This page details the services available for researchers and data-producing facilities. We define services as tools, databases, and support functions (e.g. hosting services) useful in data-driven life science. Use the search function to identify services that may be relevant for you.
Some of the services listed here are hosted by Scilifelab Data Centre. The status and uptime of all such services can be viewed on the Service status page. To check on the status and uptime of a particular service, click on the icon under ‘Support’ for that service.
We have classified the services by ‘Type’ to make it easier to understand what the service is. Each service can be accessed by clicking on the name under the thumbnail image. Where possible, we have provided direct links to support email addresses , support websites , and links to the underlying code , among others.
If you know of a relevant service that should be listed below, but is missing, please get in touch and the team will assess your suggestion ASAP.
We also have a resources section that offers information that could be useful to those working in data-driven life science (e.g. what compute resources are available in Sweden generally).
Search
Type
A collaborative effort to bring artificial intelligence models to the bioimaging community
Type: Database
Maintained by:
AI4Life BioImage Model Zoo team
Data Sharing, Policy Support, and Services for researchers in Swedish medical imaging AI.
Type: Compute resources, Database, Helpdesk
Maintained by:
AIDA Data Hub
A snakemake workflow for trimming and quality control of pair-ended FASTQ files
Type: Tool, Workflow
Maintained by:
Swedish Biodiversity Data Infrastructure
A bioinformatics analysis pipeline for somatic mutations in cancer.
Type: Tool, Workflow
Maintained by:
Clinical Genomics Stockholm
Chanjo is a sequencing coverage assessment tool useful in clinical and other sequencing contexts.
Type: Tool
Maintained by:
Clinical Genomics Stockholm
Chanjo2 is coverage analysis tool for human clinical sequencing data using the d4 (Dense Depth Data Dump) format.
Type: Tool
Maintained by:
Clinical Genomics Stockholm
CheckQC is a program designed to check a set of quality criteria against an Illumina runfolder.
Type: Tool
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.
Type: Tool
Maintained by:
Swedish Biodiversity Data Infrastructure
A meta-analysis resource showing changes in plasma proteins that occur during COVID-19.
Type: Database
Maintained by:
CoViMAPP team
Details about how researchers, research groups, and organisations can store their data using SciLifeLab FAIR Storage resources.
Type: Storage resources
Maintained by:
SciLifeLab Data Centre
A tool for exploring comprehensive protein networks of functional coupling.
Type: Tool
Maintained by:
Sonnhammer Group
GENMOD is a simple to use command line tool for annotating and analysing genomic variations in the VCF file format.
Type: Tool
Maintained by:
Clinical Genomics Stockholm
Details about how researchers, research groups, and organisations can apply for hosting via the SciLifeLab Platform.
Type: Compute resources
Maintained by:
SciLifeLab Data Centre
A molecular atlas of human prenatal development, describing every cell type in detail and showing their spatial and temporal distributions in three dimensions.
Type: Database, Tool
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
Type: Database, Portal, Tool
Maintained by:
The Human Protein Atlas
A database of orthologs between 640 species, including inparalogs for both protein domains and full-length proteins.
Type: Database
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.
Type: Tool
Maintained by:
Clinical Genomics Stockholm
Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis.
Type: Database, Portal, Tool
Maintained by:
NBIS
A community effort to collect a curated set of analysis pipelines and modules built using Nextflow.
Type: Tool, Workflow
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.
Type: Tool, Workflow
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
Type: Tool, Workflow
Maintained by:
nf-core community
nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data.
Type: Tool, Workflow
Maintained by:
nf-core community
PathBIX, Pathway Analysis with ANUBIX, is a web server that implements a novel network-based pathway enrichment analysis.
Type: Tool, Workflow
Maintained by:
Sonnhammer Group
Pathway annotation based on crosstalk derived through genome-side functional association networks.
Type: Tool
Maintained by:
Sonnhammer Group
A combined transmembrane topology and signal peptide predictor.
Type: Tool
Maintained by:
Sonnhammer Group
A tool to help to transform files in preparation for submission via the ClinVar API.
Type: Tool
Maintained by:
Clinical Genomics Stockholm
A service that gathers data about genes, transcripts, and exons from multiple sources and merge the information.
Type: Tool
Maintained by:
Clinical Genomics Stockholm
Repository for publishing any kind of research-related data, posters, presentations, and more!
Type: Database, Tool
Maintained by:
SciLifeLab Data Centre
A tool that aids researchers in creating data management plans (DMPs) using multiple choice questions
Type: Tool
Maintained by:
NBIS, SciLifeLab Data Centre
A portal containing information on research data management in Sweden
Type: Portal, Helpdesk
Maintained by:
NBIS, SciLifeLab Data Centre
SciLifeLab Serve is a platform offering machine learning model serving, data science app hosting (Shiny, Gradio, Streamlit, Dash, etc.).
Type: Tool
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.
Type: Tool
Maintained by:
Clinical Genomics Stockholm
A collection of resources centred around the subcellular localisation of proteins
Type: Database, Tool, Portal
Maintained by:
SubCellBarCode Team
Facilitates the sharing and promotion of pandemic preparedness and infectious disease data
Type: Portal, Helpdesk
Maintained by:
SciLifeLab Data Centre
Portal that highlights, aggregates, and displays genome data of non-human eukaryotic species studied in Sweden
Type: Portal, Tool, Helpdesk
Maintained by:
SciLifeLab Data Centre
A website developed to make genomic datasets more findable and accessible
Type: Database
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.
Type: Database, Portal, Tool
Maintained by:
TissUUmaps
A bioinformatics best-practice analysis pipeline to analyse RNA-Seq from rare disease patients.
Type: Tool, Workflow
Maintained by:
Clinical Genomics Stockholm
Search
Type
A web-based system for handling calls, proposal submission, reviews, decisions, and grant dossiers.
Type: Tool
Maintained by:
SciLifeLab Data Centre
Details about how researchers, research groups, and organisations can apply for hosting via the SciLifeLab Platform.
Type: Compute resources
Maintained by:
SciLifeLab Data Centre
A configurable web-based system enabling communication between units and prospective users
Type: Tool
Maintained by:
SciLifeLab Data Centre
Cloud-based system for the delivery of data from SciLifeLab units to their users
Type: Tool
Maintained by:
SciLifeLab Data Centre