Literature DB >> 28051850

BioBlocks: Programming Protocols in Biology Made Easier.

Vishal Gupta1, Jesús Irimia1, Iván Pau1, Alfonso Rodríguez-Patón1.   

Abstract

The methods to execute biological experiments are evolving. Affordable fluid handling robots and on-demand biology enterprises are making automating entire experiments a reality. Automation offers the benefit of high-throughput experimentation, rapid prototyping, and improved reproducibility of results. However, learning to automate and codify experiments is a difficult task as it requires programming expertise. Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments. The experiments can be specified, saved, modified, and shared between multiple users in an easy manner. BioBlocks is open-source and can be customized to execute protocols on local robotic platforms or remotely, that is, in the cloud. It aims to serve as a de facto open standard for programming protocols in Biology.

Keywords:  Blockly; Scratch; high-level programming language; lab automation; rapid prototyping; reproducibility

Mesh:

Year:  2017        PMID: 28051850     DOI: 10.1021/acssynbio.6b00304

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


  4 in total

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Journal:  Molecules       Date:  2018-05-29       Impact factor: 4.411

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Authors:  Peter Washington; Karina G Samuel-Gama; Shirish Goyal; Ashwin Ramaswami; Ingmar H Riedel-Kruse
Journal:  Proc Natl Acad Sci U S A       Date:  2019-03-01       Impact factor: 11.205

3.  Enabling high-throughput biology with flexible open-source automation.

Authors:  Emma J Chory; Dana W Gretton; Erika A DeBenedictis; Kevin M Esvelt
Journal:  Mol Syst Biol       Date:  2021-03       Impact factor: 11.429

4.  The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.

Authors:  Joan Hérisson; Thomas Duigou; Melchior du Lac; Kenza Bazi-Kabbaj; Mahnaz Sabeti Azad; Gizem Buldum; Olivier Telle; Yorgo El Moubayed; Pablo Carbonell; Neil Swainston; Valentin Zulkower; Manish Kushwaha; Geoff S Baldwin; Jean-Loup Faulon
Journal:  Nat Commun       Date:  2022-08-29       Impact factor: 17.694

  4 in total

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