iPhone apps every biologist needs

Check it out! http://www.the-scientist.com/news/display/56049/

Using Case It! in your classes

As you are planning your classes for spring semester, please make note of how you will present Case It! to your class, what questions you may ask of your class, and how the experience goes for your class. This information will be vital in writing up the results, so the more detailed you can be, the better.

It'd be great if you could keep a written log, but alternately you can email things to me directly and I can compile an overview for each campus.

Thanks!

BJ

Class testing

Here is what I'm thinking for how I will use Case It in class this semester. The students would generate two separate web pages/posters, one analyzing an existing case (HIV and maybe other viral diseases). The other web page will be about an open-ended bioinformatics extension - not necessarily an extension of the case but related to whatever virus the case was about.

I have 3 lab sessions scheduled for this - 4/1, 4/8, and 4/29.

4/1 - Introduce them to the software and walk them through an example case. (I think I may make up a simple case just for demo purposes so we don't have to "waste" an existing case.) After the demo, they will work through their assigned case and start to prepare their web pages. Each case has ELISA, Western blot, and a fairly simple bioinformatics piece (like what we did for the Anna case). Web pages have to be finished by 4/15.

4/8 - Check on progress with web pages. Introduce them to the problem spaces, and how to select and load sequences into Case It for analysis with MEGA 4. Get them started on coming up with their own question to test, identifying what sequences they need. These web pages will be due 4/22.

4/8-4/29 - Give them their conferencing assignments. Conferencing (asynchronous) about Case studies 4/15-4/22; conferencing about bioinformatics project 4/22-4/29. Look into setting up a time or two for synchronous conferencing.

4/29 - Last day of conferencing. BJ visits for focus group interviews

There are obviously a few details to work out... How many groups and how big should the groups be? I have 40 students in two lab sections (20/lab). 2-3 per group works best. Maybe it would be helpful if both classes had the same number of groups for the conferencing assignment? I still need to package up DNA sequences for each case and set up the problem space.

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)