Introduction to the Special Issue on Computational Synthetic Biology

2014 ◽  
Vol 11 (3) ◽  
pp. 1-5
Author(s):  
Chris J. Myers ◽  
Herbert Sauro ◽  
Anil Wipat
Keyword(s):  
Synthetic Biology ◽  
Special Issue

scholarly journals Special Issue “Metabolic Engineering and Synthetic Biology Volume 2”

Metabolites ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 35
Author(s):  
An N. T. Phan ◽  
Lars M. Blank
Keyword(s):  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Special Issue ◽  
Subsequent Increase ◽  
Increasing Demand

In times of ever-increasing demand for chemicals and the subsequent increase in CO2 in the atmosphere, we have to intensify our efforts to establish a circular (bio) economy [...]

scholarly journals Specifications of Standards in Systems and Synthetic Biology

2015 ◽  
Vol 12 (2) ◽  
pp. 1-3 ◽  
Author(s):  
Falk Schreiber ◽  
Gary D. Bader ◽  
Martin Golebiewski ◽  
Michael Hucka ◽  
Benjamin Kormeier ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Information Exchange ◽  
Computational Models ◽  
Access Point ◽  
Economic Benefits ◽  
Special Issue ◽  
Community Initiative ◽  
Central Access ◽  
Oral Presentations ◽  
Modeling In Biology

Summary Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation).Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork [1] has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/.So far the different standards were published and made accessible through the standards’ web-pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

scholarly journals Synthetic Biology Open Language (SBOL) Version 2.1.0

2016 ◽  
Vol 13 (3) ◽  
Author(s):  
Jacob Beal ◽  
Robert Sidney Cox ◽  
Raik Grünberg ◽  
James McLaughlin ◽  
Tramy Nguyen ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Molecular Biology ◽  
Best Practices ◽  
Basic Sequence ◽  
Special Issue ◽  
Biological Design ◽  
Version 2.0 ◽  
Topology Information ◽  
Synthetic Biology Open Language

SummarySynthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. 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 2.1 of SBOL that builds upon version 2.0 published in last year’s JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.

scholarly journals Synthetic Biology Open Language (SBOL) Version 2.3

2019 ◽  
Vol 16 (2) ◽  
Author(s):  
Curtis Madsen ◽  
Angel Goñi Moreno ◽  
Umesh P ◽  
Zachary Palchick ◽  
Nicholas Roehner ◽  
...  
Keyword(s):  
Experimental Data ◽  
Metabolic Engineering ◽  
Systems Biology ◽  
Synthetic Biology ◽  
Molecular Biology ◽  
Special Issue ◽  
Design Elements ◽  
Biological Design ◽  
Support Organization ◽  
Synthetic Biology Open Language

AbstractSynthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems is to improve the exchange of information about designed systems between laboratories. 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, which builds upon version 2.2.0 published in last year’s JIB Standards in Systems Biology special issue. In particular, 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. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, refinement of a number of validation rules, improved figures and examples, and clarification on a number of issues related to the use of external ontology terms.

Sign in / Sign up

Export Citation Format

Share Document