Registry Catalogue

Alfred is a comprehensive tool for quality control of next-generation sequencing alignments. It supports commonly used alignment QC metrics, RNA and DNA feature counting, and flexible feature annotation. As part of the GEAR toolbox, Alfred helps users evaluate sequencing data quality and generate quantitative summaries from aligned NGS datasets. Key benefits Provides comprehensive quality control for NGS alignments Supports commonly used alignment QC metrics Enables RNA and DNA feature counting Offers flexible feature annotation options Suitable for reproducible command-line and pipeline-based analyses Applications Quality control of NGS alignment files Assessment of sequencing and mapping performance RNA and DNA feature counting Generation of summary metrics for sequencing datasets Integration into automated NGS analysis workflows Intended use Alfred is intended for bioinformaticians, genomics researchers, sequencing facilities, and life science researchers working with aligned NGS data. It is particularly suited for users who need reproducible alignment quality control, feature counting, and reporting within genome, transcriptome, or other sequencing analysis pipelines.

BacDive (The Bacterial Diversity Database) is the world’s largest knowledge base of standardized, strain-level bacterial and archaeal information. Recognized as both an ELIXIR Core Data Resource and a Global Core Biodata Resource, BacDive mobilizes and makes freely available research data from culture collections, species descriptions, and other curated sources. The database currently contains more than three million data points on over 100,000 strains, covering taxonomy, morphology, physiology, metabolism, origin, biosafety, sequence data, and cultivation. Key benefits Comprehensive strain-level information for more than 100,000 bacterial and archaeal strains More than 1,000 standardized data fields across a broad range of biological and experimental topics Manually curated data from species descriptions and international culture collections Powerful search tools for identifying strains by phenotype, growth conditions, habitat, or isolation source Programmatic access through a RESTful API and SPARQL endpoint Recognized as an ELIXIR Core Data Resource and a Global Core Biodata Resource Applications Identification of strains with specific physiological or metabolic characteristics Search for organisms isolated from particular environments or host-associated habitats Selection of strains for cultivation and experimental studies Comparative analysis of microbial traits and phenotypes Linking strain-level information with sequence and biosafety data Large-scale data retrieval and knowledge-graph-based analyses via API or SPARQL Intended use BacDive is intended for microbiologists, microbial ecologists, taxonomists, bioinformaticians, data scientists, and biotechnology researchers who require comprehensive and standardized information on bacterial and archaeal strains. It is particularly suited for users searching for strains with defined biological characteristics or integrating curated strain-level data into large-scale computational analyses.

BakRep is a comprehensive, scalable web repository that aggregates and standardizes millions of publicly available bacterial genomes from e.g. AllTheBacteria. Each genome is enriched with uniform quality metrics, taxonomic classification, sequence typing, and annotation, enabling rapid and reproducible comparative analyses across large datasets, and integrated with accompanying submission metadata. Key Benefits Extensive data coverage with consistently processed bacterial genomes. Integrated Metadata: original submission metadata comprising e.g. sampling location, data, source. Standardized genome characterizations, including QC, taxonomy, MLST, and annotation. Powerful search and filtering to compile custom genome sets based on genomic or metadata attributes. Web interface and command-line access for both exploratory and automated high-throughput workflows. Features Unified pipeline for QC, taxonomic assignment, sequence typing, and annotation. Advanced search by species, genome size, GC content, contig count, sequence type, and more. Downloadable genome subsets for downstream computational analyses. CLI integration for large-scale or reproducible workflows. Applications Comparative genomics, phylogenetics, and population genomics. Large-scale surveys of resistance genes, virulence factors, or metabolic traits. Building curated genome datasets for benchmarking or tool development. Supporting epidemiological investigations and outbreak analyses. Intended Use BakRep is ideal for microbial genomics researchers, bioinformaticians, and epidemiologists who need reliable, standardized access to large bacterial genome collections.

BAND (Bioimage Analysis Desktop) and BARD (Bioimage Analysis Research Desktop) provide cloud-based desktop environments for bioimage analysis, accessible directly through a web browser. Applications run in fully containerized environments orchestrated by OpenStack or Kubernetes clusters, enabling users to work with GUI-based imaging tools without local installation or complex infrastructure setup. BAND/BARD are designed for both individual image analysts and course organizers who require scalable computational resources for hands-on training. The de.NBI BAND instance is hosted at the de.NBI Tübingen node and offers configurable desktops with CPU, RAM, and GPU resources. Key benefits Browser-based access to desktop environments with containerized bioimage analysis software No local installation of complex imaging software required Configurable compute resources including CPU, RAM, and GPU options Suitable for scalable training courses and workshops Persistent user storage with options to access external data sources Applications Running GUI-based bioimage analysis applications in the cloud Providing standardized desktop environments for training events Interactive image analysis without maintaining local workstations GPU-supported analysis workflows where available Accessing remote datasets through integrated tools such as Rclone Intended use BAND/BARD are intended for image analysts, bioimage researchers, trainers, course organizers, and life science researchers who need browser-accessible computing environments for image analysis. They are particularly suited for users who rely on graphical software tools, require scalable compute resources for training, or want to provide standardized analysis environments to multiple participants.

The Berlin RNA Toolbox is a comprehensive collection of bioinformatics tools and databases. The toolbox offers a wide range of resources for researchers to analyze, predict, and understand various aspects of RNA biology. Key Benefits Comprehensive analysis of RNA interactions : Identify potential binding sites of microRNAs on messenger RNAs (mRNAs) and explore the complex relationships between RNAs. In-depth analysis of circular RNAs : Discover circRNAs in RNA-seq data and explore their potential functions. Accurate prediction of protein-RNA interactions : Identify specific binding regions between proteins and RNAs. Tools PicTar : A microRNA target predictor that identifies potential binding sites of microRNAs on messenger RNAs (mRNAs). miRDeep : A probabilistic model that detects the presence of expressed animal microRNAs in deep sequencing data. PIPmiR : A tool to identify novel plant miRNA genes from a combination of deep sequencing and genomic features. NASTIseq : Expression analysis for the identification of cis-Natural Antisense Transcripts (cis-NAT) from strand-specific RNA-seq data. PARalyzer : A peak finder for protein-RNA interaction sites in PAR-CLIP data, helping to identify specific binding regions between proteins and RNAs. microMUMMIE : MicroRNA target-site prediction in PAR-CLIP data, allowing researchers to predict potential microRNA binding sites within PAR-CLIP peaks. cERMIT : A motif finder for large sequence sets e.g. from chromatin or RNA immunoprecipitation experiments, enabling users to identify conserved motifs across different sequences. Databases doRiNA : A database of RNA interactions in post-transcriptional regulation, providing insights into the complex relationships between RNAs. circBase : A database for public circular RNA datasets, allowing users to discover circRNAs in RNA-seq data and explore their potential functions. Target Audience The Berlin RNA Toolbox is designed for researchers in the fields of molecular biology, bioinformatics, and computational biology. The tools and databases provided are particularly useful for scientists interested in understanding various aspects of RNA biology, including microRNA regulation, circular RNAs, and protein-RNA interactions.

bHLH Annotator is a web-based tool for the automated identification and functional annotation of the basic Helix–Loop–Helix (bHLH) transcription factor family in plants. The tool analyzes coding or protein sequences derived from genome or transcriptome assemblies and combines homology searches, phylogenetic analysis, orthology inference, and motif detection to provide reliable functional annotations. By automating the annotation workflow, bHLH Annotator enables rapid and reproducible characterization of bHLH gene families in newly sequenced plant species. Key benefits Automated identification of plant bHLH transcription factors Functional annotation based on orthology to experimentally characterized bHLHs Combines BLAST or HMMER searches with phylogenetic classification Detects conserved bHLH domains, DNA-binding properties, and subfamily-specific motifs Supports genome and transcriptome assemblies Web-based service with reproducible analysis workflow Applications Annotation of bHLH gene families in newly sequenced plant genomes Functional characterization of transcription factors Comparative genomics of plant transcription factor families Evolutionary and phylogenetic analyses of bHLH proteins Candidate gene identification for plant functional genomics Analysis of de novo genome and transcriptome assemblies Intended use The bHLH Annotator is intended for plant biologists, genome annotation specialists, bioinformaticians, and evolutionary researchers working with plant genome or transcriptome data. It is particularly suited for researchers who require accurate and automated annotation of bHLH transcription factors for comparative genomics, gene family evolution, and functional genomics studies.

BIIGLE is a web-based software for image and video annotation that enables collaborative research on large datasets. It offers tools for manual and computer-assisted annotation, quality control and the collaboration on custom taxonomies to describe objects. BIIGLE is freely available and can be installed in cloud environments, a local network or on mobile platforms during research expeditions. The public instance on biigle.de is free for non-commercial use.

Bioconda is a community-driven software distribution for bioinformatics and life-science tools based on the Conda package manager. It provides easy access to thousands of curated software packages and supports reproducible installation and management of complex bioinformatics workflows. Bioconda packages are tightly integrated with BioContainers, enabling container-based execution of the same software. Key Benefits: Simple installation with automatic dependency resolution. Reproducible environments through versioned packages and containers. Broad coverage across genomics, transcriptomics, metagenomics, proteomics, and systems biology. Flexible execution via Conda environments or containers. Suitable for local systems, HPC, and cloud infrastructures. Features: Large, community-maintained repository of bioinformatics software packages. Automated building and testing to improve consistency and reliability. Generation of BioContainers from Bioconda packages for container-based workflows. Support for isolated Conda environments and container runtimes. Compatibility with Linux and macOS systems. Applications: Installation and management of bioinformatics software stacks. Building reproducible analysis environments for research and training. Running workflows in container-based systems and workflow managers. Standard software provisioning in research infrastructures and core facilities. Intended Use: For bioinformaticians, life-science researchers, and infrastructure providers who need reliable, reproducible software installation. Supports both Conda-based environments and containerized execution using BioContainers.

BioContextAI is a community hub that connects agentic artificial intelligence with biomedical resources and software via Model Context Protocol (MCP) servers. Its main goal is to foster the development of MCP servers for biomedical research applications that comply with the FAIR4RS principles (Findable, Accessible, Interoperable, and Reusable for Research Software). BioContextAI provides the BioContextAI Registry, a community-driven catalogue of MCP servers supporting AI-based biomedical research workflows. The Registry enables researchers and developers to discover, access, and contribute specialized MCP-based tools and databases enriched with structured metadata. Key benefits Community-driven registry of MCP servers for biomedical AI applications Supports FAIR4RS-compliant software development Enables integration of AI agents with biomedical databases and tools Rich metadata to improve discoverability and interoperability Encourages collaboration between AI developers and biomedical researchers Applications Discovery and reuse of MCP servers for AI-supported biomedical workflows Integration of large language models (LLMs) with biomedical tools and databases Development of interoperable AI-driven research applications FAIR4RS-oriented software development and community contribution Exploration of agent-based AI approaches in life science research Intended use BioContextAI is intended for biomedical researchers, AI developers, research software engineers, and data infrastructure providers who aim to integrate agent-based AI systems with biomedical resources in a FAIR-compliant manner. Optional knowledge about LLM tool usage via MCP is beneficial for advanced development and integration scenarios. Website Contact If you used this service, please help us improve by completing our short user survey.

BRENDA – Comprehensive Enzyme Information System BRENDA is one of the world's most comprehensive databases of enzyme functional information. It provides manually curated data on enzymes classified according to the Enzyme Commission (EC) nomenclature, covering thousands of EC numbers across all domains of life. The database contains experimentally validated information extracted from primary literature, including enzyme functions, kinetics, substrate specificity, regulation, and optimal reaction conditions. All entries are critically reviewed by experts to ensure high data quality and consistency. Key benefits Comprehensive, manually curated enzyme information database Covers enzymes from more than 8,800 EC numbers Includes experimentally validated functional and kinetic data Information on substrates, products, inhibitors, cofactors, and enzyme regulation Provides pH and temperature optima as well as expression data Links to metabolic pathways and related biological databases Freely accessible through a user-friendly web interface Applications Enzyme function annotation and characterization Identification of enzyme substrates, products, and inhibitors Investigation of enzyme kinetics and catalytic properties Metabolic pathway analysis and reconstruction Comparative enzymology and systems biology Support for biotechnology, metabolic engineering, and drug discovery Intended use BRENDA is intended for biochemists, molecular biologists, bioinformaticians, systems biologists, and biotechnology researchers seeking comprehensive, high-quality enzyme information. It is particularly suited for users requiring curated experimental data on enzyme function, kinetics, regulation, and metabolism for research, annotation, and computational modelling.

CalibraCurve is an R package for generating and visualizing calibration curves from targeted mass spectrometry-based quantitative data. It supports applications in proteomics, lipidomics, metabolomics, and related omics fields. The package enables users to assess linearity, determine upper and lower limits of quantification, and predict concentrations from measured intensities for absolute quantification. Key benefits Generates calibration curves for targeted quantitative MS data Supports proteomics, lipidomics, metabolomics, and related data Assesses linearity and upper/lower limits of quantification Predicts concentrations from measured intensities Produces customizable, publication-ready ggplot2-based visualizations Applications Absolute quantification in targeted mass spectrometry experiments Evaluation of calibration curve quality and measurement linearity Determination of quantification limits for omics assays Visualization of single or multiple calibration curves Integration into automated workflows using the accompanying Nextflow pipeline Intended use CalibraCurve is intended for proteomics, lipidomics, metabolomics, and mass spectrometry researchers who need reproducible tools for calibration curve generation, quality assessment, and absolute quantification. It is particularly suited for users who want flexible R-based visualization and integration into existing analysis pipelines.

CATS (Crop Analysis Tools Suite) is an online platform that brings together a diverse collection of tools and resources for plant genome analysis, crop research, and research data management. The suite supports sequence similarity searches, microsatellite identification, genome and pan-genome exploration, crop diversity analysis, and the creation of FAIR and ISA-compliant metadata. Key benefits Central access to complementary tools for crop genome analysis and data management Supports sequence search, genome annotation, visualization, and comparative genomics Provides access to current crop reference and pan-genome resources Includes tools for molecular marker and primer development Facilitates barley genomics, genebank exploration, and crop diversity research Supports FAIR and standardized metadata annotation for life science experiments Applications Homology searches against crop genome and pan-genome resources Identification of microsatellites and development of molecular markers Exploration of barley genes, orthologous groups, and genome annotations Analysis of crop diversity, phenotypic traits, and sequence polymorphisms Creation of standardized experimental metadata following ISA and MIAPPE principles Included tools Web BLAST Server – Web-based sequence similarity searches against current crop genome and pan-genome resources MISA Web – Identification of microsatellites and generation of molecular markers or primers PanBARLEX – Exploration of genes and orthologous groups across the barley pan-genome ISA Wizard – User-friendly creation of FAIR and ISA-compliant metadata for life science experiments, including support for MIAPPE-based plant phenotyping metadata BRIDGE – Exploration of the IPK barley genebank collection based on genetic diversity, phenotypic traits, and sequence polymorphisms Intended use CATS is intended for plant geneticists, crop scientists, breeders, molecular biologists, bioinformaticians, and research data managers working with crop genome data and experimental metadata. It is particularly suited for researchers who need integrated access to tools for sequence analysis, genome exploration, marker development, crop diversity analysis, and FAIR data documentation.