A European standardization framework for data integration and data-driven in silico models
for personalised medicine
Disease Model
In this section you will have the opportunity to explore cellular models:
patient-derived immortalized cell lines, and animal models
Patient-derived induced pluripotent stem cell (iPSCs)
Organoid
You can also find information regarding animal models:
Zebra Fish
Fruit fly
Mouse
Rat
Non-human primates
COmputational Modeling in BIology Network (COMBINE)
Published by COmputational Modeling in BIology NEtwork
computational modelsIn silico modelsThe “COmputational Modeling in BIology NEtwork” (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all aspects of modeling in biology
View this resource Bookmark this resource
Synthetic Biology Open Language (SBOL)
Published by Journal of Integrative Bioinformatics
SBOLSynthetic Biology Open LanguageIn silicoThe synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.3.0 of SBOL. SBOL 2.3.0 includes means of succinctly representing sequence modifications, such as insertion, deletion, and replacement, an extension to support organization and attachment of experimental data derived from designs, and an extension for describing numerical parameters of design elements.
View this resource Bookmark this resourceNeuroML is an international, collaborative initiative to develop a language and associated software tools for describing detailed models of neural systems.
View this resource Bookmark this resourceSBML is a software data format for describing models in biology. It’s a little like HTML, but for formal models instead of web pages. It’s independent of any particular software tool and not limited to any particular field of the life sciences. It’s open and free.
View this resource Bookmark this resource
Applied Concepts in PBPK Modeling: How to Build a PBPK/PD Model
Published by CPT Pharmacometrics & Systems Pharmacology
pharmacokinetic/pharmacodynamic (PBPK/PD) modelingIn silicoThe aim of this tutorial is to introduce the fundamental concepts of physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) modeling with a special focus on their practical implementation in a typical PBPK model building workflow
View this resource Bookmark this resourceJaqpot is a computational platform for in silico modelling of chemical compounds, that provides both access to its services both over a User Interface (GUI) and an Application Programming Interface (API). It is a cloud-ready application that uses the benefits of Java, R and Python, having incorporated functionality by various established and open-source machine learning and data analysis toolkits, while algorithms in any programming algorithm can be added to Jaqpot. A new version of the UI and API is in preparation and will be released within 2019
View this resource Bookmark this resource
In-silico trial of intracranial flow diverters replicates and expands insights from conventional clinical trials
Published by Nature Communications
virtual patientsClinical TrialsIn silicoIn-silico trials rely on virtual populations and interventions simulated using patient-specific model and may offer a solution to lower these costs. In this article, It is presented the flow diverter performance assessment (FD-PASS) in-silico trial, which model the treatment of intracranial aneurysms in 164 virtual patients with 82 distinct anatomies with a flow-diverting stent, using computational fluid dynamics to quantify post-treatment flow reduction
View this resource Bookmark this resourceCOSYS is an open computational platform designed for the Systems Biology community. Designed to help life scientists to easily access basilar systems biology tools, it can be also used with effectiveness by skilled systems biologists. Cooperation-driven and user-friendly, COSYS is a unified tool for biological modeling (mechanistic and constraint-based), simulation and analysis, providing users with the cutting edge of GPU-powered computation. COSYS is free of charge, and can be used by everyone.
View this resource Bookmark this resourceThis Platform helps communities find, register and benchmark software tools. These tools help researchers access, analyse and integrate biological data, and so drive scientific discovery across the life sciences.
View this resource Bookmark this resource