Service list

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.

Collaborative Spanish Variant Server (CSVS) is a crowdsourcing initiative to provide information about the genomic variability of the Spanish population to the scientific/medical community.

Supports Finnish national data custodians (biobanks) in building a data resource for Sequence Initiative Suomi and affiliated projects.

Web based portal of organism-specific cross-platform expression compendia of bacterial organisms and grapevine

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

Either as a cooperation or consultancy service.

contact [at] denbi.de

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.

Conceptual modelling, especially OntoUML, UML, BORM, DEMO and BPMN and consultancy. Software solutions design, software development and consultancy.

Expertise includes

• DNA microarray
• RNA‐Seq
• qPCR processing pipelines
• array‐CGH, SNP
• NGS data analysis

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.  

Aligns contigs from a draft genome to a closely related genome, and resolves their relative orientation based on this alignment.

OPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

COPO is a portal for scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile.

Galaxy server allowing to align complete assemblies of SARS-CoV-2 genomes with the reference genomic sequence to obtain a list of polymorphic positions and to annotate genetic variants.

A data resource for Quercus suber.

Czech COVID-19 genomics portal

Template-based predictor of RNA secondary structure. It takes a template RNA secondary structure(s) and a query RNA sequence(s) and generates secondary structure of the query sequence(s) using the provided structure(s) as a template(s). Biological reliability of the generated structures is evaluated in form of z-scores.

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

The CSC Cloud service is targeted for High Performance Computing (HPC), allowing customers to run virtual machines with exclusive access to up to 16 cores. This service includes cPouta and ePouta. 

Curare is a free analysis pipeline for reproducible, high-throughput, bacterial RNA-Seq experiments. Define standardized pipelines customised for your specific workflow, without installing all the tools by yourself.

a web application that provides a graphical interface for Seurat version 2, a popular single-cell RNA-seq (scRNA-seq) package for R. It provides an easy-to-use UI and the ability to export results as an HTML file.

Domain based ANnotation of Transposable Elements (DANTE) uses database of Viridiplantae (Metazoa in progress) protein domains derived from transposable elements (Neumann at al 2019) Domains searching is accomplished engaging LASTAL alignment tool. Domains are subsequently annotated and classified using phylogenetic approach.

ELIXIR Luxembourg provides integrated storage and archiving for curated Translational Medicine data. Data is stored on tranSMART servers or other suitable servers.

Either as a cooperation or consultancy service.

contact [at] denbi.de

Support regarding data uploads into public repositories (esp. PRIDE), standard data formats and converters.

The Data Stewardship Wizard is an international project to help serious researchers and data stewards with building smart Data Management Plans for FAIR Open Science.

Research data management platform to enable researchers to produce FAIR data by design  

System for identification of alterations using protein mass spectrometry.