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

Jane Doe 3, JGI

•  Have you used JGI's Integrated Microbial Genomes system?

Yes, but only as a resource. I do not modify or enter any new data.

•  What is your research about?

I work with environmental samples, where they've taken whole microbial samples from the environment and sequence DNA from it. We learn what's going on in the sample based on the DNA we extract.

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

In very large Excel files. I store anything from my own data to BLAST hit counts, all the BLAST results, etc. I work with 10s of thousands or 100s of thousands of genes at a time.

•  What role does manual annotation play in your work?

Manual annotation is useful to me in determining whether a particular characterization is reliable, because a lot of the information in these databases is generated completely automatically, and is thus very inaccurate. When it's actually annotated as an enzyme or something, I tend to trust it.

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

I work with so many genes, it becomes infeasible to click or annotate any gene individually. I actually try to avoid touching the system.

•  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)?

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

I don't need any information about the actual species itself, since I'm only working with fragmentary DNA.

•  How useful would it be to you to be able to make functional annotations without being able to do structural annotations?

What would be really useful is a way to find a particular use/patter/characteristic of a gene and be able to find all the genes with related characteristics. Perhaps a search of the manual annotations might be useful in identifying interesting characteristics.

•  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)?

Yeah, it would be nice to have. My level of expertise, I'm not sure whether I would know whether something was correct or not, but I think, at times, yes. I think some user would.

Trust is definitely an issue.

It would do everyone a lot of good if we could provide feedback directly to the individuals at other organizations who have made incorrect annotations. Right now, these false annotations are completely inaccessible/unchangeable to us.

If we had some sort of collaboration tool, we would need somebody out there to go and say, "hey, there are 20 people affirming this annotation, let's set it in stone."

Primary Resources:

COG, KEG, and GO

She also walked us through some comparative genomics tools, which might be useful in discovering false positives or genes annotated incorrectly. They also contain references and information about 'draft' genes, for which there are plans to do better annotations along the way, but there is still information that would be useful for comparative analysis.

At the level of work that I'm at, it's mostly structural annotation that required changes. Functional annotation is at a more detailed level than I work at.