SBML Level 3: an extensible format for the exchange and reuse of biological models
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …
complexity of computational models. To reproduce simulation results and reuse models …
Genetic circuit design automation with Cello 2.0
Cells interact with their environment, communicate among themselves, track time and make
decisions through functions controlled by natural regulatory genetic circuits consisting of …
decisions through functions controlled by natural regulatory genetic circuits consisting of …
Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii
P Crozet, FJ Navarro, F Willmund… - ACS synthetic …, 2018 - ACS Publications
Microalgae are regarded as promising organisms to develop innovative concepts based on
their photosynthetic capacity that offers more sustainable production than heterotrophic …
their photosynthetic capacity that offers more sustainable production than heterotrophic …
[HTML][HTML] Towards a fully automated algorithm driven platform for biosystems design
Large-scale data acquisition and analysis are often required in the successful
implementation of the design, build, test, and learn (DBTL) cycle in biosystems design …
implementation of the design, build, test, and learn (DBTL) cycle in biosystems design …
[HTML][HTML] Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform
Multi-scale models can facilitate whole plant simulations by linking gene networks, protein
synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further …
synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further …
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 …
facilitates the sharing of information about engineered biological systems. SynBioHub …
[HTML][HTML] The synthetic biology open language (SBOL) version 3: simplified data exchange for bioengineering
The Synthetic Biology Open Language (SBOL) is a community-developed data standard that
allows knowledge about biological designs to be captured using a machine-tractable …
allows knowledge about biological designs to be captured using a machine-tractable …
iBioSim 3: A Tool for Model-Based Genetic Circuit Design
The iBioSim tool has been developed to facilitate the design of genetic circuits via a model-
based design strategy. This paper illustrates the new features incorporated into the tool for …
based design strategy. This paper illustrates the new features incorporated into the tool for …
Design automation in synthetic biology
E Appleton, C Madsen, N Roehner… - Cold Spring Harbor …, 2017 - cshperspectives.cshlp.org
Design automation refers to a category of software tools for designing systems that work
together in a workflow for designing, building, testing, and analyzing systems with a target …
together in a workflow for designing, building, testing, and analyzing systems with a target …
[HTML][HTML] Quantification of bacterial fluorescence using independent calibrants
Fluorescent reporters are commonly used to quantify activities or properties of both natural
and engineered cells. Fluorescence is still typically reported only in arbitrary or normalized …
and engineered cells. Fluorescence is still typically reported only in arbitrary or normalized …