Improve the front page

[kimrutherford]

Remove Docs section on front page. Move GO Slim terms and Curation statistics to Genome status menu.

Remove "New publication pages (examples)".

This will give us more room for the news feed.

[kimrutherford]

I've done this but I forgot to ask where the GO Slim terms and Curation statistics should appear in the menu. Here's what it looks like for now. Please let me know any changes you'd like.

[ValWood]

Put GO slim terms -> GO slim overview Curation statistics Sequencing status -> Genome Sequence status Sequence updates -> Genome Updates Genome statistics -> Genome Feature Overview Gene Coordinate Changes New and Removed Genes Gene Characterisation -> Gene Characterization Status Priority Unstudied Genes

[kimrutherford]

I've made those changes in the dev vesion.

http://pombase-dev.bioinformatics.nz/

[ValWood]

New front page mock up

we want to highlight the GO slim and the advanced search permanently.

For the time being the current text can go in the rotating text box. Here we till highlight areas of biology, papers, feature (orthlog, unknowns) etc etc.

[kimrutherford]

I've done some of the rearranging. You'll see it in dev if you reload. It doesn't look quite like Val's mock up yet as I'm still tweaking the layout. http://pombase-dev.bioinformatics.nz/

I haven't tried it but I think the layout might look better if the rotating image was at the top right.

[ValWood]

I just had a quick play around. I think we should go more like this:

[ValWood]

So we could have 3 blocks across, or 2 up 2 down.

We would always try to have a "research or gene focus" we could have more than one, rotating. The community curation feed could be permanent ( but could have its own rotating set of icons to focus on different metrics or canto link for eg. A database or data spotlight (orthologs, unknowns, searching), a set of rotations.

Example popular pages could be above....we could even change these (gene, term etc) based on analytics maybe?) . We would just need an icon and a text snippit.

News feed could be horizontal across the bottom.

Something like this would keep the front page fresh and draw the eye to new stuff.

[Antonialock]

yeah I think this would look cool

[kimrutherford]

I like the shadows on the boxes.

[ValWood]

For each PomBase focus

Title :Step into the unknown Body: PomBase maintains an inventory of proteins with no known biological role, including their taxonomic conservation…..more More: link to http://preview.pombase.org/status/priority-unstudied-genes

image to associate

[ValWood]

Sample pages: Gene page Term page publication page Advanced search

but try above

• [x] add "about" link

[kimrutherford]

I've made some progress on the front page changes. Here's the prototype: http://pombase-dev.bioinformatics.nz/

All the text and links are just placeholders at the moment so we have something to talk about.

The configuration is in: pombe-embl/website/pombase_v2_config.json Look for the "front_page_panels" section if you're curious.

and the two test images are in this directory in Git: https://github.com/pombase/website/tree/master/frontend/src/assets

There is only one "Research spotlight" and one "Explore PomBase" configuration at the moment but the code is in place to randomly change what's on the front page.

I'll do a bit more work on this on Monday and then on Tuesday we can discuss it.

[ValWood]

Great start.

I don't think there will be too much to change!

• [x] can the boxes be wider and deeper? so the images can be larger. This will make more room for text too... don't worry if the text spots are a little empty for now.

• [x] I think the shading will be more effective if the box does not have the black line around

• [x] Titles and text need slight indentation

• [x] can we collapse the news a bit by either

2017-06-01 or New PomBase 2017-06-01

[ValWood]

; ) https://elifesciences.org/articles/28865/figures#video1 this will be so cool!

[kimrutherford]

deeper

If you mean taller, no problem. They will be taller once we add more text in the boxes - the height varies depending on content.

[ValWood]

OK . I was thinking that the image would be a "fixed size" at the top, and the text would also be a "fixed size at the bottom.

Overall I think the images should be larger.

[ValWood]

I have put 2 images for the top of the "community curation feed" rotation in the dropbox frontpage_rotations/community_curation_feed (we can rotate the images on this feed even though the text will stay the same...well will change but in a different manner...)

[ValWood]

I added another "Pombase spotlight" to the images folder. This is the accompanying draft text:

Title: Biological processes Overview Text: The fission yeast “GO slim” provides a summary of genes annotated to broad biological processes…more(link) Link http://preview.pombase.org/browse-curation/fission-yeast-go-slim-terms

so now we have 2 i) unknowns ii) slims iii) to do, query builder (this will do for release. can add more later)

[ValWood]

Overall I think the images should be larger.

don't worry about pushing the news feed down.... I think that is OK as long as the top of it will be normally visible on a small page....

[kimrutherford]

Overall I think the images should be larger.

Can you suggest an X and Y resolution? The current sample images are 240 x 150.

When you have time, can you suggest some text for the Gould lab spotlight? I only put in "Cytokinestic ring assembly." as a placeholder.

so now we have 2 i) unknowns

What should the title, text and link be for the Unknowns?

[kimrutherford]

The current sample images are 240 x 150.

Here they are for reference:

http://pombase-dev.bioinformatics.nz/assets/explore-poster-2017-10-06.png http://pombase-dev.bioinformatics.nz/assets/spotlight_gould-2017-10-06.png

[ValWood]

I can't reconcile the measurements because they look a different size to me but I think they should be ~25 % bigger.

[ValWood]

Title :Step into the unknown Body: PomBase maintains an inventory of proteins with no known biological role, including their taxonomic conservation…..more More: link to http://preview.pombase.org/status/priority-unstudied-genes

[ValWood]

we'll write the other text soon. I'll do cytokinesis today (i'm approving the paper later)

[kimrutherford]

they should be ~25 % bigger

OK, I'll try that.

[kimrutherford]

• add more space between news items
  • vw: (and reduce space between news item title header and news item slightly (make line spacing the same as body for each item)
• fix Markdown for "9th International Fission Yeast Meeting registration open" - too much space before "Conference Organizers"

[kimrutherford]

The dev site now has the new front page. I'll update the preview tomorrow after doing some checking and tidying.

[ValWood]

yes we can close this and put new requests in a new ticket. v

[kimrutherford]

The preview now has the new front page layout. The Gould lab text hasn't changed yet but it's ready to go.

[Antonialock]

shiny!

[ValWood]

freed from the limitations of Drupal....