asu-cis-capstone/z-squad

repo for project zoophy

z-squad

repo for project zoophy

ZooPhy README

Overview ZooPhy is web application aimed at providing helpful and insightful analysis on virus trajectories to researchers and public health agencies. Using ZooPhy, users from around the world can access the repository of virus samples held in ZooPhy’s databases to find histories and construct phylogenetic trees and construct a visual trajectory of the virus’ pathways in populations. Users will be able to select specific criteria from virus type to host species and can drill down even further for advanced users. ZooPhy will start their query, which may take up to a few days, and then send them a notification when the process has been completed. This will produce a phylogenetic tree of the virus and also a KML file to place against Google Earth so the trajectory of the virus through populations can be viewed geographically by the user.

List of Contributors • Dr. Matthew Scotch • Mehrad Noghrehchi • Andrew Paxia • Bryan Mercado • Jeff Recker • Hunter Bryan

Release Notes v 0.1:

README file created.

Visual mockup created. https://drive.google.com/a/asu.edu/file/d/0B6XMxKdhKp0xN1pwbnRGcUY5eVk/view?usp=sharing

Waffle.io started.

v 0.2 Current PHP/MySQL framework uploaded to Github.

Install Instruction:

1. Install WAMP server on local machine 2.Type localhost into browser to access phpmyadmin
2. Create DB with name "Users", and table "accounts" table to store user account information
3. Drop Zoophy folder into c/wamp/www directory in computer
4. Once table created, the connect folder connects the front end to DB on local machine
5. Open localhost, select Zoophy and home page loads
6. Click "login" and login page accepts account info and logs user in

v0.3 New Release: This release includes a new layout and color scheme for the site. Navigation and links are updated and sample pages with dummy data have been used for lgin and view jobs purposes.

The page also integrates Google Maps to display the desired look for mapping KML files in the future.

Instructions: To view new project, use WAMP server to load index.html and navigate through links form there as you would a regular site.

v0.4 Video Demo done. Note that not all features work. Still trying to get bugs out, but this gives a simple rundown of the service and how it will work. Address is below:

http://youtu.be/e-vd6ZP917w

v0.5 DEMO 1.2 folder is the current updated project. Things need to be done: -Connect back end (signup/login) -fix CSS styling -get web app to send/recieve correct data from web service

v0.6 Current iteration of Zoophy on our test site. Automated testing recorded. Things to be done: -double check link locations -get search function operational -hook up to web service

z-squad's Issues

Visual mock-up

Front end

Create and format the front end for the zoophy app.
.html and .css most likely.

step 1

Retrieve sequences from SQL DB.

step 2

Align sequences.

homepage

logo
view jobs/profile/logout hyperlink
basic search criteria
advanced search criteria

login page

add logo
sign in architecture,
register
lost password/id
formatting

Step 4

Phylogeography
.kml comes in here.

web hosting

Waffle board

decipher the given code

view jobs page

logo/navigation hyperlinks
queries:
list queries
status pulls
kml map/ phylogenetic tree download

Access to the test environment

Needs to be completed around the time the program passes local testing.
zoophydev.asu.edu

access to virus database

For the later stages of testing.

Readme file

step 3

Model Testing

confirmation page

logo/ hyperlinks
query confirmation/ info
return home hyperlink
a-sync architecture