Core Concepts

Understanding Kernel's core concepts helps you organize your work and collaborate effectively.

Workspaces

A workspace is a shared environment where teams collaborate on genetic design projects. Each workspace has:

• Members: Users with access to the workspace

• Repositories: Collections of constructs, parts, and notebooks

• Settings: Configuration for the workspace

You can belong to multiple workspaces and switch between them using the workspace selector in the header.

Public Workspaces

Kernel provides access to public workspaces with curated content:

• Asimov Public: Curated genetic parts from Asimov

• Uniprot Swiss-Prot: Protein sequences and annotations

• Addgene: Plasmid repository

Repositories

A repository is a container for organizing related constructs, parts, notebooks, and files. Think of it like a project folder.

Repositories support:

• Folders: Organize content hierarchically

• Sharing: Control who can view or edit

• Permissions: Admin, Editor, or Viewer roles

Constructs

A construct is a designed genetic sequence, typically a plasmid or expression vector. Constructs are built from parts and can include:

• DNA sequences

• Annotations marking features and regions

• Parts mapped to sequence regions

• Metadata like name, description, and attributes

Construct Groups

A construct group links related constructs that function together. For example, an antibody expression system might include:

• Heavy chain plasmid

• Light chain plasmid

Grouping these constructs keeps them organized and indicates they're meant to be used together.

Parts

A part is a reusable genetic element with a defined function. Parts have:

• Type: Promoter, CDS, terminator, origin, etc.

• Sequence: The DNA sequence

• Attributes: Metadata like organism, function, source

Common part types:

Type	Function
Promoter	Drives transcription
5' UTR	Untranslated region affecting translation
CDS	Coding sequence (gene)
3' UTR	Untranslated region for stability
Terminator	Ends transcription
Origin	Replication origin
Selectable marker	Antibiotic resistance or selection

Molecules

A molecule is a higher-level entity representing a protein or complex that one or more constructs encode. Molecules are particularly useful for:

• Antibodies (linking heavy and light chain constructs)

• Multi-subunit proteins

• Protein complexes

Notebooks

Notebooks are electronic lab notebook (ELN) entries for documenting experiments, protocols, and notes. Notebooks can link to constructs and parts for traceability.

Sequences

Sequences in Kernel are DNA sequences with annotations. Key concepts:

• Annotations: Named regions marking features (promoters, genes, etc.)

• Parts mapping: Linking sequence regions to part definitions

• Topology: Linear or circular (plasmids)

Next Steps

• Navigating the Interface — Learn the UI layout

• Creating Constructs — Build your first design

• Parts Library — Find reusable parts