BigDataScript: a scripting language for data pipelines.
BigDataScript: a scripting language for data pipelines.
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DOI：
10.1093/bioinformatics/btu595
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发表时间：
2015-01-01
期刊：
影响因子：
--
通讯作者：
Blanchette M
中科院分区：
文献类型：
--
作者：
Cingolani P;Sladek R;Blanchette M
动机：大型生物数据集的分析通常需要在大型计算基础设施上长时间运行的复杂处理管道。我们设计并实现了一种简单的脚本式编程语言，具有干净和极简的语法，用于开发和管理流水线执行，并提供对各种类型的软件和硬件故障的鲁棒性以及可移植性。结果如下：我们介绍了BigDataScript（BDS）编程语言的数据处理管道，它提高了抽象的硬件资源，并协助鲁棒性。硬件抽象允许BDS管道在各种计算机架构上运行而无需修改，从小型笔记本电脑到多核服务器，服务器农场，集群和云。BDS通过结合绝对序列化和惰性处理的概念来实现健壮性，从而允许管道从错误中恢复。通过在编程语言级别抽象管道概念，BDS简化了复杂生物信息学管道的实现、执行和管理，从而减少了开发和调试周期，并使代码更清晰。可用性和实现：BigDataScript在http://pcingola.github.io/BigDataScript的开源许可下可用。联系人：巴勃罗.e. gmail.com
Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. Results: We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. Availability and implementation: BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. Contact: pablo.e.cingolani@gmail.com
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影响因子：
5.8
作者：
Goodstadt, Leo
通讯作者：
Goodstadt, Leo
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
7
作者：
McKenna, Aaron;Hanna, Matthew;DePristo, Mark A.
通讯作者：
DePristo, Mark A.
DOI：
10.1093/bioinformatics/btp324
发表时间：
2009-07-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Durbin R
通讯作者：
Durbin R
影响因子：
3.7
作者：
Cingolani P;Patel VM;Coon M;Nguyen T;Land SJ;Ruden DM;Lu X
通讯作者：
Lu X