Related Resources¶
PBPK Modeling Resources¶
Software Tools¶
Commercial Tools: - GastroPlus - Advanced compartmental absorption and transit (ACAT) model - Simcyp - Population-based PBPK modeling platform - PK-Sim - Open-source PBPK modeling software - ADMET Predictor - ADMET property prediction
Open Source Tools: - PK-Sim - Open Systems Pharmacology Suite - Open Systems Pharmacology - Community-driven modeling platform - R packages - Various PBPK-related R packages - Python libraries - PBPK modeling libraries
Databases¶
Physiological Data: - ICRP - International Commission on Radiological Protection - EPA - Environmental Protection Agency physiological data - Allometric scaling databases - Species-specific parameters
Chemical Data: - ChEMBL - Chemical database of bioactive molecules - PubChem - Chemical information database - DrugBank - Drug and drug target database
Ontology Resources¶
Related Ontologies¶
Foundational Ontologies: - BFO - Basic Formal Ontology - RO - Relation Ontology - IAO - Information Artifact Ontology
Domain Ontologies: - GO - Gene Ontology - OBI - Ontology for Biomedical Investigations - SBO - Systems Biology Ontology - ChEBI - Chemical Entities of Biological Interest
Pharmacology Ontologies: - Drug Ontology - Drug-related terms - Pharmacokinetics Ontology - PK-specific terms - ToxML - Toxicology markup language
Ontology Tools¶
Development Tools: - ROBOT - OBO ontology development tool - Protégé - Ontology editor - OWL API - Java API for OWL - rdflib - Python RDF library
Validation Tools: - HermiT - OWL reasoner - Pellet - OWL 2 reasoner - Fact++ - OWL reasoner - ELK - EL reasoner
Educational Resources¶
Tutorials and Courses¶
PBPK Modeling: - PBPK Modeling Course - Online course materials - Tutorial Series - Step-by-step guides - Video Lectures - Recorded presentations - Workshop Materials - Hands-on exercises
Ontology Development: - OBO Academy - Comprehensive ontology tutorials - ROBOT Tutorial - Template-based development - Protégé Tutorial - Ontology editing - OWL Tutorial - Web Ontology Language
Books and References¶
PBPK Modeling: - "Physiologically Based Pharmacokinetic Modeling" by Reddy et al. - "PBPK Modeling and Simulation" by Rowland et al. - "Computational Toxicology" by Reisfeld and Mayeno
Ontology Development: - "Ontology Engineering" by Gómez-Pérez et al. - "Semantic Web Technologies" by Antoniou and van Harmelen - "OWL 2 Web Ontology Language" by W3C
Community Resources¶
Forums and Discussions¶
PBPK Community: - PBPK Modeling Forum - Discussion platform - LinkedIn Groups - Professional networking - Twitter - #PBPK hashtag discussions - Reddit - r/pharmacokinetics
Ontology Community: - OBO Foundry - Community discussions - Protégé Forums - Technical support - Stack Overflow - Programming questions - GitHub Discussions - Project-specific discussions
Conferences and Events¶
PBPK Conferences: - International Conference on Pharmacokinetics - PBPK Modeling Workshop - Regulatory Science Conference - Drug Development Conference
Ontology Conferences: - OBO Foundry Workshop - International Semantic Web Conference - Bio-Ontologies Workshop - Ontology Summit
Regulatory Resources¶
Guidelines and Standards¶
FDA Guidelines: - PBPK Modeling Guidance - FDA guidance document - Model-Informed Drug Development - FDA framework - Pediatric Study Plans - PBPK applications
EMA Guidelines: - PBPK Modeling Guideline - EMA guidance - Paediatric Investigation Plans - PBPK requirements - Scientific Guidelines - Regulatory requirements
ICH Guidelines: - ICH M3(R2) - Nonclinical safety studies - ICH S6(R1) - Preclinical safety evaluation - ICH E14 - Clinical evaluation of QT prolongation
Data Standards¶
Exchange Formats¶
Model Exchange: - SBML - Systems Biology Markup Language - CellML - Mathematical model description - SED-ML - Simulation experiment description - COMBINE - Standards for systems biology
Data Formats: - JSON-LD - Linked data format - RDF - Resource Description Framework - OWL - Web Ontology Language - OBO - Open Biomedical Ontologies format
Funding and Support¶
Grant Opportunities¶
Research Funding: - NIH - National Institutes of Health - NSF - National Science Foundation - EU Horizon - European Union funding - Wellcome Trust - Biomedical research funding
Open Source Support: - GitHub Sponsors - Open source funding - Open Collective - Community funding - Patreon - Creator support - Corporate Sponsors - Industry support
Contact and Support¶
Getting Help¶
Technical Support: - GitHub Issues - Bug reports and feature requests - Email - saurav.kumar@iispv.cat - Documentation - This site - Community Forums - User discussions
Collaboration: - Research Partnerships - Academic collaboration - Industry Partnerships - Commercial collaboration - Training Programs - Educational partnerships - Consulting Services - Professional services