AUTHOR=Stevens Jean-Luc R., Elver Marco , Bednar James A.
TITLE=An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook
JOURNAL=Frontiers in Neuroinformatics
VOLUME=Volume 7 - 2013
YEAR=2013
URL=https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2013.00044
DOI=10.3389/fninf.2013.00044
ISSN=1662-5196
ABSTRACT=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.