Services: Software Tools

BioTranslator enables functional interpretation of genomic experiments through pathways analysis with a variety of biomedical ontologies, regulatory genes prioritization and protein network visualization.

Primer design and ePCR method for bisulfite treated and untreated DNA sequences (cDNA, genomic)

An interactive literature‐based biomedical discovery support system

A web server integrating multiple tools for prediction of protein subcellular localization and topological features

BUSCO provides quantitative measures for the assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.

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.

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

A resource for analyzing and interpreting genetic dependencies in cancer.

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

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 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.

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

A service oriented data mining tool

Multiple Sequence Alignment package via on-line server, in collaboration with groups in Germany, the UK and France.

ClustVis is a web tool for visualizing clustering of multivariate data. This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

A server for calculating contact maps of X-ray, NMR and predicted structures.

ComplexHeatmap is an R package which flexibly arranges multiple heatmaps and self define annotation graphics.

A tool to analyze structural ensembles of proteins by assessing their compliance to structural parameters derived from NMR measurements. Can be used both for ordered and disordered proteins and includes an option to select sub-ensembles with better correspondence to the parameters chosen.

Expertise on very diverse subjects of data processing, analysis and curation as well as connections to existing infrastructure RI's like EUDAT. This expertise can be made available to research projects and organisations.