Create. Share. Learn.Using Google Sites and MediaWiki

Kam D. Dahlquist, Ph.D.Department of Biology

John David N. Dionisio, Ph.D.Department of Electrical Engineering & Computer Science

Originally presented at:Center for Teaching ExcellenceLoyola Marymount University

October 22, 2008

Outline

• Using Google Sites in a Bioinformatics Laboratory Course

• Using MediaWiki in a Biological Databases Course

• Advantages and disadvantages of each platform

What is bioinformatics?

• Application of information technology (informatics) to biological data

• Informatics:representationorganizationmanipulationdistributionmaintenanceuse

of digital information

• Interdisciplinary: biology, computer science, math,chemistry, physics, engineering . . .

DatabasesAnalytical tools

Biology 398-03: Bioinformatics Laboratory

• 1 unit laboratory course for upper-division biology majors

• Meets twice a week for 2 hours each time

• All work is conducted in the Seaver 120 Computer Lab-- stand-alone bioinformatics software-- web software and databases

• Students perform bioinformatics research using real research software--Molecular Genetics Explorer (Brian White)--HIV Problem Space (BEDROCK)--DNA microarray data analysis with GenMAPP (Dahlquist)

The Challenges of Bioinformatics Research are both Similar and Different

than Wet-lab Research

Student Expectations from a Traditional Laboratory Course

What Really Happens in a (Wet) Research Laboratory

Demo labs where answer is known Open-ended questions

How do you know if an experiment is working? The teacher/lab manual shows “ideal” results

How do you know if an experiment is working? Careful experimental design and use of appropriate controls

If experiment doesn’t work it was “experimental error”, move on to next week’s lab

If experiment doesn’t work, repeat it until it does

Stand-alone labs Long-term projects where next step is dependent on previous steps

Follow procedures like they are recipes, don’t need to think about what you are doing

Develop own procedures, catch and troubleshoot mistakes, constantly thinking about how to improve the efficiency and accuracy of an experiment

Fill out laboratory notebook the night before it is due to be turned in, purpose of lab notebook is to get a grade from the instructor

Write out the procedure each day before performing experiment, so that you know what you are going to do! take notes as you go along, analyze data as soon as you get it to decide what to do next, important scientific (and legal!) record of everything done in the lab

Laboratory reports are written the night before (hours!) before it is due, purpose of report is to get a grade from the instructor; arbitrary rules for the sections of a report and formatting

Primary research articles report the results of original research, sections and formatting convey important information to colleagues in the scientific community

Separate compartments in head for biology, chemistry, math, reliance on formulas

Pull on knowledge of biology, chemistry, math to solve problems, figure things out

Mistakes are to be avoided at all costs; the teacher tells you what is right

Mistakes are how you learn, they happen all the time, notice them and troubleshoot

Only the grade is at stake, little ownership of the research

Pursuit of knowledge and truth

Student Expectations from a Traditional Laboratory Course

What Really Happens in a (Wet) Research Laboratory

Demo labs where answer is known Open-ended questions

How do you know if an experiment is working? The teacher/lab manual shows “ideal” results

How do you know if an experiment is working? Careful experimental design and use of appropriate controls

If experiment doesn’t work it was “experimental error”, move on to next week’s lab

If experiment doesn’t work, repeat it until it does

Stand-alone labs Long-term projects where next step is dependent on previous steps

Follow procedures like they are recipes, don’t need to think about what you are doing

Develop own procedures, catch and troubleshoot mistakes, constantly thinking about how to improve the efficiency and accuracy of an experiment

Fill out laboratory notebook the night before it is due to be turned in, purpose of lab notebook is to get a grade from the instructor

Write out the procedure each day before performing experiment, so that you know what you are going to do! take notes as you go along, analyze data as soon as you get it to decide what to do next, important scientific (and legal!) record of everything done in the lab

Laboratory reports are written the night before (hours!) before it is due, purpose of report is to get a grade from the instructor; arbitrary rules for the sections of a report and formatting

Primary research articles report the results of original research, sections and formatting convey important information to colleagues in the scientific community

Separate compartments in head for biology, chemistry, math, reliance on formulas

Pull on knowledge of biology, chemistry, math to solve problems, figure things out

Mistakes are to be avoided at all costs; the teacher tells you what is right

Mistakes are how you learn, they happen all the time, notice them and troubleshoot

Only the grade is at stake, little ownership of the research

Pursuit of knowledge and truth

Things we learned “growing up” with computers (sometimes the hard way)

Are students really “Digital Natives”?

Where are the data stored? Hard drives, flash drives, web servers, network servers, FTP sites; what are directories and folders and how do you navigate them?

Frequently use e-mail attachments to store files.

File formats: .doc, .ppt, .xls, .jpg, .txt, and many others

Macs don’t use file extensions and PCs now hide them. This is OK if all you ever use is .doc, but is problematic when you use bioinformatics software. Fundamentally, students don’t often know that the different types of files store information differently.

What really happens when you drag and drop? The bane of moving PowerPoint files between Macs and PCs.

Keeping back-ups of your data Frequently use e-mail attachments to store files.

Keeping track of different versions of files Have to be taught this

Overcoming computer-phobia: not knowing how the computer works, fear of breaking something

Surprisingly large amounts of comupter-phobia: not knowing how the computer works, fear of breaking something (magical thinking)

Computer security: passwords, cookies, protecting from malware, privacy concerns

In my experience, students seem to have more problems with unstable computers than faculty

Data sourcing, sharing, and attribution Google vs. Google Scholar; proper attribution of figures found on the web; discerning quality of source and giving proper attribution

E-mail etiquette Subject lines, proper greeting and closing, proper use of reply, reply-to-all, CC, and BCC

When we say students are “Digital Natives”, what do we mean?

Google Sites <http://sites.google.com>

• Free web service that allows you to create a web site

• Site can be public or private (limited to certain users)

• 100 MB of storage space (costs $ to upgrade)

• Look and feel of web site based on limited templates (costs $ to upgrade)

• Allows attachments and images (up to the storage limit)

• Allows comments (but not threaded conversations)

• Keeps history of changes by users (but can’t compare pages)

BIOL/CMSI/HNRS 398-01: Biological Databases

• 3 unit upper division course, team-taught

• 7 biology majors5 computer science majors2 math, 1 natural science, 1 film/television

• Meets twice a week for 75 minutes each time

• Classroom, Seaver 120 Computer Lab, Keck Computer Lab (Doolan)-- relies on Computer Science Linux network and software-- also used some other web and stand-alone software

• Students perform biological database project using real research software (XMLPipeDB/GenMAPP)

<https://www.cs.lmu.edu/biodb/wiki/index.php/MediaWiki_Pedagogy>

• Open Source software used for Wikipedia and many other wikis online

• Need to learn wiki syntax• Each user has a page, each page has a discussion

“backpage”• History of changes recorded and easy to compare

versions• Can upload images and files• Used for assignments, narratives, discussion, group

projects

Google Sites MediaWiki

Free Free and open source, but you must find a free web service or you have to set it up yourself on an internal server

Similar to Blackboard in the way you work with it, easier to learn.

Requires learning wiki syntax, a little bit harder to learn.

Sometimes “autoformatting” feature makes it hard to control how you want it to look

Fine-grained control of look through wiki syntax; accepts HTML code for advanced users

Keeps history of user changes, but a little unwieldy

Keeps a sophisticated history of user changes

Easier to learn Can use this skill on Wikipedia or other public wiki sites.

• An option for using a MediaWiki site is <http://www.OpenWetware.org>• Another wiki WYSIWYG technology is <http://www.Wikispaces.com>• Research application of Wikispaces on XMLPipeDB SourceForge site

Conclusions

• Personal preference for MediaWiki

• Still a danger of a teacher-centric mode of communication (this is not fixed simply by technology)

• Like its power for organizing and storing information

• Although when using an external service, always a possibility it will go away without notice

• Although if using as internal service, then someone needs to put in the time to manage/maintain it