Literature DB >> 27744689

DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data.

Bryan S Der1, Emerson Glassey1, Bryan A Bartley2, Casper Enghuus3, Daniel B Goodman4,5, D Benjamin Gordon1, Christopher A Voigt1, Thomas E Gorochowski1.   

Abstract

DNAplotlib ( www.dnaplotlib.org ) is a computational toolkit for the programmable visualization of highly customizable, standards-compliant genetic designs. Functions are provided to aid with both visualization tasks and to extract and overlay associated experimental data. High-quality output is produced in the form of vector-based PDFs, rasterized images, and animated movies. All aspects of the rendering process can be easily customized or extended by the user to cover new forms of genetic part or regulation. DNAplotlib supports improved communication of genetic design information and offers new avenues for static, interactive and dynamic visualizations that map and explore the links between the structure and function of genetic parts, devices and systems; including metabolic pathways and genetic circuits. DNAplotlib is cross-platform software developed using Python.

Keywords:  SBOLv; biodesign automation; standardization; synthetic biology; visualization

Mesh:

Year:  2016        PMID: 27744689     DOI: 10.1021/acssynbio.6b00252

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


  17 in total

1.  Characterizing Genetic Parts and Devices Using RNA Sequencing.

Authors:  Deepti Vipin; Zoya Ignatova; Thomas E Gorochowski
Journal:  Methods Mol Biol       Date:  2021

2.  Engineering Sensors for Gene Expression Burden.

Authors:  Alice Boo; Francesca Ceroni
Journal:  Methods Mol Biol       Date:  2021

3.  Burden-driven feedback control of gene expression.

Authors:  Francesca Ceroni; Alice Boo; Simone Furini; Thomas E Gorochowski; Olivier Borkowski; Yaseen N Ladak; Ali R Awan; Charlie Gilbert; Guy-Bart Stan; Tom Ellis
Journal:  Nat Methods       Date:  2018-03-26       Impact factor: 28.547

4.  Communicating Structure and Function in Synthetic Biology Diagrams.

Authors:  Jacob Beal; Tramy Nguyen; Thomas E Gorochowski; Angel Goñi-Moreno; James Scott-Brown; James Alastair McLaughlin; Curtis Madsen; Benjamin Aleritsch; Bryan Bartley; Shyam Bhakta; Mike Bissell; Sebastian Castillo Hair; Kevin Clancy; Augustin Luna; Nicolas Le Novère; Zach Palchick; Matthew Pocock; Herbert Sauro; John T Sexton; Jeffrey J Tabor; Christopher A Voigt; Zach Zundel; Chris Myers; Anil Wipat
Journal:  ACS Synth Biol       Date:  2019-08-05       Impact factor: 5.110

5.  Synthetic neural-like computing in microbial consortia for pattern recognition.

Authors:  Ximing Li; Luna Rizik; Valeriia Kravchik; Maria Khoury; Netanel Korin; Ramez Daniel
Journal:  Nat Commun       Date:  2021-05-25       Impact factor: 14.919

6.  Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays.

Authors:  Alexander C Reis; Sean M Halper; Grace E Vezeau; Daniel P Cetnar; Ayaan Hossain; Phillip R Clauer; Howard M Salis
Journal:  Nat Biotechnol       Date:  2019-10-07       Impact factor: 68.164

Review 7.  Agent-based modelling in synthetic biology.

Authors:  Thomas E Gorochowski
Journal:  Essays Biochem       Date:  2016-11-30       Impact factor: 8.000

8.  Genetic circuit characterization and debugging using RNA-seq.

Authors:  Thomas E Gorochowski; Amin Espah Borujeni; Yongjin Park; Alec Ak Nielsen; Jing Zhang; Bryan S Der; D Benjamin Gordon; Christopher A Voigt
Journal:  Mol Syst Biol       Date:  2017-11-09       Impact factor: 11.429

9.  Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology.

Authors:  Philipp Boeing; Miriam Leon; Darren N Nesbeth; Anthony Finkelstein; Chris P Barnes
Journal:  Processes (Basel)       Date:  2018-09-15       Impact factor: 2.847

10.  Absolute quantification of translational regulation and burden using combined sequencing approaches.

Authors:  Thomas E Gorochowski; Irina Chelysheva; Mette Eriksen; Priyanka Nair; Steen Pedersen; Zoya Ignatova
Journal:  Mol Syst Biol       Date:  2019-05-03       Impact factor: 11.429

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