The RDF Knowledge-based Database for plant molecular networks.
Fouille de texte Ontologies Web sémantique Extraction de connaissances Intégration de données hétérogènes Représentation des connaissances
GPL-3.0 Mature
ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: i) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; ii) A multispecies genomic browser; iii) a Genomicus gene synteny browser.
Mature
Tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region.
An aphid genome database.
Génomique comparative Analyse de données de séquençage NGS Annotation de séquences
Curation de collections de données Protéomique
MIT Mature
A software for automated NOE assignment and NMR structure calculation.
AGPL-3.0 Mature
AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL
Ontologies Web sémantique Intégration de données hétérogènes Représentation des connaissances Analyse de données de séquençage NGS
Design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.
GPL-3.0 Mature
A unified workspace built around a Python package PADMet (Python library for hAndling metaData of METabolism), to house the reconstruction of genome-scale metabolic models.
Modélisation des réseaux métaboliques Biologie des systèmes Analyse des réseaux métaboliques Intégration de données hétérogènes
Integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.
Comparaison des génomes Génomique comparative Analyse de séquences Prédiction d'homologie/orthologie
Comparaison des génomes Annotation de séquences Recherche de motifs Bases de données et systèmes d’informations
Analyse de séquences Prédiction d'homologie/orthologie Bioinformatique structurale Prédictions des propriétés structurales Annotation de séquences
Curation de collections de données
GPL-2.0 Mature
A Next-Generation Information System for Musa genomics
Génomique (DNA-seq) Comparaison des génomes Analyse de séquences Interfaces, portails web Intégration d'outils Bases de données et systèmes d’informations
Other Emerging
BIII (BioImage Informatics Index, biii.eu) is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis. Software tools are organized as either a full protocol of analysis (workflow), a specific component to construct a workflow, or a software platform or library (collection). They are described using EDAM-bioimaging. All entries are exposed following FAIR principles and accessible for other usage with ODC-By v1.0 license.
AGPL-3.0 Mature
BioMAJ is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.
Gestion et transfert de données Données
This software is well suited for distances estimated from DNA or protein sequences. It has better topological accuracy than NJ in all evolutionary conditions; its superiority becomes important when the substitution rates are high and varying among lineages.
Evolution et phylogénie Evolution moléculaire Gènes et génomes
Environnements de calcul Cluster Intégration de données Gestion et transfert de données Données Interfaces, portails web Développements technologiques de l‘Information et de la Communication Outils Intégration d'outils Parallélisation Bases de données et systèmes d’informations
Bacterial protein tYrosine Kinase database (BYKdb). Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences.
Cluster Intégration de données Gestion et transfert de données Données Développements technologiques de l‘Information et de la Communication Parallélisation Bases de données et systèmes d’informations
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.
Analyse de séquences
