Contribution Guidelines

We integrate information from published papers and image data produced by other groups. The provenance of that information, textual or image, is always acknowledged.

There are three ways to contribute, covered below and on the pages linked from here.

Submitting new data to VFB

Tell us about your paper

Have you just had a paper published which describes new anatomical or expression information?
The best way to make us aware of your paper, and to put it on our curation list is to act on an email you will receive from FlyBase after your paper has been published. The link on the email points to the Fast-Track Your Paper Tool.
Using this tool you can provide information on what types of data your paper contains. If it has new anatomical or expression information you’ll need to fill the sections, Anatomical data or Expression, respectively, in addition to any other suitable ones.
You can also use this tool for any other, previously published paper.

Spotted a paper with cell type information?

Have you seen a publication that characterises cell types or reconciles their names? New characterisation of cell types, and synonym mapping between differently named types, are particularly valuable for the ontology behind VFB. You don’t have to be an author to flag it.

• Flagging publications with cell type information: how to raise a ticket on the ontology repo or email us, and what to include.

Do you have image data that could be incorporated into VFB?

Email us at data@virtualflybrain.org and we will advise on image requirements and arrange a way to get the files to us. Ideally, contact us when you are still in the planning stages, but if you have already generated a dataset we can still help.

Two pages cover the detail:

• Submitting image data: what we can take, what to say in that first email, and what happens next.
• Registering your images: how to align your stacks to a standard template, starting with the easiest route.

Please use data@virtualflybrain.org rather than our support address. support@ goes to a publicly archived forum, which is not a good place for unpublished or embargoed data.

How to contribute to these docs

We use Hugo to format and generate these support pages. Hugo is an open-source static site generator that provides us with templates, content organisation in a standard directory structure, and a website generation engine. You write the pages in Markdown (or HTML if you want), and Hugo wraps them up into a website.

All submissions, including submissions by project members, require review. We use GitHub pull requests for this purpose. Consult GitHub Help for more information on using pull requests.

Updating a single page

If you’ve just spotted something you’d like to change while using the docs, there’s a shortcut:

1. Click Edit this page in the sidebar on the right of the page.
2. If you don’t already have an up to date fork of the project repo, you are prompted to get one. Click Fork this repository and propose changes or Update your Fork to get an up to date version of the project to edit. The appropriate page in your fork is displayed in edit mode.
3. Make your change and open a pull request.

Reporting a problem

If you’ve found a problem in the docs, but you’re not sure how to fix it yourself, click Report an issue in the same sidebar to raise one about that specific page. You can also create an issue directly in the VirtualFlyBrain/VFB2 repo.

Useful resources

• Hugo documentation: Comprehensive reference for Hugo.
• Github Hello World!: A basic introduction to GitHub concepts and workflow.
• nbconvert: A tool to convert jupyter notebooks into markdown (md) format.
• HTML to Markdown Converter: It helps to convert your HTML to MD. This tool is super fast and processes conversion in the browser.
• How to add new query properties to VFBConnect library