GenomeGitWeb is a repository hosting site for GenomeGit, a DVCS for genomic data. The goal of this tool is to allow users to visually explore the data stored in a GenomeGit repository, including the changes between versions of an assembly. It also enhanes the project management aspect of GenomeGit by allowing registered users to create projects, mamage the visibility of the projects, invite collaborators, and add descriptiions or subit issues to a project.
After downloading the project, execute the following commands:
npm install -g @angular/clinpm installng buildnpm start
The application should now be available at http://localhost:3000 (with the developer version at http://localhost:4200).
WebCircos is the main visualisation tool used by GenomeGitWeb. It supports the visualisation of fasta, GFF, and VCF files from GenomeGit's repository to create circos plots where each file type forms a track. GenomeGitWeb also uses information from the alignment step in GenomeGit's lift-over to create a link track which links identical sequences between assembly versions. Data from a single commit/assembly version can be visualised by selecting a fasta file along with another file type. Data from different commits/assembly versions can also be visualised at the same time for comparison. By clicking on a GFF track, users can carry out more in-depth data exploration using a lightweight genome browser [Genoverse].
GenomeGitWeb can be used in a team setting for collaboration and management purposes or as a public repository for browsing projects. Users can search for projects to visualise on the homepage by using the search box or by clicking on the popular projects listed. Projects can also be visualised by selecting them from the dropdown menu on the "Plot" page.
Users can make an account by clicking on the 'Sign up' button on the homepage in the top right corner and filling out the form, inputting a user name, password, and email.
Only registered users are able to make new projects. Clicking the plus button on the "Plot" page brings up a dialog box where the project name, visibility (public or private), and an optional description can be input. Once the project has been created on GenomeGitWeb, the user can push their GenomeGit repository to GenomeGitWeb.
On the profile page, users can view details about all the projects they are part of. By navigating through the tabs, they can edit the project description, view files in the project, submit or resolve issues, and add new collaborators to a project.
This project was initially developed by Pramod Errolla, Joshua Fleming, Dylan Mead, Anton Spadar, and Ya Zuo.