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Swedish Pathogens Portal SciLifeLab

Tools catalogue

A collection of tools relevant to infectious disease research.

BIAFlows
BIAFlows
Open-source web platform to benchmark and reproducibly deploy bioimage analysis workflows.
Bioimage Informatics Search Engine (BISE)
Bioimage Informatics Search Engine (BISE)
Search engine for tools, training materials, and data in bioimage analysis.
COVID-19 Data Repository on ICPSR
COVID-19 Data Repository on ICPSR
Repository of social, behavioral, and health sciences research data on COVID-19, hosted on ICPSR’s open platform.
COVID-19 Disease Map
COVID-19 Disease Map
Collaborative knowledgebase of molecular interaction diagrams of host–pathogen interactions specific to SARS-CoV-2, built from literature evidence.
COVID-19 Social Science Research Tracker
COVID-19 Social Science Research Tracker
A curated tracker of COVID-19 related social science research projects, datasets, and initiatives.
Galaxy COVID-19 Analysis Portal
Galaxy COVID-19 Analysis Portal
Open-access platform providing curated workflows for SARS-CoV-2 analysis across genomics, cheminformatics, and proteomics. Enables variant tracking, docking, MS analyses, and real-time surveillance with mirrored datasets and training.
HPA UMAP
HPA UMAP
ImJoy plugin to explore Human Protein Atlas single-cell UMAP projections interactively in the browser.
ImJoy
ImJoy
Plugin-powered hybrid computing platform for deploying deep learning applications, including advanced image analysis tools
ITK/VTK Viewer
ITK/VTK Viewer
Web-based viewer for visualising images using ITK/VTK pipelines; supports large multidimensional biomedical data.
Kaibu
Kaibu
Web application for visualization and annotation of multidimensional images, supporting layers, shapes, and interactive settings. Runs directly in the browser.
National Library of Sweden – SweBERT models
National Library of Sweden – SweBERT models
Swedish BERT and ALBERT models for natural language processing, trained on large Swedish corpora.
scispaCy
scispaCy
Python package with spaCy models for efficient processing of biomedical and clinical text.
spaCy
spaCy
Industrial-strength NLP library integrating deep learning models for a wide range of text analysis tasks.
Swedish Public Employment Service – SweBERT models
Swedish Public Employment Service – SweBERT models
Swedish BERT language models provided by the Swedish Public Employment Service for natural language processing research.
Vizarr
Vizarr
Client-side browser tool for viewing Zarr-based images with Viv & ImJoy; embeddable into webpages for live visualisation.
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