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 5

Senior Research Associate

Center for Environmental Biotechnology (CEB)

Lawrence Berkeley National Laboratory

Berkeley, CA

Have you used JGI's Integrated Microbial Genomes system?

No.

•  What is your research about?

Bioremediation after exposure to radioactivity that allows to study gene response and a couple of other projects. All of them are after initial sequencing. I do have a lot of use of functional annotation.

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

I have built a proprietary SQL database where I store my data.

•  What role does manual annotation play in your work?

The biggest problem in manual annotation is the sourcing, how can ensure that the information is credible. In my days in biotech company, I knew who I could trust. If it is supported by a publication, that would be of help.

Trust rating? I don't think I would like to see a star rating next to my name. It might make sense if you see how many people agreed with you - may be.

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

I write my own scripts for processing sequences and doing annotation. If I use any sites, I use MicrobialOnline, not JGI. On JGI, I see a top hit, which is not necessarily helpful. Like how MO has a more descriptive, 3-letter ids. Most sites don't show results past the first few obvious hits. Other results remain in "hypothetical proteins" for years. I find most sites very difficult for doing functional comparisons between genes, for example in the same species, but different DNA strain.

•  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)?

BLAST and clusteral alignment tools. GO, KEGG, COG occasionally. Not so much anymore, it was useful in human genome. Microbs are too simple. Metabolic pathways are helpful. I don't like having just the top hit (as in KEGG), I would like a link to a map and more info.

•  What information do you need in order to understand the annotations?

Structural information - protein structure.

•  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)?

I wouldn't want to publish everything before my paper goes out. Also, some PIs have tradition in electronic collaboration, and some don't. You might be bound by that culture. I don't see any incentive to enter any annotations into someone else's system.

 

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

Yes. I would.