Concepts¶
Storage of high-level information about a laboratory¶
Most pipelines track some information about the lab, including the facilities, experiment rigs, and users. This can help track which lab members are associated with which projects or who is responsible for equipment.
Through our interviews and direct collaboration on the precursor projects, we identified the common motifs in the lab schemas. This Element works for diverse downstream pipelines and is always used in combination with other Elements for specific experiments. As such, it is validated jointly with the acquisition Elements such as Extracellular Array Electrophysiology and Calcium Imaging.
Key Partnerships¶
Over the several years, many labs have developed DataJoint-based pipelines for lab management. The DataJoint team collaborated with several and interviewed these teams to understand their experiment workflow, associated tools, and interfaces. These teams include:
- International Brain Laboratory
- BrainCoGs (Princeton Neuroscience Institute), Python pipeline, MATLAB pipeline
- MoC3 (Columbia Zuckerman Institute)
- Churchland Lab
- Costa Lab (private repository)
- Hillman Lab
Element architecture¶
lab schema (API docs)¶
| Table | Description |
|---|---|
| Lab | Table for storing general lab info. |
| Location | Location of research (e.g., animal housing, experimental rigs) |
| UserRole | Roles assigned to a user or a job title. |
| User | Table for storing user information. |
| LabMembership | Store lab membership information using three lookup tables. |
| ProtocolType | Type of protocol or issuing agency. |
| Protocol | Protocol specifics (e.g., protocol number and title). |
| Project1 | Projects within a lab. |
| ProjectKeywords1 | Project keywords or meta-information. |
| ProjectPublication1 | Project's resulting publications. |
| ProjectSourceCode1 | URL to source code for replication. |
| ProjectUser1 | Users participating in the project. |
| Source | Source or supplier of subject animals. |
project schema (API docs)¶
| Table | Description |
|---|---|
| Project | Top-level grouping of studies and experiments to investigate a scientific question. |
| ProjectPersonnel | List of individuals involved in a project. |
| ProjectKeywords | Project keywords. If the dataset is exported, this metadata is saved within the NWB file. |
| ProjectPublication | Project's resulting publications. |
| ProjectSourceCode | Web address of source code. |
| Study | A set of experiments designed to address a specific aim. |
| Protocol | Info about institutional approval (e.g., IACUC, IRB, etc.) |
| Experiment | Experimental tasks and their associated lab, study, and protocol. |