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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Ri��ler-Pipka, Nanette; Barthauer, Raisa; Buddenbohm, Stefan; Calvo Tello, Jos��; +2 Authors

    The report refers to the call for user stories for the Text+ consortium in the context of the German National Research Data Infrastructure (NFDI). The user stories summited by scholars (mainly from the Humanities) present challenges or possible infrastructural solutions related to their individual research data. The report explains the context and methodology, as well as the decisions and steps taken during the call. It also provides an analysis of the major elements and categories of the user stories, and some reflexions for future measures. The data for the analysis is published in the DARIAH-DE Repository: http://dx.doi.org/10.20375/0000-000E-67ED-4.

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    ZENODO
    Report . 2021
    License: CC BY
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    Report . 2021
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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      Report . 2021
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      Report . 2021
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Berg, Hannes; Wirtz Martin, Maria A.; Altincekic, Nadide; Alshamleh, Islam; +20 Authors

    SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. Angewandte Chemie. International Edition, 61 (46) ISSN:0570-0833 ISSN:1433-7851 ISSN:1521-3773

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    Research Collection
    Article . 2022
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      Article . 2022
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    Authors: Boerner, Ingo; Trilcke, Peer; Milling, Carsten; Fischer, Frank; +1 Authors

    While the calls for reproduction studies in Computational Literary Studies (CLS) have become louder, practical aspects, especially the interplay of the components involved in the research process (code, data, environments, infrastructures, etc.) proves to be a hurdle for reproducing research. We present a way to fully reproducible research using a Docker-based approach: We exemplarily implemented it for a network-analytic study on a corpus of about 3,000 theater plays derived from the DraCor project. We demonstrate that the use of highly portable, self-contained digital artifacts (Docker images) containing runnable research environments not only allow for a full reproduction of the study, but also offer ways to implement different scenarios of repeating research (e.g. same code, different data).

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    Article . 2023
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      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Schöch, Christof; Jannidis, Fotis;

    The workshop on Quantitative Text Analysis for Literary History was the first in a series of DARIAH-DE expert workshops and took place from November 22 to 23 at the University of Würzburg, Germany. It was organized by Fotis Jannidis and Christof Schöch of the Department for Literary Computing, University of Würzburg, and brought together experts in the computational analysis of collections of literary texts from France, Germany, Poland and the US. This report first briefly provides some context on the DARIAH expert workshops and introduces the specific goals of the workshop reported on here. Then, it summarizes the major issues raised by the participants in their initial statements and debated in the ensuing discussions. Finally, it describes the key results from the workshop, which include advances in the areas of data, tools and methods for quantitative text analysis.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Buddenbohm, Stefan;

    The SSH Open Marketplace (https://marketplace.sshopencloud.eu/), built as part of the Social Sciences and Humanities Open Cloud (SSHOC) project, is a discovery portal for the SSH research community comprising tools & services, training materials, datasets, publications and workflows. Designed as a catalogue contextualising its resources by creating links between them and showcasing their use in research scenarios (workflows), the interfaces of the SSH Open Marketplace are crucial for the discovery and reusability of its content. How does one build convenient, reliable, and accurate interfaces for a discovery portal? Which audiences (human, machines) and technologies have to be addressed by the interfaces and in which priority? What does it mean to be user-friendly for a web service in the world of research infrastructures? Three interface dimensions will guide our presentation of the beta version of the SSH Open Marketplace: The human individual interface dimension or user experience (UX) design and user interface (UI) (Graphical User Interface: https://marketplace.sshopencloud.eu/): SSH Open Marketplace is built to be a user-friendly portal designed on the principles of Human Center Designed (HCD) for the SSH community, with a low entry threshold for users' contributions. The design of the SSH Open Marketplace, developed by the Poznan Supercomputing and Networking Centre (PSNC) and implemented by the Austrian Centre for Digital Humanities and Cultural Heritage (ACDH-CH), has been built consulting target user communities. But still we seek for further feedback from the attendees of the demo session to identify possible improvements. The machine-readable interface dimension or REST Application Programming Interface (API documentation: https://s.gwdg.de/pymPIp): the SSH Open Marketplace includes a REST API allowing experienced users to search and retrieve detailed information and even to add information. Particularly the last aspect would be of interest as to discuss how to provide easy means for adding new content to the marketplace using its API, which would likely be of interest for institutional users. A hackathon relying on some of the API functions is planned for September 2021, and our demo will also allow attendees to gain an overview of the hackathon tasks or to announce interest in taking part. The social-structural interface dimensions or gateway for SSH resources in the European Open Science Cloud (EOSC): https://marketplace.eosc-portal.eu/: the SSH Open Marketplace is a contribution to the SSH branch of the EOSC, and as such it can be seen as a communication interface between the EOSC, its infrastructures and the SSH research communities interested in digital methods and practices.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    Other literature type . 2021
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    Presentation . 2021
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    Authors: Bardi, Alessia; Manghi, Paolo; Gonzalez Lopez, Jose Benito; Ariyo, Chris; +17 Authors

    Open Science calls for researchers to publish as soon as possible any type of research product in such a way their research activity can be transparently assessed, reviewed, reproduced, and rewarded in all its aspects. However, the publishing process has become more and more a burden for scientists, who must, most of the time, spend time to publish their articles, data, software, and other products in the many institutional or thematic repositories of reference. Scenarios include first-time publishing of new resource products or double-publishing of research products, to satisfy institutional mandates and community practices. Such tedious work is often incomplete, with some products ending up unpublished and others showing incomplete or imprecise metadata. Some communities investigated and realised the integration of their research performing services, from research infrastructures and clusters, with repositories for research product deposition. The integration ensures that outcomes of such services are deposited automatically, prior authorization of the users, into a given repository, giving life to an end-to-end scientific workflow, from experimentation to publishing. The limit of existing approaches is to be bound to a specific repository API and format; introducing multiple repositories as potential targets of deposition for the service, multiplies the problem, as bilateral interactions with the respective repository API must be established. For example, the Zenodo deposition API and the B2SHARE API are similar but different in many ways; a service willing to automate publishing into either repositories would require implementing and maintaining two different workflows. For the EOSC to act as enabler for Open Science practices, its Interoperability Framework should guide services of research infrastructures and clusters of the EOSC on how to implement (semi-)automated workflows for the deposition and consumption of research products. To support different integration options, two modalities are supported by these guidelines: SWORD protocol v3 for push mode and a combination of COAR Notify and Signposting for pull mode. The EOSC guidelines for research product onboarding are suggested as metadata exchange format. The guidelines are proposed by the EOSC Future Working Group on Research Product Publishing

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    Authors: Hardt, Marcus; Liampotis, Nicolas; Jensen, Jens; Sallé, Mischa; +4 Authors

    This specification defines how SP-IdP Proxies can provide hints about services towards Discovery Services to improve the user experience of the authentication process.

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    Authors: Bardi, Alessia; Manghi, Paolo; Gonzalez Lopez, Jose Benito; Ariyo, Chris; +17 Authors

    An important aspect of Open Science is the possibility to re-use existing research products (e.g. research data), deposited in repositories and accessible via their persistent identifiers (e.g. handle, doi, ark). However, there is no standard way a service can access the actual content behind persistent identifiers, as these typically resolve to the landing pages of the research products. The lack of standard for accessing the actual content identified by persistent identifiers makes the automatic consumption of research products hardly implementable and, when possible, limited to the persistent identifiers issued by a specific repository (e.g. the first prototype of the EGI Data Transfer Service integrated in the EOSC EXPLORE portal supported only DOIs from Zenodo). The EOSC Future Working Group on Research Product Publishing proposes the adoption of the Publication Boundary Pattern of the SignPosting protocol and recomends it for inclusion as interoperability guideline in the EOSC IF. The guidelines are proposed by the EOSC Future Working Group on "Research Product Publishing".

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    Authors: Ardizzone, Valeria; Bučík, Dominik František; Hardt, Marcus; Helmert, Stefan; +6 Authors

    Information about the groups a user is a member of is commonly used by relying parties in order to authorise user access to protected resources. This document provides guidelines for expressing group membership and role information across AARC BPA-compliant AAI services. Specifically, it defines a URN namespace for expressing this information using common identity federation protocols, namely SAML and OpenID Connect/OAuth2.

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    Authors: Keck, Veronika;

    While usage of social media data for research across academic disciplines is growing, a lot of questions are arising about research methods, and potential standards, e.g., representativeness and reproducibility. Furthermore, researchers are concerned about ethics and data protection. These concerns, questions, and possible solutions were discussed during an online bootcamp session that took place on the 8th and 11th February 2021. The outcomes of the bootcamp are summed up in this blog post that was published on the SSHOC web page: https://www.sshopencloud.eu.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Ri��ler-Pipka, Nanette; Barthauer, Raisa; Buddenbohm, Stefan; Calvo Tello, Jos��; +2 Authors

    The report refers to the call for user stories for the Text+ consortium in the context of the German National Research Data Infrastructure (NFDI). The user stories summited by scholars (mainly from the Humanities) present challenges or possible infrastructural solutions related to their individual research data. The report explains the context and methodology, as well as the decisions and steps taken during the call. It also provides an analysis of the major elements and categories of the user stories, and some reflexions for future measures. The data for the analysis is published in the DARIAH-DE Repository: http://dx.doi.org/10.20375/0000-000E-67ED-4.

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    Authors: Berg, Hannes; Wirtz Martin, Maria A.; Altincekic, Nadide; Alshamleh, Islam; +20 Authors

    SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. Angewandte Chemie. International Edition, 61 (46) ISSN:0570-0833 ISSN:1433-7851 ISSN:1521-3773

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    Authors: Boerner, Ingo; Trilcke, Peer; Milling, Carsten; Fischer, Frank; +1 Authors

    While the calls for reproduction studies in Computational Literary Studies (CLS) have become louder, practical aspects, especially the interplay of the components involved in the research process (code, data, environments, infrastructures, etc.) proves to be a hurdle for reproducing research. We present a way to fully reproducible research using a Docker-based approach: We exemplarily implemented it for a network-analytic study on a corpus of about 3,000 theater plays derived from the DraCor project. We demonstrate that the use of highly portable, self-contained digital artifacts (Docker images) containing runnable research environments not only allow for a full reproduction of the study, but also offer ways to implement different scenarios of repeating research (e.g. same code, different data).

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