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

John Doe 4

Staff Scientist

Center for Environmental Biotechnology (CEB)

Lawrence Berkeley National Laboratory

Berkeley, CA

Have you used JGI's Integrated Microbial Genomes system?

No.

Potential IMG user?

•  What is your research about?

Microbial diversity and extreme environments: high/low temperature, high/low pH, chemical contamination, anaerobic environment, etc. I collect environmental samples, it is called bioprospecting - carefully choosing a habitat where interesting micro-organisms live. Once the samples are collected, we (1) study what the microbial community is (without any culturing), (2) applications for biotechnology and agriculture, biomedicine. I have a couple of other projects that have to do with applications for national securtiiy.

•  How do you keep track of information about each gene?

Spreadsheets, it's very difficult to have a good idea of what we have. We have about 10,000 samples and no good way of data-management.

•  What role does manual annotation play in your work?

None. Two major biotech companies do screening for us, and if they find anything interesting we go back and try to reverse engineer them. But there is no annotation because these organisms are not sequenced. So we use "brute force" in trying to find the gene that might be responsible for certain functions. But it doesn't mean that I would not have use for it in other projects. There I would be looking at the annotation information available.

(Refers us to John Doe 5 and John Doe 6.)

•  If you do annotation at all, can you walk us through the use of whatever annotation tools you use now? (Do you use IMG?)

Never gone past the home page on IMG. It would be nice to be able to see what the gene is coding for and if there are links to genes in other organisms with similar capabilities. I have two proposals right now, both of which would have a great use for that. One of which is studying radiation in fungi, more specifically, DNA repair or DNA damage tolerance. Comparative analysis to sequenced organisms would be of great use.

•  Which ontologies would you like to see represented in the annotation fields? What other features would you like to see added or removed (e.g. all the BLAST hits)?

I use GO, KEGG, COG.

•  Would you be interested in using a collaborative annotation tool that allowed anyone who wanted to obtain a login if the system provided assessments of the validity of their annotations (based on feedback from other users)?

For another project we have 2500 organisms from Chernobyl that are already identified. We will have them sequenced, and we might even add them to a database (or create our own) and there we might be interested in looking into annotation.

•  How much information would you be willing to share with the scientific community?

All of it.

 

Would you like to offer further direction into the development of this project at a later date?

Yes, absolutely, I would like to be a guinea pig.