SciLifeLab data services are tools, repositories, and support functions (e.g. hosting services) that can be used in research. Extra information about uptime (), contact (), guidelines/support (), source code (), and usage () is linked, where available.
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Eligible for accounts
Service owner
A collaborative effort to bring artificial intelligence models to the bioimaging community
Eligible for accounts: Everyone
Maintained by:
AI4Life BioImage Model Zoo team
Data Sharing, Policy Support, and Services for researchers in Swedish medical imaging AI.
Eligible for accounts: Swedish Research Institute Affiliation
Maintained by:
AIDA Data Hub
A snakemake workflow for trimming and quality control of pair-ended FASTQ files
Eligible for accounts: Everyone
Maintained by:
Swedish Biodiversity Data Infrastructure
A bioinformatics analysis pipeline for somatic mutations in cancer.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
Enables state-of-the-art analyses for image data using computer vision, machine learning, and bioinformatics.
Eligible for accounts: Everyone
Maintained by:
NBIS
NBIS produces tailored bioinformatics solutions for multi-omics, single cell genomics, proteomics, metabolomics, structural biology and more.
Eligible for accounts: Everyone
Maintained by:
NBIS
Chanjo is a sequencing coverage assessment tool useful in clinical and other sequencing contexts.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
Chanjo2 is coverage analysis tool for human clinical sequencing data using the d4 (Dense Depth Data Dump) format.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
CheckQC is a program designed to check a set of quality criteria against an Illumina runfolder.
Eligible for accounts: Everyone
Maintained by:
SNP & SEQ Technology Platform, NGI
A tool that downloads sequences and metadata from GBIF and formats sequences for use with downstream metabarcoding analyses.
Eligible for accounts: Everyone
Maintained by:
Swedish Biodiversity Data Infrastructure
A meta-analysis resource showing changes in plasma proteins that occur during COVID-19.
Eligible for accounts: Everyone
Maintained by:
CoViMAPP team
Data stewards can provide guidance on multiple elements of data management, e.g. Data Management Plans.
Eligible for accounts: Everyone
Maintained by:
NBIS, SciLifeLab Data Centre
Data stewards can provide support for submitting data to the relevant research repository.
Eligible for accounts: Everyone
Maintained by:
NBIS
Enables sensitive data from Swedish omics research in a responsible, safe, and legally compliant way.
Eligible for accounts: Everyone
Maintained by:
NBIS
A tool for exploring comprehensive protein networks of functional coupling.
Eligible for accounts: Everyone
Maintained by:
Sonnhammer Group
GeneSPIDER(v2) is a Matlab toolbox for gene regulatory network inference and benchmarking with controlled network and data properties.
Eligible for accounts: Everyone
Maintained by:
Sonnhammer Group
GENMOD is a simple to use command line tool for annotating and analysing genomic variations in the VCF file format.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
A molecular atlas of human prenatal development, describing every cell type in detail and showing their spatial and temporal distributions in three dimensions.
Eligible for accounts: Everyone
Maintained by:
Human Developmental Cell Atlas
The Human Protein Atlas aims to map all the human proteins in cells, tissues, and organs using an integration of various omics and imaging technologies
Eligible for accounts: Everyone
Maintained by:
The Human Protein Atlas
A database of orthologs between 640 species, including inparalogs for both protein domains and full-length proteins.
Eligible for accounts: Everyone
Maintained by:
Sonnhammer Group
A tool to keep track of variant observations from genome sequencing data. Handles a large flow of samples, and samples can be added continuously.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis.
Eligible for accounts: Everyone
Maintained by:
NBIS
A community effort to collect a curated set of analysis pipelines and modules built using Nextflow.
Eligible for accounts: Everyone
Maintained by:
nf-core community
nf-core/raredisease is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients.
Eligible for accounts: Everyone
Maintained by:
nf-core community
nf-core/rnafusion is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes
Eligible for accounts: Everyone
Maintained by:
nf-core community
nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data.
Eligible for accounts: Everyone
Maintained by:
nf-core community
A database of human disease orthologs.
Eligible for accounts: Everyone
Maintained by:
Sonnhammer Group
PathBIX, Pathway Analysis with ANUBIX, is a web server that implements a novel network-based pathway enrichment analysis.
Eligible for accounts: Everyone
Maintained by:
Sonnhammer Group
Pathway annotation based on crosstalk derived through genome-side functional association networks.
Eligible for accounts: Everyone
Maintained by:
Sonnhammer Group
A combined transmembrane topology and signal peptide predictor.
Eligible for accounts: Everyone
Maintained by:
Sonnhammer Group
A tool to help to transform files in preparation for submission via the ClinVar API.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
A service that gathers data about genes, transcripts, and exons from multiple sources and merge the information.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
Databases showing publications from research fellows affiliated with SciLifeLab.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
A web-based system for handling calls, proposal submission, reviews, decisions, and grant dossiers.
Eligible for accounts: Everyone
Maintained by:
SciLifeLab Data Centre
Access to Jira, Confluence, and Trello is available for those affiliated with SciLifeLab.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
Cloud-based system for the delivery of data from SciLifeLab units to their users
Eligible for accounts: SciLifeLab Units
Maintained by:
SciLifeLab Data Centre
A service describing the data services available at SciLifeLab.
Eligible for accounts: Everyone
Maintained by:
SciLifeLab Data Centre
Repository for publishing any kind of research-related data, posters, presentations, and more!
Eligible for accounts: Swedish Research Institute Affiliation
Maintained by:
SciLifeLab Data Centre
A tool that aids researchers in creating data management plans (DMPs) using multiple-choice questions
Eligible for accounts: Swedish Research Institute Affiliation
Maintained by:
NBIS, SciLifeLab Data Centre
Details about how researchers, research groups, and organisations can store their data using SciLifeLab FAIR Storage resources.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
Contact Data Centre for access to SciLifeLab Google Workspace (including aquiring a @scilifelab.se email addresses).
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
Databases showing publications involving SciLifeLab infrastructure units.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
Nextcloud enables real-time document editing and file sharing.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
Instances of a configurable web-based system that enable communication between units and prospective users.
Eligible for accounts: SciLifeLab Units
Maintained by:
SciLifeLab Data Centre
Links to multiple data sources, including quality registers and KIARVA (an open-source immunology database).
Eligible for accounts: Everyone
Maintained by:
SciLifeLab Data Centre
Licences are provided for those affiliated with SciLifeLab to use protocols.io - used for the creation, sharing, and versioning of laboratory and computational protocols.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
Free consultations and support on all aspects of data management for those working in in Swedish life science research
Eligible for accounts: Everyone
Maintained by:
NBIS, SciLifeLab Data Centre
An instance of an order portal used to collate information about SciLifeLab affiliated researchers and infrastructure units.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
SciLifeLab Serve is a platform offering machine learning model serving, data science app hosting (Shiny, Gradio, Streamlit, Dash, etc.).
Eligible for accounts: Swedish Research Institute Affiliation
Maintained by:
SciLifeLab Data Centre
Access to Slack to enable collaboration and communication.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
A cloud-based file sharing and storage service.
Eligible for accounts: SciLifeLab Affiliation
Maintained by:
SciLifeLab Data Centre
Portal that highlights, aggregates, and displays genome data of non-human eukaryotic species studied in Sweden
Eligible for accounts: Swedish Research Institute Affiliation
Maintained by:
SciLifeLab Data Centre
Contact Data Centre to create dynamic forms with Typeform.
Eligible for accounts: SciLifeLab Operations
Maintained by:
SciLifeLab Data Centre
A visualiser for variant call format (VCF) files. It helps to manage multiple patient cases in an single, user-friendly interface, and enables collaboration between groups.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm
NBIS produces and maintains easy-to-use bioinformatics tools to investigate research results.
Eligible for accounts: Everyone
Maintained by:
NBIS
A collection of resources centred around the subcellular localisation of proteins
Eligible for accounts: Everyone
Maintained by:
SubCellBarCode Team
Facilitates the sharing and promotion of pandemic preparedness and infectious disease data
Eligible for accounts: Everyone
Maintained by:
SciLifeLab Data Centre
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample.
Eligible for accounts: Everyone
Maintained by:
TissUUmaps
A bioinformatics best-practice analysis pipeline to analyse RNA-Seq from rare disease patients.
Eligible for accounts: Everyone
Maintained by:
Clinical Genomics Stockholm