Sustaining Software for Biological Collections Computing

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!

The experimental work was carried out at National Tsing Hua University, Institute of Photonics Technologies, supported by the Ministry of Science and Technology, Taiwan (grants 105-2112-M-007-030-MY3, 105-2112-M-001-030 and 104-2112-M-007-012-MY3). The concept of isolated circularly polarized attosecond pulses was developed by C.H.-G., D.D.H., M.M.M., C.G.D., H.C.K., A.B. and A.J.-B.. C.H.-G. acknowledges support from the Marie Curie International Outgoing Fellowship within the EU Seventh Framework Programme for Research and Technological Development (2007–2013), under Research Executive Agency grant agreement no. 328334. C.H.-G. and L.P. acknowledge support from Junta de Castilla y Leon (SA046U16) and the Ministerio de Economia y Competitividad (FIS2013-44174-P, FIS2016-75652-P). C.H.-G. acknowledges support from a 2017 Leonardo Grant for Researchers and Cultural Creators (BBVA Foundation). M.M.M. and H.C.K. acknowledge support from the Department of Energy Basic Energy Sciences (award no. DE-FG02-99ER14982) for the concepts and experimental set-up. For part of the theory, A.B., A.J.-B., C.G.D., M.M.M. and H.C.K. acknowledge support from a Multidisciplinary University Research Initiatives grant from the Air Force Office of Scientific Research (award no. FA9550-16-1-0121). A.J.-B. also acknowledges support from the US National Science Foundation (grant no. PHY-1734006). This work utilized the Janus supercomputer, which is supported by the US National Science Foundation (grant no. CNS-0821794) and the University of Colorado, Boulder. This research made use of the high-performance computing resources of the Castilla y Leon Supercomputing Center (SCAYLE, www.scayle.es), financed by the European Regional Development Fund (ERDF). J.L.E. acknowledges support from the National Science Foundation Graduate Research Fellowship (DGE-1144083). L.R. acknowledges support from the Ministerio de Educacion, Cultura y Deporte (FPU16/02591).

Funding agencies and research councils around the world rely on peer review to assess the potential impacts of proposed research. This article compares the procedures of two major public science agencies — the US National Science Foundation and the European Commission's 7th Framework Programme — for evaluating ex ante the potential societal impact of research proposals. In this paper we survey the state of the art and discuss some of the conceptual questions that arise in using ex ante peer review to assess the societal impact of scientific research. Copyright , Beech Tree Publishing.

Developing a major national resource such as the US National Science, Technology, Engineering, and Mathematics education Digital Library (NSDL) requires policy and technical expertise. Policy issues are as much a challenge as infrastructure in the construction of such a major digital library. This paper focuses on the policy making structures that have developed since 2000 when the US National Science Foundation began its funding for NSDL. The authors are the Vice Chair and Chair of the NSDL Policy Committee and report here on issues of voice, authority, and central issues for policy construction as these have emerged in the NSDL context.

The US National Science Foundation (NSF) in 2015 awarded funding for a first-of-a-kind distributed cyberinfrastructure (DCI) system called Jetstream. Jetstream will be the NSF's first production cloud for general-purpose science and engineering research and education. Jetstream, scheduled for production in January 2016, will be based on the OpenStack cloud environment software with a menu-driven interface to make it easy for users to select a pre-composed Virtual Machine (VM) to perform a particular discipline-specific analysis. Jetstream will use the Atmosphere user interface developed as part of iPlant, providing a low barrier to use by practicing scientists, engineers, educators, and students, and Globus services from the University of Chicago for seamless integration into the national cyberinfrastructure fabric. The team implementing Jetstream has as their primary mission extending the reach of the NSF's eXtreme Digital (XD) program to researchers, educators, and research students who have not previously used NSF XD program resources, including those in communities and at institutions that traditionally lack significant cyberinfrastructure resources. We will, for example, use virtual Linux Desktops to deliver DCI capabilities supporting research and research education at small colleges and universities, including Historically Black Colleges and Universities (HBCUs), Minority Serving Institutions (MSIs), Tribal colleges, and higher education institutions in states designated by the NSF as eligible for funding via the Experimental Program to Stimulate Competitive Research (EPSCoR). Jetstream will be a novel distributed cyberinfrastructure, with production components in Indiana and Texas. In particular, Jetstream will deliver virtual Linux desktops to tablet devices and PDAs with reasonable responsiveness running over cellular networks. This paper will discuss design and application plans for Jetstream as a novel Distributed CyberInfrastructure system for research education.

In this article we compare two different perspectives on the National Science Foundation (NSF) grant proposal and funding process: that depicted by the genre-dominant NSF Web site and that articulated by several successful NSF-funded researchers. Using genre theory and play theory to map the respective processes, we found that a systems-based refocusing of audience analysis—namely, genre field analysis—allows researchers a more accurate understanding of their roles as agents within the system.

Promotion of collection importance is paramount in securing a future in research and outreach through the exposure of diverse stakeholders to the incredible resource of biological collections. One outlet to increase exposure to collections’ data is through data aggregation. Data aggregation allows for a wide array of research, education and outreach activities that would otherwise be impossible. As the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation - iDigBio has made large contributions to collections with regards to communication, outreach and community training. Two facets of iDigBio’s mission statement are: to facilitate the aggregation of collections data and to promote its use. Recently, a new resource for fish collections (fishfindR.net) has contributed to both the aforementioned missions. FishFindR utilizes data aggregated by iDigBio to explore, share and compare fish collection data as it is presented in the iDigBio portal via a web resource. The data is shown in accessible, easy to use and easy to read interfaces. This resource also provides the fish research community with a way to reconcile collection data to institutions from the iDigBio recordsets. This gives fish collections stakeholders data and tools that will be useful in communicating their value, advocating for support, applying best practices to their data publishing and improving collections’ sustainability as a community. Going forward, it is the hope that this resource will provide other taxonomic disciplines with a framework to provide similar services for their stakeholders and that through a network of taxonomic specific collection resources that collections’ staff will become similarly empowered to use their own data as a communication tool.

Brian joined OCLC Research in 1996. Since that time, he has worked on projects in many areas, including digital preservation, cooperative print management, and data-mining of bibliographic resources. He was a co-founder of the working group that developed the PREMIS Data Dictionary for preservation metadata, and served as co-chair of a US National Science Foundation blue-ribbon task force on economically sustainable digital preservation. Brian's academic background is in economics; he has a Ph.D. in agricultural economics. Brian's current research interests include stewardship of the evolving scholarly record, analysis of collective collections, and the system-wide organization of library resources.

SESYNC - National Socio-Environmental Synthesis Center, US National Science Foundation (Grant # DBI-1052875); USDA Forest Service Urban Forestry South; Resources For the Future

Nell’attuale fase di evoluzione del capitalismo, caratterizzata dal ruolocrescente della conoscenza come risorsa strategica per la crescita e la com-petitivita, l’efficacia dei sistemi scientifici costituisce un fattore fondamenta-le per il benessere delle nazioni. In particolare, la struttura istituzionale e leprestazioni di un sistema scientifico influiscono sulle capacita di un paesedi sviluppare ed utilizzare le nuove tecnologie derivanti direttamente da co-noscenze e da competenze accademiche (Guerrieri, 1999; Pavitt, Patel1999; Whitley, 2003), come nei settori dell’informatica e delle biotecnologie(Mansfield, 1995; McKelvey, 1996; Narin

A discussion session held at a National Science Foundation-sponsored Herbarium Networks Workshop at Michigan State University in September of 2004 resulted in a rallying objective: make all botanical specimen information in United States collections available online by 2020. Rabeler and Macklin 2006 outlined a toolkit for realizing this ambitious goal, which included: a review of relevant and state-of-the-art web resources, data exchange standards and, mechanisms to maximize efficiencies while minimizing costs. a review of relevant and state-of-the-art web resources, data exchange standards and, mechanisms to maximize efficiencies while minimizing costs. Given that we are now in the year 2020, it seems appropriate to examine the progress towards the objective of making all US botanical specimen collections data available online. Our presentation will attempt to answer several questions: How close have we come to meeting the original objective? What fraction of “digitized” specimens are minimally represented by a catalog number, a determination, and/or a photograph? What fraction has been thoroughly transcribed? How close have we come to attaining a seamlessly integrated, comprehensive, and national view of botanical specimen data that guides a stakeholder to appropriate resources regardless of their entry point? What “holes” in this effort still exist and what might be required to fill them? How close have we come to meeting the original objective? What fraction of “digitized” specimens are minimally represented by a catalog number, a determination, and/or a photograph? What fraction has been thoroughly transcribed? How close have we come to attaining a seamlessly integrated, comprehensive, and national view of botanical specimen data that guides a stakeholder to appropriate resources regardless of their entry point? What “holes” in this effort still exist and what might be required to fill them? Given our interest in the success of both the Global Biodiversity Information Facility (GBIF) and the Integrated Digitized Biocollections (iDigBio), as well as the overwhelming likelihood that either one of these initiatives is the usual entry point for someone seeking US-based botanical data, we approached the answers to the above questions by first crafting a repeatable data download and processing workflow in early July 2020. This resulted in 25.6M records of plant, fungi, and Chromista from 216 datasets available through GBIF and 32.8M comparable records available through iDigBio from 525 recordsets. We attempted to align these seemingly discordant sets of records and also chose Darwin Core terms that were best suited to match the four hierarchical levels of digitization defined in the Minimal Information for Digital Specimens (MIDS) (van Egmond et al. 2019). During the analysis/comparison of the datasets, we found several examples where the number of data records from an institution seemed much lower than expected. From a combination of analyzing record content in GBIF/iDigBio and consulting regional/taxonomic portals, it became evident that, besides datasets only being included in either GBIF or iDigBio, there was a significant number of records in regional/taxonomic portals that were not yet made available through either GBIF or iDigBio. Progress on digitization has benefited greatly from the US National Science Foundation's creation of the Advancing Digitization of Biodiversity Collections (ADBC) program, and funding of the 15 Thematic Collection Networks (TCN). The launching of new projects and the ensuing digitization of herbarium collections have led to a multitude of new specimen portals and the enhancement of existing software like Symbiota (Gries et al. 2014). But, it has also led to insufficient data sharing among projects and inadequately aligned data synchronization practices between aggregators. Consistency in terms of data availability and quality between GBIF and iDigBio is low, and the chronic lack of record-level identifiers consistently restricts the flow of enhancements made to records. We conclude that there remains substantial work to be done on the national infrastructure and on international best practices to help facilitate collaboration and to realize the original objective of making all US botanical specimen collections data available online.

<p>Changes in the Arctic system have increased the vulnerability of permafrost coasts to erosion and altered coastal morphologies, ecosystems, biogeochemical cycling, infrastructure, cultural and heritage sites, community well-being, and human subsistence lifestyles. Better understanding the pace and nature of rapid changes occurring along permafrost coastlines is urgent, since a high proportion of Arctic residents live on or near coastlines, and many derive their livelihood from terrestrial and nearshore marine resources</p><p>The US National Science Foundation’s AccelNet and Arctic System Sciences Programs, recently awarded a collaborative grant funding the Permafrost Coastal Systems Network (PerCS-Net). PerCS-Net focuses on leveraging resources from existing national and international networks that have a common vision of better understanding permafrost coastal system dynamics and emerging transdisciplinary science, engineering, and societal issues in order to amplify the broader impacts by each individual network. PerCS-Net strengthens linkages between existing networks based in Germany, Russia, Norway, Denmark, Poland, and Canada with the activities of several active US NSF-funded networks as well as several local, state, and federally funded US-based networks.</p><p>PerCS-Net will benefit the US and international research communities by (1) developing internationally recognized protocols for quantifying the multitude of changes and impacts occurring in Arctic coastal permafrost systems, (2) sustaining long-term observations from representative coastal key sites, (3) unifying annual and decadal-scale observations of circum-arctic permafrost-influenced coasts, (4) refining a circum-arctic coastal mapping classification system and web-based delivery of geospatial information for management planning purposes and readily accessible information exchange for vulnerability assessments, (5) engaging local communities and observers to capture impacts on  subsistence and traditional livelihoods, and (6) promoting synergy across networks to foster the next generation of students, postdoctoral scholars, and early-career researchers faced with the known and unknown challenges of the future Arctic System.</p><p>Ultimately, PerCS-Net will develop a circumpolar alliance for Arctic coastal community information exchange between stake-, rights- and knowledge holders, scientists, and land managers. There is increasingly diverse interest in permafrost coastal system issues and currently no unified source of information on the past, present, and potential future state of permafrost coastal systems that provide the level of detail needed to make decisions at scales relevant for indigenous communities across the Arctic. Such new engagement will inform intergovernmental agencies and international research and outreach programs in making science-based decisions and policies to adapt to changing permafrost coastal system dynamics. PerCS-Net will build a network of networks to assess risks posed by permafrost coastal system changes to local and global economies and well-being and facilitate knowledge transfer that will lead to circum-arctic adaptation strategies.</p>

Over the last decade, the United States paleontological collections community has invested heavily in the digitization of specimen-based data, including over 10 million USD funded through the National Science Foundation’s Advancing Digitization of Biodiversity Collections program. Fossil specimen data—9.0 million records and counting (Global Biodiversity Information Facility 2024)—are now accessible on open science platforms such as the Global Biodiversity Information Facility (GBIF). However, the full potential of this data is far from realized due to fundamental challenges associated with mobilization, discoverability, and interoperability of paleontological information within the existing cyberinfrastructure landscape and data pipelines. Additionally, it can be difficult for individuals with varying expertise to develop a comprehensive understanding of the existing landscape due to its breadth and complexity. Here, we present preliminary results from a project aiming to explore how we might address these problems. Funding from the US National Science Foundation (NSF) to the University of Colorado Museum of Natural History, Smithsonian National Museum of Natural History, and Arizona State University will result in, among other products, an “ecosystem map” for the paleontological collections community. This map will be an information-rich visualization of entities (e.g. concepts, systems, platforms, mechanisms, drivers, tools, documentation, data, standards, people, organizations) operating in, intersecting with, or existing in parallel to our domain. We are inspired and informed by similar efforts to map the biodiversity informatics landscape (Bingham et al. 2017) and the research infrastructure landscape (Distributed System of Scientific Collections 2024), as well as by many ongoing metadata cataloging projects, e.g. re3data and the Global Registry of Scientific Collections (GRSciColl). Our strategy for developing this ecosystem map is to model the existing information and systems landscape by characterizing entities, e.g. potentially in a graph database as nodes with relationships to other nodes. The ecosystem map will enable us to provide guidance for communities working across different sectors of the landscape, promoting a shared understanding of the ecosystem that everyone works in together. We can also use the map to identify points of entry and engagement at various stages of the paleontological data process, and to engage diverse members within the paleontological community. We see three primary user types for this map: people new(er) to the community, people with expertise in a subset of the community, and people working to integrate initiatives and systems across communities. Each of these user types needs tailored access to the ecosystem map and its community knowledge. By promoting shared knowledge with the map, users will be able to identify their own space within the ecosystem and the connections or partnerships that they can utilize to expand their knowledge or resources, relieving the burden on any single individual to hold a comprehensive understanding. For example, the flow of taxonomic information between publications, collections, digital resources, and biodiversity aggregators is not straightforward or easy to understand. A person with expertise in collections care may want to use the ecosystem map to understand why taxonomic identifications associated with their specimen occurrence records are showing up incorrectly when published to GBIF. We envision that our final ecosystem map will visualize the flow of taxonomic information and how it is used to interpret specimen occurrence data, thereby highlighting to this user where problems may be happening and whom to ask for help in addressing them (Fig. 1). Ultimately, development of this map will allow us to identify mobilization pathways for paleontological data, highlight core cyberinfrastructure resources, define cyberinfrastructure gaps, strategize future partnerships, promote shared knowledge, and engage a broader array of expertise in the process. Contributing domain-based evidence FAIRly*2 requires expertise that bridges the content (e.g. paleontology) and the mechanics (e.g. informatics). By centering the role of humans in open science cyberinfrastructure throughout our process, we hope to develop systems that create and sustain such expertise.

The US National Science Foundation’s (NSF’s) Division of Policy Research and Analysis (PRA) supported academic research related to, among many other things, measurement of the returns to private and public R&D, during the early 1980s. The findings from this body of research became a foundation for a number of technology and innovation policies promulgated in the aftermath of the US productivity slowdown in the 1970s, and, as we suggest in this paper, a foundation for many contemporary technology and innovation policy initiatives. We argue that there are lessons to be learned from PRA’s successes from its sponsorship of research in this area, and we suggest one possible area of future emphasis for NSF’s ongoing Science of Science and Innovation Policy program.

The fields of computer and information science and engineering (CISE) are central to nearly all of society's needs, opportunities, and challenges. The US National Science Foundation (NSF) was created 70 years ago with a broad mission to promote the progress of science and to catalyze societal and economic benefits. NSF, largely through its CISE directorate which has an annual budget of more than $1B, accounts for over 85% of federally-funded, academic, fundamental computer science research in the US. My talk will give an overview of NSF/CISE research, education, and research infrastructure programs, and relate them to the technical and societal trends and topics that will impact their future trajectory. My talk will highlight opportunity areas for education and workforce development across the computing and information sciences, with a particular emphasis on parallelism and advanced computing and information topics.