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SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology

The SynBioHub repository (https://synbiohub.org) is an open-source software project that facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a …

A brief history of COMBINE

Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to transport information reliably, to apply a variety of tools to their problems, and to reproduce scientific results. Over the past …

Toward Community Standards and Software for Whole-Cell Modeling

Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell …

Sharing Structure and Function in Biological Design with SBOL 2.0

The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real …

Introduction to the Special Issue on Computational Synthetic Biology

The goal of this special issue is to introduce the field of computational synthetic biology to engineers and computer scientists. The first article gives an introduction to the key biological principles and experimental techniques that support …

Stochastic Model Checking of Genetic Circuits

Synthetic genetic circuits have a number of exciting potential applications such as cleaning up toxic waste, hunting and killing tumor cells, and producing drugs and bio-fuels more efficiently. When designing and analyzing genetic circuits, …

libSBOLj 2.0: A Java Library to Support SBOL 2.0

The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic …

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form …

A new assertion property language for analog/mixed-signal circuits

This book brings together a selection of the best papers from the sixteenth edition of the Forum on specification and Design Languages Conference (FDL), which was held in September 2013 in Paris, France. FDL is a well-established international forum …

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

COMBINE (Computational Modeling in Biology Network) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE's aim is to act as a coordinator, facilitator, and …