A Computational Workflow for the Automated Generation of Models of Genetic Designs

ACS Synthetic Biology
Goksel MisirliAnil Wipat

Abstract

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the ...Continue Reading

References

May 15, 2004·Progress in Biophysics and Molecular Biology·Catherine M LloydPoul F Nielsen
May 17, 2005·Genome Biology·Karen EilbeckMichael Ashburner
Apr 17, 2009·Journal of the Royal Society, Interface·Michael Pedersen, Andrew Phillips
May 23, 2009·Nature Reviews. Molecular Cell Biology·Priscilla E M Purnick, Ron Weiss
Aug 12, 2009·Nature Biotechnology·Nicolas Le NovèreHiroaki Kitano
Jan 25, 2011·Integrative Biology : Quantitative Biosciences From Nano to Macro·James T MacDonaldGuy-Bart V Stan
Oct 27, 2011·Molecular Systems Biology·Mélanie CourtotNicolas Le Novère
Mar 31, 2015·ACS Synthetic Biology·Nicholas RoehnerChris J Myers
Dec 4, 2015·PLoS Biology·Jacqueline Y QuinnHerbert M Sauro
Dec 24, 2015·ACS Synthetic Biology·Tramy NguyenChris J Myers
Apr 2, 2016·Science·Alec A K NielsenChristopher A Voigt
Oct 22, 2016·ACS Synthetic Biology·Göksel MısırlıAnil Wipat
Apr 26, 2016·ACS Synthetic Biology·Nicholas RoehnerChris J Myers
Mar 2, 2017·Cold Spring Harbor Perspectives in Biology·Evan AppletonDouglas Densmore
Apr 26, 2017·ACS Synthetic Biology·Michael ZhangChris J Myers
Jun 18, 2017·Biochemical Society Transactions·Chris J MyersZach Zundel
Jan 11, 2018·ACS Synthetic Biology·James Alastair McLaughlinAnil Wipat

❮ Previous
Next ❯

Citations

Feb 6, 2020·Journal of Bioinformatics and Computational Biology·Tatsuya SekiguchiMasahiro Okamoto
Jun 2, 2020·Frontiers in Bioengineering and Biotechnology·Richard J R KelwickPaul S Freemont
Oct 6, 2020·Frontiers in Bioengineering and Biotechnology·James Alastair McLaughlinChris J Myers
Dec 11, 2020·Metabolic Engineering·Rosanna YoungPaul S Freemont
Nov 25, 2020·International Journal of Molecular Sciences·Minjeong KangSuhyung Cho
Aug 14, 2020·ACS Synthetic Biology·Pedro FontanarrosaChris Myers
Jun 27, 2018·ACS Synthetic Biology·Leandro WatanabeChris Myers
May 1, 2019·ACS Synthetic Biology·Jing Wui YeohChueh Loo Poh
Nov 11, 2021·ACS Synthetic Biology·Nicholas RoehnerJacob Beal

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.