Experiment Design

SeqCMD uses a simple but expressive model for describing experimental design and meta-data.

Experiment Data Model

To describe an experiment SeqCMD uses three concepts: Samples, Attributes, and Groups. Samples are used to represent the source of material for a sequencing experiment, e.g. a plate of cells, or a piece of tissue from a particular donor. Each Sample is described by any number of arbitrary Attributes. These Attributes are used to specify properties of the sample, e.g. the Sample could have Attributes "Species:Human" and "Age:73". To facilitate downstream analysis and data retrieval Samples can be organized into Groups, which are named collections of Samples.

Registering Experiments

To make small modifications the Sample, Attribute, and Group information can be manually edited using buttons provided in the user interface. To register more complex experiments a CSV describing the experimental details can be uploaded.

Editing Experimental Design

Errors in the original sample sheet specification can sometimes happen, as well as sample-swap mixups. To enable these errors to be corrected the sample attributes can be edited without disturbing the relationship between samples and downstream data artifacts.