benjamin-lee/viroiddb

A curated database of all available viroid-like RNA sequences

viroiddb

Build Setup

# install dependencies
$ npm install

# serve with hot reload at localhost:3000
$ npm run dev

# build for production and launch server
$ npm run build
$ npm run start

# generate static project
$ npm run generate

For detailed explanation on how things work, check out Nuxt.js docs.

viroiddb's Issues

Layout and missing submit buttom

Single column layout / shortish line wrapping, on regular MD pages (e.g. screen cap)
Also, submit page - form lacks a "submit" button.

sequence list page - color coding types and more

1. Types color coding is no more by design?
2. satRNAs, Virus need fluffing, Viroids need sources.
3. Sequence list landing page - replace Lorem ipsum

Don't display RZ hits if none present

Unify + and - SS view

List rotationally identical sequences

Make SS view at bottom of page

Capitalize type in search page

Sequence viewer flukes

1. "Copy FASTA" button not implemented. Suggestion: discard it (users can ctrl+c if they want).
2. Suggestion - instead of single-click download, offer other stuff via drop down box.
   e.g. Download ⮧

• Fasta nucleic
• DBN
• Metadata filled JSON
• forna pic as svg
  etc etc

3. "MFE" and "Bases paired" not sourced

Move SS legend to the SS card

Add page listing versions and changes

Add page with direct data download links

Fix sequence routing

Only a few of the routes actually work.
ie http://viroids.org/sequences/JF746187.1 is invalid

Restyle the new search results

With more attributes the results look bloated. This is not a huge deal

Add clear results button to search

I added keep-alive to <Nuxt /> to fix the fact that it was clearing and losing place. However, now the only way to clear the search is manual. Could we get a button for that?

Fix the navbar in a medium view

The addition of "community" tab makes the navbar overflow in certain sizes

Link out to NCBI GenBank page for each rotationally identical sequence

Sequence hub flukes

• Green - allow numerical / alpha-beit sorting by column value
• Red - sequence name should be clickable (instead / in addition to "View" button)
• Blue - Allow multiple clicks on the groups tick boxes (currently only one check-ed box allowed), and make the table auto-hide sequences from unticked boxes.

Hide load more button on cluster page if all sequences loaded

Use periods consistently in seq view page

Add copy/download buttons to Infernal output