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Among the Concord Consortium's many projects are several that relate to understanding the submicroscopic world of atoms and molecules.
Outlined below is a detailed description of each piece of software, how to install it, and how to use it either with the database or as a stand alone application. Java is a platform independent programming language, which means that someone can write software on one type of machine and it should run everywhere regardless of the operating system.
In Java versions 1.4 and later, an additional technology called Java WebStart was included in the standard installation.
Some of our software is small enough that each user will end up with a copy of that application in their user's WebStart cache (i.e.
Not every one of our activities uses Quicktime, so some of them will run without installing Quicktime. Note: (Windows only issue) If this window comes up but tells you that Quicktime is not installed properly, but you are sure you followed the installation instructions correctly, restart your machine and run the test software again.
Once the core technologies described above have been installed, you can begin to use the molecular based applications, each of which is described below. The Molecular Workbench is a piece of software , the primary function of which, is to run molecular dynamics models.
Java WebStart checks to see if the Molecular Workbench already exists in the user's WebStart cache. Then, Java WebStart launches the Molecular Workbench and tells it to show the activity that was specified in the .jnlp file.
The Molecular Workbench can be launched as described above, but it can also be run independently of any specific activity.
Double-click on the downloaded file to launch the Molecular Workbench from your webstart cache.
If this is to be used in a multi-user environment, make sure everyone has read and write permissions for this file. Java WebStart checks to see if a small Pedagogica Launcher application exists in the user's Web Start cache.
Then, Java WebStart starts the Pedagogica Launcher, passing the information about which activity to launch. The Pedagogica Launcher will search your drive in typical installation locations for the workspace.jar file inside of the PedagogicaActivities folder. Pedagogica can be launched as described above, but it can also be run independently of any specific activity. Open the installed PedagogicaActivities folder and double-click on workspace.jar - the application for browsing installed Pedagogica activities. Pedagogica Activities.jnlp - a Java Web Start script for launching Pedagogica so that a window allowing you to browse and launch Pedagogica activities appears. PedagogicaActivities - a folder containing all the supporting software and files for running Pedagogica activities.
Then just drag the PedagogicaActivities folder to one of our recommended installation locations. Place the Pedagogica Activities.jnlp file in a convenient location if you would like to launch Pedagogica activities independently of using web page links.
If you are installing Pedagogica in a multi-user environment, then you must set the permissions properly for both the PedagogicaActivities folder and the Pedagogica Activities.jnlp file. As mentioned above, the Molecular Workbench can also be run as a separate application (i.e. Within the typical school environment where each machine is behind a firewall, http requests pass through a proxy server, internet filtering software is used for all data passing through the http port of the proxy server, and many different users use many different computers, some technical issues occasionally arise.
All files and folders which are installed by dragging them to the hard drive after downloading them from our web site need their permissions set so that all users have read and write access to those files and folders.
Unfortunately, to use Java Web Start's GUI, this will need to be done once for each user*, so the user will need to open Java WebStart, edit the preferences, and manually enter the proxy information.


Open Java WebStart by either double-clicking on the Java WebStart icon that is on your desktop, or finding javaws.exe and double-clicking on that. Note: if an individual user sets these preferences by using the GUI method above, the user's preferences will override the global preferences. Pedagogica repeatedly loses the connection and pops up a window asking if you want to reconnect. Use an outside proxy server that utilizes a different port than the one your proxy server is currently filtering.
If webstart seems to be having a problem, follow the instructions above for manually entering this information into the Java Web Start preferences. If Pedagogica seems to be having a problem, edit (or create if not already present) the command.properties text file located in the PedagogicaActivities folder as described above, and change the proxy info to match the new proxy server you intend to use. Some proxy servers require authentication, which often means that you have to input a user name and password to access the internet. If this solution works, Pedagogica should ask you for a user name and password, followed by the launching of your requested activity. When determining a location for the PedagogicaActivities folder, it is recommended that it be installed in one of the following directories.
Three major pieces of software have been developed to facilitate this understanding: The Molecular Workbench, The Molecular Viewer, and Pedagogica (which is a general activity creation tool). All of our software is Java based, and some of it uses other core technologies that are freely available if not already installed on your system. There are also many instructions for how this is to be done in a multi-user environment, such as the typical school computer lab. Because we want users of all platforms to have the ability to run our software, we chose to use this programming language. This technology allows someone to write a small script, which is stored in a file with a .jnlp extension. However, it is highly recommended that this installation is done to avoid having some activities not function properly. If this doesn't work, then it is likely that you have multiple versions of Java on your machine. Along with dynamic models, a Molecular Workbench page can display text, images, and questions.
If it finds this file, Pedagogica is launched and the activity specified in the original .jnlp file will be displayed. The others will be installed in each user's Java Web Start cache folder the first time an activity using either the Molecular Workbench or the Molecular Viewer is launched via a web page link. If you choose not to place the PedagogicaActivities folder in one of those locations, then a window will pop up the first time you try to launch a Pedagogica activity, asking you to either find the workspace.jar file (which is located inside the PedagogicaActivities folder) or to install Pedagogica.
If you need assistance in setting permissions, see the Guide to Setting Permission for Multi-user Environments.
However, there are some instances when this doesn't happen and manual proxy information needs to be entered. User preferences are stored in a text file also called deployment.properties, but it is stored in the user's home directory (ex. However, this needs to be entered once per machine, not once per user, and can be done by whoever is installing Pedagogica instead of having each student enter this information. In other words have requests to and from any concord.org IP address bypass the proxy and internet filtering software.
It is highly recommended that you set up your own second proxy if possible, because you don't have control over the stability of any publicly available proxy. Usually, this means that both Java Web Start and Pedagogica should request this information from you. If this doesn't solve your problem, then you may want to consider bypassing that proxy server altogether.


If installed in a recommended directory, it can easily be found by the Pedagogica Launcher application which is launched when you click on a Java Web Start link in our database. An online database which links to activities created using the previously mentioned software has also been made available.
To facilitate the launching of differing pieces of software for various activities, we use Java Webstart which provides for the ability to create a standard web page link which, when clicked, will launch the appropriate software from your hard drive (and even download it if necessary). For most people, the simple instructions outlined on the software downloads page will suffice. Pedagogica) to make this practical, so a separate installation must be done such that all users can share this common set of activities. You can also search for j2se and j2sdk to make sure all folders that contain these character sequences have been removed from your system. The editing environment for creating these pages has been modeled after a typical word processor, so no programming knowledge is necessary for the authoring of these pages.
If the Molecular Workbench already exists in the cache, then WebStart will check if there is a newer version available on our server, and update the cached software if possible.
Programming knowledge is required to be able to author activities in this way, so, typically, Pedagogica is used only to launch pre-made activities designed here at the Concord Consortium. If the launcher already exists in the cache, then Web Start will check if there is a newer version available on our server, and update the cached software if possible.
If it can't find the workspace.jar file, then a window will pop up asking you to either locate it yourself, or to download a new Pedagogica installation, after which the activity will be launched. The full Pedagogica installation is around 35 MB, so, it is recommended that this is installed prior to launching any Pedagogica activities. This can either be done via Java WebStart or by installing a separate version of this application outside of the Web Start cache.
For those schools where no access to the hard drive is allowed for security purposes this folder can be hidden so that users won't manually change or delete this folder. If you find that Java Web Start is not working, it is a good idea to try typing in the proxy information manually. The first time Pedagogica is launched it will pop up a window requesting the proxy server information.
Whoever is offering this publicly available proxy may at any time decide to no longer make it public or just stop running it.
In the cases where Java Web Start does ask for authentication and Pedagogica does not, then you need to modify a file called command.properties, located in your PedagogicaActivities folder. If you decided to install other pieces of software from the Concord Consortium, then it is safe to place everything inside a folder called CC Software inside of one of the directories listed below. If you have trouble installing the software or want more detailed information on the variety of ways this software can be used, the information provided below should help.
For this Java player to work Quicktime needs to be installed on your system as well as some special Quicktime for Java classes that will allow us to interface our Java activities with the native Quicktime installation. Teachers (and students) are encouraged to not only view premade activities, but to create their own. Because Pedagogica is a more generic tool, the software and all molecular related activities require about 35MB of disk space. Enter the information and Pedagogica will store this for future use in a text file called command.properties.
Therefore, the bulk of this software is not kept in the individual user's Web Start cache folder.



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