Registry Catalogue

The FAIRDOMHub is a publicly available repository managed and supported by the FAIRDOM consortium (https://fair-dom.org/). It’s build using the FAIRDOM-SEEK software (http://fairdomseek.org), an open source web platform for storing, sharing and publishing research assets of biology projects. The assets include FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models. FAIRDOMHub enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship. FAIRDOMHub includes special support for the Systems Biology community.

The Freiburg RNA Toolbox provides a comprehensive set of online tools for RNA research, covering various aspects such as sequence-structure alignments, clustering, interaction prediction, identification of homologs, sequence design, and more. Tools Interaction Prediction CopraRNA : A tool for sRNA target prediction that combines whole genome IntaRNA predictions using homologous sRNA sequences from distinct organisms. IntaRNA : A tool for predicting RNA-RNA interactions, including mRNA target sites for non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs). metaMIR : A framework to predict interactions in human between miRNAs and clusters of genes. Seq-Str Alignment LocARNA : A tool for multiple alignments of RNAs based on their sequence and structure similarity, considering the whole ensemble of secondary structures for each RNA. CARNA : A tool for multiple alignment of RNA molecules based on their full ensembles of structures, computing the alignment that fits best to all likely structures simultaneously. MARNA : A tool for multiple sequence-structure alignments considering a single fixed structure for each sequence only. ExpaRNA : A fast, motif-based comparison and alignment tool for RNA molecules. CRISPR CRISPRmap : A tool providing a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems. CRISPRloci : A full suite for CRISPR locus characterization that includes CRISPR array orientation, detection of conserved leaders, cas gene annotation, and subtype classification. Sequence Design AntaRNA : An Ant-Colony Optimization based tool solving the RNA inverse folding problem, designing RNA sequences satisfying a set of constraints. INFORNA : A server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. SECISDesign : A server for the design of SECIS-elements within the coding sequence of an mRNA with both structure and sequence constraints. Splicing NIPU : A tool allowing to display splicing regulatory motifs and single-stranded regions. SNP & Mutation CopomuS : A tool rating and ranking possible compensatory mutations of IntaRNA predictions. MutaRNA : A tool predicting and visualizing the mutation-induced structure changes of a single-nucleotide polymorphism (SNP) in an RNA sequence. RaSE : An offline tool using the graph vectorization technique to compute a score indicative of the structural stability responsibility of each nucleotide in an RNA sequence. Classification BrainDead : A tool learning a two-class model for short RNA sequences based on accessibility-enhanced k-mer features and applying it for class prediction of unknown RNAs. Gene set extension DiGI : A tool predicting and ranking a list of unknown genes based on their probabilities to be related to a given genetic disease. Additional Resources The Freiburg Bioinformatics Group also provides: MoDPepInt Server : A simple and interactive webserver for predicting the binding partners of three different modular protein domains. CPSP-Tools Server : An exact and efficient approach to identify optimal structures of lattice proteins within the hydrophobic-polar (HP) model. Galaxy Project - Uni Freiburg : A framework for scientists on e.g. NGS data analyses, genome annotation analyses, proteomics, and metabolomics analysis. CMV server : Tools for the visualization of RNA family models, also known as co-variance models (CM) and Hidden Markov Models (HMM).

Galaxy Docker provides a ready-to-use Docker-based distribution of the Galaxy platform, enabling users to deploy Galaxy quickly and reproducibly on local machines, servers, or cloud environments. It offers a convenient way to start a fully functional Galaxy instance without manual installation of dependencies, making it well suited for testing, training, and portable analysis setups. Key benefits: Fast and reproducible deployment of a Galaxy instance using Docker No complex local installation—dependencies and configuration are packaged into the container Portable setup for local use, servers, and cloud/HPC-adjacent environments Useful for training courses, workshops, demos, and prototyping Open-source and maintained in a public repository Applications: Rapid setup of Galaxy for teaching, workshops, and hands-on tutorials Testing Galaxy configurations, tools, or workflows in an isolated environment Providing a portable Galaxy environment for teams or collaborations Quick prototyping of analysis environments prior to production deployment Intended use: Galaxy Docker is intended for bioinformatics users, trainers, and service operators who want to deploy Galaxy quickly for temporary or reproducible environments. It is particularly suited for users who prefer a containerized approach for setup and maintenance, or who need a reliable Galaxy instance for training and testing scenarios.

The Galaxy Help Forum provides an open, community-driven platform for user support, troubleshooting, and discussion related to the Galaxy platform. Researchers can ask questions about workflows, tools, installations, errors, and best practices, and receive guidance from Galaxy developers, service operators, and experienced community members. The forum serves as a central knowledge hub for resolving technical issues and improving Galaxy-based analyses. Key benefits: Open and transparent support platform for Galaxy-related questions Direct interaction with developers, administrators, and experienced users Publicly searchable knowledge base of previously answered questions Community-driven troubleshooting and best-practice guidance No cost for scientific users Applications: Troubleshooting Galaxy workflows and tool execution errors Guidance on workflow design and optimization Support for Galaxy installation and configuration Advice on tool selection and parameter settings Exchange of best practices for reproducible analysis Intended use: The Galaxy Help Forum is intended for researchers, bioinformaticians, and Galaxy service users who require assistance with Galaxy workflows, installations, or analysis strategies. It is particularly suited for users seeking community-based support and transparent knowledge exchange in an open forum environment.

Galaxy TIaaS (Training Infrastructure as a Service) is provided by the European Galaxy Server (usegalaxy.eu) to support hands-on training events within the Galaxy training community. TIaaS offers dedicated computational infrastructure for workshops and courses, ensuring stable performance and sufficient resources for all participants during practical sessions. Key benefits: Dedicated computing resources for Galaxy training events Stable and predictable performance during hands-on sessions No local installation required for trainers or participants Scalable infrastructure supporting small and large courses Integrated within the European Galaxy ecosystem Applications: Hands-on bioinformatics workshops using Galaxy University courses and training schools Online and hybrid Galaxy training events Community-driven training initiatives within ELIXIR and de.NBI Intended use: Galaxy TIaaS is intended for trainers, educators, and workshop organizers who conduct hands-on Galaxy courses and require reliable computational infrastructure for participants. It is particularly suited for events where consistent performance and centralized resource management are essential for a smooth training experience.

GeoMine is a tool for the automated mining of protein–ligand binding sites. It enables users to define custom queries and search large collections of protein–ligand complexes and binding pockets for specific spatial interaction patterns. GeoMine supports ligand-based radius pockets as well as predicted pockets generated with DoGSite3 and provides matched binding-site superpositions together with geometric statistics. Key benefits Automated search for spatial patterns in protein–ligand binding sites Custom query design for specific interaction geometries Searches large, regularly updated collections of protein structures and pockets Supports ligand-based and DoGSite3-predicted binding pockets Available through a graphical interface and REST service Provides structural superpositions and statistics on distances, angles, and matching points Applications Identification of recurring interaction patterns in protein binding sites Comparison of geometrically similar binding pockets Analysis of conserved ligand-binding arrangements Discovery of structurally related binding sites across different proteins Support for structure-based drug discovery and ligand design Generation of reference sets for binding-site classification and validation Intended use GeoMine is intended for structural biologists, medicinal chemists, computational chemists, and bioinformaticians working with protein–ligand complexes and binding-site geometries. It is particularly suited for users who want to search large structural datasets for custom spatial interaction patterns and compare matched binding sites in detail.

Goslin is a software tool that facilitates the parsing and normalization of lipid nomenclatures. It provides a standardized way to represent lipids in a computationally accessible format. Key Features: Lipid ontology : Goslin uses a comprehensive lipid ontology to cover various lipid classes and subclasses. Nomenclature parsing : The tool can parse different lipid nomenclatures, including shorthand notations and systematic names. Normalization : Goslin normalizes lipid structures to a standardized format for efficient comparison and analysis. Benefits: Standardization : Goslin enables researchers to easily compare and integrate lipidomics data across different studies and platforms. Improved data quality : The tool's normalization capabilities help ensure accurate and consistent lipid structures. Availability: Goslin is available as a software library that can be downloaded from the LIFS Tools website, or used through its web-based application.

HyPPI is a web-based tool for classifying protein–protein complexes as permanent, transient, or crystal artifacts. Permanent complexes are stable only in their associated state, whereas transient complexes can remain stable both as complexes and as individual subunits. Crystal artifacts are non-biological contacts formed during crystallization. HyPPI performs the classification using two structural properties of the protein–protein interface: its hydrophobicity (ΔGhydrophobic) and the interface quotient (IF-quotient), which reflects the symmetry of the interacting surfaces. Key benefits Automated classification of protein–protein complexes Distinguishes permanent and transient interactions from crystal artifacts Uses interpretable structural interface descriptors Supports assessment of the biological relevance of crystallographic contacts Web-based analysis without local software installation Applications Classification of protein–protein interactions in crystal structures Identification of potentially biologically relevant protein complexes Detection of non-functional crystallization contacts Analysis of interface hydrophobicity and symmetry Support for structural interpretation and protein interaction studies Intended use HyPPI is intended for structural biologists, protein scientists, bioinformaticians, and computational biologists working with three-dimensional protein complex structures. It is particularly useful for researchers who need to assess whether an observed protein–protein interface represents a permanent or transient biological interaction or is likely to be a crystal artifact.

JAMDA is a tool for preparing protein structures and docking small molecules into selected, preprocessed binding sites. It simplifies protein–ligand docking through automated workflows for protein preparation, binding-site setup, ligand conformer generation, docking, and scoring. Users can apply default settings or customize the preparation process to account for protein ensembles, relevant water molecules, and cofactors. Key benefits Automated preparation of proteins and binding sites Integrated docking and scoring of small-molecule ligands Flexible configuration for protein ensembles, water molecules, and cofactors Automated ligand conformer generation using Conformator Supports externally generated ligand conformations Designed for reproducible and streamlined docking workflows Applications Prediction of protein–ligand binding poses Virtual screening of small-molecule compounds Evaluation of alternative ligand conformations Docking into single structures or protein ensembles Investigation of the influence of binding-site waters and cofactors Support for structure-based drug discovery and ligand optimization Intended use JAMDA is intended for structural biologists, medicinal chemists, computational chemists, and researchers in structure-based drug discovery who need an automated and configurable workflow for protein–ligand docking. It is particularly suited for users who want to combine standardized preprocessing with flexible control over protein structures, binding-site components, and ligand conformations.

KIPEs (Knowledge-based Identification of Pathway Enzymes) is a web-based tool for the automated identification and functional annotation of enzymes involved in plant biosynthetic pathways. Using curated reference sequences, functionally relevant amino acid residues, and orthology-based inference, KIPEs identifies candidate genes in coding DNA (CDS), peptide, or transcriptome datasets and predicts their likely biological functions. The current release supports the annotation of enzymes involved in flavonoid biosynthesis (including decoration enzymes and transport proteins) as well as carotenoid biosynthesis. The tool is designed to facilitate the rapid characterization of metabolic pathways in newly sequenced plant species without requiring manual preparation of reference datasets. Key benefits Automated identification of pathway enzymes from CDS, peptide, or transcriptome data Functional annotation based on orthology and conserved functional residues Detection of functionally important amino acid motifs and catalytic sites No manual preparation of reference datasets required Fast and reproducible annotation workflow for newly sequenced species Produces annotated candidate sequences together with detailed summary reports Applications Annotation of enzymes involved in plant biosynthetic pathways Identification of candidate genes in genome and transcriptome assemblies Functional characterization of metabolic pathways Comparative genomics of biosynthetic gene families Evolutionary analysis of plant metabolism Candidate gene discovery for functional genomics and metabolic engineering Intended use KIPEs is intended for plant biologists, genome annotation specialists, bioinformaticians, and evolutionary researchers working with plant genome or transcriptome data. It is particularly suited for users seeking an automated and standardized workflow for the identification and functional annotation of enzymes involved in specialized plant metabolism.

LifeSoaks is a tool for identifying and characterizing solvent channels in macromolecular crystal structures determined by X-ray crystallography. It automatically evaluates channel accessibility by calculating bottleneck radii for solvent channels and small-molecule binding sites. By replacing time-consuming manual inspection, LifeSoaks supports the selection of suitable crystal forms and experimental conditions before soaking experiments. Key benefits Automated detection and analysis of solvent channels in crystal structures Calculation of bottleneck radii to estimate molecular accessibility Supports both solvent channel and small-molecule binding-site analysis Reduces the need for manual inspection of macromolecular crystal structures Rapid analysis, typically completed within seconds to minutes Helps prioritize promising crystal forms and soaking conditions Applications Planning of ligand- and fragment-soaking experiments Assessment of solvent channel accessibility in protein crystals Comparison of alternative crystal forms Identification of potential access routes to binding sites Selection and optimization of experimental soaking conditions Support for X-ray-based fragment screening Intended use LifeSoaks is intended for structural biologists, crystallographers, medicinal chemists, and researchers in structure-based drug discovery working with macromolecular crystal structures. It is particularly suited for users who want to assess whether small molecules can access binding sites before conducting soaking experiments.

LIFS (Lipidomics Informatics for Life Science) is a web portal providing a comprehensive suite of stand-alone and web-based tools for targeted and untargeted mass spectrometry-based lipidomics analysis. The platform supports lipid identification, quantification, quality control, visualization, and lipidome comparison, while also serving as an information hub for lipidomics resources, training, publications, and community activities. Key benefits Comprehensive ecosystem for lipidomics data analysis Combination of stand-alone software and web-based applications Supports both targeted and untargeted lipidomics workflows Standardized and reproducible analysis methods Interactive visualization and structure-based lipidome comparison Central hub for lipidomics software, courses, publications, and conferences Applications Lipid identification and annotation from mass spectrometry data Quantitative and qualitative lipidome comparison Quality control and post-processing of lipidomics datasets Generation of targeted transition lists for mass spectrometry workflows Parsing and normalization of lipid nomenclatures Statistical analysis and visualization of lipidomics experiments Included tools LipidXplorer – Shotgun lipidomics software using MFQL (Mass Spectrometry Formula Query Language) Lipidome Projector – Web application for structure-based lipidome comparison lxPostman – Post-processing and quality control for LipidXplorer outputs Goslin – Libraries and web tools for lipid nomenclature normalization LipidCreator – Creation of lipid-specific targeted transition lists LipidCompass – Interactive exploration and comparison of quantitative lipidomes LipidSpace – Interactive QC, lipidome comparison, statistical analysis, and visualization Intended use LIFS is intended for researchers in lipidomics, metabolomics, systems biology, and mass spectrometry-based life science research who require integrated tools for lipid identification, quantification, comparison, and visualization. The platform is particularly suited for users seeking standardized and reproducible lipidomics workflows supported by both web-based and stand-alone applications.