I. Goals of project
II. A view of the future
III. Make your own suggestions
I. Goals of project
To take advantage of the breadth and connectivity within the cyanobacteriological community and the genomic resources available to build an interactive tool to access and manipulate integrated experimental and genomic knowledge regarding cyanobacteria, building upon CYORF, an active web-based community knowledge base.II. A view of the future
- Inclusive: Bring bioinformatics tools and programming techniques to the vast majority of scientists who have little acquaintance with computer science
- Friendly: Aim to engage all users by offering an intuitive interface, online context-sensitive help, and offline human help.
- Familiar: Present a common interface to access tools and to display results, so that users need not climb a new learning curve every time they try a new technique.
- Flexible: Facilitate asking questions unanticipated by the developers of the site
- Open: Allow graphical interfaces to be bypassed so that sophisticated users can access the databases and capabilities of the site through scripts.
- Evolving: Permit the easy addition of new tools and capabilities
- Rooted: Link each assertion to the evidence behind it, or make plain the lack of supporting evidence.
- Global: Curate incomplete cyanobacterial sequences in such a way that encourages their use.
- Connective: Encourage easy communication amongst user/annotators
Obviously, the proposed website does not yet exist. Nonetheless, you can get an idea of the utility of the site through mock screen shots (as PowerPoint presentations) that have been designed to simulate how people might use the site to address certain questions. Please let these examples inspire you to think about what features YOU would want in a database and interface. If you have any trouble viewing these scenarios, please let me know.III. Make your own suggestionsScenario 1: Knowledge entry: Orf of which little is known; Overview of annotation page
Scenario 2: Knowledge entry: Orf with available experimental data; Propagation of assertions to other records
Scenario 3: The anotation process: Start-site testing; Dynamic alignments
Scenario 4: Analysis: Discovery of possibly coregulated genes; Loops and Boolean operations
Scenario 5: Analysis: Discovery of possible regulatory motifs; Set operations
Scenario 6: Analysis: Tools for directly examining sequence and features
Graduate School of Bioagricultural Sciences
Chikusa, Nagoya 464
Nagoya, JP-464-8601 JAPAN
Tel: +81 52 789 4106
Fax: +81 52 789 4107
Dept. of Biology & Center for the Study of Biological Complexity
1000 W. Cary St.
Virginia Commonwealth University
Richmond, VA 23284 U.S.A.