Tool:Webapollo: Browser-Based Sequence Annotation Editor

Question

[girlwithglasses]

WebApollo is a browser-based tool for visualisation and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process.

A brief list of some of the features of WebApollo:

• History tracking, including browsing of an annotation's edit history and full undo/redo functions
• Real time updating: edits in one client are instantly pushed to all other clients
• Convenient management of user login, authentication, and edit permissions
• Two-­stage curation process: edit within a temporary workspace, then publish to a curated database
• Ability to add comments, either chosen from a pre-defined set of comments or as freeform text.
• Ability to add DB-xrefs (e.g. for GO functional annotation)
• Can set start of translation for a transcript or let server determine automatically
• Flagging of non-canonical splice sites in curated annotations
• Edge matching to selected feature: matching edges across annotations and evidence tracks are highlighted
• Option to color transcript CDS by reading frame
• Loading of data directly from GFF3, BigWig, and BAM files, both remotely and from user's local machine.
• Configurable heat map rendering of BigWig data
• Per-session track configuration to set annotation colors, height, and other properties
• Export of annotation tracks as GFF3 and optionally other formats
• Search by sequence residues using server-side interface to BLAT or other sequence search programs

WebApollo is distributed as free, open-source software as part of the Generic Model Organism Database (GMOD) project. The latest release can be downloaded from the GMOD website, and there is also a WebApollo demo server.

Answer 1

[Istvan Albert]

Can I make a basic usability observation: when you create a demo site just have it jump directly to the visualization itself.

Making the site so that one first lands on a very rudimentary page, then has to click a link, then has to log in, then has to select some tracks - every single step loses a large number of potentially interested people. Load up the a nice fast page right away. Then point out other features.

And then after I went through all that - I was left confused, is this working at all? I saw some tracks but it was not obvious how to get anything visualized. Turns out I have to click edit? to see the tracks. I found that counterintuitive.

[girlwithglasses]

Thank you for the comment - I will pass that on to the WebApollo devs! Would a video demo be preferable to being thrown in the deep end with the demo site?

[Istvan Albert]

These decisions need to be made relative to audience that you want to reach and involve. A video may work better with a less-technical audience - but if you wanted give someone with more experience a practical perspective then it would be preferable to let them immediately get a sense for the performance, look and feel of the site and let them explore the interface unhindered.