SynBiopython: an open-source software library for Synthetic Biology

IF 3.2 4区生物学 Q1 Agricultural and Biological Sciences

Synthetic Biology Pub Date : 2021-01-01 DOI:10.1093/synbio/ysab001

Jing Wui Yeoh, Neil Swainston, Peter Vegh, Valentin Zulkower, Pablo Carbonell, M. B. Holowko, Gopal Peddinti, C. Poh

{"title":"SynBiopython: an open-source software library for Synthetic Biology","authors":"Jing Wui Yeoh, Neil Swainston, Peter Vegh, Valentin Zulkower, Pablo Carbonell, M. B. Holowko, Gopal Peddinti, C. Poh","doi":"10.1093/synbio/ysab001","DOIUrl":null,"url":null,"abstract":"Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.","PeriodicalId":22158,"journal":{"name":"Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.2000,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"7","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Synthetic Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/synbio/ysab001","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}

引用次数: 7

Abstract

Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.

查看原文本刊更多论文

SynBiopython:合成生物学的开源软件库

合成生物学实验室硬件自动化的进步还没有完全与软件自动化相匹配。这种自动化实验室，现在通常被称为生物代工厂，需要软件解决方案来帮助许多专业任务，如批量DNA设计，样本和数据跟踪，以及数据分析等。通常情况下，生物铸造厂面临的许多挑战都是共同面临的，但许多实验室并行开发类似软件解决方案的轮式再发明也很频繁。在本文中，我们将首次尝试创建一个标准化的开源Python包。许多工具将被集成和开发，我们设想这些工具将成为全球生物代工厂内软件开发项目的明显起点。具体地说，我们描述了可用软件的当前状态、当前的使用场景和针对常见问题的案例研究，最后描述了未来开发的计划。SynBiopython可在以下地址公开获取:http://synbiopython.org。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Synthetic Biology Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

CiteScore

4.50

自引率

3.10%

发文量

审稿时长

25 weeks