Saturday, October 18, 2014

100K views on my YouTube channel

I passed the 100,000 views mark on my YouTube channel. That's not very much by YouTube standards but I'm still surprised given the pretty dry videos I tend to make.  Most of these videos were made for teaching of some kind, so I am happy that a few other folks found them useful.

Anyway, here are the top 5 videos with number of views.

Illustrating Entropy  19,674 (20%)

Tunneling and Scanning Tunneling Microscopy 10,331 (10%)

The Computational Chemistry Movie 9,203 (9.2%)

Molecular basis of differential scanning calorimetry 5,450 (5.4%)

Four simple examples of the Schrödinger equation 5,438 (5.4%)


This work is licensed under a Creative Commons Attribution 4.0 

Sunday, September 28, 2014

PM6, DFTB, GAMESS, enzyme design, protein-ligand binding, and protein structure validation

The publication of this paper got me thinking and this blog post is an attempt to organize my thoughts.

Background
A while back my group developed a method for high-throughput calculation of the effect of mutations on enzyme barrier heights.  The newly developed PM6 method was key to this: it was fast enough and predicted the right reaction mechanism, which AM1 and PM3 did not.

Around that time Mike Gilson and Stefan Grimme published studies were they predicted good absolute binding energies of host-guest complexes using hydrogen bond- and dispersion-corrected PM6. Again PM6 was fast enough to compute the vibrational frequencies needed for the free energy correction.

Parallel to this we have been working in protein structure determination using chemical shifts.  I am starting to suspect that the best way to validate the predicted position of key side chains is to compute their chemical shifts ab initio.  The first step this process might be a complete or partial geometry optimization using something like PM6-D3H+, followed by an QM/MM-like ab initio chemical shift calculation.  Or perhaps a similar check of all side chains.

PM6 in GAMESS
Using PM6 in MOPAC gave all sorts of problems. At that time the only other option for PM6 was Gaussian, without dispersion and hydrogen bond corrections. So the only option was to put PM6 in GAMESS, or more precisely:
1. implement PM6
2. implement dispersion and hydrogen bond correction
3. interface to PCM
4. linear-scaling FMO implementation.
5. interface to QM/MM?

+Jimmy Charnley Kromann has done 1-2 and +Casper Steinmann has done 3, both for elements up to F. Heavier elements require d-functions.  We have the d-integral code.

DFTB in GAMESS
Now Nishimoto, Fedorov, and Irle have implemented dispersion-corrected DFTB and FMO2-DFTB in GAMESS, leaving the implementation of a hydrogen bond correction and interface to PCM.

Where does that leave us?
Is DFTB as good as PM6?
For binding and frequencies the answer appears to be "yes" (see for example Table 5 and Table I). For TSs I'm not really sure, but perhaps a little better (Table 4).  We should definitely test this on our little database.
One worry is that DFTB is available for fewer elements than PM6.

What's more work: implementing PM6 for the remaining elements, and d-integral PCM implementation, and FMO2 or implementing hydrogen bond corrections and the PCM interface for DFTB? 
I think the latter.  However I should definitely ask the authors if they have similar plans and when we can get our hands on their code.  Should we decide to go ahead with FMO-PM6 this paper will be very helpful.

What about QM/MM?
AMBER now has dispersion and hydrogen bond corrected PM6 and DFTB, complete with interface to a continuum solvent method and, of course, the AMBER FF. Do we really need to treat all the atoms with SE-QM?  If not, we could go straight to applications!

One problem is that we have no real experience with AMBER. How easy is it to use? Would we get the help we need if we get stuck?  How easy is it to modify the code?

There is really only one way to find out.


This work is licensed under a Creative Commons Attribution 4.0 

Friday, July 25, 2014

Flipping your classroom: getting started

Completely flipping your classroom with videos, clicker questions, etc. is a lot of work.  One way to make it happen is to do it in stages.  It is better to do a little bit than nothing at all.

The alarm clock approach
The most common use of clicker-questions is to give a multiple choice clicker question about half-way through the lecture to wake students up. This begs the question "why put them to sleep in the first place" but it's better than letting them sleep.  It also gives you some feedback on how much the students have absorbed.

If you feel you can't even spare 5 minutes for a clicker question because you are always hopelessly behind in the lectures then there is something seriously wrong with the way you teach.

An experiment: is lecture necessary?
1. Make a 2-3 question reading quiz on a topic you would like to skip in lecture and that you feel the book explains well.

2. Give 1-2 in-class clicker questions that, if answered correctly by >75% of the student, makes you comfortable skipping the topic in lecture.

3. Repeat a very similar in-class question on same topic next week (yes, you'll need to repeat material to make it stick).

Convinced? Good, now:

The first year
Look through your lecture notes and replace part of lectures where you mostly repeat the textbook with reading quiz and in-class questions.

The second year
Record video lectures where you deviate from the textbook and use the entire lecture period for questions.  This will also free up time for review questions on previously covered topics.

The third year
Rethink the course in light of what you have learned. Is the book helping or hurting the course? Does it cover what you want in the order you want it? If not, consider getting rid of the textbook and replacing it entirely with video lectures. When doing so, consider reducing the curriculum compared to the textbook.

Workload
Clicker questions. In my experience I get through about 6 good clicker-questions per 45 min period: about 3 review questions and 3 questions on new topics. It's OK to re-use or only slightly modify questions that you haven't used for at least a week (if you don't believe me, try it).

It's hard to write good clicker questions. Be prepared to replace questions that are too easy or too hard the following year.

Reading quizzes. You need to give a reading quiz before every lecture period where you give clicker questions on new material. The reading quiz shouldn't be more than at most 7 easy-to-answer (if you have done the reading or watched the video) questions. I often use true/false.  It usually takes me 15-20 minutes to write such a quiz.

Video lectures. The optimum length for a video is about 7 minutes. If you already have lecture notes or Powerpoint slides and are comfortable with the recording software you use then making a 7 minute video takes about 15-30 minutes depending on the amount of editing you do. This does not include the upload to Youtube, which can be up to 30 minutes depending on internet speeds, but you can do other things during that time.

Recording live lectures
Another option is to record your live lectures in year 1 for use in subsequent years.  If you lecture with Powerpoint you can use screencasting software to record and use an external microphone.  If you lecture on the blackboard you will have to get someone to record it with a video camera.  Ask your university e-learning office to borrow one.

In either case you should edit the recording into shorter videos no longer than 10 minutes. It is just a boring and off-putting to watch a 45 minute lecture on-line as it is live. If possible insert a question at the end of each video to activate the students.

Other universities have recorded lectures on put them on-line, so you might be able to find what you need just by Googling or searching on Youtube.  Notice that if you only want the students to see part of a video you can specify the start time in the Youtube link.

This post is part of an ongoing series of post on teaching tools and tips collected here.


This work is licensed under a Creative Commons Attribution 4.0



Thursday, July 24, 2014

Making video lectures: pencasts



The above video shows a pencast - i.e. a video lecture mimicking a blackboard lecture (it's in Danish but you get the idea).  This is an alternative to the Powerpoint based video lectures that I wrote about here.

The iPad + Explain Everything app
The pencast is made using an iPad and a $3 app called Explain Everything. In addition I used the headphones/microphone that came with my iPhone (which makes the audio recording a bit better) and a stylus.  Using a good stylus is really key to this approach and I have good experiences with both the Jot Script and the Jot Pro (I can't quite make up my mind whether the Script was wort the extra money).



There are many other pencasts apps for the iPad but all the other ones I have seen only give you one finite size page, whereas Explain Everhing gives you unlimited number of pages of infinite size (see 2:20 min of the video immediately above.  The video at the top of this post uses one infinite size page.

While I usually upload the video to Youtube directly from the app, it is also possible to save the movie file on Dropbox and import it into a video editing program such as Screenflow to edit out mistakes.

Note that you can import pictures, pdf files, and even entire powerpoint presentations into Explain everything to use as part of your pencasts

Other ways of making pencasts
While the Explain Everything app is cheap investing in an iPad just to make screencasts is relatively expensive.  I have also tried to cheaper alternative methods to making pencasts (NB: I haven't used either for a while so this may be outdated):

The Echo Smart Pen.  The main advantage of this pen is that it is an actual pen writing on real paper so the writing process will seem more natural.  Another advantage is that it produces an animated pdf file that makes it easy to skip or fast forward through the presentation.

The disadvantages are that (1) I found the file management (transfer, upload, etc) very cumbersome and non-intuitive, (2) no way to edit out mistakes (3) no way to import pictures or files, and (4) only one color.

Graphics tablet & pen. In this approach, made famous of Salman Khan, you use such a tablet to write in a graphics program (I used this one) on your computer while recording using screencasting software.  While low-end tablets are much cheaper than the iPad, it is much harder to learn to write one place (the tablet) while the text appears another place (the computer screen).  I, for one, quickly gave up.

Powerpoint or pencast presentation (repeated from this post):
For live lecturing students tend to favor chalk-board lectures over Powerpoint lectures, because the pace of chalk-board lectures tends to match that of note-taking.  The relatively slower pace of chalk-board lecturing also means that fewer new concepts are introduced during lecture.

In the case of video lectures these differences largely disappear.  Students can pause and repeat Powerpoint video lectures. Pen-cast lectures (the video equivalent of chalk-board lectures) are no longer restrained by the available lecture time and can cover just as much as Powerpoint lectures.

It it telling that it is possible to view Powerpoint video lectures on the on-line platform Coursera at 1.5 or 2 times the regular speed. There seems to be no demand for slowing the Powerpoint lectures down!

I tend to make Powerpoint video lectures rather than pen-casts because I often present rather complicated equations or diagrams that are laborious to write or sketch by hand. However, if I want to demonstrate some thought process (e.g. solving a problem) then I use pen-casts.

In any case, I always give students access to the Powerpoint slides or the handwritten notes I base the video on. It is much faster to read these notes than to watch the video. If the written material is clear, there is no need to view the video.

Good video lectures
* The optimal length is about 7 minutes
* One specific topic per video
* At least one multiple choice question per video
* Students can handle no more than 7 such videos (new topics) per lecture period.

This post is part of an ongoing series of post on teaching tools and tips collected here


This work is licensed under a Creative Commons Attribution 4.0

Tuesday, July 22, 2014

Making video lectures: Powerpoint screencasts



I have previously discussed the many advantages of video lectures compared to live lectures. Here discuss how I make most of my video lectures.

Almost all my video lectures are screencasts of Powerpoint presentations made using the screencasting software Screenflow.  Screenflow only works on Macs but there is a very similar program for Windows called Camtasia.

The two videos above nicely illustrate how I do it: you simply go through your Powerpoint presentation of your computer and Screenflow records what's happening on the screen and what you say.Then, usually after a bit of editing, I upload the video to my Youtube account.



There are two main differences between the videos and my approach: One difference is that I use the earphones with microphone that came with my iPhone for a better audio recording. The other difference is that I don't record myself talking with my webcam because I personally find these "talking heads" distracting when I watch such videos.

There are other ways of recording Powerpoint presentations.  The reason I used Screenflow is that
it has very powerful, yet easy-to-use, editing capabilities for fixing mistakes. The same is true for Camtasia and this video gives an example of a correcting a mistake.




Some practical tips
* Once you start a recording, don't stop.  If you make a mistake, keep quiet for a moment and start that part over.  You can fix the mistake by editing and the quiet moment allows you to cut without interrupting the narration.

* Keep quiet for a second before and after changing slides. This allows you fix errors on a particular slide without affecting other slides.

* Once you finish recording a video your first instinct will be to delete it.  Try waiting a day and listening to it again. I bet you'll feel better about it.

* Hosting your videos on Youtube has many advantages such as optimized views for mobile devices and good buffering for slow internet connections.  You can control who can access your videos on Youtube, though there is really no good reason not to share the video with everyone.

* However, if you want to host the video in a place not recognized by Screenflow or Camtasia, such as a university server, you can export the movie to a file and upload the file.

Other uses of screencast
Screencasting in general, and Screenflow and Camtasia in particular, are very versatile tools that can be used for many other things.

For example, I frequently use Screenflow to grab fragments of Youtube videos or simulations to include in my Powerpoint slides.  Here are some examples:



A screencast is also an excellent way to show how to use a particular program or website.  Here I show how to use a particular feature of the program MAPLE.


 This post is part of an ongoing series of post on teaching tools and tips collected here


This work is licensed under a Creative Commons Attribution 4.0

Thursday, July 17, 2014

My new research impacts this week


Your new research impacts this week

Jan Jensen

50000+ profile SlideShare views
You've now got a total of 50168 SlideShare views on your profile, thanks to 305 new SlideShare views this week!
Congrats on passing the 50000 mark!
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9000+ profile PLOS html views
You've now got a total of 9028 PLOS html views on your profile, thanks to 199 new PLOS html views this week!
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800+ PLOS html views
This article attracted 20 new PLOS html views this week, bringing it up to 807 total. It marks your 7th product to get this many html views on PLOS. Nice work!
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900+ PLOS html views
This article attracted 10 new PLOS html views this week, bringing it up to 906 total. It marks your 5th product to get this many html views on PLOS. Nice work!
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800+ PLOS html views
This article attracted 20 new PLOS html views this week, bringing it up to 807 total. It marks your 7th product to get this many html views on PLOS. Nice work!
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200+ SlideShare views
This slides attracted 54 new SlideShare views this week, bringing it up to 240 total. That's good--only 36% of 2014 slide decks on Impactstory have that many. It marks your 30th product to get this many views on SlideShare. Nice work!
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3 new Scopus citations
That brings this article up to 205 Scopus citations total. Impressive! Only 1% of 2011 Biological Sciences articles on Impactstory have reached that many citations. It's your 4th product to get this many citations on Scopus. Nice work!
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3 new Scopus citations
That brings this article up to 355 Scopus citations total. Impressive! Only 1% of 2007 Biological Sciences articles on Impactstory have reached that many citations. It's your 2nd product to get this many citations on Scopus. Nice work!
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3 new Scopus citations
That brings this article up to 748 Scopus citations total. Impressive! Only 1% of 2005 Biological Sciences articles on Impactstory have reached that many citations. It's your 1st product to get this many citations on Scopus. Nice work!
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2 new Scopus citations
That brings this article up to 338 Scopus citations total. Impressive! Only 1% of 2008 Biological Sciences articles on Impactstory have reached that many citations. It's your 3rd product to get this many citations on Scopus. Nice work!
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Sunday, June 29, 2014

Video lectures


Video lectures vs live lectures
Advantages
* You can watch them anytime you want (e.g. when you are most alert)
* You can watch them pretty much anywhere you want (e.g. on the bus on your smartphone)
* You can pause and repeat part of the lectures.
* You can watch all or some the lectures again and again (e.g. while doing a homework problem or  preparing for an exam).
* Good video lectures are short (max 7-10 minutes) and focussed on one specific topic.
* As a teacher you can't "get behind" on your lecturing.
* Video lectures free up valuable class time for discussion, e.g. using peer instruction.

Disadvantages
* Students cannot ask questions right away.
- In most large courses this is practically impossible anyway.
- In my experience questions occur very infrequently, even in smaller courses.

* If you use your lectures to inspire and motivate students that is probably better done live
- While students enjoy such lectures, there is no evidence that they learn more from them than "boring" lectures.

* Students won't watch the videos
- I really recommend "reading" quizzes
- Students also skip your live lectures.

Video lectures vs assigned reading
* If your lectures (or some of them) are basically repetition of the textbook, just assigning the reading instead of making the video lectures. Make sure they read it using "reading" quizzes

* Another alternative to making videos are detailed lecture notes, if you have them already.  If you don't, making video lectures is much faster than writing detailed lecture notes.

Powerpoint vs chalk-board (pen-cast) lectures
For live lecturing students tend to favor chalk-board lectures over Powerpoint lectures, because the pace of chalk-board lectures tends to match that of note-taking.  The relatively slower pace of chalk-board lecturing also means that fewer new concepts are introduced during lecture.

In the case of video lectures these differences largely disappear.  Students can pause and repeat Powerpoint video lectures. Pen-cast lectures (the video equivalent of chalk-board lectures) are no longer restrained by the available lecture time and can cover just as much as Powerpoint lectures.

It it telling that it is possible to view Powerpoint video lectures on the on-line platform Coursera at 1.5 or 2 times the regular speed. There seems to be no demand for slowing the Powerpoint lectures down!

I tend to make Powerpoint video lectures rather than pen-casts because I often present rather complicated equations or diagrams that are laborious to write or sketch by hand. However, if I want to demonstrate some thought process (e.g. solving a problem) then I use pen-casts.

In any case, I always give students access to the Powerpoint slides or the handwritten notes I base the video on. It is much faster to read these notes than to watch the video. If the written material is clear, there is no need to view the video.

Good video lectures
* The optimal length is about 7 minutes
* One specific topic per video
* At least one multiple choice question per video
* Students can handle no more than 7 such videos (new topics) per lecture period.

You can see some examples video lectures that I made here.

Making the videos
Here is how I make Powerpoint video lectures and pen-casting video lectures.

This post is part of an ongoing series of post on teaching tools and tips collected here.

This work is licensed under a Creative Commons Attribution 4.0