DOI: 10.3897/rio.11.e179253

Authors: Ronny Gey, Daniel Mietchen, Oliver Karras, Tim Wittenborg, Moritz Schubotz, Jan Bumberger

Abstract: Across essentially all fields of research, many aspects of the respective research processes – whether experimental, theoretical, empirical or outright computational – are closely related to software. Yet the process of finding software that is directly suitable or at least a good starting point for a given research task is cumbersome.This project aims to develop a community-driven system that provides potential users of research software with a diversity of pathways towards actually finding software that closely matches their research needs if such software exists. Conversely, it will provide software developers with mechanisms to make their software findable for research-related tasks and it will highlight mismatches between software supply and demand for specific tasks.To this end, we will document how various stakeholders of the research landscape have been searching for – or stumbling upon – research software so far, identify variables associated with successful search outcomes and build workflows that assist in describing software and associated concepts in a standardised fashion. These descriptions will then be aligned across various sources of relevant information and integrated into Wikidata, the knowledge graph that anyone can edit and that already contains considerable breadth and depth of information related to research, software and their interactions.While keeping an eye on similar approaches to software discovery that might work in parts of the research ecosystem, existing Wikidata content and workflows will be reviewed and built upon. Additional documentation, tooling and workflows will be developed to enrich, expand, curate, query and explore this content, both for specific use cases and with ongoing engagement of the communities involved in research software, open data or collaborative curation. Within its three years, the project seeks to establish a dedicated community overseeing a well-documented and smoothly running infrastructure for software discovery and to devise a plan for how this can be sustained for the longer term.

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DOI: 10.3897/rio.10.e134840

Authors: Talia Karim, Erica Krimmel, Holly Little, Lindsay Walker

Abstract: A stakeholder engagement workshop was held in May 2024 as part of the "Community-driven enhancement of information ecosystems for the discovery and use of paleontological specimen data" project, which is funded under the United States National Science Foundation (NSF) Geosciences Open Science Ecosystem (GEO OSE) program. This report describes the activites and outcomes of the workshop.

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DOI: 10.3897/arphapreprints.e106369

Authors: Christos Arvanitidis, Ron Dekker, Andreas Petzold, Niklas Blomberg, Giovanni Lamanna, Rudolf Dimper, Cristina Isabel Huertas Olivares, Ana Mellado, Matthew Viljoen, Sally Chambers, Montserrat González, Sophie Viscido

Abstract: The Special Collection of articles on the Science Projects of the EOSC Future project, funded by the European Commission, refers to one of the essential components of the project. This editorial article explains how the Science Projects fit to the EOSC Future, the way their concept has been developed and evolved during the preparation and the implementation of the project and it also makes an introduction to the templates developed by the Science Projects as a plan to carry out their activities.

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DOI: 10.3897/rio.4.e32449

Authors: Katja Seltmann, Sara Lafia, Deborah Paul, Shelley James, David Bloom, Nelson Rios, Shari Ellis, Una Farrell, Jessica Utrup, Michael Yost, Edward Davis, Rob Emery, Gary Motz, Julien Kimmig, Vaughn Shirey, Emily Sandall, Daniel Park, Christopher Tyrrell, R. Sean Thackurdeen, Matthew Collins, Vincent O'Leary, Heather Prestridge, Christopher Evelyn, Ben Nyberg

Abstract: Georeferencing is the process of aligning a text description of a geographic location with a spatial location based on a geographic coordinate system. Training aids are commonly created around the georeferencing process to disseminate community standards and ideas, guide accurate georeferencing, inform users about new tools, and help users evaluate existing geospatial data. The Georeferencing for Research Use (GRU) workshop was implemented as a training aid that focused on the creation and research use of geospatial coordinates, and included both data researchers and data providers, to facilitate communication between the groups. The workshop included 23 participants with a wide background of expertise ranging from students (undergraduate and graduate), professors, researchers and educators, scientific data managers, natural history collections personnel, and spatial analyst specialists. The conversations and survey results from this workshop demonstrate that it is important to provide opportunities for biocollections data providers to interact directly with the researchers using the data they produce and vice versa.

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DOI: 10.3897/rio.4.e24430

Authors: Adewale Amosu, Hamdi Mahmood, Paul Ofoche

Abstract: Reservoir modeling of carbonate rocks requires a proper understanding of the pore space distribution and its relationship to permeability. Using a pigeonhole fractal model we characterize the fractal geometry of moldic pore spaces and extract the fractal dimension. We apply the Kozeny-Carman equation and equations relating the tortuosity and the porosity to the fractal dimension to derive an empirical relationship between permeability and porosity.

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DOI: 10.3897/rio.4.e23676

Authors: Adewale Amosu, Hamdi Mahmood

Abstract:

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DOI: 10.3897/rio.2.e11321

Authors: Florian Leese, Florian Altermatt, Agnès Bouchez, Torbjørn Ekrem, Daniel Hering, Kristian Meissner, Patricia Mergen, Jan Pawlowski, Jeremy Piggott, Frédéric Rimet, Dirk Steinke, Pierre Taberlet, Alexander Weigand, Kessy Abarenkov, Pedro Beja, Lieven Bervoets, Snaedís Björnsdóttir, Pieter Boets, Angela Boggero, Atle Bones, Ángel Borja, Kat Bruce, Vojislava Bursić, Jens Carlsson, Fedor Čiampor, Zuzana Čiamporová-Zatovičová, Eric Coissac, Filipe Costa, Marieta Costache, Simon Creer, Zoltán Csabai, Kristy Deiner, Ángel DelValls, Stina Drakare, Sofia Duarte, Tina Eleršek, Stefano Fazi, Cene Fišer, Jean-François Flot, Vera Fonseca, Diego Fontaneto, Michael Grabowski, Wolfram Graf, Jóhannes Guðbrandsson, Micaela Hellström, Yaron Hershkovitz, Peter Hollingsworth, Bella Japoshvili, John Jones, Maria Kahlert, Belma Kalamujic Stroil, Panagiotis Kasapidis, Martyn Kelly, Mary Kelly-Quinn, Emre Keskin, Urmas Kõljalg, Zrinka Ljubešić, Irena Maček, Elvira Mächler, Andrew Mahon, Marketa Marečková, Maja Mejdandzic, Georgina Mircheva, Matteo Montagna, Christian Moritz, Vallo Mulk, Andreja Naumoski, Ion Navodaru, Judit Padisák, Snæbjörn Pálsson, Kristel Panksep, Lyubomir Penev, Adam Petrusek, Martin Pfannkuchen, Craig Primmer, Baruch Rinkevich, Ana Rotter, Astrid Schmidt-Kloiber, Pedro Segurado, Arjen Speksnijder, Pavel Stoev, Malin Strand, Sigitas Šulčius, Per Sundberg, Michael Traugott, Costas Tsigenopoulos, Xavier Turon, Alice Valentini, Berry van der Hoorn, Gábor Várbíró, Marlen Vasquez Hadjilyra, Javier Viguri, Irma Vitonytė, Alfried Vogler, Trude Vrålstad, Wolfgang Wägele, Roman Wenne, Anne Winding, Guy Woodward, Bojana Zegura, Jonas Zimmermann

Abstract: The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.

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DOI: 10.3897/rio.2.e10528

Authors: Adrian Glover, Thomas Dahlgren, Sergio Taboada, Gordon Paterson, Helena Wiklund, Andrea Waeschenbach, Amber Cobley, Pedro Martínez, Stefanie Kaiser, Sarah Schnurr, Sahar Khodami, Uwe Raschka, Daniel Kersken, Heiko Stuckas, Lenaick Menot, Paulo Bonifacio, Ann Vanreusel, Lara Macheriotou, Marina Cunha, Ana Hilário, Clara Rodrigues, Ana Colaço, Pedro Ribeiro, Magdalena Błażewicz, Andrew Gooday, Daniel Jones, David Billett, Aurélie Goineau, Diva Amon, Craig Smith, Tasnim Patel, Kirsty McQuaid, Ralph Spickermann, Stefan Brager

Abstract:

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DOI: 10.3897/rio.2.e8827

Authors: Jennifer McWhorter, Darren Wright, Julie Thomas

Abstract:

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