PyMICE – a Python library for analysis of IntelliCage data

Source of the article

Authors

• Jakub M. Dzik
• Alicja Puścian
• Zofia Mijakowska
• Kasia Radwanska
• Szymon Łęski

Introduction

In order to meet the standarts of reproducibility and enable a reproducibility review we decided to publish the data and complete source of the article.

Requirements

We claim that all results presented in the article may be reproduced on a Linux machine with an interpreter of Python programming language v. 2.7.3, PyMICE v. 1.1.0, NumPy v. 1.6.1, matplitlib v. 1.1.1rc, dateutil v. 1.5 and pytz v. 2012c.

We have not tested if the results are reproducible on other operating systems, however it is likely.

To reproduce the article itself (generate a new PDF document based on the reproduced results), pdflatex (v. 3.1415926), BibTeX (v. 0.99d), and Pweave (v. 0.24) tools are necessary.

Reproduction of the article

To automatically generate a custom version of the article based on reproduced results rather than on the results claimed by the authors, perform the following procedure: copy content of the repository to the working directory.

In case the GNU Make tool (or similar) is installed in the system, to reproduce the article run:

$ make article.pdf

If GNU Make tool is not installed, you need to weave the texw files. It is important to weave get_example_data.texw as the first file, since example data are saved in the working directory during its weaving.

$ Pweave -f tex get\_example\_data.texw
$ Pweave -f tex pymice\_overview.texw
$ Pweave -f tex pymice\_reproducibility.texw
$ Pweave -f tex example1.texw
$ Pweave -f tex -F figures example2.texw
$ Pweave -f tex -F figures example3.texw
$ Pweave -f tex -F figures example4.texw

After all files have been weaved, compile the LaTeX source.

$ pdflatex article.tex
$ bibtex article
$ pdflatex article.tex
$ pdflatex article.tex

The article.pdf file contains the reproduced article.

Reproduction of the supplementary materials

To automatically generate a custom version of the supplementary materials perform the following procedure: copy content of the repository to the working directory.

In case the GNU Make tool (or similar) is installed in the system, to reproduce the supplementary materials run:

$ make supplementary\_materials.zip

The archive supplementary_materials.zip contains the complete supplementary materials.

If GNU Make tool is not installed, you need to generate the supplementary materials manually.

First tangle and execute script providing the raw data.

$ Ptangle get\_example\_data.texw
$ python get\_example\_data.py

Tangle the examples.

$ Ptangle example1.texw
$ Ptangle example2.texw
$ Ptangle example3.texw
$ Ptangle example4.texw

Weave the reproducibility statement.

$ Pweave -f tex supplementary\_reproducibility.texw

Eventually compile the LaTeX source.

$ pdflatex supplementary\_materials.tex
$ bibtex supplementary\_materials
$ pdflatex supplementary\_materials.tex
$ pdflatex supplementary\_materials.tex

The supplementary_materials.pdf file contains description of supplementary materials.

Acknowledgements

JD, KR and SŁ supported by a Symfonia NCN grant UMO-2013/ 08/W/NZ4/00691. AP supported by a grant from Switzerland through the Swiss Contribution to the enlarged European Union (PSPB-210/2010 to Ewelina Knapska and Hans-Peter Lipp).

KR and ZM supported by an FNP grant POMOST/2011-4/7 to KR.