An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook.
An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook.
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DOI：
10.3389/fninf.2013.00044
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发表时间：
2013
影响因子：
3.5
通讯作者：
Bednar JA
中科院分区：
文献类型：
--
作者：
Stevens JL;Elver M;Bednar JA
Lancet是一个新的，独立于模拟器的Python实用程序，用于简洁地指定，启动和整理来自大批量相互关联的计算需求程序运行的结果。本文演示了如何将联合收割机Lancet与IPython Notebook相结合，为完全可重复的科学研究提供灵活、轻量级和敏捷的工作流程。这种非正式和实用的方法使用IPython Notebook来捕获科学计算中的步骤，因为它逐渐自动化并准备发布，而无需强制使用任何可能限制科学探索和创新的单独应用程序。由此产生的笔记本简明地记录了即使是非常复杂的计算过程中所涉及的每个步骤，这些计算过程导致了特定的数字或数值结果，从而允许自动复制完整的事件链。Lancet最初旨在帮助解决计算神经科学中的问题，例如分析复杂模拟对各种参数的敏感性，或收集不同随机起点的多次运行的结果。然而，由于永远不可能提前知道未来的任务可能需要什么工具，因此Lancet被设计为完全通用的，支持任何类型的程序，只要它可以作为进程启动，并可以以文件的形式返回输出。例如，Lancet也被一位作者在一个单独的研究小组中大量使用，用于启动批量微处理器模拟。这种总体设计将使《柳叶刀》能够继续支持特定的研究项目，即使基础方法和工具发生变化。
Lancet is a new, simulator-independent Python utility for succinctly specifying, launching, and collating results from large batches of interrelated computationally demanding program runs. This paper demonstrates how to combine Lancet with IPython Notebook to provide a flexible, lightweight, and agile workflow for fully reproducible scientific research. This informal and pragmatic approach uses IPython Notebook to capture the steps in a scientific computation as it is gradually automated and made ready for publication, without mandating the use of any separate application that can constrain scientific exploration and innovation. The resulting notebook concisely records each step involved in even very complex computational processes that led to a particular figure or numerical result, allowing the complete chain of events to be replicated automatically. Lancet was originally designed to help solve problems in computational neuroscience, such as analyzing the sensitivity of a complex simulation to various parameters, or collecting the results from multiple runs with different random starting points. However, because it is never possible to know in advance what tools might be required in future tasks, Lancet has been designed to be completely general, supporting any type of program as long as it can be launched as a process and can return output in the form of files. For instance, Lancet is also heavily used by one of the authors in a separate research group for launching batches of microprocessor simulations. This general design will allow Lancet to continue supporting a given research project even as the underlying approaches and tools change.
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影响因子：
3.5
作者：
Bednar JA
通讯作者：
Bednar JA
影响因子：
3.5
作者：
Goodman, Dan;Brette, Romain
通讯作者：
Brette, Romain
影响因子：
3.5
作者：
Antolík J;Davison AP
通讯作者：
Davison AP
影响因子：
2.1
作者：
Davison, Andrew P.
通讯作者：
Davison, Andrew P.
影响因子：
4.3
作者：
Nordlie E;Gewaltig MO;Plesser HE
通讯作者：
Plesser HE