IS213 Projects Home

Assignment 1

• Problem Statement
• Project Members

Assignment 2

• Personas
• Task Analysis
• Appendices
• Work Distribution

Assignment 3

• Scenarios
• Comparative Analyses
• Initial Design 1
• Initial Design 2
• Initial Design 3
• Work Distribution

Assignment 4

• Introduction
• Low-Fi Prototype
• Methods
• Test Measures
• Results
• Discussion
• Appendices
• Work Distribution

Assignment 5

• Design Revisions
• Revised Scenarios
• 1st Hi-Fi Prototype
• Storyboards
• Instructions for Use
• Slide Presentation
• Work Distribution

Assignment 6

• Heuristic Evaluation
• Work Distribution

Assignment 7

• 2nd Hi-Fi Prototype
• Responses to HEs
• Work Distribution
• Instructions for Use

Assignment 8

• Introduction
• Method
• Test Measures
• Results
• Discussion
• Appendices
• Work Distribution
• Slide Presentation

Final Write-up

• Problem Statement
• Solution Overview
• Final Personas
• Final Scenarios
• Revised Storyboards
• Final Interface Design
• Design Evolution
• Interactive Prototype
• Instructions for Use
• Work Distribution
• Slide Presentation

 

Interview with John Doe 6

(John Doe 6 works with John Doe 4 at Lawrence Berkeley National Lab)
He could only give us ten minutes, so we asked only the most important questions.

Have you used IMG?
No, he has seen it but not gotten past the first page.

What is the role of manual annotation in your work?

Hi group recently sequenced Yersinia pestis, did automated annotation, manually corrected annotations originally done at Oak Ridge. Now they are looking at Salmonella using Affymetrix gene chips, 200,000,000 probes on a chip. They use 8 different probes, ACGT and reverse strand ACGT, across 210 genomes, looking at SNPs (total number and number of synonymous SNPs).
FYI from Annette: a SNP (Single Nucleotide Polymorphism, "snip") is a variation in a single nucleotide in a gene sequence (like ACCTTG and ATCTTG). A group of three bases (a codon) codes for one amino acid, and many amino acids are strung together to make a protein. For some amino acids, there are multiple three-base combinations that yield the same amino acid. These codons are said to be synonymous. Synonymous SNPs don't change the protein coded for, because the possible codons are synonymous.

What tools do you use?
She has scripts to automate the manual annotation process.
Looking for differences between SNPs in different COGs

Which ontologies are important to you?
COG

What features would you expect to see in an annotation tool?
Kinda likes to have the most info possible on the current list, so he doesn't have to go out an search elsewhere, see his protein of interest and the other homologs.

What information do you need to understand an annotation?
He has very basic needs, just what the homology is to, predicted function, whether it's hypothetical. How it's gotten to be where it is (who did it)

How useful is functional without structural?
Very, they dont' really concern themselves with structural annotation.

Would you be interested in a collaborative annotation tool?
Yeah, he's all for transparency, recognizes the limitation of locked annotations.

Would a history be useful?
Yeah, that would be good.

Can we contact you in the future?
Limitedly