(Note :
Initial Requirements Specifications Document with
customer for review)
I. Brief
This
document forms the requirement specification of
GenExplorer. The text to follow shall delineate the
scope and the specifics of the proposed product. This
document shall cover most of the details of the system
that we shall try to model and implement as a part of
the project.
II. Project
Description
1.
Product Perspective
The
idea behind the project is to help beginning biology
students understand the central dogma of molecular
biology in an interactive way. The gene expression
process is a very important concept, which is a
necessity for every beginning biology student. This
application is build keeping in mind that the end user
of this application would have minimum computer skills.
So, a lot of thought has been put in its user interface
design. There are a couple of tutorials available on
World Wide Web, which shows the gene expression process.
But what they lack is user interaction. In this
application the student can input a gene sequence of
his/her choice and visualize the entire gene expression
process.
We
propose to develop new software that shall be platform
independent thus allowing any user working on any
platform to learn gene expression. Our product is in no
way competing against any product currently available in
the market today. But yes, we shall be competing in
terms of the higher standards of quality that our
product will try to deliver.
2.
Project Scope
GenExplorer
(or GeneX for short) shall allow students to simulate
the gene expression process. This software shall be
distributed with a public license and shall be available
for download from a dedicated website. For further
elucidation on the proposed project scope refer to the
following: Vision
3.
Vision Statement
GenExplorer
is a simulation that provides an opportunity for
beginning students to understand the “central dogma”
of molecular biology. The process by which information
is extracted from the nucleotide sequence of a gene and
used to make a protein is essentially the same for all
living things on Earth and is described by the grandly
named “central dogma” of molecular biology. The goal
of this application is to help students visualize this
very important concept. GenExplorer provides a
graphically interactive environment for the students to
interpret the information encoded in a DNA sequence.
In
order to interpret the information in a DNA sequence,
the students input the sequence into GenExplorer. The
program then starts scanning the sequence for promoter
and terminator and graphically displays every step of
gene expression (transcription, splicing and
translation) from a nucleotide sequence into protein.
GenExplorer provides students with the freedom to mutate
a nucleotide sequence and track the effect of mutation
down to the protein sequence. Students would also be
able to visually interpret the involvement of a
nucleotide base or a protein in each step of the entire
process of gene expression.
GenExplorer
can be run in either strict mode (where single sequence
exactly match - for easier interpretation) or relaxed
mode (where mismatches are allowed – a closer
simulation of real life).
GenExplorer
is designed such that even a naïve computer user can
smoothly navigate and use all the features of the
application. Other important software features include:
·
extreme robustness and reliability since
it will be used by beginning students.
·
platform independence and ability to run
on any browser application
·
easy-to-use and colorful/animated GUI
GenExplorer
when completed will be used by over 350 biology students
a year in UMass itself. GenExplorer is being
designed and developed by a team of final year graduate
students of Computer Science Department at UMass Boston.
4.
Development methodology (Design and Implementation
Constraints)
The
initial idea was conceived with a web-based application
in mind. Because
there is no request to access a database, save and open
works, there will no back end design in this project.
All of the possible operations on this application will
be done on a major browser.
The system will be developed restrictedly with
MVC model as matter of doing small release and designing
an open system. (more…)
5.
Product Release
5.1
User’s Documentation
The
product will be essentially shipped as a single
component. It will be shipped with User-manuals written
in both .txt and .html format. The .html format will
actually be available centrally from the Product Release
and Distribution web site.
(more…)
III. Expected
Users of the System
1.
Assumptions and Dependencies
During
the course of the projects various factors could play
their role in restricting the achievable requirements.
To this end the only visible factor that could account
for this is time. We
would be changing the requirements if at all we do think
it is imperative based on the amount of time available
to complete the project on time.
We
also take the following as assumed:
a.
The
user has access to the web
b.
User
has basic skills of using computer and basic Internet
surfing skills.
2.
Users
Beginner
level biology students as well as intermediate level
biology students will well identify with our
software’s targeted audience.
There is another class of user that is in the form of an
administrator (i.e. the instructor) who will handle the
various types of default parameters for students to work
with. Both classes of users identified above are not
expected to be computer literate. Being totally computer
illiterate shall not prevent them from using the
software.
IV. System Requirement
1.
External Interface Requirement
1.1
User Interface
(more…)
2.
Functional Requirement
2.1
Instructor Side
The administrator side of GenExplorer will allow
the user to do the following:
·
Specify
the default gene sequence
·
Specify
the default promoter and terminator sequence
·
Specify
the number of protein required for a successful
completion of the assignment
·
Use
help on any of the above stated functionality and UI
components.
2.2
Student Side
The student side of GeneX will allow for the user
to do the following:
·
Input
a new gene sequence
·
Edit
the base
·
Highlight
any base/protein in the gene expression process
·
Print
the work to a printer or to a file
·
Work
under interactive mode
·
Work
under relaxed mode
·
Use
help on any of the above stated functionality and UI
components
·
Invoke
balloon help on any clickable component in the software
3.
Nonfunctional Requirement
The
qualitative characteristics that GeneX will address no
matter what are
Robustness:
The software must not crash under any conceivable
conditions.
Reliability:
The software must be accurate
Portability:
The software must work on any platform
V. System Features
The
features that this product aims to provide shall be
illustrated in the form of use-cases. The use-cases are
divided into two parts on the basis of the kind of user
it addresses (i.e. user as a student or a user as an
administrator).
VI.
Hardware and Software Environment
1.
Operating System
Platform
independence has probably been the big mantra behind
this project. Needless to say, the product would be web
based and would be able to run on any kind of browser
and all major operating systems like Windows, Unix,
Linux and Mac.
2.
Hardware Requirements
3.
Miscellaneous
To
allow for GenExplorer to send user’s work as e-mail
the system should have:
·
Internet
connectivity
·
E-mail
client
Appendix
A: Glossary
Applet
An
applet is a small program that is intended not to be run
on its own, but rather to be embedded inside another
application. For further information refer Java 2
Platform Std. Ed. v1.4.1
GUI
Graphical
user interface
Linux
A
Unix based Operating System
Mac
A
brand of PC
Unix
An
Operating System
Web-browser
A
computer program used for accessing sites or information
on a network
Windows9x
Version
of Microsoft Windows Operating System
WWW
World
Wide Web
Appendix
B: Analysis Models
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