CS 411W LAB I - PRODUCT DESCRIPTION DOCUMENT
1
INTRODUCTION
1. Societal Problem
a. Biology Protein Prediction
b. Website
2. Solutions
a. API
i. Extends Scorpion
ii. Adds to ODU Research Standing
b. Website
i. More Professional
ii. Added functionality
iii. User statistics
2
SCORPION PRODUCT DESCRIPTION
1. RESTful API
a. application agnostic, communicate over http
b. queue and schedule jobs
2. Website
a. User friendly
b. Added features(Login)
c. Tracking and Statistics
2.1
Key Product Features and Capabilities
1. API
a. API allows more people to use Scorpion
b. Security and Protection
c. Common interface
2. Website Functionality
a. Improved Design
b. Competitive Features
i.
History tracking
ii.
Automated input sanitization
2.2
Major Components (Hardware/Software)
1. Hardware-API
a. Scorpion Neural Network
b. PHP Server
2.
1.
2.
3.
3
c. PSI-BLAST
d. PC
Software/Virtual- API
a. RCSB Protein Database-Provided
b. Dunbrack Labs Protein Database - Provided
c. RESTful API
i.
GET/POST
ii.
Input Sanitization
iii.
Queueing jobs
Hardware - Website
a. PC
b. PHP Web Server
c. PSI-BLAST (Third Party/Provided)
d. Scorpion Neural Network
Software/Virtual - Website
a. Web browser + Internet connection
b. Webpage design template
c. Google Analytics (Third Party/Provided)
d. Database
i.
Protein sequence & user database
1. Open ID table
2. Sequence submissions table
3. User data table
4. User sequence submissions link table
Algorithms - Website
a. Protein sequence submission
i.
Input sanitation
ii.
Estimated prediction time
IDENTIFICATION OF CASE STUDY
1. Scorpion
a. History
b. Highest Accuracy
2. Target Audience
a. Professor Li
b. Biologist around the world (overall scientific knowledge)
c. More researchers
4
SCORPION PRODUCT PROTOTYPE
DESCRIPTION
1. Interface
a. protein chain input - no reduced functionality
i. data sanitization
ii. character counting to produce estimated time of prediction
2. PROTOTYPE FUNCTIONAL GOALS and OBJECTIVES
1. Improve the interface to scorpion
a. Website
i.
Improved website 508 compliance
b. API
i.
platform agnostic, using an API, users can use their language and
platform of choice over http. Allows a hook to SCORPION
4.1
Prototype Architecture (Hardware/Software)
<How will the prototype be structured to demonstrate key features of the 410 product.
Prototype MFCD provided and described.>
1. API
a. API -Backend
i.
Dr.Li’s c3Scorpion Binary
ii.
Handling POST Requests
1. Security (Attacks)
2. General POST Handling -PHP
3. Returning Job ID and Information -PHP
iii.
Sending Data through the NN
iv.
Getting Job Information
1. One Job
2. All Current Jobs
v.
Emailing Result
b. API - Frontend
i.
GET format of return
1. XML/JSON
2. User Friendly
2. Website
a. Server-side code in PHP
i.
Already used in the website before solution
ii.
Module based for ease of addition/removal of functions
b. SQL
i.
Standard in database profession
ii.
Why SQL instead of NOSQL
iii.
Sqlite3 chosen for ease of use
iv.
Separate database from training part of project
c. HTML/Javascript
i.
Benefits - Uses client processor instead of server
ii.
JQuery - Standard in web development
iii.
Openid.net for login - A known product used by other websites
4.2
Prototype Features and Capabilities
Demonstrates
1. API
a.
b.
c.
d.
Submit and schedule requests over http
Get Status of Jobs over on queue
Get status of a single job
Public Documentation for the public to use
2. Website
a. Web layout in compliance with 508 web standards
b. Offer client tools for users to sanitize input
c. Opt in User registration system
d. User tracking solution to track registered and unregistered users usage
Mitigate Risk
1. backwards compatible with existing C3 Scorpion system
2. Use open source and free tools solutions to solve user registration and tracking
4.3
Prototype Development Challenges
1. Website
a. 508 compliance
b. New, unfamiliar webpage design
c. Accuracy of estimated prediction time
d. User security
2. API
a. Public facing API has to be secured
b. Interfacing with existing scorpion infrastructure and codebase
c. Ensuring that Admin can access statistics
Glossary:
Amino Acids/Residues: The building blocks of proteins
Training set: Set of instances from the problem domain used to train the algorithm.
Data cleansing: The process of removing non-representative instances from the data
set.
Cross-validation Training: The process of dividing training data into k mutually
exclusive subsets (folds), of roughly equal size where some subsets are used for
training, validating, and testing. The process is repeated k times.
PSSM: Position-Specific Scoring Matrix which includes information about evolutionary
relatives of the original protein sequence
PSI-BLAST: Position-Specific Iterative Basic Local Alignment Search Tool used for
deriving the PSSM
References:
1. "Biological Macromolecular Resource." RCSB Protein Data Bank. N.p., n.d. Web.
20
Feb. 2014. <http://www.rcsb.org/pdb/home/home.do>.
2. CS410 Blue Team. "Scorpion Protein Prediction Timed Experiment." N.p., 11
Feb.
2014. Web.
<www.cs.odu.edu/~410blue/CS410ScorpionProteinPredictionTimeEx
periment.xlsx>.
3. Ashraf Yaseen and Yaohang Li. “Context-based Features Enhance Protein
Secondary
Structure Prediction Accuracy”.
4. "Section 508." United States Department of Health and Human Services. N.p.,
n.d.
Web. 15 Mar. 2014. <http://www.hhs.gov/web/508/index.html>.
5. "Section 508 Of The Rehabilitation Act." Section 508 Home. N.p., n.d. Web. 15
Mar.
2014. <http://www.section508.gov/Section-508-Of-The-RehabilitationAct>.