Hi folks. I'll appologize in advance for the long
message, but I wanted to make you aware of a free NSF funded application that we
have been developing at the Concord Consortium (CC) (http://www.concord.org) for the past
several years. The jMol part of it is in beta stage right now, but I think we
already have solutions to some of the issues that have been brought up recently
in the jMol forum, and I think we are ready for some suggestions from the jMol
community.
About the Concord
Consortium:
- We are a collection of folks working to realize
the potential for using technology to improve education. Most of the projects we
are working on are National Science Foundation (NSF) funded, and we make all our
software available free to the public.
About the Molecular Workbench
(MW):
- MW began as a simple molecular dynamics
engine developed by Qian "Charles" Xie. It began as a program for doing dynamic
computational modeling of interactions between atoms and molecules. Users could
interact with the model, change temp, etc. and discover emergent
properties.
- Over the past five years this has developed into
an educational tool which we have used to model simple gas laws, thermodynamics,
chemical reations, DNA hybridization, protein folding, x-ray diffraction, the
initial work for modeling light/matter interactions, and now 3D models via
jMol.
- MW is a cross-platform Java application with a
WYSIWYG editor. So you can type text, add images, add controls (sliders,
buttons, spinners), add graphs, add questions (multiple choice, essay, etc.),
and modeling containers (chemical reactions, atom/molecule interactions, protein
folding and synthesis, DNA models, and jMol models). One of the buttons
allows you to make a report which collects all of the students questions/answers
and annotated screen shots of models.
- So far we have been using this application to
develop activiteis for middle, high school, and college level classes. It is
considered an educational research tool, so the reports generated above
have a "submit" button at the bottom which sends the report back to our servers.
We have been thinking of ways to expand the use of this report/submit feature to
allow teachers and other developers to create their own activities and have the
reports sent to locations other than CC servers.
- Becasue MW is a Java application you could launch
an MW activity or page from a web browser (or PPT presentation) via a standard
web-link that connects to a Java Web Start JNLP file. For example, you can
launch the application with its default home page/activity by clicking on this
link (assuming you have Java installed): http://xeon.concord.org:8080/modeler/webstart/MW.jnlp Clicking on that link will start Java Web Start, read
the script in the jnlp file, check to see if you MW already in your webstart
cache and download it if necessary, then launch the application with the
parameters specified in the jnlp file.
- You can save the MW.jnlp file to disk if you want
access to launching the application when you are offline. Java Web Start will
cache the application so that it can be launched locally if you don't have an
internet connection.
About jMol and MW:
- Right now you can drop a jMol container onto the
page.
- The container has a menu bar, a toolbar, and a
status bar. However you can customize the look of this so that all or none of
these are showing, including the frame, so the molecule can appear as if
floating on the page.
- You can configure the molecule via menus and
buttons, as well as, through using a customization panel which allows
you to set an initializtion script, background color, etc.
- If you manipulate the model by just using the
menus, then the state of the model will be saved, so no scritping is even
necessary if you can get the model to look the way you want by just using menus.
(For now, only "style", zoom, orientation, and spin are saved, but more menu
choices might be saved in the future. If you provide an initialization script
via the customization panel, then it will be executed after the molecule has
been shown after the saved style, zoom, orientation, and spin have been
applied.)
- You can also drop a jMol console (the one that is
normally available from the application) onto the page so you can provide a
custom script window.
- One feature which can be turned on via a menu is
a set of animation controls which appear in the upper left of
the jMol window.
Future plans for jMol
integration:
- Provide sliders, buttons, spinners, etc. to
control all aspects of the model, which can be added as other components to the
page. So, a user could build a custom interface for working with the model. All
of this will be part of the WYSIWYG editor, so no HTML or _javascript_ knowledge
will be needed to build custom activities using jMol (as well as all of our
other model components).
- At some point in the future we would like to
adapt the jMol environment as a view for a 3D molecular dynamics simulation
(what we currently do in 2D).
- Possibly make the MW page exportable as HTML. Of
course some functionality would be lost (for example the ability to ask
questions and make reports), but we might be able to get the sliders and buttons
to be converted into _javascript_.
Getting started:
- You can learn more about the Molecular Workbench
as a general tool here: http://workbench.concord.org/modeler/index.html
- Launch MW by clicking on the following link:http://xeon.concord.org:8080/modeler/webstart/MW.jnlp
- You can see the current jMol demo page by
launching MW and clicking on the Jmol (3D molecular viewer)
arrives! link that appears in the Recent models and activities:
section.
- If you want to play with editing that page and
configuring the jMol viewers there, then save the page to your hard drive and
click on the Editor button that will appear in the tool
bar. Then try using the jMol menus and right-clicking on the currently loaded
jMol models.
- For a more detailed set of instructions on how to
create MW pages go back to the home page (by clicking on the back button, or on
the little home button in the toolbar), and the click on the
support link there.
- If you want to easily share your creation with
folks you can even upload your new activity to our server using the
collaboration, menu in MW. Then you can send people to the
upload area or even create your own jnlp file by viewing the uploaded activity
by going to the user upload area and then
right-clicking on the link to your activity. This will allow you to
create a JNLP file which you can link to on a web site or even
send as an attachment to an email.
- BTW I could have provided web/jnlp links to take
you directly to all of those pages, but I wanted to have you explore MW by using
the built in links making easier for you to find this stuff later on your own
without clicking on links in the email.
- We have an entire databse of activities found at:
http://molo.concord.org Most of these
activities were written with MW, some with MW encapulated in Pedagogica (see
below), and a couple are Flash. Anyway, you just launch any of these by clicking
on a web link. If it is a link to a jnlp file then java web start will run (and
install if necessary) the java application and load that particular activity.
You can also just browse around using the links found on the MW homepage when
you launch MW, but the web based database provides you with some search
features. Because jMol is so new you won't find any jMol based activities here,
but you might find some other activities of interest to those of you teaching
basic biology, chemistry, or physics. (Note: a couple of the activities need
Quicktime for Java to be installed, but you don't need this to see 95% of the
activities. You can find detailed installation information at http://molo.concord.org/software).
BTW, we have another appliction which requires
programming knowledge called Pedagogica that allows us to place any java
components on a page and link them together via an underlying script. The
adavantage of this is that you can truely customize the user's experience and
program the script to watch what the user is doing and respond appropriately.
However, this type of activity must be fully configured using a scripting
language, so each actvitiy is, in a sense, it's own application. My guess is
that much of what the jMol community might need in a customizable activity
creator could be served by the Molecular Workbench which is much more user
friendly.
-Dan Damelin
P.S. I'll be speaking at the upcoming ACS meeting
in San Diego if anyone wants to meet in person. Hopefully, I'll "unveil" this as
part of my talk.
P.P.S. If you want to contact me directly, please
use my Concord email - [EMAIL PROTECTED]
