About The Project:
Saving lives by improving logistics and data accuracy! Infectious diseases kill more than 17 million people every year. When outbreaks occur it
is difficult to determine the source of the pathogen causing them. Our sponsor, TGen North, uses forensic DNA sequencing to determine the origin of
the pathogens so outbreaks can be stopped as close to the source as possible; unfortunately, this life saving science is often put on hold while the
scientists track samples and perform significant amounts of error prone, manual data entry. You can read more in depth by looking at
TGens Proposal
Over the past 9 months Team Viraltech has been implementing a full stack web application that will automatically accomplish the logistical tasks while
improving data accuracy, so that the scientists at TGen North can spend more time saving lives.
Problems:
Data Entry
Manual data entry done by scientists
Non-standardized data collection
Collaborators are using their own methods of submitting data via different spreadsheets
Non-dynamic data submission
Data associated with samples is dynamic, often changing on a case by case basis, the current process does not account for this
Current Workflow:
Our Solution:
We envision solving solving the problem by creating a Website for TGEN & their contributors, that also communicates with their current database. In this app, users could log in securely, then be able to enter in all the required data about their samples.
Team Members
Jialei Chen
Release ManagerCoder
Carl Porter
Team LeadCommunicator
Coder
Colton Spector
ArchitectRecorder
Coder
Weiheng Su
CoderProject Requirements Key Features, High Level Requirements, & Technology Used
Key Features
- A secure modern Web2.0 web application, to allow access from any modern web browser.
- User accounts and profiles with secure authentication to strictly control access to the system(only known users/domains should be able to view/add data).
- A dashboard for authenticated users, allowing them to view their submitted jobs and the current status of those jobs, as well as submitting new jobs.
- The ability to generate custom labels that collaborators may attatch to the samples they send us, instead of using their own (haphazard) in-house labeling systems.
- A clean, configurable forms-based interface. Based on the job characteristics selected by users, the GUI will gather precisely the information relevant for that job.
- Intergration with TGens internal database and workflow managment system, so that entered data can be easily and automatically stored.
- Provide shipping instructions and printable shipping labels to the collaborator after they have entered their data.
High Level Requirements
- Users will be able to submit their sample information through the Collaborator Web Portal
- Users will have a generated QR code for their sample which will allow Workflow tracking
- Users will have been generated a shipping label to place on their package, which is trackable
- System will submit sample data from the Collaborator Web Portal to the TGen North database
- System must allow for highly flexible/customizable metadata
Technologies Used
- Google Authentication was requested by our client to avoid having to create our own authentication system for their scientists and their clients.
- PostgreSQL is currently being used by TGen for their PIMS system, and they wish to continue their use of PostgreSQL since it is more stable, and has better performance for larger databases.
- We will continue the implementation of QR codes in our project, since it provides assistance in linking the data submitted to the PIMS database.
- Dynamic data entry accomplished with JSON tuples stored in the database
Deliverables Our work
Collaborator Entry Point - Demo
Codebase - GitHub
All Team Meetings
Technological Feasability Document
Schedule
Since September we have been in the process of gathering requirements for our project. We met with TGen North bi-weekly. Our meetings started with general information as well as a tour of the TGen North facilities. From there we began iterative conceptual prototyping in order to workshop the functionality of the website. We went through three iterative cycles, with the first prototype being drawn on paper and the next two modeled in photoshop. Once we had a pretty good idea of how the website would look we translated the visual prototypes to technical requirements. We went over the requirements line by line with TGen North and discussed changes and additions to be made.
Outside of our meetings with TGen North we created team standards and team inventory documents. We created our team website. We wrote a technological feasibility document. We did our design review, presenting our projects progress. And we completed our tech demo where we implemented software locally to get data from a PostgreSQL server, to the back-end, to the javascript, to the html and back again.
Going into our second semester we are confident that we can bring this project to completion. We plan on hopefully increasing our meetings with TGen north to be weekly instead of bi-weekly. Our second semester is focused on the implementation part of the development process. Our first goal in the second semester is to produce a software design document that goes into the technical design and implementation of our website. Our design document will involve UML diagrams, explicit data flow scenarios, function documentation for our back-end, etc. While we’re completing the design document our plan is to start an iterative implementation cycle. We plan on creating the basic functionality of the front-end and back-end in our first iteration, and then linking them together in our second. We plan on completing our prototype by Feb 20th.