Showing posts with label DGU. Show all posts
Showing posts with label DGU. Show all posts

Wednesday, December 5, 2012

Teaching high school students to fold proteins in less than a day


Program

1. The Computational Chemistry Movie

2. Brief introduction to computational chemistry (slides nr 2-6)

3. The Protein Structure Activity using Molecular Workbench

4. Start on the introductory puzzles for Foldit

5. Lunch

6. Four Peer Instruction questions using Socrative (slides nr 7-13)

7. More puzzles on Foldit

8. Tour of the Department



Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 Unported License.  

Sunday, July 1, 2012

Using PeerWise to assign homework



PeerWise
This past quarter I used a new tool called PeerWise in a physical chemistry course I co-taught.  The main idea behind PeerWise, which is a free web-based service developed by Paul Denny at the University of Auckland, is that students write multiple choice questions for each other.  I didn't quite have the courage to say "Want homework? Write your own" so instead I used it as a supplement to the normal homework assignments, i.e. I reformulated most of the homework assignments as multiple choice questions and posted them on PeerWise, in addition to the usual homework assignment.

Some information about the course
The course is attended by about 170 chemistry and biochemistry majors and covers thermodynamics and kinetics - more specifically chapters 13-20 in Atkin's Quanta Matter and Change.  It's taught in a 9-week quarter and the students take one other course at the same time.  There are four other faculty members involved who also pick homework problems associated with their lectures.  The students were divided into six teams of roughly 30, and each team has six contact hours with TAs who can help them with the assignments.

Advantages of PeerWise
1. Feedback to the students.  PeerWise allows you to give extensive descriptions (you can even use videos: example 1 and example 2) on how to solve the problem immediately after the student has picked an answer.   The quality of the help provided by the TAs tend to vary greatly, and I hoped this would help even things out a bit.
2. Breaking complex problems up into more manageable pieces.  A standard question usually asks you to compute x given some conditions.  In PeerWise this can be broken up into, for example, a) which of the following equations would you use to compute x? and then b) what is the value x given these conditions.  Answering the first question lets people now whether they are on the right track before proceeding.
3. Feedback to me.  Students can leave questions or comments for each problem, which often helps me improve the explanation or identify errors in the problem.  Students can also rate the quality and difficulty of each question, which is very valuable.  I also get all sorts of detailed data including how many students answered the question correctly (more on that below).

Some data
I put 120 questions up on PeerWise and 119 students answered at least one question.  From what I understand many students worked in pairs and only one would answer on PeerWise.  39 students answered 100 questions or more.  For almost all problems, the majority of students picked the right answer, so they are not just clicking randomly to get the explanation as one could have feared.  For example, for the question with the most (86) answers was answered correctly by 57% while the question voted the hardest was answered correctly by 47% of the 76 students who answered it.

While I encouraged students to write their own questions, only 9 questions were written.  One of these questions was "Do you find PeerWise helpful?"  41 students answered, 38 said yes.  Also several students commented positively on PeerWise with one caveat (see below).



Clearly, many students used PeerWise as a study aid before the exam as seen on this figure.


One main problem: errors
The main complaint by the students was the many errors that crept in to the questions, multiple choice answers, and solutions.  The multiple choice format exacerbates the problem, since many students will work for hours trying to reproduce one of the answers.  This is of course impossible if there is an error and this is very frustrating to the student!

There are several sources of errors.
1. Several errors were introduced by me when I typed in the multiple choice answers (for example, using Joules when I meant kiloJoules) and explanations.
2. Several errors were already in the problems and was copied into PeerWise.
3. Several errors were in the answers provided in the solution manual of the text book and were copied into PeerWise by me.  Often the you would simply get a different numerical answer based on the numbers provided.

The error rate was about 1-2 questions per week and all (hopefully) will be fixed next year.


Tips 
1. By default the questions are listed in the reverse order they are created (i.e. newest one first), so in cases where the order was important I would write the first question last, e.g. exercise 1b and then exercise 1a.
2. Each question comes with a one line preview, so the first sentence in the question should be the name of the exercise, e.g. Exercise 1a.
3. Each question can also be labelled by subject, so I would use labels like "week 1".  With one click one can then display the questions on for a single week only.
4. Many of the comments left by the students said "I punch the solution into my calculator and get a different answer".  It's of course hard to know what the problem is, but in these cases I leave a link to the worked out solution on Wolfram|Alpha (example), which is basically on on-line calculator.
5. You add equation through one of several editors  (I recommend using the Latex editor) that create and image of the equation, which you can't edit. If you view the page in HTML format there is a Latex code you can copy and paste into the editor and change, rather than typing everything in from scratch.

Changes for next year (When was the last time you learned anything by doing it once?)
Overall PeerWise was a hit, and I will use it next year for this course.  I plan to make the following changes:
1. I will add 10-20 math and conceptual training questions every week.  Questions one should be able to answer in 1 second: What is $e^{-0}$?  If $\Delta G^\ominus <1$ what can you say about the equilibrium constant?  Some of these will show up every week! 
2. I will add 1-2 "regular" questions based on topics from previous weeks.
3. I will try to have the explanations include a screenshot of the solution done in Maple.  For three reasons: a) it will make me double check the answer in the solution manual, b) it will remove one source of error if I don't have to retype something, and c) it will encourage the students to use Maple (students who use Maple efficiently are done in a fraction of the time compared to others).

Finally, I am racking my brain on how to get more students to write their own questions.

Thursday, May 3, 2012

Computing molecular properties with molecular dynamics - part 2

These videos represent a lecture from my course Molecular Statistics that gives brief introduction to computing molecular properties with molecular dynamics.  The lectures are in Danish.  The lecture notes can be found here.  See also this blog post.

a. Computing molecular properties
b. Computing the free energy difference part 1
c. Computing the free energy difference part 2

Technical details
The first video was made with ScreenFlow and Molecular Workbench
The remaining videos was made with an iPad, Apple head-phones, the Explain Everything app, and a Bamboo Stylus.

Tuesday, May 1, 2012

A brief introduction to periodic boundary conditions (in Danish)

These videos represent a lecture from my course Molecular Statistics that gives brief introduction to periodic boundary conditions.  The lectures are in Danish.  The lecture notes can be found here.  See also this blog post.

a. The boundary problem
b. Periodic boundary conditions: a sketch
c. Periodic boundary conditions: an animation
d. Cutoffs - Part 1
e. Cutoffs - Part 2

Technical details
The first video was made with ScreenFlow and Molecular Workbench
The remaining videos was made with an iPad, Apple head-phones, the Explain Everything app, and a Bamboo Stylus.

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 Unported License.

Saturday, April 28, 2012

Brief introduction to molecular dynamics (in Danish)

These videos represent 2 lectures from my course Molecular Statistics, that gives a brief introduction to Lennard-Jones Potentials and molecular dynamics.  The lectures are in Danish.  The lecture notes can be found here.

a. Modeling gases and liquids
b. Newtons equation of motion underlies molecular dynamics-part 1
c. The Lennard-Jones Potential
d. Newtons equation of motion underlies molecular dynamics-part 2
e. Initialization
f. Computing the force and taking the step
g. The step size (The video contains a small mistake which is corrected here)
h. Equilibration and constant E vs constant T simulations

Technical details
The first video was made with ScreenFlow and Molecular Workbench
The remaining videos was made with an iPad, Apple head-phones, the Explain Everything app, and a Bamboo Stylus.

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 Unported License.

Saturday, December 10, 2011

Bond lengths, Avogadro, Google Docs, and gamification

Recently a colleague of mine, Henrik, lamented that at a recent oral exam many first year students had no clue what a typical bond length in a molecule is.  I am not a big fan of memorizing something that can be easily Googled, but we're talking order of magnitude here, not the last decimal place.

Read the rest of the entry over at Molecular Modeling Basics

Friday, November 4, 2011

Pen- and screencasting

Some links for todays "educational" seminar on pen- and screencasting

Tools for pencasting
The Smartpen
The Replaynote app for the iPad Limited to 10 min recordings
The Wacom Bamboo Tablet/Screenflow (Mac) or Camtasia (Windows)

Miscellaneous
Free screencasting software, limited to 15 min recordings
The Khan Academy collection of thousands of pencasts
9. klasses matematikpensum som pencasts

Uses for pencasting
Review of lectures
Supplementary lectures
Homework problems/solutions

Other uses for screencasting
Powerpoint lectures
How to use programs such as Maple
Research presentations
Summary of research papers
Animation in Powerpoint

Wednesday, October 26, 2011

Tools for the lazy teacher


Here are my slides for my talk at the meeting of the Theoretical Chemistry section of the Danish Chemical Society.

Here are links to the sites and programs I discuss:
Polleverywhere.com (Socrative.com)
The cyclohexane Jmol example
ChemDoodle Web Components demo using Molgrabber
Molecular Workbench model of entropy (link to Molecular Workbench)
ChemTube3D
Avogadro model builder (see also this post on the autoopt tool)
Pen- and Screencasts
Khan Academy
Wolfram-Alpha (see also this post)
Online homework using Peerwise (I recommend the last video on this page)

Update: check out the Molecule Calculator!

Questions?  Leave a comment below!

Monday, September 26, 2011

Derivatives and heat capacities for a simple system

Here are three videos I made on computing the heat capacity for a simple two-state system and plotting them using either Maple or Wolfram-Alpha.  The videos are in Danish.

The pencast video was made with an iPad, the ReplayNote app and a Just Mobile AluPen.  The other two videos where made with the Screenflow screencasting software.



Wednesday, September 7, 2011

My first pencast: Partition functions and conformational probabilities of a simple polymer


Tools: A MacBook Pro, the headphones with microphone that came with my iPhone, A Wacom Bamboo Tablet, SketchBookExpress, and ScreenFlow.

Saturday, August 20, 2011

Education at its best: my poster for the assessment meeting



Here is my poster for the assessment meeting for the Education at its Best (Den gode uddannelse, DGU) initiative.

Here is a translation with links and supplementary information:

Simulation and Visualization (tools and resources being developed with support from DGU)
* Vibrating molecules
* The Quantum Calculator
* Student wiki-projects
* Video software manuals
* Link collections for courses

Active learning and peer instruction
* Web clickers (two videos about peer instruction)
* Web lectures (pencasts, Khan Academy type videos)
* Simulation based peer instruction questions

Other activities
* Web quizzes
* Using MAPLE in chemistry teaching
* Interactive chemistry e-book prototype
* Mini seminars on education


What was the money used for?

Student helpers
* Janus Eriksen
* Toke Fritzemeier
* Anne Schou Hansen

Software
* Polleverywhere (web-clicker)
* Screenflow/Camtasia (screencast software)
* iPad apps

Hardware
* Wacom Bamboo tablet
* iPad
* Web server

Suggestions for future funding
* Fund people instead of projects
Example: Hughes investigators. "By appointing scientists as Hughes investigators, rather than awarding them grants for specific research projects, the investigators are provided with long-term, flexible funding that gives them the freedom to explore and, if necessary, to change direction in their research. Moreover, they have support to follow their ideas through to fruition—even if that process takes a very long time."

* Make outreach a funding requirement
To continue to receive funding you should demonstrate that you are sharing your new teaching techniques with your colleagues.

* Students should be required to have a laptop
This is self-evident but apparently it needs to be said: You cannot incorporate IT deeply into your teaching unless you can be sure that all students have a laptop.  Why isn't the University of Copenhagen doing this yet?
 
* Power in classrooms and exams
If we want the students to use their computers we must provide them with basic necessities like power.  Right now most classroom have 1-2 power outlets, and the students do not have any access to power outlets during exams. 

* Control over internet access at exams
Many exam rooms do not have WiFi, so we can't write exams that require internet access to complete.  Conversely, many more teachers would embrace the use of computers if they can be sure access to the internet (for example using 3G) is not possible during exams.  This can be done with with "WiFi jammers".




Thursday, July 28, 2011

Wacom Bamboo tablet

And headphones with mike.
Let the pencasts begin!

Thursday, May 26, 2011

Outline Jan's edu-seminar: Using simulation and visualization in chemical education

Here are the main points of my seminar which I give tomorrow:

Chemistry deals with complicated three-dimensional structures and the complex motion of many particles, both of which are usually reduced to static two-dimensional structures on blackboards and Power Point Slides when teaching.  This is one of the things that makes chemistry a "difficult subject".  In the talk I show some examples (listed below) of how this can be overcome using three free software packages called Jmol, Molecular Workbench, and ChemDoodle Web Components.

I discuss four ways of using simulation and visualization when teaching chemistry:

1. Make an e-resource page (for example on Absalon) with links to simulations or visualizations you find on the web.  Examples: the DGU site and Jean Claude Bradley's page.
Try Googling "jmol and xxx" where xx is your topic of interest, such as "inorganic chemistry" or "chirality".  Or look through the library of simulations that come with Molecular Workbench.

2. Use them in lecture. Examples: illustrating energy states and molgrabberOther examples in physical chemistry.

3. Use them in peer instruction.  Examples: cyclohexane and illustrating entropy. See more examples hereSee two videos on peer instruction here.
I use Polleverywhere.com for voting.  It is free for 30 or less students.  I have bought a 1-year license for larger courses.  If anyone at KIKU or COMS wants to use it, contact me for login instructions.

4. On-line quizz or practice pages.  Examples: cyclohexane, chirality, and molgrabber.

If someone in KIKU or COMS is interested in pursuing some of this further, please contact me.  We have money to hire student helpers.

Sunday, May 15, 2011

Peer instruction without clickers

I have written about my first experience with peer instruction over at Molecular Modeling Basics.  Click here to read, and please leave any comments over there.

I have bought an instructors version of polleverywhere.  If anyone at KIKU or COMS is interested in using it, just contact me.