Services

Overview of the tools and datasets available via this Platform.

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
AI4Life BioImage Model Zoo
A collaborative effort to bring artificial intelligence models to the bioimaging community
Type: Database
Maintained by: AI4Life BioImage Model Zoo team
Support:
AIDA Data Hub
Data Sharing, Policy Support, and Services for researchers in Swedish medical imaging AI.
Type: Compute resources, Database, Helpdesk
Maintained by: AIDA Data Hub
Support:
Amplicon-multi-cutadapt
A snakemake workflow for trimming and quality control of pair-ended FASTQ files
Type: Tool, Workflow
Support:
BALSAMIC
A bioinformatics analysis pipeline for somatic mutations in cancer.
Type: Tool, Workflow
Support:
Chanjo
Chanjo is a sequencing coverage assessment tool useful in clinical and other sequencing contexts.
Type: Tool
Support:
Chanjo2
Chanjo2 is coverage analysis tool for human clinical sequencing data using the d4 (Dense Depth Data Dump) format.
Type: Tool
Support:
CheckQC
CheckQC is a program designed to check a set of quality criteria against an Illumina runfolder.
Type: Tool
Support:
CoiDB
A tool that downloads sequences and metadata from GBIF and formats sequences for use with downstream metabarcoding analyses.
Type: Tool
Support:
COViMAPP
A meta-analysis resource showing changes in plasma proteins that occur during COVID-19.
Type: Database
Maintained by: CoViMAPP team
Support:
Cutadapt
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Type: Tool
Maintained by: NBIS
Support:
FAIR storage
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
Support:
FunCoup
A tool for exploring comprehensive protein networks of functional coupling.
Type: Tool
Maintained by: Sonnhammer Group
Support:
GENMOD
GENMOD is a simple to use command line tool for annotating and analysing genomic variations in the VCF file format.
Type: Tool
Support:
Hosting on the Data Platform
Details about how researchers, research groups, and organisations can apply for hosting via the SciLifeLab Platform.
Type: Compute resources
Maintained by: SciLifeLab Data Centre
Support:
Human Developmental Cell Atlas
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
Support:
Human Protein 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
Support:
InParanoiDB
A database of orthologs between 640 species, including inparalogs for both protein domains and full-length proteins.
Type: Database
Maintained by: Sonnhammer Group
Support:
LoqusDB
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
Support:
Metabolic Atlas
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
Support:
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
Type: Tool
Maintained by: Seqera
Support:
nf-core
A community effort to collect a curated set of analysis pipelines and modules built using Nextflow.
Type: Tool, Workflow
Maintained by: nf-core community
Support:
nf-core/raredisease
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
Support:
nf-core/rnafusion
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
Support:
nf-core/Sarek
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
Support:
OrthoDisease
A database of human disease orthologs.
Type: Database
Maintained by: Sonnhammer Group
Support:
PathBIX
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
Support:
PathwAX
Pathway annotation based on crosstalk derived through genome-side functional association networks.
Type: Tool
Maintained by: Sonnhammer Group
Support:
Phobius
A combined transmembrane topology and signal peptide predictor.
Type: Tool
Maintained by: Sonnhammer Group
Support:
PreClinVar
A tool to help to transform files in preparation for submission via the ClinVar API.
Type: Tool
Support:
Schug
A service that gathers data about genes, transcripts, and exons from multiple sources and merge the information.
Type: Tool
Support:
SciLifeLab Data Repository
Repository for publishing any kind of research-related data, posters, presentations, and more!
Type: Database, Tool
Maintained by: SciLifeLab Data Centre
Support:
SciLifeLab Data Stewardship Wizard
A tool that aids researchers in creating data management plans (DMPs) using multiple choice questions
Type: Tool
Support:
SciLifeLab RDM Guidelines
A portal containing information on research data management in Sweden
Type: Portal, Helpdesk
Maintained by: NBIS, SciLifeLab Data Centre
Support:
SciLifeLab Serve
Platform for sharing machine learning models and data science applications, such as Shiny and Dash apps.
Type: Tool
Maintained by: SciLifeLab Data Centre
Support:
Scout
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
Support:
SubCellBarCode
A collection of resources centred around the subcellular localisation of proteins
Type: Database, Tool, Portal
Maintained by: SubCellBarCode Team
Support:
Swedish Pathogens Portal
Facilitates the sharing and promotion of pandemic preparedness and infectious disease data
Type: Portal, Helpdesk
Maintained by: SciLifeLab Data Centre
Support:
SweFreq
A website developed to make genomic datasets more findable and accessible
Type: Database
Maintained by: SciLifeLab Data Centre
TissUUmaps
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
Support:
Tomte
A bioinformatics best-practice analysis pipeline to analyse RNA-Seq from rare disease patients.
Type: Tool, Workflow
Support:
Search
Type
Anubis
A web-based system for handling calls, proposal submission, reviews, decisions, and grant dossiers.
Type: Tool
Maintained by: SciLifeLab Data Centre
Support:
Hosting on the Data Platform
Details about how researchers, research groups, and organisations can apply for hosting via the SciLifeLab Platform.
Type: Compute resources
Maintained by: SciLifeLab Data Centre
Support:
Order Portal
A configurable web-based system enabling communication between units and prospective users
Type: Tool
Maintained by: SciLifeLab Data Centre
Support:
SciLifeLab Data Delivery System
Cloud-based system for the delivery of data from SciLifeLab units to their users
Type: Tool
Maintained by: SciLifeLab Data Centre
Support: