trivial. Finally, we argue that the reliability of smoking gun–type claims can be greatly enhanced by releasing comprehensive datasets, discussing alternative scenarios, and disclosing the total volume of study.

Frolov, S. M. [Univ. of Pittsburgh, PA (United Sta

Open Science for Life in Space: Data Sharing and Tools for Knowledge Discovery

The next era in human space exploration is rapidly approaching. The use of health countermeasures and biomonitoring systems for space missions are required to counteract space health hazards and to support life to thrive in deep space (e.g., humans, animals, plants, crops; entire ecosystems within spacecrafts/habitats/spacesuits). The development of these mission components will be highly dependent on our understanding of basic biological and health responses to myriad space hazards (ionizing radiation, altered gravitational fields, altered day-night cycles, confined isolation, hostile-closed environments, distance-duration from Earth, planetary dust-regolith, and extreme temperatures/atmospheres). The fast-growing array of space biological and mission telemetry data, which in the past was simply archived after minimal analysis, holds great potential once applied to these mission challenges if it can be reorganized and formatted for Open Science. Organizing the data for such analysis is a challenge because of its multi-hierarchical, multi-modal, and heterogenous nature (molecular, cellular, tissue, organ, whole organism, behavior, ecosystem, microbiome; tabular, omics, imaging, video, biospecimen, environmental physical-chemical telemetry). This session focuses on current approaches in this domain such as: making space biological data FAIR (findable, accessible, interoperable, reusable), effective data ingestion/dissemination, observational versus experimental data, Open Science collaborations, data analysis techniques, AI/ML/knowledge graph/modeling methods, and data integration/discovery tools.

open science

Collaborative Arrival Planning: Data Sharing and User Preference Tools

Air traffic growth and air carrier economic pressures have motivated efforts to increase the flexibility of the air traffic management process and change the relationship between the air traffic control service provider and the system user. One of the most visible of these efforts is the U.S. government/industry "free flight" initiative, in which the service provider concentrates on safety and cross-airline fairness, and the user on their business objectives and operating preferences, including selecting their own path and speed in real-time. In the terminal arrival phase of flight, severe restrictions and rigid control are currently placed on system users, typically without regard for individual user operational preferences. Airborne delays applied to arriving aircraft into capacity constrained airports are imposed on a first-come, first-serve basis, and thus do not allow the system user to plan for or prioritize late arrivals, or to economically optimize their arrival sequence. A central tenant of the free-flight operating paradigm is collaboration between service providers and users in reaching air traffic management decisions. Such collaboration would be particularly beneficial to an airline's "hub" operation, where off-schedule arrival aircraft are a consistent problem, as they cause serious air-port ramp difficulties, rippling airline scheduling effects, and result in large economic inefficiencies. Greater collaboration can also lead to increased airport capacity and decrease the severity of over-capacity rush periods. In the NASA Collaborative Arrival Planning (CAP) project, both independent exchange of real-time data between the service provider and system user and collaborative decision support tools are addressed. Data exchange of real-time arrival scheduling, airspace management, and air carrier fleet data between the FAA service provider and an air carrier is being conducted and evaluated. Collaborative arrival decision support tools to allow intra-airline arrival preferences are being developed and simulated. The CAP project is part of and leveraged from the NASA/FAA Center TRACON Automation System (CTAS), a fielded set of decision support tools that provide computer generated advisories for both enroute and terminal area controllers to manage and control arrival traffic more efficiently. In this paper, the NASA Collaborative Arrival Planning project is outlined and recent results detailed, including the real-time use of CTAS arrival scheduling data by a major air carrier and simulations of tactical and strategic user preference decision support tools.

Zelenka, Richard E.

Share Data with OPeNDAP Hyrax: New Features and Improvements

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in 1. server installation, 2. server configuration, 3. Hyrax aggregation capabilities, 4. support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS), 5. support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

OPeNDAP

2025 TEM Workshop

The TEM Data Management Workshop will take place on August 26 from 9 a.m. to 12 p.m. MT, and will be held virtually on TEAMS. The primary goal of this workshop is to engage NSUF users and stakeholders in discussions about the data needs for the utilization of AI and ML in the analysis of TEM data. Key topics to be covered include data storage, data sharing, data tagging, metadata inclusion, standardized data formats, data augmentation, and annotated training datasets. Additionally, the workshop will provide valuable insights into resources such as the Nuclear Research Data System (NRDS) for data storage and sharing, as well as open-source codes for data analysis.

Bachhav, Mukesh

CLIPS, AppleEvents, and AppleScript: Integrating CLIPS with commercial software

Many of today's intelligent systems are comprised of several modules, perhaps written in different tools and languages, that together help solve the user's problem. These systems often employ a knowledge-based component that is not accessed directly by the user, but instead operates 'in the background' offering assistance to the user as necessary. In these types of modular systems, an efficient, flexible, and eady-to-use mechanism for sharing data between programs is crucial. To help permit transparent integration of CLIPS with other Macintosh applications, the AI Research Branch at NASA Ames Research Center has extended CLIPS to allow it to communicate transparently with other applications through two popular data-sharing mechanisms provided by the Macintosh operating system: Apple Events (a 'high-level' event mechanism for program-to-program communication), and AppleScript, a recently-released scripting language for the Macintosh. This capability permits other applications (running on either the same or a remote machine) to send a command to CLIPS, which then responds as if the command were typed into the CLIPS dialog window. Any result returned by the command is then automatically returned to the program that sent it. Likewise, CLIPS can send several types of Apple Events directly to other local or remote applications. This CLIPS system has been successfully integrated with a variety of commercial applications, including data collection programs, electronics forms packages, DBMS's, and email programs. These mechanisms can permit transparent user access to the knowledge base from within a commercial application, and allow a single copy of the knowledge base to service multiple users in a networked environment.

Compton, Michael M.

Jell-Molds and Cookie-cutters: Shrinkwrap Isn't Just for Leftovers Anymore

So what is Shrinkwrap all about? For those of you who may not know about it, Shrinkwrap is a type of data structure that can manifest itself as a feature or model. It is cleverly covered up, almost hidden, and doesn't get the press or widespread use of a solid or surface. The shrinkwrap feature is located under the data sharing submenu of the feature menu. The shrinkwrap feature, as described by PTC, is a collection of surfaces and datum features of a model that represents the exterior of the model . The advantages and applications of the shrinkwrap feature are in the creation of minimal memory guzzling representations of assemblies. These can be used to represent subassemblies in parent assemblies, and can handle control of dependency issues, geometry represented, and additional references through the use of the shrinkwrap feature options. The shrinkwrap model is an option available under the save as umbrella. Its function, as described by PTC, is to share data with internal and external design groups and improve performance in large assembly design . Some of the benefits of the shrinkwrap model include being able to represent complex assemblies with a single, lightweight part that protects design intent and parametric data, and the ability to improve performance of large assembly modeling in the area of less load time. The proper-scale models can be saved as IGES, STEP, and VRML (for fly-throughs).

Randazzo, John