Tag: network model


Found 38 sources
Source Match ReputationScore*

Comparative Toxicogenomics Database


Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...
100%

Systems Biology Markup Language


The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. By su ...
96%

NeuroML


NeuroML is a model description language developed in XML (extensible Markup Language) that was created to facilitate data archiving, data and model exchange, database creation, and model publication in the neurosciences. One of the goals of the Neuro ...
84%

BioModels


BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...
81%

Systems Biology Graphical Notation


The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes. The mission of SBGN project is to develop high quality, standard graphical languages for representing biolo ...
81%

The Network Data Exchange (NDEx)


NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytosc ...
67%

VirHostNet 2.0


VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.
66%

VirusMentha


VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions. vir ...
63%

Sol Genomics Network


The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.
63%

Arabidopsis Information Portal


The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...
63%

ModelDB


ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. ModelDB is tightly coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downl ...
62%

Termini-Oriented Protein Function INferred Database


TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alte ...
62%

Protein Interaction Network Analysis platform


Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated ...
61%

MetaNetX


MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. Meta ...
61%

SignaLink


SignaLink is an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. it allows browsing of signaling pathways, cross-talks and multi-pathway proteins; selection of transcriptional, post- ...
59%

YEASTNET: A consensus reconstruction of yeast metabolism


This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from ...
59%

PyNN


The PyNN API aims to support modelling at a high-level of abstraction (populations of neurons, layers, columns and the connections between them) while still allowing access to the details of individual neurons and synapses when required. PyNN provide ...
57%

Signaling Pathway Integrated Knowledge Engine


SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...
55%

GeneNetwork


GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists togethe ...
54%

Pathway Ontology


The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes o ...
54%

KEGG Mark-up Language


The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KGML enables automatic drawing of KEGG pathways and provides facilities for computational analysis and mo ...
53%

Bacterial Protein Interaction Database


Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.
52%

BioModels Ontology


OWL Representation of the models in the BioModels repository.
52%

GeneNet Engine


GeneNet Engine is an exploratory tool to aid hypothesis and biomarker development at a systems-level for genotype-phenotype relationships. Expressed phenotypes may arise due to interactions between multiple genes in a system and effects from the surr ...
52%

Interaction Network Ontology


The Interaction Network Ontology (INO) aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It models general interactions (e.g., molecular interactions) and interact ...
51%

DyNet


DyNet is a Cytoscape application that provides a range of functionalities for the visualization, realtime synchronization, and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the mos ...
50%

Brainstem Connectome


Database of all known neuronal connections of the rat brainstem. Connections are directed, weighted and bilateral. It is built using the neuroVIISAS platform. The Brainstem Connectome is a highly structured neuroontology composed of datasets from ove ...
48%

Enzyme Mechanism Ontology


The "Enzyme Mechanism Ontology " describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.
48%

Genome-wide Integrated Analysis of gene Networks in Tissues 2.0


GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional ...
47%

DNAtraffic


A database for systems biology of DNA dynamics during the cell life.
45%

Automatic molecular interaction predictions


InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interac ...
44%

Animal Trait Correlation Database


A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene express ...
43%

Translocatome


Translocatome is a database that collects and characterises manually curated and predicted translocating proteins from human cells. The prediction is made by a gradient boosting based machine learning algorithm (XGBoost), using highly curated positiv ...
40%

Human Interaction Network Ontology


The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has incorporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed following the OBO Foundry principle ...
38%

Compartmentalized Protein-Protein Interaction


The compartmentalized protein-protein interaction database (ComPPI), provides qualitative information on the interactions, proteins and their localizations integrated from multiple databases for protein-protein interaction network analysis.
38%

MDL reaction Format


MDL reaction Format is used to describe the kinetics of chemical reactions and the chemical structure of the reactants and products.
36%

DBpedia


DBpedia is a crowd-sourced community effort to extract structured content from the information created in various Wikimedia projects. This structured information resembles an open knowledge graph (OKG).
36%

eXtensible Graph Markup and Modeling Language


XGMML (eXtensible Graph Markup and Modeling Language) is an XML application based on GML which is used for graph description. XGMML uses tags to describe nodes and edges of a graph. The purpose of XGMML is to make possible the exchange of graphs betw ...
36%

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