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This is a work in progress!

Quick Start

Registration

You can view public repositories on CellRepo without signing up for an account. To get the most out of CellRepo, we recommend creating an account. To do so:

  • Sign up for the application by clicking the ‘Join Now’ button on the CellRepo homepage

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  • Choose an avatar, enter your name, email address and a secure password on the registration form and click ‘Register’. If you do not wish to select an avatar, your initials will be displayed in place of an avatar. However, an avatar would make it easier for those you know to identify you in CellRepo

  • Check your email inbox for an email from CellRepo to confirm your account

  • If you see this email, click the link in the email to confirm your email address with CellRepo.

  • You may need to check your spam folder. If you still haven’t received your confirmation instructions after 10 mins, follow the link for ‘Didn’t receive confirmation instructions?’

  • Once you are confirmed, you can sign in using your email address and password

If you have registered, confirmed and signed in successfully, you should see the CellRepo homepage

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Species

Here you can set up the species that you base your repositories from
  • Click the 'Species' link in the navigation bar at the top of the screen.

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  • Select the databank type from the dropdown option

  • Add in the ID for the species from the external databank source. Click the (?) icon to see the images of how to get the ID and NAME for various external sources

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  • Add in the NAME for the species from the external databank source. Click the (?) icon to see the images of how to get the ID and NAME for various external sources

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  • Click on 'Create' to save your species

Now you’ll see the species under ‘My Species’ list and it will be checked - this means it will appear in the species dropdown on the new repository page and edit repository page. Click on the icon next to the species name to get the link out to your species on it's external page

Alternatively, there will be a link to add a new species for use during the creation of a Repository, should you wish to skip this step

Teams

Teams are a way to work with other users on CellRepo. You can define as many teams as you need, and they can consist of one or as many other users as you like. You can give permissions to those in your team to be able to either View or Edit the team-based repositories you have

  • Navigate to the ‘Teams’ page using the navigation bar at the top of the page or the card on the homepage Click the + button to create a team

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  • Create a name for your new team

  • Enter the name of someone you would like to add to the team in the text box on the team page

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  • Select from the dropdown whether you’d like to give that person ‘Viewer’ or ‘Editor’ permissions for your team repositories

  • Click ‘Add’ when you are ready to add that person to your team
  • Continue this for as many team members as you would like to add

You can remove team members on this page, too, as well as delete the team

When you delete a team, any repositories associated with that team become private so that no one apart from you can access that repository. You can change the repository settings, but this is the default behaviour once you delete a team that has repositories associated with it

Repositories

Repositories are what contain all of your experiment data. Each repository represents an experiment on a cell line

  • Navigate to the ‘Repositories’ page using the navigation bar at the top of the page or the card on the homepage

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  • Browse the different tabs to see different categories of repositories

  • My repositories are repos that you have created

  • Public are repos which are visible to the public which do not belong to you

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  • You can see repositories you have followed, too

  • Any repository that is not yours which you have collaborated on appears here

  • Click Add button to create a new repository

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  • Select a species from the dropdown - remember to add any more species you’d like to use by clicking the link under the box

  • Give your repository a name, a description, and set the visibility level of your repository

  • Optionally, you can choose to associate your repository with a team. This will NOT work for private repositories!

  • You can also add a README which contains any information that another user would need in order to be able to use or read your repository

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  • You can perform actions on your repository using the actions menu

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Commits

A commit adds the latest changes to the repository. It contains information about the changes to the cell line, who did it, references, barcodes, documents etc. Commits are a representation of a cell line at an exact moment in history.

  • Select 'New Commit' from the Actions menu to add a commit to the repository

  • Fill in the commit form with information about your change. Add any files you want to upload that supplement the commit.

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  • You can view your commit once you have added and saved all of your data

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  • A commit, once saved, with remain in its ‘Editable’ state UNTIL you click ‘Finalise Commit’ at which point it can no longer be edited or deleted

  • Click on a document to download that file

Strains

Strains are the new things you create by editing genotype, phenotype, and plasmid information as part of commits. You can view all the ones you have created in CellRepo under the Strains view

Branches

Branches contain commits and belong to repositories, and represent different versions of work on the same parent project

  • Create a new branch by going to a commit, clicking the 'Action' menu and filling in the 'New Branch' field with a name for your new branch, and then click the little icon button next to the field to create the branch. The new branch will only show up properly in the graph once you have added a commit to this branch

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  • Switch branches in your repository by clicking on the branch name in the branch dropdown

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Search

Search within CellRepo for things you or other CellRepo users have created. At the moment, we suggest using full terms to search as the application does not currently support partial word or term search.

  • Enter your term in the search bar on the navigation menu

  • Click this button to search

  • Click on a search result to view the resource

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Account

You have access to your account settings should you wish to update your name, email address, password, avatar, notification settings, or delete your account

  • Click on your avatar in the top right corner of the navbar

  • Change any fields you wish and click the 'Update' button to save your changes

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  • To delete your account, click the delete button

Ideas, suggestions, feedback and bug reports are always welcome through the ‘Feedback’ area of the Knowledge Base

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