Synthetic Biology Open Language (SBOL)

Published by Journal of Integrative Bioinformatics

SBOLSynthetic Biology Open LanguageIn silico

The 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.

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Systems Biology Markup Language (SBML)

Published by SBML

In silicoSBML

SBML 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.

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Jaqpot 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

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In-silico trial of intracranial flow diverters replicates and expands insights from conventional clinical trials

Published by Nature Communications

virtual patientsClinical TrialsIn silico

In-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

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COSYS 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.

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