element-animal 0.1.1

DataJoint Element for Animal Management

DataJoint Element - Animal

• element-animal features a DataJoint pipeline design for subject and genotyping management.

• element-animal is not a complete workflow by itself, but rather a modular design of tables and dependencies.

• element-animal can be flexibly attached to any DataJoint workflow.

• See the Element Animal documentation for the background information and development timeline.

• For more information on the DataJoint Elements project, please visit https://elements.datajoint.org. This work is supported by the National Institutes of Health.

Element architecture

There are two modules in element-animal:

• subject: contains the basic information of subject, including Strain, Line, Subject, Zygosity, and SubjectDeath information
• genotyping: this module is designed for labs that keep track of colony management and genotyping results, containing information of breeding, weaning, housing, and genotyping.

Subject Diagram

Genotyping Diagram

Installation

pip install element-animal

If you already have an older version of element-animal installed using pip, upgrade with

pip install --upgrade element-animal

Element usage

• element-animal is not a complete workflow by itself, but rather a modular design of tables and dependencies that can be flexibly attached to any DataJoint workflow.

• See the workflow-session repository for example usage of element-animal.

• Also refer to the workflow-calcium-imaging and workflow-array-ephys repositories for example usages of element-animal when combining with other elements.

Citation

• If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.

• DataJoint for Python or MATLAB

  • Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658

  • DataJoint (RRID:SCR_014543) - DataJoint for <Select Python or MATLAB> (version <Enter version number>)

• DataJoint Elements

  • Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358

  • DataJoint Elements (RRID:SCR_021894) - Element Animal (version <Enter version number>)