A workflow is a sequence of research processes that are performed to answer a research question or synthesize new material, for e.g. synthesizing a new set of proteins from supernatants or improving the transduction process. Think of it as a pipe that helps information flow through all the connected steps.
A reusable template that defines an ordered collection of stages and the connections between them.
Workflow templates are:
- Fully configurable
- Versioned so that you can track changes made over time and compare the results generated from different versions
- Access controlled so that you determine who can see and edit them
A step in the workflow that modifies or analyzes a biological entity. Each stage defines:
- A default entry template that can be used as a blueprint for entries created for that stage.
- Results that need to be recorded for that stage
- Who is working on it
One execution of a stage in a workflow. It connects all the inputs that lead to a set of outputs for a given condition.
A stage can be executed multiple times in a workflow.
An enhanced table that enables automatic extraction of data from a Notebook entry. Data recorded in result tables can be searched for across entries.
Result tables have the following properties:
- Data shown in search results and the workflows summary dashboard.
- Data is synced with the warehouse.
- Configurable Schemas, enables a consistent set of information can be recorded every time
- Automatically generated rows for the samples in the entry
Input samples table
Shows the starting samples that are being worked with in this entry. Think of it as an inbox for samples that need to be used. Because the input samples table is linked through the workflow, the output samples marked in the previous stage are automatically filled in as inputs to this stage.
Output samples table
Set of valid samples that will be passed on to the next stage. These can either be new samples generated during this stage or the list of inputs that were characterized and should be used by a downstream stage. Think of it as an ‘outbox’.
A table used for registering batches of an entity to the Benchling Bioregistry from within a Notebook entry. For each batch, the user can specify the following in a registration table:
- Properties about the entity
- Properties about the batch
- Container location
It is useful because it allows users to capture information about the samples they are creating without having to switch context.
- Each registration table only registers entities of a specific entity type.
- A Notebook entry can have more than one registration table.
Aggregated workflow view that shows all the workflows, who is working on them, the project they are a part of, current status, and when the last stage was completed.
Workflow summary view
Workflow Summary Dashboard aggregates information and shows:
- Stages and how they are connected to each other
- Current status
- Inputs and outputs to each stage
- Critical data fields, extracted from structured tables
Each stage can be performed multiple times.