update README and fix environment

README.md

@@ -1,4 +1,5 @@
 # Cobrawap Publication Code Archive
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10210141.svg)](https://doi.org/10.5281/zenodo.10210141)
 
 This is the code and data archive accompanying the publication
 > 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. (2023). "Using a modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets". Cell Reports Methods
@@ -9,7 +10,7 @@ The above publication also introduces the software
 ## How to reproduce the results/figures from the publication
 
 ### Setup
-- Setup the Python environment (`conda create -f environment.yaml`) and activate it.
+- Setup the Python environment (`conda env create -f environment.yaml`) and activate it.
 - Setup Cobrawap with `cobrawap init` and follow the instructions to 
     - set the cobrawap output path (\<cobrawap_output\>),
     - set the cobrawap config path (\<cobrawap_configs\>)
@@ -32,6 +33,7 @@ The above publication also introduces the software
 ```
 cobrawap run --profile=<profile>
 ```
+*Note: the folder cobrawap_output/ contains example output for the profiles IDIBAPS_WBS_WT4 and LENS_M2_t1.* 
 
 **Profiles:** The names that are used for the individual recordings and their corresponding configurations are listed in *project\_utils/profiles.txt*.
 
@@ -48,11 +50,15 @@ In the folder *aggregate\_pipeline\_output* run snakemake (`snakemake -c1`) to c
 - *wavefronts\_\<measure-type\>\_trend\_measures.csv* containing the moments of each measure for the downsampled (|macrodim) calcium imaging data,
 - *wavemodes\_\<measure-type\>\_avg\_measures.csv* containing the measures per wavefront averaged for each wavemode.
 
+*Note: the folder cobrawap_output/aggregated_output/ already contains these precomputed dataframes.*
 
 ### Plot the figures
 In folder *plot\_figures*:
 - Run `snakemake -c1` to produce Figure 5 and 6.
 - Execute `plot_wavemodes_dashboard.ipynb` to produce Figure 4 and S3 (change profile name in notebook accordingly).
 - Execute `plot_trigger_detection_f-anesthesia.ipynb` to produce Figure S4.
+    - *Note: requires running the analysis pipeline for the IDIBAPS_PM recordings, for which the pipeline output is not contained in this repository.*
 - Execute `plot_examples_frames.ipynb` to produce wave frames in Figure 2.
-    - Note: to plot the ECoG waves frames data, it requires the additional pipeline run of the corresponding profile with reduced rate `cobrawap run --profile=IDIBAPS_WBS_WT4|25Hz`.
+    - *Note: to plot the ECoG waves frames data, it requires the additional pipeline run of the corresponding profile with reduced rate `cobrawap run --profile=IDIBAPS_WBS_WT4|25Hz`.*
+
+*Note: the folder figures/ already contains these generated figures.*

datacite.yml

@@ -1,128 +0,0 @@
-# Metadata for DOI registration according to DataCite Metadata Schema 4.1.
-# For detailed schema description see https://doi.org/10.5438/0014
-
-## Required fields
-
-# The main researchers involved. Include digital identifier (e.g., ORCID)
-# if possible, including the prefix to indicate its type.
-authors:
-  -
-    firstname: "Robin"
-    lastname: "Gutzen"
-    affiliation: "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany"
-    id: "ORCID:0000-0001-7373-5962"
-  -
-    firstname: "Giulia"
-    lastname: "De Bonis"
-    affiliation: "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy"
-    id: "ORCID:0000-0001-7079-5724"
-  -
-    firstname: "Chiara"
-    lastname: "De Luca"
-    affiliation: "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland"
-    id: "ORCID:0000-0003-3488-0088"
-  -
-    firstname: "Cristiano"
-    lastname: "Capone"
-    affiliation: "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy"
-    id: "ORCID:0000-0002-9958-2551"
-  -
-    firstname: "Anna Letizia"
-    lastname: "Allegra Mascaro"
-    affiliation: "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Neuroscience Institute, National Research Council, Pisa, Italy"
-    id: "ORCID:0000-0002-8489-0076"
-  -
-    firstname: "Francesco"
-    lastname: "Resta"
-    affiliation: "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy"
-    id: "ORCID:0000-0002-9605-5852"
-  -
-    firstname: "Arnau"
-    lastname: "Manasanch"
-    affiliation: "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain"
-    id: "ORCID:0000-0002-8306-0759"
-  -
-    firstname: "Francesco Saverio"
-    lastname: "Pavone"
-    affiliation: "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, Italy"
-    id: "ORCID:0000-0002-0675-3981"
-  -
-    firstname: "Maria V."
-    lastname: "Sanchez-Vives"
-    affiliation: "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain"
-    id: "ORCID:0000-0002-2356-4509"
-  -
-    firstname: "Maurizio"
-    lastname: "Mattia"
-    affiliation: "Natl. Center for Radiation Protection and Computational Physics, Istituto Superiore di Sanità (ISS), Rome, Italy"
-    id: "ORCID:0000-0003-2829-2220"
-  -
-    firstname: "Sonja"
-    lastname: "Grün"
-    affiliation: "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany"
-    id: "ORCID:0000-0003-2829-2220"
-  -
-    firstname: "Pier Stanislao"
-    lastname: "Paolucci"
-    affiliation: "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy"
-    id: "ORCID:0000-0003-1937-6086"
-  -
-    firstname: "Michael"
-    lastname: "Denker"
-    affiliation: "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany"
-    id: "ORCID:000-0003-1255-7300"
-
-# A title to describe the published resource.
-title: "Cobrawap Publication Code"
-
-# Additional information about the resource, e.g., a brief abstract.
-description: |
-  Code and data repository accompanying the publication "Using a modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets" by Gutzen et al. (2023)
-
-# Lit of keywords the resource should be associated with.
-# Give as many keywords as possible, to make the resource findable.
-keywords:
-  - "neuroscience",
-  - "neurophysiology",
-  - "electrophysiology",
-  - "statistics",
-  - "data-analysis"
-
-# License information for this resource. Please provide the license name and/or a link to the license.
-# Please add also a corresponding LICENSE file to the repository.
-license:
-  name: "BSD 3-Clause 'New' or 'Revised' License"
-  url: "https://spdx.org/licenses/BSD-3-Clause.html"
-
-
-
-## Optional Fields
-
-# Funding information for this resource.
-# Separate funder name and grant number by comma.
-funding:
-  - "EU, 785907"
-  - "EU, 945539"
-
-
-# Related publications. reftype might be: IsSupplementTo, IsDescribedBy, IsReferencedBy.
-# Please provide digital identifier (e.g., DOI) if possible.
-# Add a prefix to the ID, separated by a colon, to indicate the source.
-# Supported sources are: DOI, arXiv, PMID
-# In the citation field, please provide the full reference, including title, authors, journal etc.
-references:
-  -
-    id: "arxiv:10.48550/arXiv.2211.08527"
-    reftype: "IsSupplementTo"
-    citation: "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. (2023). "Using a modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets".
-  -
-    id: "doi:10.5281/zenodo.10198749"
-    reftype: "IsSupplementTo"
-    citation: "Gutzen et al. (2023) Cobrawap 0.1.0"
- 
-
-# Resource type. Default is Dataset, other possible values are Software, DataPaper, Image, Text.
-resourcetype: Software
-
-# Do not edit or remove the following line
-templateversion: 1.2

environment.yaml

@@ -5,7 +5,7 @@ channels:
   - defaults
 dependencies:
   - python==3.9
-  - pip==19.3.1
+  - pip==22.3.1
   - pip:
     - cobrawap==0.1
     - seaborn==0.13.0