Recently added (10)#
Collaborative Working and Version Control with git[hub]#
Robert Haase
Published 2024-01-10
Licensed CC-BY-4.0
This slide deck introduces the version control tool git, related terminology and the Github Desktop app for managing files in Git[hub] repositories. We furthermore dive into:* Working with repositories* Collaborative with others* Github-Zenodo integration* Github pages* Artificial Intelligence answering Github Issues
DL4Proteins-notebooks#
Michael Chungyoun, Courtney Thomas, Britnie Carpentier, GabeAu79, puv-sreev, Jeffrey Gray
Published 2024-09-04T12:24:24+00:00
Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
Tags: Bioinformatics
Content type: Github Repository, Collection
LSM example J. Dubrulle#
Salama Lab Fred Hutchinson Cancer Center
Published 2024-12-17
Licensed CC-BY-4.0
Large Language Models: An Introduction for Life Scientists#
Robert Haase
Published 2024-12-12
Licensed CC-BY-4.0
This slide deck introduces Large Language Models to an audience of life-scientists. We first dive into terminology: Different kinds of Language Models and what they can be used for. The remaining slides are optional slides to allow us to dive deeper into topics such as tools for using LLMs in Science, Quality Assurance, Techniques such as Retrieval Augmented Generation and Prompt Engineering.
Modular training resources for bioimage analysis#
Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Gonzalez Tirado, Sebastian, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
Published 2024-12-03
Licensed CC-BY-4.0
Resources for teaching/preparing to teach bioimage analysis
NFDI4BIOIMAGE data management illustrations by Henning Falk#
NFDI4BIOIMAGE Consortium
Published 2024-11-29
Licensed CC-BY-4.0
These illustrations were contracted by the Heinrich Heine University Düsseldorf in the frame of the consortium NFDI4BIOIMAGE from Henning Falk for the purpose of education and public outreach. The illustrations are free to use under a CC-BY 4.0 license.AttributionPlease include an attribution similar to: “Data annoation matters”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping.
Terminology service for research data management and knowledge discovery in low-temperature plasma physics#
Becker, Markus M., Chaerony Siffa, Ihda, Roman Baum
Published 2024-12-11
Licensed CC-BY-4.0
Abstract: Terminology services (TS) [1,2] play a pivotal role in achieving structured metadata by providing controlled vocabularies and ontologies that standardize the description of data. This is a crucial aspect of research data management (RDM) in all scientific disciplines. In addition, TS facilitate the use of a common vocabulary within a scientific community also in a more general context, e.g. to annotate scientific papers, patents or other content for better discoverability, as envisaged by the Open Research Knowledge Graph (ORKG) [3] or the Patents4Science project [4]. To make use of these opportunities, terminologies, ontologies and knowledge graphs must be developed and made available as TS where they do not yet exist. This step is currently being taken by the research community in low-temperature plasma (LTP) physics. LTP physics explores partially ionized gases and its technological applications. This vibrant field offers innovative solutions for societal challenges, ranging from developing efficient lighting and solar cells to revolutionizing healthcare through plasma medicine. Various activities and projects have been started in the past years to support the RDM in LTP research and development and to facilitate the application of data-driven research methods. These activities are supported in parts by the NFDI4BIOIMAGE consortium, active work in the NFDI section “(Meta)data, Terminologies, Provenance”, and the basic service Terminology Services 4 NFDI (TS4NFDI) funded by Base4NFDI. Recently, the ontology Plasma-O [5–7] for LTP physics has been developed at INP in collaboration with FIZ Karlsruhe – Leibniz Institute for Information Infrastructure, providing a framework for structuring metadata and building a knowledge graph for scientific information within the field. The present contribution will show how a TS utilizing this resource can support different aspects of RDM and knowledge discovery using concrete examples. The application cases include (i) standardizing data annotation: By providing researchers with a controlled vocabulary of LTP-specific terms and their relationships, ensuring consistent and unambiguous data descriptions; (ii) enabling semantic search: Moving beyond keyword-based searches, TS allow for complex queries based on the relationships between concepts, significantly improving data discoverability; (iii) facilitating data integration: By mapping data from different sources to a common ontology, TS enable seamless integration and analysis of heterogeneous datasets, which is crucial for data-driven research and development. The TS Suite of TS4NFDI with the provided widgets [8] fits perfectly to the requirements of these three application cases and will support the harmonization of metadata in LTP physics. The implementation of a public TS is required to provide the domain-specific metadata in a standardized format and will be instrumental in unlocking the full potential of the TS widgets for RDM and knowledge discovery by LTP researchers. Furthermore, the results can provide insights to other domains on how to apply TS to their specific needs. The work was supported in parts by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – [NFDI46/1] – 501864659 and project number 496963457 as well as by the Federal Ministry of Education and Research (BMBF), project number 16KOA013A. References:
[1]
S. Jupp, T. Burdett, C. Leroy, H. Parkinson, “A new Ontology Lookup Service at EMBL-EBI”, Workshop on Semantic Web Applications and Tools for Life Sciences (2015), https://ceur-ws.org/Vol-1546/paper_29.pdf (accessed: 2024-09-20).
[2]
P. L. Whetzel, N. F. Noy, N. H. Shah, P. R. Alexander, C. Nyulas, T. Tudorache, M. A. Musen, “BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications”, Nucleic Acids Res. 39 (2011) W541–W545, https://doi.org/10.1093/nar/gkr469.
[3]
Open Research Knowledge Graph, https://orkg.org/ (accessed: 2024-09-20).
[4]
Patents4Science – Establishing an Information Infrastructure for the Use of Patent Knowledge in Science, https://www.patents4science.org/ (accessed: 2024-09-20).
[5]
H. Sack, F. Hoppe, “Verbundprojekt: Qualitätssicherung und Vernetzung von Forschungsdaten in der Plasmatechnologie - QPTDat; Teilvorhaben: Wissensgraph und Ontologieentwicklung zur Vernetzung von Metadaten : Schlussbericht des Teilvorhabens”, 2023, https://doi.org/10.2314/KXP:1883436974.
[6]
I. Chaerony Siffa, R. Wagner, L. Vilardell Scholten, M. M. Becker, “Semantic Information Management in Low-Temperature Plasma Science and Technology with VIVO”, 2024, preprint, https://doi.org/10.48550/arXiv.2409.11065.
[7]
I. Chaerony Siffa, R. Wagner, L. Vilardell Scholten, M. M. Becker, “Plasma Ontology and Knowledge Graph Initial Release v0.5.0”, 2024, Zenodo, https://doi.org/10.5281/zenodo.13325226.
[8]
J. Sasse, V. Kneip, R. Baum, P. Zimmermann, J. Darms, J. Schneider, V. Clemens, P. Oladazimi, L. Kühnel, “ts4nfdi/terminology-service-suite: v2.6.0”, 2024, Zenodo, https://doi.org/10.5281/zenodo.13692297.
V4SDB_Winter_School_2025#
Joanna Pylvänäinen
Published 2025-01-13T08:29:22+00:00
Training materials for V4SDB Student Winter School, 28th-31st January 2025 at ELTE Eötvös Loránd University in Budapest, Hungary
Tags: Cell Tracking, Bioimage Analysis
Content type: Github Repository, Collection
Working Group Charter. RDM Helpdesk Network#
Judith Engel, Patrick Helling, Robert Herrenbrück, Marina Lemaire, Hela Mehrtens, Marcus Schmidt, Martha Stellmacher, Lukas Weimer, Cord Wiljes, Wolf Zinke
Published 2024-11-04
Licensed CC-BY-4.0
Support is an essential component of an efficient infrastructure for research data management (RDM). Helpdesks guide researchers through this complex landscape and provide reliable support about all questions regarding research data management, including support for technical services, best practices, requirements of funding organizations and legal topics. In NFDI, most consortia have already established or are planning to establish helpdesks to support their specific communities. On a local level, many institutions have set up RDM helpdesks that provide support for the researchers of their own institution. Additional RDM support services are offered by RDM federal state initiatives, by research data centers, by specialist libraries, by the EOSC, and by providers of RDM-relevant tools. Helpdesks cover a wide range of institutions, disciplines, topics, methodologies and target audiences. However, the individual helpdesks are not yet interconnected and therefore cannot complement one another in an efficient way: Given the wide and constantly increasing complexity of RDM, no single helpdesk can provide the expertise for all potential support requests. Therefore, we see great potential in combining the efforts and resources of the existing RDM helpdesks into an efficient and comprehensive national RDM support network in order to provide optimal and tailored RDM support to all researchers and research-related institutions in Germany and in an international context.
[Workshop] Research Data Management for Microscopy and BioImage Analysis#
Christian Schmidt, Tom Boissonnet, Michele Bortolomeazzi, Ksenia Krooß
Published 2024-09-30
Licensed CC-BY-4.0
Research Data Management for Microscopy and BioImage Analysis
Introduction to BioImaging Research Data Management, NFDI4BIOIMAGE and I3D:bioChristian Schmidt /DKFZ Heidelberg OMERO as a tool for bioimaging data managementTom Boissonnet /Heinrich-Heine Universität Düsseldorf Reproducible image analysis workflows with OMERO software APIsMichele Bortolomeazzi /DKFZ Heidelberg Publishing datasets in public archives for bioimage dataKsenia Krooß /Heinrich-Heine Universität Düsseldorf
Date & Venue:Thursday, Sept. 26, 5.30 p.m.Haus 22 / Paul Ehrlich Lecture Hall (H22-1)University Hospital Frankfurt
https://zenodo.org/records/13861026
https://doi.org/10.5281/zenodo.13861026