Category Archives: Software

Network Status Update

On the morning of December 24th, Rutgers experienced an intermittent DDoS attack, directed primarily at  OIT worked with our provider on mitigation and has advised law enforcement of the attack.Users may experience difficulty accessing Sakai until the problem is resolved.

We are continuing to monitor the status.

We apologize for the inconvenience.  Thank you for your patience as we work through the issues.
848-445-HELP (4357)

OIT Update: & Cloud Service Update

List of Software available on and

Math & Science                  Desktop                         Programming

APBS 1.3.0                           Acrobat Reader *       CoqIDE 8.3

Avogadro 1.0.3                   Blender 2.7.0               Coq – Emacs

Cadabra 1.29                      Firefox *                           Eclipse IDE

Chemtool 1.6.13                Google Chrome *      GNU C/C++ 4.7

FSL 5.0                                 Google Earth 7.1.1   GNU Fortran 4.7

FSL View 4.0                       Gummi 0.6.3                 Google Android SDK *

Genome Workbench 2.4            Libre Office *       Meld 1.6

Gephi 0.8.1-1                      Pidgin IM 2.10             Netbeans IDE *

GNU Octave  3.6.2             Thunderbird *             Ox 7

Icarus Verilog 0.9.5            Pep8

Maple 18 – 100 user limit                Perl 5.14

Mathematica 10.0.0           PHP 5.3.28

Matlab 2014a                       Proof General 4.2

Maxima 5.27                          Python 2.7.3


PSPP 0.7.9

Quantum GIS 2.4

R 3.1.1-3

RStudio 0.98.1025

Sage 5.10-1

SAS 9.4-1

SPSS 21 – 50 user limit

Stata MP2 13 (MP4 on Apps.HPC)

Weka 3.6.9

XDrawChem 2.0

*denotes packages that are regularly updated.

Likely updates by September include:

Sage Math



Android SDK/NDK


New users (any Rutgers user with a NetID) can access Apps and Apps.HPC resources by first selecting “activate services” via  Then just point your browser at and login. Getting started info is referenced on the  start up page.

Note that Stat Transfer has been deleted since licensing no longer supports servers.

To keep in touch with Apps updates, read or join the Apps User Community by signing up at   For further information, please send email to

Apps HPC Will Provide Accees to GPU Capability for Instruction – We are looking for folks to test the GPUs. will be debuting access to some GPU capability in April, but now we are looking for some users who would test this service and provide feedback before it is made generally available. Please send email to indicatting your interest in testing this GPU capability.

Any Apps user will be able to submit assignments and basic research programs to the GPU cluster which is comprised of 500 core Tesla GPUs from Nvidia. There are 8 GPUs on a node. This system will allow users to submit parallelized code using Matlab, Mathematica, R, and other packages. Cloud Service Update(s)

2/27/14 – FSL 5.0 and FSL View have been added to for more info refer to for more info

1/20/14 – With the assistance of some folks who helped to test, anyone can now use this new HPC Apps service. Read more about this capability below.

1/20/14 – As browsers no longer support Java applications, the older Java Login page will be less useful and associated descriptions in documentation (flagged with **JAVA) will be deleted.

Please note that webdrive (highlighted in the “Start up Document” at is very easy to use for file transfers.

To keep in touch with Apps updates as they happen, join the Apps User Community by signing up at For further information, please send email to

Apps Debuts HPC Capability for Instruction and Longer Running Jobs debuts HPC capability in support of instruction and some elementary research. Any Apps user can submit jobs to Apps.HPC.

One can test their code on Apps as usual. Then save their program and submit the job to Apps.HPC via the srun command from a terminal window. Note that is prioritized for interactive use while Apps.HPC only prioritized to run HPC and longer running jobs.

Apps HPC system is a single node with 32 cores and 750 gig of memory. This system will allow users to submit longer running jobs as well as run parallelized code with Matlab, Mathematica, R, Stata MP4, and other packages.

Refer to for basic info to get started. For further info, send email to

Matlab Training November 15

Please join MathWorks at complimentary MATLAB seminars for educators, academic researchers, and students at Rutgers University:

Date: Friday, November 15, 2013
Location: Busch Campus Center – room 120ABC
Time: 9:30am – 11:00am
11:15am – 12:45pm

> > Register Here Now.

Our event features two technical sessions presented by a MathWorks engineer:

9:30am – 11:00am: Session 1: Data Analysis with MATLAB
Learn how to access data, use interactive tools, automate and capture your work and share your results.

11:15am – 12:45pm: Session 2: Parallel Computing with MATLAB
Learn how to solve and accelerate computationally and data-intensive problems using multicore processors, GPUs, and computer clusters and then generate readable and portable C and C++ code from your MATLAB algorithms using MATLAB Coder.

View complete session descriptions and register here.

Site Licensed Software Updates

Rutgers Community funded site licenses have been extended and include the following applications:

Software Category

  • Mathematical
  • Statistical
  • Chem&Bio Draw
  • Survey (SaaS)
  • Bibliographic (SaaS)
  • Qualitative Anal.
  • Bio Anal. (SaaS)
  • Measurement & Control



General Highlights:

– ChemBioDraw site license has been upgraded to ChemBioOffice and includes ChemBioDraw, eNotebook, and more.
– Matlab site license now includes the Matlab Distributed Computing Server (MDCS) Toolbox (for 32 or less workers/nodes) and the OPC Toolbox.
– RefWorks site license now includes Flow. Flow incorporates the general bibliographic capabilities of RefWorks plus full text and annotation as well as improved processes for collecting references, collaboration, and ease of use.

Rutgers Biomedical and Health Sciences (RBHS) Community updates:

– ChemBioOffice, ChemDoodle, Matlab, Mathematica, Maple, Stata, Origin Pro, RefWorks & Flow, NVivo, LabVIEW, and Ingenuity IPA have been extended to include RBHS faculty, staff, and students.
– RBHS users do not yet have access to Qualtrics (cloud survey tool) and Stata (a statistical package).

Downloads and installation instructions are available via the software portal at To keep up to date regarding a specific site license, sign up for its sakai listserv via the respective links listed with the software package either at the site or on the software portal.

For further information, refer to or send your queries to Cloud Service Update – Summer 2013 Updates

– R updated to version 3.0.1-3 (summer 2013)

– SAS updated to version 9.2-3 (7/30)

– Stat Transfer updated to version 12 (7/30)

– Stata updated to version 13 (7/22)

– SPSS updated to version 21 (7/22)

– Maple updated to version 17 (6/10)

– Matlab updated to version 2013a (6/11)

– Sage updated to version 5.10-1 (6/27)

– RBHS users can now access Apps and all packages except Stata (they need to select activate services via

To keep in touch with Apps updates as they happen, join the Apps User Community by signing up at For further information, please send email to