Service list

Collection of tools whose goal is to aid researchers in carrying out scientific analyses on a multitude of cloud computing platforms. It concerns itself with providing functionality in four broad areas: Provisioning; Configuration Management; Workflow Management; Operations Management.

ELIXIR-NL can help organise standard events that make data sources more FAIR by applying Linked Data, or help make data repository software more FAIR. Such meetings focus on one or two data sources, and will bring together your experts on the data content and on the usage of the data with experts in data modeling. As an important side-effect such events also educate the participants on what it means to make data FAIR in practice.

General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts.

Unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. Allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways.

Tool for calibration of targeted MS‐based measurements.

A highly successful, well-attended bioinformatics, biostatistics and data science training programmes, which are respected by others within and outside the University of Cambridge.

It provides a broad range of mostly postgraduate, hands-on training courses focused on data science, bioinformatics and computational biology.

Additionally, the Bioinformatics Training Facility is involved in running several undergraduate courses. The Facility continues to manage the Bioinformatics undergraduate Minor Subject as part of the NST Part II Biological and Biomedical Science. This Subject is open to both Natural Science and Medical students and has received extremely positive feedback every year since its inception in 2016.

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. 

An online platform for testing the enrichment of cancer hallmark genes

Gold standard of oncology clinical cases annotated with CIE-O 3 terminology

A resource for analyzing and interpreting genetic dependencies in cancer.

Functional platform for gene expression changes and mutational status in solid tumours

A classification of protein structures and sequences that groups protein domains into superfamilies. 

Collection of tools for plant genome sequence analysis (MISA-web, Kmasker Plants, IPK BLAST server, BRIDGE).

Tool for analysis of molecular channels in proteins. CAVER Analyst allows interactive visualization of the channels and cavities in protein structures.

Tools for processing the topology and structure of transmembrane proteins

An R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.

CellNetAnalyzer is a MATLAB toolbox for analyzing the structure and function of biological networks.

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes.

A knowledge resource on cell lines.

A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.

ChEBI (Chemical Entities of Biological Interest) is a dictionary of small molecular entities. It is manually annotated and provides a chemical ontology to describe small molecules, including their biological and chemical roles.

ChEMBL is a database of bioactive compounds that focuses on interactions between small molecules and their macromolecular targets, including medicinal chemistry, clinical development and therapeutics data.

ChIPSummitDB is a comprehensive database of transcription factor binding sites verified by human ChIP-seq experiments

A web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets

An R package that provides tools for the comprehensive analysis chromatin accessibility data. 

An R package used for efficient unraveling of the inherent dynamic properties of pathways.

Circlize is an R package used to generated circular visualization.

CLASTR, the Cellosaurus STR similarity search tool enables users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication and detecting potential contamination and misidentification cases.

• Cineca Cloud farm
• Cloud@ReCaS-Bari
• Cloud Veneto
• CRS4 Orione Cloud farm
• GARR Cloud

IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology.