cobrawap 0.1.1

Concept

For researchers to be able to effectively reproduce results and build on each other’s progress, it is important to not only make results openly accessible and to facilitate data sharing, but also to build the analysis workflows in a shareable and reusable manner.

Making analysis scripts available alongside results and datasets is good. What is even better is to design the analysis workflows for specific research questions in such a manner that they are general and flexible enough to be actively reused in further research. In this way, the rigor of the analysis workflow is increased, and the design of the analysis process is simplified for the researcher

Cobrawap brings together existing analysis methods, tools, and data standards and interfaces them for the analysis and characterization of cortical wave-like activity and UP/DOWN state detections. Cobrawap serves as a space to gather the various data types exhibiting wave activity and their various analysis approaches into the same pipeline. Besides generating easily reproducible and curated results, Cobrawap facilitates the rigorous comparison between datasets of different laboratories, studies and measurement modalities. Furthermore, Cobrawap can be used in the context of model validation and benchmarking of analysis methods. Cobrawap may also act as a template for implementing analysis pipelines in other contexts.

Cobrawap features…

• a user-friendly command line interface guiding the setup and usage

• a hierarchical and modular pipeline framework based on the Snakemake workflow management tool

• reusable method implementations (stages and blocks) for standalone applications or integration into workflows

• analysis methods for electrophysiological and optical data on the characterization of cortical wave activity and local oscillations

• visualization of the analysis steps and the intermediate results

• intermediate results curated with annotated metadata

For further developments and feature requests refer to the Github Issues.

Citation

To refer to the Cobrawap software package in publications, please use:

Cobrawap (doi:10.5281/zenodo.10198748; RRID:SCR_022966)

To cite a specific version of Cobrawap please see version-specific DOIs at:

doi:10.5281/zenodo.10198748

To cite Cobrawap, please use:

Gutzen, R., De Bonis, G., De Luca, C., Pastorelli, E., Capone, C., Allegra Mascaro, A. L., Resta, F., Manasanch, A., Pavone, F. S., Sanchez-Vives, M. V., Mattia, M., Grün, S., Paolucci, P. S., & Denker, M. (2022). Comparing apples to apples—Using a modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets. arXiv:2211.08527. https://doi.org/10.48550/arXiv.2211.08527

License

Cobrawap is open-source software and is licensed under the GNU General Public License v3.

Involved partners

Cobrawap was originally developed in the context the Human Brain Project and is part of the EBRAINS infrastructure. Partners involved in the collaboration and use case within the project (WaveScalES) are:

• Forschungszentrum Jülich, Germany: Robin Gutzen, Michael Denker

• Istituto Nazionale di Fisica Nucleare (INFN), Roma, Italy: Giulia De Bonis, Pier Stanislao Paolucci, Elena Pastorelli, Francesco Simula, Cristiano Capone, Chiara De Luca, Cosimo Lupo, Irene Bernava

• Istituto Superiore di Sanità (ISS), Roma, Italy: Maurizio Mattia, Antonio Pazienti.

• Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain: Arnau Manasanch, Miguel Dasilva, Maria V. Sanchez-Vives.

• European Laboratory for Non-Linear Spectroscopy (LENS), Firenze, Italy: Anna Letizia Allegra Mascaro, Francesco Resta, Francesco Pavone.

• University of Milano (UniMi), Italy: Andrea Pigorini, Thierry Nieus, Marcello Massimini

• Unité de Neurosciences, Neuroinformatics Group, CNRS, France: Andrew Davison

Further Context