4/24/15
Unverified Join Viewer
Red Team
Red Team: Unverified Join Viewer
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Red Team Members
● Joseph Cooper
● Tim Holmes
● Catalin Pop
Red Team: Unverified Join Viewer
● James Dailey
● John Berlin
● James Ord
● Abhishek Biswas (Mentor)
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Presentation Outline
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Domain Information
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Solution Design
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Hardware and Software Requirements
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Algorithm Flowcharts
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Risk Analysis
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Genome Assembly
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● The genome must be split so modern machines can
sequence the pieces
● After sequencing, the pieces must be reassembled
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Assembly Output
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● Sequencers attempt to reconstruct the genome, but the
process is prone to errors
● Some assemblers simply leave out repeated sequences
● The assembly process is a “black box.” Users cannot see
why a join is or is not made
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Unverified Join Viewer
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When presented with a file that contains the appropriate join
feature annotations, UJV will allow the user to view the
evidence used to make a particular join
C.A.R.P., a case study, lacks a compatible Graphical User Interface
(GUI) and viewer
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Projected Customers
● Biologists
○ Verifying joins on a genome is currently a timely and
expensive process
○ The ability to view join evidence quickly can save
time and money in a lab
● Software Developers
○ Open-source development invites the programming
community to expand the product to fit new solutions
as well as make improvements to the current system
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Current Process Flow
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Proposed Solution
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● Display a genome sequence in a circle
● Show justifications used for sequence fragments
● Have an intuitive interface
● Be open source based
● Export to GenBank format
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Solution Process Flow
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Functional Components
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Hardware Requirements
● Must have one of the following minimum GPUs:
● Radeon HD 2400
● GMA 4500
● GeForce 8
● Memory of 2GB
● Any of the following CPU Architecture
● Vista x86
● OS x64
● Linux x86
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Software Requirements
● Java JDK 8
● Operating System:
● Windows Vista SP2
● OS X 10.7.3
● Linux Ubuntu 10.4+
● Windows Required installation
● DivX Plus Codec Pack
● Linux Required installation
● Ibavcodec53 and libavformat53 on Ubuntu Linux 12.04 or
equivalent
● GLIB 2.28 for JavaFx Media
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Development Process
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Java Technology Stack
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JavaFX
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GitLab
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Agile Development Model
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2 week sprints
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100 man hours per sprint
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Unverified Join Viewer
Overview
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User Interface
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Algorithms
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Exporting File
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Select
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Layout
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Viewer
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Scaling
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Mock Up
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Risk Matrix
Technical Risk:
Customer Risk:
● T1: Domain Experience
● C1: Incorrect Product
● T2: New Framework Technology
● C2: Lack of Product
Adoption
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4/24/15
Technical Risks
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Domain Experience T1
● Due to limited domain experience of the team the learning curve of how to
properly express a solution within the domain will be high
● Impact 2
● Probability 3
● Mitigation: Agile development and working beside domain experts.
New framework Technology, JavaFX T2
● JavaFX, Oracle's proposed replacement for SWING, is still a fairly new user
interface framework; With that comes the difficulty of finding resources to
glean information about how to properly utilize it
● Impact 2
● Probability 3
● Mitigation: Even though the API is new the team has is comprised of members
that are Oracle certified Java programmers who can guide the team in right
direction and by utilizing FX's new API's performance the team will be able to
build a view that will surpass its Swings counterparts
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Customer Risks
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Incorrect Product C1
● The lack of a proper requirements gathering phase could lead to
a product that does not match the needs of the customer
● Impact 4
● Probability 3
● Mitigation Strategy: In addition to the drafting of a formal SRS
document, every step of the development process will feature
rigorous validation and verification with the customer through
mockups of the viewer and implemented functionality
Lack of Product Adoption C2:
● Due to the high level of technical experience of the target
customers the delivered product may fall short of expectations
● Impact 3
● Probability 3
● Mitigation Strategy: The product offers functionality that is not
featured in any other viewer on the market. Additionally,
because the project is open-source, community involvement
could aid in the development of more features commonly seen
in industry-level viewers.
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References
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Oracle JDK 8 and JRE 8 Certified System Configurations. (n.d.). Retrieved April 23,
2015, from
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http://www.oracle.com/technetwork/java/javase/certconfig-2095354.html
Release: JavaFX 2.2. (n.d.). Retrieved April 23, 2015, from
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https://docs.oracle.com/javafx/2/system_requirements_2-2/jfxpubsystem_requirements_2-2.htm
CGView - Overview. (n.d.). Retrieved April 23, 2015, from
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http://wishart.biology.ualberta.ca/cgview/
Mycobacterium shottsii. (n.d.). Retrieved April 23, 2015, from
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http://gcm.wfcc.info/speciesPage.jsp?strain_name=Mycobacterium shottsii
Additional resources available here:
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http://www.cs.odu.edu/~410red/resources.html
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