FAQ

Frequently asked questions about Kernel.

General

What is Kernel?

Kernel is a genetic design platform for engineering biology. It combines sequence design tools, team collaboration features, and workflow automation to accelerate biotechnology development.

Who is Kernel for?

Kernel is designed for:

• Molecular biologists designing constructs

• Antibody engineers

• Synthetic biologists

• Research teams collaborating on genetic projects

• Bioinformaticians managing sequence data

How do I get started?

1. Sign up at kernel.asimov.com

2. Join or create a workspace

3. Follow the Quick Start Guide

Account & Access

How do I reset my password?

1. Go to the login page

2. Click "Forgot password"

3. Enter your email address

4. Follow the reset link sent to your email

Can I belong to multiple workspaces?

Yes. You can be a member of multiple workspaces and switch between them using the workspace selector in the header.

How do I invite team members?

1. Go to Settings > Members

2. Click Invite

3. Enter email addresses

4. Select their role

5. Send invitations

Constructs & Parts

What file formats can I import?

Kernel supports:

• GenBank (.gb, .gbk)

• FASTA (.fasta, .fa)

• DNA (.dna) - SnapGene format

What file formats can I export?

• GenBank (.gb)

• FASTA (.fasta)

• DNA (.dna)

• PNG images (schematic, circular map)

What's the difference between a part and an annotation?

Parts are reusable genetic elements stored in your library. They have defined properties and can be used across multiple constructs.

Annotations are labels on sequence regions. They can be standalone or linked to part definitions.

How do I create a construct from parts?

1. Create a new construct

2. Open Part match in the right sidebar

3. Search for parts

4. Drag parts into the schematic view

5. Arrange as needed

See Drag and Drop Assembly.

Collaboration

How do I share a repository?

1. Open the repository

2. Click Share

3. Add users or workspaces

4. Set permission levels

5. Click Share

What are the permission levels?

• Admin: Full control including settings

• Editor: Can create and modify content

• Viewer: Read-only access

Can I share with people outside my organization?

Yes. Share repositories with any Kernel user by email, or share with other workspaces.

Tools & Features

What is codon optimization?

Codon optimization replaces rare codons with more common synonymous codons for your target expression host. This can improve protein expression while maintaining the same amino acid sequence.

What is the Compiler?

The Compiler automatically designs expression constructs from antibody amino acid sequences. It handles codon optimization, signal peptide selection, and vector assembly.

What is SecureDNA?

SecureDNA is a biosecurity screening service that checks sequences for potentially hazardous content. It's often required by synthesis providers.

What simulations can Kernel run?

Kernel's Simulator predicts:

• RNA polymerase flux

• Ribosome flux

• RNA concentrations

• Protein concentrations

Technical

Is there an API?

Yes. Kernel provides REST and GraphQL APIs, plus a Python SDK. See API Overview.

What browsers are supported?

Kernel works best in:

• Chrome (recommended)

• Firefox

• Safari

• Edge

Is my data secure?

Yes. Kernel uses industry-standard security:

• Encrypted data in transit and at rest

• Role-based access control

• Regular security audits

Troubleshooting

Why can't I edit a construct?

Possible reasons:

• You have Viewer permission (need Editor or Admin)

• The construct is locked

• You're viewing a public repository

Contact the repository admin for access.

Why is my search not finding results?

Try:

• Check spelling

• Use fewer search terms

• Remove filters

• Search in "All repositories" instead of "This folder"

Why did my simulation fail?

Common causes:

• Invalid sequence format

• Missing annotations

• Incomplete construct

• Check the error message for details

Support

How do I get help?

• Check this documentation

• Use Kernel AI for guidance

• Email [email protected]

How do I report a bug?

Email [email protected] with:

• What you were trying to do

• What happened

• Steps to reproduce

• Screenshots if helpful

How do I request a feature?

Email [email protected] with your feature request. We review all suggestions.