Services: Software tools
Name of service | Tag | Related links* | Key collection | |
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2Dprots |
A database including visualizations of protein secondary structure via 2D diagrams. The 2D diagrams are based on whole protein family and they take into account 2D structure of the protein family members. |
bio.tools | ||
AcivityFinder |
ActivityFinder establishes a connection between crystallographic data stored in the PDB database and the activity values stored in the ChEMBL database. |
TeSS | ||
ACT |
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. |
bio.tools | ||
Alfred |
Alfred is a comprehensive NGS alignment quality control method that supports commonly used QC metrics, RNA and DNA feature counting and flexible feature annotation. |
bio.tools | ||
AMYL-PRED 2 |
A Consensus Method for Amyloid Propensity Prediction |
bio.tools | ||
ANASTASIA |
ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository. |
bio.tools | ||
ANISEED |
ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser. |
bio.toolsFAIRsharing | ||
Annotating principal splice isoforms (APPRIS) |
Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation. |
bio.tools | ||
Argot |
Annotation Retrieval of Gene Ontology Terms using semantic similarity in Gene Ontology. |
bio.tools | ||
ARIA |
ARIA (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the assignment process through the use of an iterative structure calculation scheme. |
bio.tools | ||
ARIES |
A customised Galaxy instance for the genomic characterisation of microoganisms in particular and data intensive biomedical research in general. |
bio.tools | ||
ASA3P |
Automated high-throughput assembly, annotation and feature analysis of microbial genome cohorts |
bio.tools | ||
ASAP |
ASAP (Automated Single-cell Analysis Portal) is a web-based, collaborative portal aimed at democratizing single-cell omics data analyses and to render it more accessible to researchers. ASAP does not require any installation and enables standardized analyses that can be run in minutes by any user without requiring significant computing power. The entire single-cell analysis pipeline is available in ASAP, allowing users to choose from a panel of tools, and guiding them through tutorials. |
bio.tools | ||
Atomic Charge Calculator |
Atomic Charge Calculator - web application using the Electronegativity Equalization Method. |
bio.tools | ||
AuReMe |
AuReMe, is an adaptable workspace for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. It is adapted to the metabolic study of non-conventional organisms and microbiomes to ensure that the process is reproducible and documented regardless of the combination of tools used. Among others, modules included in the AuReMe environment are a model-management PADmet module, a wiki-export module, a gap-filling tool for non-conventional organism (meneco), a tool for the reduction of microbial communities based on metabolic complementarities (miscoto) and a package to handle the analysis of large-scale microbiota (Metage2Metabo). |
bio.tools | ||
BaCelLo |
Predicts the subcellular localization of proteins in eukaryotes. |
bio.tools | ||
Bakta |
Bakta is a tool for the rapid and standardised annotation of bacterial genomes and plasmids. It provides dbxref-rich and sORF-including annotations in machine-readable JSON and bioinformatics standard file formats for automatic downstream analysis. |
bio.tools | ||
Berlin RNA Toolbox |
Online access to tools and databases related to miRNAs binding site predictions, RNA Binding protein binding sites, circular RNAs, CLIP data analysis and transcriptome analysis |
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Beyondcell |
Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments. |
bio.tools | ||
BIBIServ |
The Bielefeld Bioinformatics Server (BiBiServ) hosts bioinformatics tools from the Bielefeld groups and close collaborators. |
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BIIGLE |
BIIGLE is a web service for the efficient and rapid annotation of still images and videos. |
bio.tools | ||
bio.tools |
Web portal for tools registry and discovery, incorporating tool benchmarking and service monitoring information and the use of EDAM for precise scientific tool description. |
bio.tools | ||
BiocompR |
BiocompR is an R package that improves visualisations commonly used in biology and genomics for data comparison and dataset exploration. |
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BioConda & BioContainers |
Build, test and convert Cloud and HPC software into Linux containers. |
bio.tools | ||
BiocWorkflowTools |
This bioconductor authoring tool links the journal’s manuscript management system with the Bioconductor nightly build system, thus enabling “continuous Integration”, automated quality control and guaranteed workflow functionality even as underlying resources and tools evolve. A package and tutorial publication are underway, and we have actively helped several authors from the community with workflow authoring. |
bio.tools | ||
BioExcel Building Blocks (BioBB) |
Biobb (BioExcel building blocks) are Python building blocks wrapping popular computational biomolecular tools. |
bio.tools | ||
BioImage Informatics Index (BISE) |
BIII Bio Image informatics Index (www.biii.eu) is a knowledge database of software tools, test image databases and training materials for bio image analysis. Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection). They are described using Edam Bio Imaging, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage with (ODC-By) v1.0 license. |
bio.tools | RIR | |
biomaRt |
Provides an R interface to BioMart services. In particular this is the most widely used programmatic access route to query EMBL-EBI’s Ensembl database. |
bio.tools | ||
Biophysical Proteome Atlas |
Website offering a comprehensive framework for constructing Biophysical Proteomes. |
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BioTextQuest(+) |
Knowledge integration platform for literature mining and concept discovery |
bio.tools |