Todos & progress for the development about ampspherewebsite HOT 8 CLOSED

Potential useful resources

• Bubble map
• HTML embedding

from ampspherewebsite.

Update on AMP page (frontend)

• Add "branchvalues": 'total' for sunburst plots ref.
• Retrieve host lineages using living-tree-toolkit from NCBI taxonomy ID (backend).
• Smaller secondary structure pie chart, make the relationships table full-width.
• Fix the colors in geo-distribution map (backend).
• Round the number of biochemical features to 3 decimals (backend).
• Distribution: habitats and hosts -> three distribution graphs: habitats, hosts and origins (switch using Plot.js buttons)
• Sidebar: fix the issue on default-openeds.
• Implement/adopt layout for line/bar/volcano plot.
• Browse page: a single table that can be filtered using host, habitat, family, etc.

from ampspherewebsite.

About 3D structure prediction @celiosantosjr

Pep-fold has neither a standalone version that can be used locally, nor an API service that can be called regularly, so embedding Pep-fold3 in our server is not possible for now.
I'll try to find another 3d structure prediction approach for such embedding.
If you have such good resources, please attach them here and I'll also try them. Thanks!

from ampspherewebsite.

• Just keep three tables in the AMP page: GMSC, Genome/Sample, Scientific name.

from ampspherewebsite.

• Merge complete_table_origins.tsv.gz, fna table, Metadata (db), and AMP (db) and generate a single table in the database

from ampspherewebsite.

mmseqs easy-search QUERY.fasta AMPSphere/AMPSphere_v.2021-03.faa.gz alnRes.m8 tmp

from ampspherewebsite.

• Implement helical wheel generating on the frontend side (mimic the modlamp api).

from ampspherewebsite.

PRIORITY

Already finished

• open a new API to get overall statistics of the entire ampsphere database
• implement distribution API
• test the backend API at a large scale - using pytest (https://fastapi.tiangolo.com/tutorial/testing/).
• integrate the backend and the frontend (fix the numbers on the home page).
• include a series of pagination buttons on the relationships table.
• include graphs (geoDistribution, habitatDistribution, hostDistribution, and PieChart - genomes and metagenomes) using the Carousel API of element plus.

DataBase (first week)

• create a statistics table #7
• refactor the repository structure of the database and necessary pre-computed files (finalize file structure)
• insert helical wheel paths in the AMP table

Backend (first week)

• include gene sequence in the /v1/amps/{accession} API
• change response code to 200 when no AMPs or families can be returned using browse API
• Host backend to the AWS server
• add total number of items (and total pages) for each paginated API.
• implement the download API (only four tsv tables in the database, should be done once new server is ready)
• fix the colors in geo-distribution map (backend, lower priority).

Frontend

• update the AMP page to use real data from the backend (first week)
• include gene sequences in the downloaded relationships table
• implement a browse page and a search result page (integrated with the backend API)
• browse page: a single table that can be filtered using host, habitat, family, etc.
• implement a family page (integrated with the backend API)
• implement other pages (integrated with the backend API when necessary)
• download page: four buttons for four tsv tables in the database, --- and link to the Zenodo repository
• include Fudan, ISTBI, BDB logo and info...
• include badges indicating qualities of amps (similar to github badges)
• sidebar: fix the issue on default-openeds.

Performance optimization

• optimize text search performance, LOW PRIORITY
• finalize frontend layout: enhance responsiveness

from ampspherewebsite.