Access to Mathematica and Wolfram Workbench

Mathematica

We strongly encourage you to install Mathematica on a machine that you can bring to class and use for your assignments. Here are three methods for doing that.

Downloading Mathematica

Go to http://bio5495.wustl.edu/files/ . You will need the username and password provided in class or in my first email.

Download the Windows, Mac, or Linux version of Mathematica. If more than one release is available, pick the highest release number available.

Install Mathematica. (To install on a Linux machine,  run ‘sudo bash Mathematica_11.0.0_LINUX.sh’ substituting your version number for 11.0.0)

Connecting to our license server

This method requires you to be on a network when you use Mathematica.
Most networks, both inside and outside the university should work, including WUFI-S, which you log in to with your WUSTL key. However, some networks, including WUFI-GUEST, only open a limited number of ports for things like web browsing and so won’t work. If you don’t have access to a network in the classroom that works for the license server please let me know.

After you have installed Mathematica, open it.

When asked for an activation key, click "Other ways to activate" .

Select “Connect to a network license server”.

Enter the server name: mathlm-75216.cgs.wustl.edu

Alternative method 1: Obtaining a stand-alone license

This may be the best method for many people.

No cost. If you are a graduate student, postdoc, or other person receiving a salary or stipend through the School of Engineering, you are covered by the School’s site license and do not have to pay. There is some murkiness about whether this applies only to university-owned computers (including those bought by a professor on a grant or startup fund). How you handle that is between you and the software licensing office -- I believe it’s an honor system rather than something they check up on.

$25 Cost. Any student can obtain a license through the university for use on personal machines for $25. Considering most textbooks cost more like a $100 and this class doesn’t require any textbook purchase, I think $25 is very reasonable.

In either case, you can get an initial download that’s good for 15 days while you figure out whether you need to pay and if so how you will pay. To get the free download:

Go to the Wolfram User Portal to create a Wolfram User ID (click or copy https://user.wolfram.com/portal/login.html). Use your school email address to create an account and then log in.

Click on Wolfram Activation Key Request Form, sign in with your Wolfram User ID, complete the request form and submit it. You will receive an activation key that is valid for 15 days.

To get your license key extended for the full year, send an email to one of the employees of Software Licensing, whose contact information should be listed at: http://sl.wustl.edu/staff.php (this link only works when you’re in the wustl.edu domain or using a vpn to get into it virtually). Either indicate that you think you are entitled to a free license or alternatively that you are in my class and intend to pay $25 for a license.

To pay by credit or debit card, call someone at Software Licensing (see URL above).  They can process your card information.

To pay by check, make payable to Washington University and send by campus mail to Campus Box 1110, Attn: Software Licensing.

Alternative method 2: x forwarding (note: this approach has serious drawbacks -- use it as a last resort).

If you cannot install Mathematica or your installation is giving you trouble for some reason, you can run it on our server and use X forwarding to make the interaction window appear on your machine. This works best if the machine you are sitting at is a Linux or Macintosh machine -- if you want to do this on Windows, you’ll have to install some kind of unix-like software that runs under Windows, such as cygwin.

Drawback: Once you complete platform-specific instructions below, each time you open a Mathematica notebook you will want to follow the instructions here http://support.wolfram.com/kb/12406 to permenantly disable the suggestions bar and autocompletion features. This is not strictly required, but if you don’t do it you will see some annoying blips on the screen as you type and the interactions could get a little laggy.

Mac

Install X11.  X11 is not included with Mountain Lion. Apple has their own version of X11 called Xquartz.  

Download the Xquartz.dmg file

Follow on-screen directions

Log out and log back in

Run X11:

Start XQuartz by clicking in a Finder window, Applications → Utilities → XQuartz. A new XQuartz terminal window will open.

Ssh to the class server by typing ssh -X username@bio5495-work.wustl.edu, where username is your username. The -X option enables X11 forwarding.

Linux    

Install X11: X11 was most likely installed by your Linux distribution’s installer.  If not, you can build if from source following the directions here http://www.linuxfromscratch.org/blfs/view/cvs/x/xorg7.html

Run X11: ssh to the class server by typing ssh -X username@bio5495-work.wustl.edu, where username is your username. The -X option enables X11 forwarding.

Windows

X11 is possible.  Talk to the instructor or TAs for instructions.

Eclipse integrated development environment and Mathematica plug-in

Please read the following instructions for installing Eclipse IDE and Mathematica plug-in, note that you have to install Java Development Kit 8(JDK8) which includes Java Runtime Environment (JRE) before installing Eclipse.

Download Java Development Kit 8 by following this link: http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html. Choose the version according to your operating system.

Download and run Eclipse installer (https://eclipse.org), now the newest version is Eclipse Oxygen, and please install Eclipse IDE for Java Developers.

MathematicaAccess_1.gif

Then follow the step-by-step guide on the instruction page (http://support.wolfram.com/kb/27221), which will guide you to install the Mathematica Workbench plug-in.

Workbench (do this only if you have a problem getting Eclipse and the plug-in to work)

Workbench is the integrated development environment that goes with Mathematica. After you’ve installed Mathematica, you can install Workbench as follows:

Go to http://bio5495.wustl.edu/files/ . You will need the username and password provided in class.

Download the Windows, OSX, or Linux version of Workbench 3.0.0beta. Do not download Workbench 2.0.0 unless instructed to.

Install Workbench (to install on a Linux machine, run ‘sudo bash Workbench_3.0.0-5136968_LINUX.iso’)

Windows users: If you get an error message when you try to run a notebook from Workbench by using the “Run As -> Wolfram” menu, the following may fix it.

Copy the file "C:\Program Files\Wolfram Research\Mathematica\11.0\SystemFiles\Libraries\Windows-x86-64\ml64i3.dll"
into your system folder "C:\Windows\System32"

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