icosa

The common library used by the websites (hivdb.stanford.edu and covdb.stanford.edu) created by HIVDB team. This library uses React to create views and components.

Views and Components

HIV Analysis Program

The HIVdb/HIVseq/HIValg programs share the same code base src/views/hiv. Config JSON files are hosted on cms.hivdb.org for the different programs. Here are the source YAML files:

• HIVdb: https://github.com/hivdb/hivdb-cms/blob/master/pages/sierra-hivpol.yml
• HIVdb-capsid: https://github.com/hivdb/hivdb-cms/blob/master/pages/sierra-hivca.yml
• HIVdb-HIV2: https://github.com/hivdb/hivdb-cms/blob/master/pages/sierra-hiv2.yml
• HIVseq: https://github.com/hivdb/hivdb-cms/blob/master/pages/sierra-hivseq.yml
• HIValg: https://github.com/hivdb/hivdb-cms/blob/master/pages/sierra-hivalg.yml

These YAML files need to be built into JSON format by make build command of hivdb/hivdb-cms repo before deployed to cms.hivdb.org.

SARS-CoV-2 Analysis Program

The src/views/sars2 is the code base for the SARS-CoV-2 analysis program. It shares core components with HIV Analysis Program but has individual views and configurations for obivious reasons. The config JSON file is also hosted on cms.hivdb.org. Here is the source YAML file:

• https://github.com/hivdb/chiro-cms/blob/main/pages/sierra-sars2.yml

Like HIV Analysis Program, this YAML file also need to be built into JSON format by make build command of hivdb/chiro-cms repo.

Markdown renderer

The src/components/markdown component wraps and extends react-markdown for rendering Markdowns from cms.hivdb.org. It is the core component of the /page/ prefixed pages on hivdb and covdb websites.

Genome map

The src/components/genome-map component plots a genome map and mutations according to input definitions. It is the core component of the SARS-CoV-2 variants page.

Simple table

The src/components/simple-table component renders a sortable table using input column definitions and table data. Many tables hosted on hivdb and covdb websites depends on this component.

Development

The development environment of Icosa requires NodeJS and Yarn. Once the latest versions installed:

cd icosa
yarn && yarn start

This command will host a service on http://localhost:3009. It requires Sierra-HIV/Sierra-SARS2 running as the backends for running/developing the HIV/SARS-CoV-2 Sequence Analysis Programs.