This quarter, I'm using a wiki with my bioinformatics class and posting sometimes about the things that I learn.
Two things I've been experimenting with are:
- Setting up pages for individual students so they can take notes while they're working.
- Embedding a Google form into one of my wiki pages for student assessment.
Here's a diagram showing some of the pages in my bioinformatics class wiki site.
- Syllabus: I suppose this reflects on my own lack of organization, but I use the syllabus as a dynamic document, making changes and adding information throughout the course. There are links to activities, assignments, and other materials. I used to try and use Blackboard for this, but pbwiki is so much easier to use.
I learned that students got confused sometimes, when clicking syllabus links, because some of the links go to pdf documents. Depending on the web browser, clicking a pdf might open the document, or the document might get downloaded to your desktop, either one is okay with me, but for the students this can be a bit mysterious because there isn't any kind of affordance or indication that the file got downloaded. So, they keep clicking the link expecting something to happen.
Now, I'm trying addressing this by putting a ".pdf" after links to pdf documents. That way, they should know that the link goes to a document and not a web page.
- Activities: Bioinformatics is a hands-on course when I teach it, with lots of activities. I have links to pages with instructions for doing the labs.
- Individual student note pages: During the years that I've taught bioinformatics classes, I've learned that students rarely bring paper along when they're working with a computer. At first this came as a surprise, now I'm come to expect that behavior.
The problem is that sometimes I want students to take notes. The wiki gives me a way to do this. I set up a page with questions and tables that I want students to answer and complete while they're working.
After making the page, I tagged it as a "template." Then I used that template to make a page for each student. Then, for each student I added their own unique part of the assignment. In this assignment, each student works with a different DNA structure and students only have access to their unique wiki note page.
I found it was essential that I make myself a student account, too, so I could tell for certain which pages students could see and which pages they couldn't see.
I should mention that all of these pages can be downloaded from the wiki site, in any location, as pdf documents, so students can capture a written record of their work, on their own computers.
- Assessment questions: Working on the internet and using diverse sites does present a bit of difficulty for people when they confront diverse user interfaces or get lost when going from place to place. To get around this problem and improve usability, I decided to test putting one of my Google assessment forms into my wiki site.
I set up my assessment questions in a Google form. Then, I copied the embed code from the Google site, and using the HTML plug-in from Pbwiki, I pasted the code in a page.
That placed my questions into a wiki page. Students completed the questions and clicked the submit button. This sent the answers to my Google account, so I could log in, get my spread sheet and I see all their answers at once along with a bit of data analysis from Google.
For some of my questions, I expected to see different answers from each student, so the Google analysis didn't always make sense, but for other questions it was pretty handy.
This method worked okay except for one thing. If students entered information in the form and navigated away from the page, the information was lost. A few web-savvy students realized that they could work around this challenge by opening the form in a new tab, or new window, but this wasn't an obvious solution to everyone (or me).
Next time, I'll use that example and make my wiki links so that those assessment pages open in a new tab or window when the links are clicked. I think that will make the process of completing the forms friendlier for all of the students.
If you want to try a free wiki, you can test these out at different places. I'm using pbwiki, but there are some other sites, too.
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That sounds really cool!
I just graduated with my B.S., and I wish that some of my classes had been like that. I did have a Molecular Biology laboratory course that allowed students to group their own files as they wished to on an online directory for which they controlled the permissions. It made group work MUCH easier (the final project for this class was to write a grant application on a topic of our choosing; I think that the team I worked with uploaded about ~5Gb of files to our directory).
Other questions:
I am currently working in Microbiology/Immunology as a Technician, and wish to move into Computational Biology/Bioinformatics for graduate school. If you are able to answer these questions for me, could you please answer in email at quatsch_AT_med.umich.edu?
1) Which schools do really well for computational biology for graduate studies? All I've been able to find so far are clusters of professors doing interesting things, but no real departmental-level renown yet.
2) Do you use Perl? I'm trying to learn it using Strawberry Perl on a Vista system and I understand how to write a program, but I'm a bit lost when it comes to making the Perl shell run a script. I've tried "$chmod a+x 'filename'" but this and variations upon it don't seem to do anything. Any ideas?
This is fabulous!
I may take some cues from your techniques. I am a biosciences/bioinformatics librarian at Northwestern University's Feinberg School of Medicine, and I'm in the process of getting a Master's degree in Computational Biology and Bioinformatics. I teach single-session classes in bioinformatic tools and databases, but I am always looking for new ways to teach electronically. You've done a really nice job of parsing your content into manageable packages and logical sections.
Your insights on Blackboard, other Wikis and Google assessment forms are really appreciated and provide some inspiration. Thanks again for sharing your ideas. I really do enjoy following your blog.
Thanks Pamela!
Toaster: Let's see.
I use Perl on a Mac (i.e. UNIX) with a bash shell (and rarely even then) so there are probably differences with using it on VISTA. You should probably check the Perl FAQ for VISTA to see how that works.
As far as graduate programs, I don't know the answer but I'm willing to query readers. We'll see what they have to say.
For organizing my notes, I use a personal wiki called Luminotes. I can see several notes on different subjects all at once, and unlike many wikis, I don't have to click "edit" and then "save" every time I want to update something.
I run EcoliWiki, which is part of the NIH-funded EcoliHub project. We're working on having instructors use EcoliWiki for courses where students will participate in the ongoing annotation of E. coli K-12, its phages, plasmids, and mobile genetic elements. And we welcome users who want to come up with other uses for EcoliWiki and GONUTS, our other wiki project for the Gene Ontology, for teaching.
I can't tell if you're using MediaWiki or a different platform (looks like a different one, but perhaps its a custom skin?). If you are, we also have a bunch of MediaWiki extensions we've built that we hope will be useful for teaching. For example, we have an extension that lets instructors follow where and when their students have been editing pages. We've modified the Cite extension to make it easy to add references as PubMed IDs, and we've build a forms-based generic table editor. All of these are open source. We recently added the ability to embed a CoverItLive chat session in wiki pages, with the idea of supporting journal clubs and annotation jamborees in cyberspace.
We're not the only ones, of course. There is a proliferation of wikis for science. We're trying to link to as many of them as we can.
Hi Jim,
We use MediaWiki where I work, but I don't like it much because it's not very user-friendly. I used pbwiki in my examples. Pbwiki is a bit buggy, but it's really, really, easy to use.
Hi Pamela,
Thanks for taking the time to post this information. I immediately began experimenting with the use of assessments in Pbwiki for my students based on your example.
I have one question for you,however, how can I associate student names with responses that are collected in the Google Spreadsheet? I would like all of the students to fill out the assessment from a single wiki page - but still be able to discriminate among them.
Sean: I'm not Pamela, but that's okay.
I use a text field in the Google form and ask students to enter their names when they do the assessment. It's true that I can't verify whether a student lies about their name or not, but I do get the time they completed the form from Google and since I gave them their log in info, I can look at the wiki log in records to see if the right student was logged in at the right time.
Hi Sandra,
Thank you for your thoughtful response to my question. I'm sorry I didn't post your correct name with my inquiry:-)