Literature DB >> 29944839

iBioSim 3: A Tool for Model-Based Genetic Circuit Design.

Leandro Watanabe1, Tramy Nguyen1, Michael Zhang1, Zach Zundel1, Zhen Zhang2, Curtis Madsen3, Nicholas Roehner4, Chris Myers1.   

Abstract

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 DNA circuit design, design analysis, and design synthesis, all of which can be used in a workflow for the systematic construction of new genetic circuits.

Keywords:  COMBINE archive; SBML; SBOL; SED-ML; genetic design automation; standards

Mesh：

Substances：

Year:  2018        PMID： 29944839     DOI： 10.1021/acssynbio.8b00078

Source DB:  PubMed          Journal:  ACS Synth Biol        ISSN： 2161-5063            Impact factor:   5.110


  15 in total

1.  Modelling co-translational dimerization for programmable nonlinearity in synthetic biology.

Authors:  Ruud Stoof; Ángel Goñi-Moreno
Journal:  J R Soc Interface       Date:  2020-11-04       Impact factor: 4.118

2.  BioUML-towards a universal research platform.

Authors:  Fedor Kolpakov; Ilya Akberdin; Ilya Kiselev; Semyon Kolmykov; Yury Kondrakhin; Mikhail Kulyashov; Elena Kutumova; Sergey Pintus; Anna Ryabova; Ruslan Sharipov; Ivan Yevshin; Sergey Zhatchenko; Alexander Kel
Journal:  Nucleic Acids Res       Date:  2022-05-10       Impact factor: 19.160

Review 3.  Best Practices for Making Reproducible Biochemical Models.

Authors:  Veronica L Porubsky; Arthur P Goldberg; Anand K Rampadarath; David P Nickerson; Jonathan R Karr; Herbert M Sauro
Journal:  Cell Syst       Date:  2020-08-26       Impact factor: 10.304

4.  BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data.

Authors:  Fedor Kolpakov; Ilya Akberdin; Timur Kashapov; Llya Kiselev; Semyon Kolmykov; Yury Kondrakhin; Elena Kutumova; Nikita Mandrik; Sergey Pintus; Anna Ryabova; Ruslan Sharipov; Ivan Yevshin; Alexander Kel
Journal:  Nucleic Acids Res       Date:  2019-07-02       Impact factor: 16.971

5.  Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs.

Authors:  Uriel Urquiza-García; Tomasz Zieliński; Andrew J Millar
Journal:  Synth Biol (Oxf)       Date:  2019-06-20

6.  BioModels-15 years of sharing computational models in life science.

Authors:  Rahuman S Malik-Sheriff; Mihai Glont; Tung V N Nguyen; Krishna Tiwari; Matthew G Roberts; Ashley Xavier; Manh T Vu; Jinghao Men; Matthieu Maire; Sarubini Kananathan; Emma L Fairbanks; Johannes P Meyer; Chinmay Arankalle; Thawfeek M Varusai; Vincent Knight-Schrijver; Lu Li; Corina Dueñas-Roca; Gaurhari Dass; Sarah M Keating; Young M Park; Nicola Buso; Nicolas Rodriguez; Michael Hucka; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

7.  SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts.

Authors:  Esteban Martínez-García; Angel Goñi-Moreno; Bryan Bartley; James McLaughlin; Lucas Sánchez-Sampedro; Héctor Pascual Del Pozo; Clara Prieto Hernández; Ada Serena Marletta; Davide De Lucrezia; Guzmán Sánchez-Fernández; Sofía Fraile; Víctor de Lorenzo
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

8.  Modular assembly of dynamic models in systems biology.

Authors:  Michael Pan; Peter J Gawthrop; Joseph Cursons; Edmund J Crampin
Journal:  PLoS Comput Biol       Date:  2021-10-13       Impact factor: 4.475

9.  The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.

Authors:  James Alastair McLaughlin; Jacob Beal; Göksel Mısırlı; Raik Grünberg; Bryan A Bartley; James Scott-Brown; Prashant Vaidyanathan; Pedro Fontanarrosa; Ernst Oberortner; Anil Wipat; Thomas E Gorochowski; Chris J Myers
Journal:  Front Bioeng Biotechnol       Date:  2020-09-11

10.  The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).

Authors:  Dagmar Waltemath; Martin Golebiewski; Michael L Blinov; Padraig Gleeson; Henning Hermjakob; Michael Hucka; Esther Thea Inau; Sarah M Keating; Matthias König; Olga Krebs; Rahuman S Malik-Sheriff; David Nickerson; Ernst Oberortner; Herbert M Sauro; Falk Schreiber; Lucian Smith; Melanie I Stefan; Ulrike Wittig; Chris J Myers
Journal:  J Integr Bioinform       Date:  2020-06-29
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