PathRover
“tools for Rover & Analysis systems medicine disease map”
Focus on “systems medicine disease map(SMDM)” and modeling on them…
Biological Pathway
“A biological pathway or molecular interaction maps (MIMs) is a sequence of molecular interactions in a cell that results in a specific outcome or a modification in the cell. It can initiate the formation of new molecules, such as a fat or protein, activate or deactivate genes, or stimulate a cell to move.”
Systems medicine disease map (SMDM)
A Systems Medicine Disease Map (SMDM) is a detailed, expert-led representation of disease mechanisms, acting as a conceptual model of a disease. It features interconnected signaling, metabolic, and gene regulatory pathways, stored in standard formats such as SBGN, SBML and BioPAX.
The involvement of domain experts, including clinicians and biologists, ensures comprehensive coverage of all disease hallmarks and accurate representation of relevant knowledge.
The Disease maps are the networks (disease molecular pathways) themselves, displayed by the MINERVA Platform in a web browser, where user can explore and analyse them.
LINK: portal for communication, news, guidelines, and other information about the Disease Maps Project.
minerva-entity-explorer
This tool was created due to the fact that “disease molecular maps projects” are not integrated in a database and there is no engine for simultaneous search in them.
minerva-detail-explorer
This tool extracts and displays the detailed information of the components by using existing epi maps. Considering that the “disease molecular maps projects” presented on the Minerva platform do not provide the detailed information of the maps, this tool can help researchers Help in this regard.
CASQ
Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap between static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner.
MetaLo
MetaLo, an open-source Python package that enables the coupling of Boolean models inferred from process description MIMs with generic core metabolic networks. MetaLo provides a framework to study the impact of signaling cascades, gene regulation processes, and metabolic flux distribution of central energy production pathways. MetaLo computes the Boolean model’s asynchronous asymptotic behavior, through the identification of trap-spaces, and extracts metabolic constraints to contextualize the generic metabolic network. MetaLo is able to handle large-scale Boolean models and genome-scale metabolic models without requiring kinetic information or manual tuning.
MINERVA NET
MINERVA Net is a registry of publicly shared disease maps projects.MINERVA Net enables the users to share information about their projects on the central server via dedicated API.
Cell Collective
Cell Collective is an interactive, open and collaborative modeling platform for Biological Networks for researchers, students and teachers worldwide.
CoLoMoTo
CoLoMoTo (Consortium for Logical Models and Tools) is a consortium of research groups interested in logical modelling: modelers, curators and developers of methods and tools. The consortium works on the definition of standards for model representation and interchange (especially the SBML qual format), and on the comparison of methods, models and tools.
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Logical Qualitative Modelling toolkit
Java library for the manipulation and conversion of logical models
BoolNetR
package for the simulation, reconstruction and analysis of various types of Boolean networks
The Cell Collective
Web-based plateform for the construction and simulation of Boolean models
CellNetAnalyzer
A MATLAB package with graphical user interface for structural and functional analysis of cellular networks
CellNOpt (CellNetOptimizer)
CellNOpt is a free open-source toolbox for creating logic-based models of signal transduction networks, and training them against high-throughput biochemical data.
EpiLog
Simulation of epithelial patterning using multi-cellular multivalued logical models
GINsim
Java software for the construction and analysis of multivalued models
Genetic Network Analyzer (GNA)
Genetic Network Analyzer (GNA) is a computer tool for the qualitative modeling, analysis, and simulation of gene regulatory networks
JSBML
Java API library for parsing and writing SBML files and for in-memory manipulation of SBML data structures
LogicModelClassifier
A comprehensive number of Python scripts that allow the specification, management and analysis of model pools
MaBoSS
Continuous time Boolean modeling
Pint
Static analyzer for transient dynamics of automata networks
PyBoolNet
Python API for the analysis of Boolean networks
SQUAD & BoolSim
Standardized continous simulation of logical models
TemporalLogicTimeSeries
Translates discretized time series data into LTL and CTL specifications for NuSMV model checking
“type of maps and standards”
Disease map
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Pathways databases
- KEGG Pathway database is a popular pathway search database highly used by biologists.
- WikiPathways is a community curated pathway database using the “wiki” concept. All pathways have an open license and can be freely used.
- Reactome is a free and manually curated online database of biological pathways.
- NCI-Nature Pathway Interaction Database is a free biomedical database of human cellular signaling pathways (new official name: NCI Nature Pathway Interaction Database: Pathway, synonym: PID).
- PhosphoSitePlus is a database of observed post-translational modifications in human and mouse proteins; an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation.
- BioCyc database collection is an assortment of organism specific Pathway/Genome Databases.
- Human Protein Reference Database is a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome (the last release was #9 in 2010).
- PANTHER (Protein ANalysis THrough Evolutionary Relationships) is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products.
- TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles (provided by geneXplain GmbH).
- MiRTarBase is a curated database of MicroRNA-Target Interactions.
- DrugBank is a comprehensive, high-quality, freely accessible, online database containing information on drugs and drug targets.
- esyN is a network viewer and builder that allows to import pathways from the biomodels database or from biogrid, flybase pombase and see what drugs interact with the proteins in your network.
- Comparative Toxicogenomics Database (CTD) is a public website and research tool that curates scientific data describing relationships between chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules; CTD illuminates how environmental chemicals affect human health.
- Pathway commons is a project and database that uses BioPAX language to convert, integrate and query other biological pathway and interaction databases.
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