Use Case ID

GENEX01

Use Case Name

Highlighting Nucleotides

Created by

Sumana

Last Updated by

Sumana 

Date Created

10/7/03

Date Last Updated

10/31/03

Actor 

Student, Instructor, Tester

Description

When clicked on a nucleotide base in DNA sequence, highlighting corresponding nucleotide in mRNA sequence and amino acid.

Preconditions 

GenExplorer must be running

Post conditions 

Highlighting parts show up

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. User clicks once on DNA nucleotide base

2.Highlights the DNA base nucleotide and corresponding mRNA nucleotide and amino acid

Alternative Course

1. User clicks once on DNA nucleotide base  

2. Highlights DNA nucleotide only, as corresponding mRNA, amino acid are not present

Exceptions

1. User clicks on promoter/terminator

2. Displays an alert message 

Includes (another use case id) 

Special requirements

DNA, mRNA and Amino acid sequences must be present

Assumptions

Notes and issues

Use Case ID

GENEX02

Use Case Name

Highlighting

Created by

Sumana

Last Updated by

Sumana

Date Created

10/7/03

Date Last Updated

10/31/03

Actor 

Student, Instructor, Tester

Description

When clicked on a nucleotide base in pre-mRNA sequence, highlighting corresponding nucleotide in DNA sequence and amino acid.

Preconditions 

GenExplorer must be running

Post conditions 

Highlighting parts show up

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. User clicks once on mRNA nucleotide base.

2.Highlights the pre-mRNA, mRNA nucleotide and corresponding DNA nucleotide and amino acid.

Alternative Course

Actor Actions 

System Responses

1. User clicks once on mRNA nucleotide base  

2. Highlights mRNA and DNA nucleotide only, as corresponding amino acid is not present

Exceptions

Includes (another use case id) 

Special requirements

DNA, mRNA and Amino acid sequences must be present

Assumptions

Notes and issues

Use Case ID

GENEX03

Use Case Name

Highlighting

Created by

Sumana

Last Updated by

Sumana

Date Created

10/7/03

Date Last Updated

10/31/03

Actor 

Student, Instructor, Tester

Description

When clicked on a nucleotide base in mRNA sequence, highlighting corresponding nucleotide in DNA sequence and amino acid.

Preconditions 

GenExplorer must be running

Post conditions 

Highlighting parts show up

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. User clicks once on mRNA nucleotide base.

  2.Highlights the  mRNA nucleotide and corresponding DNA nucleotide and amino acid.

Alternative Course

1. User clicks once on mRNA nucleotide base  

2. Highlights mRNA and DNA nucleotide only, as corresponding amino acid is not present

Exceptions

Includes (another use case id) 

Special requirements

DNA, mRNA and Amino acid sequences must be present

Assumptions

Notes and issues

Use Case ID

GENEX05

Use Case Name

Editing

Created by

Sumana

Last Updated by

Sumana

Date Created

10/7/03

Date Last Updated

10/31/03

Actor 

Student, Instructor, Tester

Description 

Editing a DNA nucleotide base in the input sequence

Preconditions 

GenExplorer must be running and a valid DNA sequence must be present

Post conditions 

DNA nucleotide changed to the entered value

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. User double-clicks on a DNA nucleotide

3. Enters new nucleotide

2. Requests for the new nucleotide base

4. If the nucleotide base matches with its pair, changes all DNA, mRNA and amino acid sequences, otherwise displays error message

Alternative Course

1. User double-clicks on a DNA nucleotide

3. Enters new nucleotide

2. Requests for the new nucleotide base

4. If the value is not one of A, C, G, T displays an error message

Exceptions

Includes (another use case id)

Special requirements

DNA, mRNA and Amino acid sequences must be present

Assumptions

Notes and issues

Use Case ID

GENEX06

Use Case Name

Help

Created by

Sumana

Last Updated by

Sumana

Date Created

10/7/03

Date Last Updated

10/31/03

Actor 

Student, Instructor, Tester

Description 

When the user requests for help on a subject, displays the help information

Preconditions 

GenExplorer must be running

Post conditions 

Help information presented

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. User selects ‘Help’ option and enters/selects a help topic

2. Opens the customer's lab manual in new window

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX07

Use Case Name

Resetting DNA Sequence

Created by

Sumana

Last Updated by

Sumana

Date Created

10/7/03

Date Last Updated

10/31/03

Actor 

Student, Instructor, Tester

Description 

Resets the DNA sequence to a default value or clears the screen

Preconditions 

GenExplorer must be running and at least once sequence exists on the screen.

Post conditions 

Screen cleared or sequence set to a default value .

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. User selects ‘Reset DNA sequence’ option

3. Selects ‘Yes’ to confirm

2. Asks for user confirmation to reset

4. No changes made

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Any of the sequences must be present

Assumptions

Notes and issues

Use Case ID

GENEX08

Use Case Name

Printer Friendly Version

Created by

Sumana

Last Updated by

Sumana

Date Created

10/7/03

Date Last Updated

10/31/03

Actor 

Student, Instructor, Tester

Description 

To display a printer friendly version of all sequences

Preconditions 

GenExplorer must be running and at least once sequence exists on the screen

Post conditions 

Printer friendly version of sequences displayed

Priority: (low/medium/high) 

High

Frequency of Use 

Low/Medium

Normal Course

1. User selects ‘Printer Friendly Version’ option

2. Displays printer friendly version of all sequences in a new window

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Any of the sequences must be present

Assumptions

Notes and issues

Use Case ID

GENEX09

Use Case Name

Testing for promoter and terminator in Relaxed Mode

Created by

Prasoon

Last Updated by

Prasoon

Date Created

10/7/03

Date Last Updated

10/23/03

Actor 

Developer

Description 

Checking for promoter and terminator in the relaxed mode

Preconditions

GenExplorer must be running

Post conditions 

Promoter and Terminator are identified

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. Runs the application in test mode.

3. If found display the promoter and the terminator

2. Look for the promoter/terminator which is specified in the input file by the instructor.

4. If found display the promoter and the terminator

5.  Display the detailed system response

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX10

Use Case Name

Specifying default DNA sequence by the instructor

Created by

Prasoon

Last Updated by

Prasoon

Date Created

10/7/03

Date Last Updated

10/23/03

Actor 

Instructor

Description 

Instructor specifies the DNA sequence which would be used as a default sequence

Preconditions

GenExplorer must be running and an instructor is logged in the application.

Post conditions 

The specified sequence is entered in the input file.

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. Login as an instructor

3.

2. Enter the DNA Sequence

4.  System displays a message saying that the sequence has been updated.

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Only an instructor can change the default gene sequence

Assumptions

Notes and issues

Use Case ID

GENEX11

Use Case Name

Instructor specifies the promoter/terminator sequence to be used by the students

Created by

Prasoon

Last Updated by

Prasoon

Date Created

10/7/03

Date Last Updated

10/23/03

Actor 

Instructor

Description 

Instructor specifies the default promoter/terminator sequence

Preconditions

GenExplorer must be running and an instructor is logged in the application

Post conditions 

The specified promoter/terminator is enterd in the input file.

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. Login as an instructor

3. Enter the promoter and terminator

2.  

4.  System displays a message saying that the file has been updated.

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Only an instructor can change the required parameter

Assumptions

Notes and issues

Use Case ID

GENEX12

Use Case Name

Specifying number of proteins required by the instructor

Created by

Prasoon

Last Updated by

Prasoon

Date Created

10/7/03

Date Last Updated

10/23/03

Actor 

Instructor

Description 

Instructor specifies the number of protein which would be required to complete the assignment by the students.

Preconditions

GenExplorer must be running and an instructor is logged in the application.

Post conditions 

The specified number is enterd in the input file.

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

1. Login as an instructor

3. Enter the number of protein

2.  

4.  System displays a message saying that the file has been updated.

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Only an instructor can change the required parameter

Assumptions

Notes and issues

Use Case ID

GENEX13

Use Case Name

Check Input Sequence

Created by

Chitra

Last Updated by

Chitra

Date Created

10/08/03

Date Last Updated

10/31/03

Actor 

User (Instructor, Student, T.A.)

Description 

Check if the user entered the valid letter (T, A, G, C which represents the four types of Nucleotides) while entering the gene sequence.   

Preconditions

GenExplorer is running

Post conditions 

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

Actor Actions   

System Responses   

1. User types in a letter.

2a.  if the length of gene on typing the letter does not exceed the valid gene length then

2a1. if the letter typed is a T   or A or G or C then, return to the user and read in the next letter and check for the Valid input letter.

2a2. Else throw an error message.

2b. Else throw error message.

Alternative Course

Actor Actions   

System Responses   

Exceptions

Actor Actions   

System Responses   

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

TOP

Use Case ID

GENEX14

Use Case Name

Transcription in Interactive Mode

Created by

Chitra

Last Updated by

Chitra

Date Created

10/08/03

Date Last Updated

10/31/03

Actor 

System

Description 

To transcribe a strand of DNA sequence into an mRNA.   

Preconditions

GenExplorer is running

Post conditions 

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

Actor Actions   

System Responses   

1. The system provides a gene sequence that the user had input.

2. The sequence gets transcribed into a premature mRNA.     

Alternative Course

Actor Actions   

System Responses   

Exceptions

Actor Actions   

System Responses   

1. There is no input from the system as the user did not input the right promoter or terminator sequence for the gene.

2. Error Message will be thrown.

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX15

Use Case Name

Splicing in Interactive Mode

Created by

Chitra

Last Updated by

Chitra

Date Created

10/08/03

Date Last Updated

10/31/03

Actor 

User ( Student, Instructor, T.A. )

Description 

To separate the introns and the exons from the premature mRNA.   

Preconditions

GenExplorer is running

Post conditions 

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

Actor Actions   

System Responses   

1. The user presses “splice”.

4. The Resulting mRNA is displayed on the screen.    

2. The system starts Scaning the pre-mRNA at the 5’ end and looks for the “start intron" sequence  

2a1. If the start Intron is found then move towards the 3' end and look for the end Intron sequence

2b1. If the end intron found then mark intron and continue scanning to the 3’ end, goto step – 2a.

2b2. else no intron found continue scanning to the 3’ end, goto step – 2a.

2a2. else mature RNA = pre-mRNA.

3. Separates the exons from the introns such that all the exons combine to form mature mRNA.

Alternative Course

Actor Actions   

System Responses   

Exceptions

Actor Actions   

System Responses   

1. There is no input from the system as the user did not input the right promoter or terminator sequence for the gene.  

2. Error Message will be thrown.

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX16

Use Case Name

Translation in Interactive Mode

Created by

Chitra

Last Updated by

Chitra

Date Created

10/08/03

Date Last Updated

10/31/03

Actor 

User (Instructor, Student, T.A.)

Description 

To translate the mature mRNA into a protein sequence.

Preconditions

Valid promoter and terminator sequence of the gene exists.  

Post conditions 

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

Actor Actions   

System Responses   

1. The user presses “Translate”.

3. The resulting protein sequence or the error message is displayed on the screen.

2. The system starts Scanning the mature mRNA at the 5’ end and looks for the “AUG” codon

2a1.If the “AUG” codon is found then start the protein chain with “met” protein being the first protein. Keep scanning to the 3’ end.

2b1. if stop codon is found then end the protein

2b2.else Display  ‘Error Msg’ 

2a2. else no protein made.  

Alternative Course

Actor Actions   

System Responses   

Exceptions

Actor Actions   

System Responses   

There is no input from the system as the user did not input the right promoter or terminator sequence for the gene.

Error Message will be thrown.

Includes (another use case id)

GENEX17

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX17

Use Case Name

Testing for Codon

Created by

Chitra

Last Updated by

Chitra

Date Created

10/08/03

Date Last Updated

10/31/03

Actor 

Developer

Description 

To translate the given sequence of codon into an amino acid.   

Preconditions

Valid promoter and terminator sequence of the gene exists.  

Post conditions 

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

Actor Actions   

System Responses   

1. The system provides a codon sequence.

2. The system finds the corresponding amino acid and returns.

Alternative Course

Actor Actions   

System Responses   

Exceptions

Actor Actions   

System Responses   

1. There is no corresponding amino acid for the codon sequence.

2. Error Message will be thrown.

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX18

Use Case Name

Scanning for a Valid Promoter or Terminator Sequence.

Created by

Chitra

Last Updated by

Chitra

Date Created

10/08/03

Date Last Updated

10/31/03

Actor 

User (Instructor, Student, T.A.)

Description 

To check for valid promoter/terminator sequences based on the Mode (Strict/Non Strict) the user chooses to work in.  

Preconditions

The user has defined the mode (Strict/Non Strict).   

Post conditions 

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

Actor Actions   

System Responses   

1. The user types in the gene sequence.

2. The system checks the mode in which the user is running the application

2a1. If it is strict mode then the system checks for the default promoter and terminator sequences in the DNA sequence typed by the user.

2a2.else one variation from the default promoter or terminator sequence is allowed.

3. The system returns. 

Alternative Course

Actor Actions   

System Responses   

Exceptions

Actor Actions   

System Responses   

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX19

Use Case Name

Scanning for Valid Start and End Intron

Created by

Chitra

Last Updated by

Chitra

Date Created

10/08/03

Date Last Updated

10/31/03

Actor 

User (Instructor, Student, T.A.)

Description 

To check for valid Start and End Intron sequences based on the Mode (Strict/Non Strict) the user chooses to work in.

Preconditions

The user has defined the mode (Strict/Non Strict).   

Post conditions 

Priority: (low/medium/high) 

High

Frequency of Use 

High

Normal Course

Actor Actions   

System Responses   

1. The system provides the DNA sequence.

2. The system checks the mode in which the user is running the application

2a1. If it is strict mode then the system checks for the default Start and End Intron sequences in the DNA sequence provided by the system.

2a2.else one variation from the default Start or End Intron sequence is allowed.

3. The system returns.

Alternative Course

Actor Actions   

System Responses   

Exceptions

Actor Actions   

System Responses   

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX22

Use Case Name

QuestionMark

Created by

Ziping

Last Updated by

Date Created

10/08/03

Date Last Updated

Actor 

Students

Description 

To help students retrieve in a easy way an explanation on a selected target.

Preconditions

Post conditions 

User-specified target related information shows up.

Priority: (low/medium/high) 

Medium

Frequency of Use 

Medium

Normal Course

1. Users activate the question mark.

3. Move the icon to the target and activate the target

2.  Question mark function is highlighted and its icon shows up.

4.  Target related information shows up.

Alternative Course

Exceptions

Includes (another use case id)

Special requirements

Assumptions

Notes and issues

Use Case ID

GENEX25

Use Case Name

ZoomInOut

Created by

Ziping

Last Updated by

Date Created

10/08/03

Date Last Updated

Actor 

Students, Instructors

Description 

To help users to see an enlarged gene sequence section in order to get specific detail of some parts of gene sequence.

Preconditions

Gene sequences exist

Post conditions 

The file is closed and disappeared from screen.

Priority: (low/medium/high) 

Medium

Frequency of Use 

Medium

Normal Course

1. Activates ZoomInOut feature.

3. Enlarge action on a target sequence segment

2.  Ready to execute ZoomInOut

4.  Responds by a size changed target sequence.

Alternative Course

1. Giving a specific size request

3. Giving a fraction of original size.

2. Shows up the required sequence.

4. Shows up the size-changed sequence.

Exceptions

1. Continuously doing same action on a same target

2. Keeping size change until reach a preset size limit.

Includes (another use case id)

GENEX01,GENEX02, GENEX03, GENEX04,GENEX08, GENEX21

Special requirements

Do not use mouse right click for the reason of using Mac.

Assumptions

Notes and issues