update repo naming

.zenodo.json

@@ -1,144 +0,0 @@
-{
-    "creators": [
-      {
-        "orcid": "0000-0001-7373-5962",
-        "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",
-        "name": "Gutzen, Robin"
-      }
-    ],
-    
-    "contributors": [
-        {
-        "orcid": "0000-0001-7373-5962",
-        "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",
-        "name": "Gutzen, Robin",
-        "role": "Project Member"
-        },
-        {
-        "orcid": "0000-0001-7079-5724",
-        "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy",
-        "name": "De Bonis, Giulia",
-        "role": "Project Member"
-        },
-        {
-        "orcid": "0000-0003-3488-0088",
-        "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland",
-        "name": "De Luca, Chiara",
-        "role": "Project Member"
-        },
-      {
-        "orcid": "0000-0001-7079-5724",
-        "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy",
-        "name": "De Bonis, Giulia",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0003-3488-0088",
-        "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland",
-        "name": "De Luca, Chiara",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0003-0682-1232",
-        "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy",
-        "name": "Pastorelli, Elena",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0002-9958-2551",
-        "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy",
-        "name": "Capone, Cristiano",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0002-8489-0076",
-        "affiliation": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Neuroscience Institute, National Research Council, Pisa, Italy",
-        "name": "Allegra Mascaro, Anna Letizia",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0002-9605-5852",
-        "affiliation": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy",
-        "name": "Resta, Francesco",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0002-9605-5852",
-        "affiliation": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy",
-        "name": "Resta, Francesco",
-        "role": "Data Collector"
-      },
-      {
-        "orcid": "0000-0002-8306-0759",
-        "affiliation": "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain",
-        "name": "Manasanch, Arnau",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0002-0675-3981",
-        "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",
-        "name": "Pavone, Francesco Saverio",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0002-8437-9083",
-        "affiliation": "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain",
-        "name": "Sanchez-Vives, Maria V.",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0002-2356-4509",
-        "affiliation": "Natl. Center for Radiation Protection and Computational Physics, Istituto Superiore di Sanità (ISS), Rome, Italy",
-        "name": "Mattia, Maurizio",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0003-2829-2220",
-        "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",
-        "name": "Grün, Sonja",
-        "role": "Project Member"
-      },
-      {
-        "orcid": "0000-0003-1255-7300",
-        "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",
-        "name": "Denker, Michael",
-        "role": "Project Leader"
-      },
-      {
-        "orcid": "0000-0003-1937-6086",
-        "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy",
-        "name": "Paolucci, Pier Stanislao",
-        "role": "Project Leader"
-      }
-    ],
-  
-    "title": "Cobrawap Manuscript Code Archive",
-  
-    "keywords": [
-      "neuroscience",
-      "neurophysiology",
-      "electrophysiology",
-      "statistics",
-      "data-analysis"
-    ],
-  
-    "license": {
-      "id": "BSD 3-Clause 'New' or 'Revised' License"
-    },
-
-    "related_identifiers": [
-      {
-        "scheme": "doi",
-        "identifier": "10.48550/arXiv.2211.08527",
-        "relation": "isDocumentedBy",
-        "resource_type": "publication-preprint"
-      }
-    ],
-    
-    "grants": [
-      {"id": "785907"},
-      {"id": "945539"}
-    ],
-  
-    "upload_type": "software"
-  }

README.md

@@ -1,4 +1,4 @@
-# Cobrawap Manuscript Code Archive
+# Cobrawap Publication Code Archive
 
 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
@@ -24,7 +24,8 @@ The above publication also introduces the software
     - IDIBAPS\_PM: [10.25493/WKA8-Q4T](https://doi.org/10.25493/WKA8-Q4T)
     - LENS\_M: [10.25493/QFZK-FXS](https://doi.org/10.25493/QFZK-FXS)
     - LENS\_ISO: [10.25493/XJR8-QCA](https://doi.org/10.25493/XJR8-QCA)
-- Set the path parameter (`DATA\_SETS`) in the *stage01\_data\_entry/config/config\_<profile>.yaml* files to the corresponding data locations.
+- Set the path parameter (`DATA\_SETS`) in the *stage01\_data\_entry/config/config\_\<profile\>.yaml* files to the corresponding data locations.
+
 
 ### Run the analysis pipeline
 - To produce all the possible pipeline outputs *\<cobrawap\_output\>/\<profile\>\<variant\>/stage05\_(channel\_)wave\_characterization/\<event-type\>\_\<measure-type\>\_measures.csv*, set the event-type and measure-type accordingly and execute:
@@ -40,12 +41,14 @@ cobrawap run --profile=<profile>
 
 **Event types:** The wave characterization in the pipeline output can be either given for all **wavefronts** or all **wavemodes** (wavemode = average of similar wavefronts). You can select between them by setting the parameter `EVENT_NAME` in the corresponding *stage05* config file. Also change the prefix of the `STAGE_OUTPUT` accordingly as `wavefronts` or `wavemodes`.
 
+
 ### Aggregate the output of the analysis pipeline
 In the folder *aggregate\_pipeline\_output* run snakemake (`snakemake -c1`) to create the combined dataframes from the individual pipeline outputs:
 - *\<event-type\>\_\<measure-type\>\<variant\>\_measures.csv* containing the pipeline outputs for all profiles,
 - *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.
 
+
 ### Plot the figures
 In folder *plot\_figures*:
 - Run `snakemake -c1` to produce Figure 5 and 6.

environment.yaml

@@ -1,4 +1,4 @@
-name: cobrawap_ms
+name: cobrawap_env
 channels:
   - conda-forge
   - bioconda

project_utils/project_paths.py

@@ -4,14 +4,14 @@ class project_paths_class:
     """
     Define the custom paths in this project.
     """
-    working_dir = Path.home() / 'Projects' / 'cobrawap_ms_code'
+    working_dir = Path.home() / 'Projects' / 'cobrawap_publication_code'
 
     def __init__(self):
         """
         Optionally set alternative paths for the execution on a compute cluster.
         """
         if self.iam_on_cluster():
-            self.working_dir = Path('/users') / 'gutzen' / 'cobrawap_ms_code'
+            self.working_dir = Path('/users') / 'gutzen' / 'cobrawap_publication_code'
             
         self.pipeline_output = self.working_dir / 'cobrawap_output'
         self.figures = self.working_dir / 'figures'