Welcome to CellRepo! This onboarding guide will help you get started with our platform, ensuring you have a smooth and efficient experience.
1. For our Beta product (currently available), you can join the platform in one of two ways
On the CellRepo.com homepage, click on the 'Join Waitlist' button, fill in and submit the form. Our team will receive your request and will send you a one-time signup link for you to access the platform
Email us directly and we can send you one-time signup links
2. Either way, once you click on your signup link, you can register your CellRepo.com account
3. Fill in your details (name, email, password).
4. Verify your email address through the confirmation link sent to your inbox.
5. Log in to your new account.
Header Navigation:
The top navigation bar includes links to key sections:
Home
Projects
Repositories
Catalogue
Labs
Organisation
Tools
A search bar and user profile icon (with sign-out option) are on the right.
Enter search terms into the Search bar and click the Search button to find data on CellRepo
Click on your User Icon to view your account page and settings
User Profile Card:
This area welcomes the you, displaying at a glance your user’s avatar, name , and your associated labs or organisations, as well as your activity metrics, with links to your user profile
Recently Added Cells:
This section lists the strains and plasmids you've recently added to the CellRepo platform
Recent Repositories:
Displays your most recent repositories, created by you
Recent Projects:
See the projects that you have been working on most recently
Repositories You’re Following:
You can follow other repositories. Your most recently followed repositories will appear here
Claim Your Genosignature Kit: If you have received a Genosignature Kit from GitLife Biotech, enter the Claimable ID below to link all Genosignatures in your kit to your CellRepo account!
Being part of your organisation makes it quick and easy to collaborate with your colleagues and view data generated on CellRepo by your organisation
Users can request to join an organisation, or, if they are the the first member of that organisation on CellRepo, they will be able to add, remove and manage other users in that organisation
Users can have different roles within an organisation
Owner:
Has the highest level of access and control within the organisation.
Can edit organisations, projects, user roles, and members.
Can assign, approve, deny, and remove members.
Full access and control.
Admin:
Can add to the organisation and projects.
Has the ability to approve, deny, and assign members.
Supports the owner in managing the organisation.
Manages additions and approvals.
Member:
Can view the organisation and its members.
Can view projects and contribute by adding labs and repositories to projects.
Primarily for contributors within the organisation.
Viewer:
Can view the organisation and its projects.
Has read-only access to the organisation's resources.
Projects enable you to collaborate across multiple organisations, labs and repositories. It is a container for you to assign more than one repository to an overarching project.
You can also add as many users, labs and organisations as you require for the project.
Similar to repositories, you can have the project visible to the public, or only to it's collaborators (which is the default behaviour)
In the context of CellRepo for strain and plasmid engineering, version control is used to track and manage the development and modification of biological designs over time. It ensures that changes to engineered strains or plasmids are well-documented, reversible, and open to collaboration.
Repositories: A repository is a dedicated space where the entire history of a strain or plasmid development is recorded. It tracks every modification, experiment, and design iteration, providing a complete and organised view of the biological engineering process.
Branches: A branch allows researchers to explore new modifications or variations in a strain or plasmid without affecting the main development line. These branches enable parallel experiments or approaches, and they can be merged back into the primary strain once the new designs are validated.
Commits: Commits capture specific alterations or updates made to the strain or plasmid. They represent snapshots of progress, documenting every adjustment in the engineering process, from genetic edits to experimental outcomes, allowing for detailed tracking and the ability to revert to earlier stages of development if needed.
A repository is a centralised storage location where users can manage and track the development of engineered strains. It facilitates version control, collaboration, and organisation of genetic data, experiments, and related resources. Each repository contains branches and commits, which store strain files, plasmid data, and other essential information. This structure ensures that every change is documented, promoting reproducibility and collaboration across projects.
A repository can have one of three visibility levels:
Everyone - The repository is viewable by CellRepo users and non-CellRepo users alike
You can add individual users as 'Viewers' (Read only access) and 'Editors' (Read and Write access) to these repositories via the 'Edit Repository' page (see below)
Only me and my lab - The repository is associated with a Lab (the lab must exist prior to selecting this option, and you must select the Lab you wish to link to this repository) and is viewable by other members of the lab.
Note - Lab members can only view the repository, not edit it or add commits to it. You must add individual users as Editors (see below) in order to allow other users to add Commits to the Repository, or to manage the Repository
Only me - The repository is private and can only be viewed by you by default.
As above, you can add individual users as 'Viewers' (Read only access) and 'Editors' (Read and Write access) to these repositories via the 'Edit Repository' page (see below)
Below: Repository Overview page, showing two tabs containing each set of Repositories
In CellRepo, forking a repository allows you to create an independent copy of an existing repository, which you can then modify without affecting the original. This is especially useful for experimenting with new changes, developing alternative versions of a strain or plasmid, or contributing to someone else's work.
When you fork a repository, the entire history and structure of the original strain development, including its branches and commits, are copied into your personal workspace. You can then edit, experiment, or add new elements as needed
In the Actions menu on a repository, select the 'Repository Report' option and a PDF version of this repository will be downloaded to your computer
A branch is a separate line of development used to explore new modifications or alternative approaches to strain or plasmid engineering. It allows researchers to experiment with changes—such as introducing new genetic components or optimizing plasmid structures—without impacting the main or stable version of the strain. This means multiple branches can exist simultaneously, each focusing on different aspects or experiments. Once a branch's modifications are tested and validated, it can be merged back into the main development line, integrating the new advancements while maintaining the integrity of the core project, or can remain as different 'versions' of that strain or plasmid
Below: A Tree showing Branches in the blue lines with Commits in pink on each branch
A commit represents a documented point of change in the engineering process of a strain or plasmid. Commits exist on branches - think of commits as leaves or nodes on branches of a tree. Each commit captures the specific biological modifications, such as gene edits, plasmid insertions, or experimental results, at a particular stage in the design. By committing these changes, users create a permanent record of their work, ensuring that each modification is traceable. This allows for precise tracking of the engineering process, facilitating collaboration and enabling a return to previous states in the strain’s development if needed, ensuring reproducibility and accuracy.
You can also create 'headless' commits that aren't attached to branches - see the video above under branching for more details, but you will see a checkbox right at the top of the page when you create a commit that you can check in order to save that commit without attaching it to the tree of your repository
CellRepo enables you to create a digital twin of your engineered cells, establishing a physical link to their real-world counterparts through Genosignature. Our CellRepo platform generates these Genosignatures, which can be seamlessly integrated into your cells, creating a traceable and defensible connection between your actual cells and their engineering history.
You have the flexibility to select the type of Genosignature for each commit. Every commit will feature a unique digital signature, and you will choose the preferred physical signature type for each one, where desired.
If you do not insert a new signature during a commit, but the parent commit includes one, our system will automatically recognize that your cell retains the previously inserted signature and associate it with the unique digital signature of that commit.
Genostamp Genostamp is our entry-level Genosignature, offering a concise representation that is shorter in length and contains less digital data encoded within its genetic counterpart. It is designed for those seeking an accessible introduction to genetic identification. Genoguard Genoguard is our advanced Genosignature, providing a more secure and robust option. With a longer length, it incorporates cryptographically encoded components of your digital twin, ensuring enhanced protection and integrity of your genetic data.
If you have received a kit from GitLife that includes Genosignatures, please claim your kit using the Claimable ID found on your CellRepo Dashboard. Once you do this, your Genosignatures will be available in the dropdown menu, allowing you to select and assign them to a commit.
CellRepo accepts user-defined restriction enzymes on Plasmid, and also in Genosignature generation. We allow you to specify which restriction enzymes you would like to exclude from your Genosignature, as well as a list of sensible defaults, ensuring that your Genosignature is restriction site free. Please note, we don't exclude enzymes whose sequences are less than five nucleotides long. To see how you can do this in detail, please view the explainer below
Adding Restriction EnzymesLabs are a way to group together users and share repositories between them. Labs can be added to Projects and Organisations and can be associated with Repositories
The Catalogue page lists all the bioassets you have created, or have been given access to, in a table that you can sort and filter using the tools directly available within the catalogue table. You can also view the publicly available bioassets in CellRepo on the 'Public' tab
You can also view the Catalogue of bioassets that has been produced by an Organisation by searching for the Organisation in question, either within the global CellRepo catalogue, or by searching for and viewing an Organisation's CellRepo page
Here we will have standalone tools that you can use independently of the version control system
We can generate a number of neutral sites that are suitable as landing paths for barcode insertion. This can be requested
On the 'Tools' Page, where you can upload your genome sequence for us to analyse and produce the sites
By ticking the 'Request Landing Paths' Checkbox when creating or editing a Commit
1. Click your Avatar on the top bar
2. Update your personal information as needed.
3. Save changes by clicking 'Update'
1. Untick the 'Email me when' options as appropriate
2. Save changes by clicking 'Update'
~Feature coming soon~
View files containing landing paths that you have requested from us and have been created for you here. You'll also receive an email when we have generated and uploaded them for you.
If you wish to delete your CellRepo account, we have a button on your User account page that will take you through the process of deleting your account
There are options for you to decide what to do with your data that exists on CellRepo. Some of these actions include obfuscating user details from public or published data, transferring ownership of shared data, and reassignment of ownership or relationhips between other sets of data or CellRepo constructs such as Labs and Projects
Follow the on-screen form and select what you wish to happen to each piece of data or construct you own, and once complete, your account will be deleted.
If you need further assistance, reach out to our support team via:
- Email: [email protected]
Thank you for choosing CellRepo! We are excited to have you on board and look forward to supporting you as you manage your cell inventory efficiently. If you have any questions, don't hesitate to reach out!