GenExplorer - Summary of Client meeting -3

1.The client wanted to make sure that we check out the systems where the application will be running, experiment with both the old as well as the new version of Java, mainly with Java 1.1.
2.Make sure that the application will run on any browser (New as well as the primitive ones) .
3. Handed the First Version of the Requirements Analysis to the client for review.
4.Discussed the Version 2 of the Use Cases reviewed by the client.
We have to make sure of the following conditions in order to submit the next version of the Use Cases to the client such that they meet all the basic and important functionalities involved in the project. So we went over the highlighting part once again with the client so that we thoroughly understand what all has to be done.
Highlighting

A) When clicked on a nucleotide base in one of the following regions

·        Promoter sequence region

·        Terminator sequence region,

·        Region before the promoter sequence and

·        Region after the terminator sequence

Then, that base along with its complementary base in the opposite strand of the DNA strand will be highlighted.

B) The Promoter sequence and the Terminator sequence doesn’t take part in formation of the pre-mRNA, and the region between the Promoter and the Terminator is called the Transcription unit which takes part in the transcription of one of the complementary DNA strand to a pre-mRNA.

C) The Transcription unit is composed of the Coding Regions (which gets converted to exons in the mRNA sequence) and the Non Coding Regions (which gets converted to Introns in the mRNA sequence).

Coding Region in DNA strand -> Exon in pre-mRNA    -> Exon in mRNA -> Protein

By clicking on the nucleotide base that is in the Coding Region of the DNA strand, the following portions get highlighted:

·        The current base of the DNA strand on which the user has clicked

·        The complimentary base in the opposite DNA strand

·        The corresponding base in Exon region of pre-mRNA sequence.

·        The corresponding base in Exon region of mRNA sequence.

·        The corresponding Protein formed.

Non Coding Region -> Intron in pre mRNA

By clicking on the nucleotide base that is in the Non-coding Region of the DNA strand, the following portions get highlighted:

·        The current base of the DNA strand on which the user has clicked.

·        The complimentary base in the opposite DNA strand.

·        The corresponding base in the Intron region of mRNA sequence.

D) Poly A tail and the 5’Cap in the mature mRNA

After splicing the pre-mRNA sequence into Exons and Intron, the mature mRNA is formed by combining all the Exons in the pre-mRNA. The ploy A tail is then attached at the end of the mature mRNA and a 5’cap (a nucleotide added to the 5’end) is attached to the beginning of the mRNA. The poly A tail and the 5’cap are a form of a flag that are stuck to the mature mRNA only once the pre mRNA is spliced and signifies that the message is complete. If they are not present in the mRNA then the messages are not exported and translated to Protein sequences.

5. Start and End Intron in the pre-mRNA : The client made it clear that the start intron and the end intron in the pre mRNA does not take part in the mRNA sequence.
6. Start and Stop Codon in mRNA : The start codon is the “AUG” sequence in the mRNA that has both the 5’ cap at the front and the poly A tail at the other end of the mature mRNA. The stop codon is one of the following sequences: “UAA” , “UGA” , “UAG”.

The start codon sequence “AUG” takes part in the protein formation but the stop codon sequence does not take part in the protein formation since there is no amino acid encoded from the stop codon sequences.

While running the application in the relaxed mode the user is not given the flexibility such that, any mismatch in the Start and the Stop codon sequence is permitted.

7. Discussion on the Initial version of our User Interface Designs:

a) The client specified that he would like the application only in the Interactive mode rather than to have the option of both the Interactive and the Non Interactive Mode as the main purpose of this application is for the students to know the steps in Protein formation.

b) He has given us snapshot of how he wants the UI of the application to look like.

c) The client would like to have all the functionality buttons (Transcription, Splicing, Translation, Express Gene, Reset Gene…) at the top of the page and based on clicking on any of the buttons only the matter displayed on the applet screen should change instead of changing the whole screen into a new screen.

d) He would like to have a button on the application screen for turning the animation ON/OFF.

e) He looked at our UI designs and would not like the DNA strands to appear in a helix form. He mentions that, although the helix shape for the DNA strand would be cool to have but it would be confusing for the students and would distract them from the actual task of the application. Hence we would like to have the DNA strands in the application as decoupled straight parallel complementary strands.

f) We discussed the editing feature of the application. He liked our idea of having a drop down list with the options of deleting, inserting… or modifying (changing the current base to A, G, C, T) the existing nucleotide base on which the user has double clicked.

g) The client specified that the student would be able to modify/edit only the DNA sequence and edit should update every part of the gene expression. The base edited should be highlighted thought out the entire representation of the gene expression process. He also mentioned that the student should be given the option to undo the last edit they made.

h) The client mentioned that he wanted a way to hide the promoter and the terminator part of the DNA sequence and so in his current version of the GenExplorer he has shown the Promoter and the Terminator with different colors. He also mentioned that he would like to set a map for the Exon and the Intron parts of the pre mRNA strand so that the exons labeled as exon1, exon2, … inside black boxes above the actual exon sequences and the introns are labeled above the intron sequences and are not labeled. This should be the case for both while displaying the splicing part in the application as well as in the printer friendly option of the application.

i) Sequences should also be clearly visible when printed on a Black and White printer for the Printer friendly version.

j) He is comfortable with the idea of scrolling to get the picture of the whole DNA strand for the printer friendly version rather than having them as a line after line.

K) He was happy with the idea of graying out the inactive buttons, for example the splicing button is not highlighted until the user has clicked on the translation button and the translation process has been completed.

8) The client mentioned that each of the labs will have different sequences of the Promoter, Terminator, Start Intron and the End Intron sequences and so he might have different links to the different lab sections and those setting would be changes by the TA by giving separate config. files as an input parameter to the application.
9) The client mentioned that in about a month (the week of 1st December) he would be putting his version of the GenExplorer into experiment by his biology students. This is the time when the GeneX team would like to go in and review how the students react and behave to the different functionality of the application and also get the feel of the problems that the naïve computer users face while taking up the introductory biology course.