what does research look like?

I was reviewing the notes from the last conference call in preparation for today, and saw that Mary had posed a question about what it would look like if students did open-ended bioinformatics research. To me, that means they would ask a question that could be addressed using bioinformatics (bascially sequence comparisons), determine what data (sequences) they need to collect, analyze the data (alignments, trees, etc.) and use the results to answer their question. The first step, posing a question, seems to be especially hard for students - so providing some sample question and some constrained data sets will probably make them more successful.

update

Hi all, and Happy New Year! I thought I'd summarize what I'm working on for the next few weeks, including the SCOPE workshop. If anyone has any suggestions or other comments, they would be welcome!

-Getting sequences together for a few more of the existing HIV cases, using sequences available at the Bedrock problem space (as a start, anyway; http://www.bioquest.org/bedrock/problem_spaces/hiv/sequence_data.php) and coming up with plausible bioinformatics scenarios for these cases

-Organizing our own problem space for some of the existing cases (HIV, influenza), compiling sequences and other information/resources that students can use to add bioinformatics extensions. How should this material be organized? Some models include the BEDROCK problem spaces and the Biology Student Workbench interactive lessions (http://www.bsw-uiuc.net/moodle/workbench.php).

-For the Puerto Rico conference, working up a Dengue fever example and expanding the malaria example

-Trying out the software that Chi found that generates sequences to fit trees

-Gathering sequences for the Dreamweed case that Eric Ribbens developed at our August conference (phylogenetic analysis to identify a new plant)