About
The system being developed by Team 2133 is an application which can provide information and predictions about Covid-19 and its variants in a given geographic region. We aim to enable the general public to make informed decisions about travel and make predictive determination of likely Covid-19 genomic mutations in a specific area. It could also be used by epidemiologists and COVID researchers as a means of assessing recent variants through multiple genome alignment, and analyze developments through the aid of a predictive model which highlights components of the genome affected by mutations.
The Team
| Name | Roles | |
|---|---|---|
| Bennett Burns | bburns39@gatech.edu | Summarizer, Compromiser, Encourager |
| Andrew Friedman | afriedman38@gatech.edu | Information Giver, Harmonizer |
| Noel Igbokwe | nigbokwe3@gatech.edu | Information Seeker, Summarizers |
| John Rehme | jrehme3@gatech.edu | Information Seeker, Feeling Expressers |
| Nihar Shah | nshah400@gatech.edu | Energizers, Clarifiers |
| Max Tang | mtang80@gatech.edu | Information Giver, Harmonizer |
| Daniel Varzari | dvarzari3@gatech.edu | Energizer, Clarifier, Compromiser, Organizer, Information Seeker |
Team Resources & Instillation Guides
Release Notes
v0.5.0
Features
- Multi node compute resource for notebooks
- Confidence Model is now reachable as an endpoint (this is yet to be connected to the frontend)
- Confidence Model has historical metrics and confusion matrix shown to display results
- MLflow in Azure setup to record and deploy model experiments as versioned histories
- API calls to the backend to receive accurate and full accession data
- iOS and MacOS support
- New versions of Variant Card, Country Card, and (now) Continent Card - support for multi-card activity and map zoom
- New Settings page to adjust different parts of the app - account, accessibility, and more
Bug Fixes
- Worked around memory issues within the notebooks by using smaller training sets
- Fixed Google Maps zoom behavior
- Multiple card behavior is now intended, not a bug
Known Issues
- unable to pad csr matrix to be accepted by the MLflow API - could be solved by moving frontend to Azure as well
- unable to run large memory blocks like the unified tables found in clustering notebook
v0.4.0
Features
- Added new variant card - selecting a variant from a region pulls up additional info about the genome sequence, a link to the vairant on NCBI, and the ability to add the variant to a user's Saved list
- New relational database created in Azure - will allow final connection between backend and frontend to populate website with data
- New Postgres SQL commands allow us to filter genomes by region, date, etc. - 650,000 have been segregated so far
- [Minor] Moved FAQ menu to new button in bottom right of home screen - cleans up home screen tabs selection
Bug Fixes
- Data cleaning has allowed us to finally store and work with genomic sequence data
- Made "card" feature universal - can now instantiate and remove cards at will
Known Issues
- New variant card throws null error for non-logged in users
- API request needs to be created for relational database
v0.3.0
Features
- Saved variant table added to user accounts - will allow saving of variants in future version of application
- Added animated Google Maps functionality when selecting a region
Bug Fixes
- Fixed Google Maps Controller to support changing of map
Known Issues
- Still able to open multiple region cards - due to unique implementation to support card feature
- Still running data cleaning - expected to end by this week or next due to the sheer volume of data
- Architecting the model has proven to be more difficult than initally presumed, at least to the degree of accuracy desired
v0.2.0
Features
- Multiselect for variants - can select group of variants to copy from a list displayed to the user
- New copy & compare button – copies list of selected variants and can open BLAST to compare
- Azure Databricks setup – have a place to run our notebooks from
- Azure Functions – allows us to port data as JSON from blob storage to notebook
Bug Fixes
- Country name now correctly shows in Variant View for the selected country
Known Issues
- Able to open the same region card multiple times
- Title for region cards shrinks when too long
- FASTA format is not sufficient to give us all the data we need – consider .gbff
- Azure is not connected as endpoint
v0.1.0
Features
- Region card view – this extends from our search functionality for regions, and where we can start to see variant views.
- Variant view – redirects to database link
- Variant table view – can view more variants for a particular region
Bug Fixes
- Fixed Google Maps agreement issue (was out-of-date)
Known Issues
- Able to open the same region card multiple times
- Title for region cards shrinks when too long