This python package provides basic functionality to read and write datasets following the Tabulated Experimental Data (TED) format for electrophysiology raw data (e.g., ion channel data collected under the Comprehensive in vitro Proarrhythmia Assay [CiPA] initiative).
For a use case example, see Alvarez-Baron et. al "hERG block potencies for 5 positive control drugs obtained per ICH E14/S7B Q&As best practices: impact of recording temperature and drug loss". J Pharamacol Tox Methods 2022. https://doi.org/10.1016/j.vascn.2022.107193. The original raw recordings as well as derived TED datasets, analysis scripts, tabulated results, figures, and reports generated using this package are also available at https://osf.io/6w5vn/.
See LICENSE and DISCLAIMER at the end of this document.
These instructions assume you already have python 3.7.7 or conda installed in your system.
- Create the cipa-suite directory
cd ~/code mkdir cipa-suite
-
Create a python virtual environment. Here we create the cipavenv environment in ~/code/cipa-suite
cd ~/code/cipa-suite python -m venv cipavenv -
Next, activate the virtual environment.
source ~/code/cipa-suite/cipavenv/bin/activate -
Upgrade pip to the most recent version
pip install --upgrade pip
-
Create a python virtual environment. Here we create the cipavenv environment in ~/code/cipa-suite:
cd ~/code/cipa-suite conda create -p cipavenv -
Activate the new conda environment:
conda activate .\cipavenv -
Install python 3.7.7:
conda install python==3.7.7
Clone the cipated repository from https://github.com/FDA/cipated or get a copy of the source code.
-
Change to the directory where you have the source code of cipated
cd ~/code/cipa-suite/cipated -
Install cipated in editable mode so you can both use it and make changes without reinstalling it.
This will also install the package dependencies
pip install -e .
To create a source and wheels distributions, type
python setup.py sdist bdist_wheel in the command line.
Install the following additional requirements:
pip install sphinx sphinx-autobuild sphinx-autodoc-typehints mock autodoc myst-parser
Next, assuming you have a copy of the source code in ~/code/cipa-suite/cipated, you can generate a local html version of the documentation from the command line as follows:
cd ~/code/cipa-suite/cipated/docs
make html
Jose Vicente Ruiz <jose.vicenteruiz@fda.hhs.gov>
Senior Staff Fellow
Division of Cardiology and Nephrology
Office of Cardiology, Hematology, Endocrinology and Nephrology
Office of New Drugs
Center for Drug Evaluation and Research
U.S. Food and Drug Administration
Manni Mashaee <manni.mashaee@fda.hhs.gov>
ORISE Fellow
Division of Cardiology and Nephrology
Office of Cardiology, Hematology, Endocrinology and Nephrology
Office of New Drugs
Division of Applied Regulatory Science
Office of Clinical Pharmacology, Office of Translational Sciences
Center for Drug Evaluation and Research
U.S. Food and Drug Administration
This code is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal Public Domain Dedication. This example is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See DISCLAIMER section below, the COPYING file in the root directory of this project and https://creativecommons.org/publicdomain/zero/1.0/ for more details.
FDA assumes no responsibility whatsoever for use by other parties of the Software, its source code, documentation or compiled executables, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. Further, FDA makes no representations that the use of the Software will not infringe any patent or proprietary rights of third parties. The use of this code in no way implies endorsement by the FDA or confers any advantage in regulatory decisions.