New!!! Allen Institute for Artificial Intelligence (Ai2) Announces Launch of #Asta: Accelerating #Science Through Trustworthy Agentic #AI https://www.infodocket.com/2025/08/26/allen-institute-for-artificial-intelligence-ai2-announces-launch-of-asta-accelerating-science-through-trustworthy-agentic-ai/ #ai2 agenticai #researchtools #scholcomm #libraries
#researchtools
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New tool for philosophers, scientists, & thinkers:
The Ontological Model Assessment Framework (OMAF) is now live on GitHub.
Evaluate _any_ ontology — in any domain — with clarity, structure, and rigor.
https://github.com/johnmackay61/omaf
#ontology #philosophy #researchtools #openscience
GitHubGitHub - johnmackay61/omaf: Ontological Model Assessment FrameworkOntological Model Assessment Framework. Contribute to johnmackay61/omaf development by creating an account on GitHub.
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Alongside the taxonomy, we built 
the GAIDeT Declaration Generator - a free, open-source tool to help researchers quickly create standardized disclosures about the use of generative AI in their manuscripts.
The tool guides you step-by-step:
Identify who is responsible for AI use
Specify the #AI tool and version
Select the research tasks delegated to AI
Generate a ready-to-use declaration for your submission
Try it here 
https://panbibliotekar.github.io/gaidet-declaration/index.html
Thrilled to present EMBL's #EBISearch at the world’s biggest #Bioinformatics conference ISMB/ECCB 2025, made by the EMBL-EBI team to make life science data more discoverable. 
Learn more about EBI Search: https://www.ebi.ac.uk/ebisearch/about
More on the event: https://lnkd.in/dhxBsBC9
Missing a dataset? Tell us: https://www.ebi.ac.uk/about/contact/support/ebi-search
New Preprint Alert!
We're excited to share our latest work on #ChemRxiv! MARCUS (Molecular Annotation and Recognition for Curating Unravelled Structures) is a web-based platform for extracting chemical information from scientific papers.
Preprint: https://doi.org/10.26434/chemrxiv-2025-9p1q1
Try it out: https://marcus.decimer.ai
ChemRxivMARCUS: Molecular Annotation and Recognition for Curating Unravelled StructuresThe exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions operate in isolation, which limits their scalability for comprehensive literature curation. Here we present MARCUS (Molecular Annotation and Recognition for Curating Unravelled Structures), a tool to aid curators in performing literature curation in the field of natural products. This integrated web-based platform combines automated text annotation, multi-engine OCSR, and direct submission capabilities to the COCONUT database. MARCUS employs a fine-tuned GPT-4 model to extract chemical entities and utilises an ensemble approach integrating DECIMER, MolNexTR, and MolScribe for structure recognition. The platform aims to streamline the data extraction workflow from PDF upload to database submission, significantly reducing curation time. MARCUS bridges the gap between unstructured chemical literature and machine-actionable databases, enabling FAIR data principles and facilitating AI-driven chemical discovery. Through open-source code, accessible models, and comprehensive documentation, the web application enhances accessibility and promotes community-driven development. This approach facilitates unrestricted use and encourages the collaborative advancement of automated chemical literature curation tools.
We dedicate MARCUS to Dr Marcus Ennis, the longest-serving curator of the ChEBI database, on the occasion of his 75th birthday.
New features now available in CONNECT & EXPLORE!
-Upload OA versions to Zenodo in clicks
-Smarter filters for better discovery
-New tools for gateway managers
-Improved accessibility & more
Read the article & see what's new: https://www.openaire.eu/new-features-in-connect-and-explore
Have you tried Brite Connect yet?
Our intuitive fNIRS data acquisition software works seamlessly with the entire Brite family of devices, making it easier than ever to collect high-quality data—whether you're measuring online or offline.
In our latest video, we show just how fast and simple it is to set up a session.
Watch it now on YouTube: https://youtu.be/uI5qcE7u_Cw
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Just a quick update on my search for a qualitative data analysis tool that works with Linux:
I found a list of tools and am checking them one by one.
If you have any experience of using any of the tools mentioned in the list, especially in a Linux environment, I would love to hear from you!
https://www.predictiveanalyticstoday.com/top-free-qualitative-data-analysis-software/
At #EGI2025, OSTrails received the Best Poster Award for showcasing practical, cross-domain tools that support #FAIR, open, and reproducible science.
Our contribution focused on making research workflows more efficient and researcher-centric, not more complex.
-Read our reflections and outcomes from the event: https://shorturl.at/nnfs0
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(6/X) Migration update: Moving from Windows to Linux!
After 4 intense days, I’m pausing the move as I’ve run out of time. The biggest hurdle is migrating my research data. As a research librarian working on systematic reviews, I rely on reference managers and qualitative analysis tools, but I am struggling with compatibility issues — for example, EndNote/Atlasti (Windows) vs. Zotero/ Taguette (Linux).
#EndOf10 #Linux #Compatibility #ResearchTools #OpenSource #Technology #AskFedi @zotero
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Switching from EndNote to Zotero? Not as smooth as I hoped.
Wanted:
export EndNote library with PDFs, notes & group structure
Got:
* no group export via RIS/XML, had to do it manually,
* double records for refs in multiple groups
* lost (research) notes
* syncing to Zotero web = painfully slow
* limited storage 2GB (have to pay 120$/year for unlimited storage)
#Zotero #EndNote #ResearchTools #ReferenceManager
#EndOf10 #Linux #LinuxMint #Compatibility #OpenSource #Technology #AskFedi
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This is awful. I'm backing up my research data from EndNote + Atlas.ti because I can't use them on Linux. I tried switching to Zotero and Taguette, but the data migration process is problematic: I lost groups with Zotero and Taguette doesn't support QDPX file import. 
Does anyone know of a QDA tool for Linux that supports QDPX file import (Project Exchange Format for Qualitative Data)?
#EndOf10 #Linux #LinuxMint #ResearchTools #QDA #QDAsoftware #Compatibility #OpenSource #Technology #AskFedi
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(3/X) Migration update: Moving from Windows to Linux!
Before switching to Linux for good, I made some backups. I saved my private and research files on an external hard disk. I also stored a backup of my research files on my employer's server.
Are there any other steps I should consider?
#Linux #EndOf10 #ResearchTools #EducationTools #OpenSource #Technology #AskFedi @Endof10
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@zotero Hello Zotero! I would love to migrate my EndNote library to Zotero. Is it possible to migrate not only the references within my groups, but also the entire group structure? I haven't been able to find a way to do this yet, so I would be very grateful if you could guide me through the process.
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So far, I have been unable to find a solution to also export my EndNote group structure. Unfortunately, I think I will have to use Python to complete this migration, but I am a beginner when it comes to Python. Fingers crossed!
#Linux #ResearchTools #EndNote #Zotero #OpenSource #Technology #AskFedi
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(2/X) Migration update: Moving from Windows to Linux!
Most of my software have solid alternatives — switched from EndNote to Zotero for reference management.
But migrating everything (attachments, file structure/groups) from EndNote is proving tricky.
If you know how to fully export an EndNote library with PDFs and folder structure, let me know!
Researchers, data scientists, and Open Science enthusiasts!
Curious about the #EOSCEUNode?
Join our Ask Me Anything session on 8 July | 14:00–15:30 CEST
With Peter Szegedi, Spiros Athanasiou & Maja Dolinar
Register: https://shorturl.at/fGTqQ
Researchers, data scientists, and Open Science enthusiasts!
Curious about the #EOSCEUNode?
Join our Ask Me Anything session on 8 July | 14:00–15:30 CEST
Discover how to:
Analyse data with Jupyter & VMs
Reuse & share data securely
Explore tools, training & policies
With Peter Szegedi, Spiros Athanasiou & Maja Dolinar
-Add to calendar: https://shorturl.at/CEEWa
SAVE THE DATE: "3D-Annotation mit Kompakkt" – Ein Bring-your-own-data-Lab
Am 06. und 07. Oktober 2025 findet das BYODL (Bring-your-own-data-Lab) zum Thema "3D-Annotation mit Kompakkt" an der Universität Trier From-Lunch-To-Lunch statt.
Mit Øyvind Eide und Maria Sotomayor als Expert*innen.
Zur Anmeldung/bei Fragen wenden Sie sich gerne an: konstanciak@uni-trier.de
Now we’re talking – Episode 5:
Meet the gel permeation chromatograph! This machine helps us understand how big (or small) molecules really are — and plays a key role in basic research at Hof University of Applied Sciences.