GenExplorer - Summary of Client meeting -2
1.Since Professor Brian White uses primitive browser in his lab, he would like to have the web page to be able to run on those too. He likes the background, images and layout.
2.Option to select Introns: There should be an option to select starting and ending Introns. There should be a default value for these and a parameter to overwrite those values as necessary. User (Student) cannot change or see these values. Only Instructor/TA should be able to edit these values. If there is only start sequence and no end sequence, all are exons and there is no mRNA and hence no amino acids formed. Starting and ending sequence for Introns is enough. It is not required to have starting and ending sequence for Exons too as it would be redundant. Strict mode and Relaxed mode exists for both Promoter/Terminator in DNA during transcription and Starting and Ending sequence for pre-mRNA during splicing. In Relaxed mode there can only be one variation in the base sequence.
3.Modes : Batch mode: Professor White is not very excited about having a batch mode. It would be sort of useful for grading but not very useful.
4.Saving work: Professor White would like to have the student's copy and paste the sequence in their e-mail to TA. The Biology lab is not well equipped to have these save features and the application would be mostly used in the lab. As far as having a "button" like submit which on clicking would save the work and also send to TA (who just runs a script- completely automated for TA)—in the current system Professor is asking students to print the sequence and submit a hard copy to TA who can then comment on it too. So he thinks this is better than batch mode, which would be of no real use for him. It would be more useful to have an effective printing mode than a to have a batch mode. He would most probably ask the students to get a hard copy than submit electronically.
5.Highlighting: a.When a student clicks on a Promoter/Terminator to locate the path for the process, it would just highlight the opposite base in DNA strand, as they are not present in mRNA and amino acids b.Similarly when a student clicks on the bases not used in the process in pre-mRNA, it should just highlight the opposite base. There need not be any warning message as part of the assignment for the students is to understand what this means.
6.Being able to edit mRNA / amino acid a.No one should be able to edit the mRNA or amino acid as mutations are changes in DNA and no one should be able to mutate other stuff. b.There could be a mode where the student can see the amino acid sequence at the bottom of the screen and they mutate the DNA sequence accordingly to form the required amino acid sequence. Generally their  assignment would be to find an amino acid sequence with at least 4 or 5 proteins.
7.There would be a maximum of 300-400 bases in the sequence.
8.Students should be able to change promoter/terminator in DNA sequence. They can do anything with their DNA.
9.Help / Tutorial a.Help: It would be better to have "Question mark" help, which when clicked on the subject displays a short message regarding the subject. For Example: when clicked on DNA strand it should display "This is a DNA strand and can be mutated. It is used in Transcription". b.Tutorial: Professor would more likely have a link to his lab manual and exercises.
10.Interactive Interface: For the user to be able to click on each step of the process instead of system just showing the process step by step. Professor likes this concept, but would like to have it modes where you can turn it on/off.
11.There would be a default DNA sequence when the application starts and user/instructor/TA can edit that sequence.
12.Animation mode: To show the animation of the process. For transcription there would be a circle representing RNA polymerase going over DNA sequence and RNA appears base by base. There is no need to show DNA strand separating. For splicing too, there can be a very simple animation to find the start and end sequence and splice.
13.Professor Ethan Bolker has some ideas on Folding on his web page at www.cs.umb.edu/~eb/folding
14.There would be no back end saving on server as it would add negative effect in terms of errors made by students during saving the files, expiration of files etc.