Proposed priority for the first release

[ruiwanguk]

@jadianes @jgriss @noedelta Since our last dev release, we had a lot of releases and discussions for the potential improvements. After discussing with Jose and Johannes, here are a proposed list of todos for the first production release (they are ordered by priority)

For the peptide search result page:

• Show modifications for the peptide sequences
• Faceting peptide search results for both species and modifications
• Improve the relevance score for the search results (#spectra first, then max ratio)
• Hide bubble chart

For the cluster summary page:

• Show modifications together with peptide sequence
• Fix the problem with the strange character with paging the original projects
• Fix the problem with the modification pie chart at both the web service level and the front end level
• Improve the paging of the unique peptide section, hide the pagination when results can be fitted on one page
• Remove the number of modifications from the summary section
• Sort by the number of PSMs for the table of unique peptides
• Show modifications on the peptides at the table of unique peptides
• Add number of projects for unique peptides

For the home page:

• Provide real cluster statistics
• Provide detailed descriptions for each sections
• Provide newly structured home page as the mockup suggests
• Provide documentations on the help page and the about page
• Add citation as part of PRIDE Cluster summary

For spectrum library page:

• Update introduction
• Update the code snippets
• Move the release date and version next to the title “Latest Release” with smaller font
• Change “Using the PRIDE Spectrum Libraries” to “How to use spectrum libraries"
• Increase the gap between “Latest release” and “ Using the PRID Spectrum libraries"

ToDo for the future:

• Add sorting to the peptide search page
• Provide bubble chart as suggested by the mockup for the peptide search page
• Improve performance of loading original projects for the cluster summary page
• Add downloading of consensus spectrum as MGF
• Click the unique peptides to view PSM details

Let me know if I have missed anything, I would suggest that we tick off these todos once they are done.

[jadianes]

I've added:

• Show modifications together with peptide sequence to the Cluster summary page (that I use to call Cluster details page by the way :) )

[ruiwanguk]

I have fixed the web service side of the problem on providing modifications and species distribution. Will deploy this in the afternoon.

[ruiwanguk]

I have added the number of projects to the unique peptide WS end point, so that we can display the number of projects for each unique peptide.

[ruiwanguk]

Improve the performance of retrieving project details using multi threaded approach. This is still limited by the speed of PRIDE Archive web service, which can be slow at times.

• Improve performance of loading original projects for the cluster summary page

[ruiwanguk]

The general statistics are now provided

• Provide real cluster statistics

[jadianes]

Done

• Hide bubble chart

[jadianes]

Done

• Improve the paging of the unique peptide section, hide the pagination when results can be fitted on one page
• Remove the number of modifications from the summary section
• Show modifications on the peptides at the table of unique peptides
• Add number of projects for unique peptides