ITC Research Computing Support Newsletter - November 2006
This is the November 2006 newsletter for ITC Research Computing Support. If you have any questions or concerns regarding the information presented here, please contact ITC Research Computing Support by emailing Res-Consult@virginia.edu, or phoning either the Research Computing Lab in Brown Library at 243-8799 or the Scholars Lab in Alderman Library at 243-8800.
Contents
- Software and Hardware
- Secure Access Only to Linux Clusters
- Mathematica 5.2.2 Available for Intel-Based Macs
- N'Vivo 7 Now Available!
- Increase in CMS and HDS Quotas
- Wolfram Workbench: A Mathematica Integrated Development Environment
- SecureCRT Upgrade Available
- SecureFX Upgrade Available
- Events and Announcements
- Technical Session: Using MATLAB & Simulink in Life Sciences on November 16
- Thanksgiving Holiday Schedule for Research Computing Support
- Fall Research Computing Colloquia
- Immediate Opening for Research Computing Student Consultants
- Mathematica Free Online Seminars
- Stay Informed About SAS Users Group Activities!
- SESUG Website Updated with Presentation Lineup and FAQ
- Virginia Visualization Group to Meet on November 28 in New Visualization Studio
- IronPort Spam Tagging for the Central Mail Service
Software and Hardware..........
Secure Access Only to Linux Clusters
In the interest of security, ITC has disabled off-Grounds direct ssh access to the new Dogwood Linux cluster as well as the older Birch and Cedar Linux clusters. In order to access these systems from off Grounds, you must use either the UVa Anywhere VPN client (http://www.itc.virginia.edu/desktop/pki/vpn/) or your normal ssh client, such as SecureCRT, to log in to blue.unix.virginia.edu initially.
If you log in to blue.unix and you have had an ITC profile for a while, you may be confronted with the text menu system known as "umenu" and it is archaic. One of the options is to turn it off, and we suggest you do so. Once umenu is turned off, when you log in to blue.unix you will be at a normal shell prompt.
If you need to log on to Dogwood (or Birch or Cedar) before disabling umenu, choose "9" for "go to Unix" and this will drop you to a shell prompt.
For instance, from the shell prompt, type
ssh dogwood.itc.virginia.edu
or
slogin dogwood.itc.virginia.edu
(these two commands have the identical result) and you will be on Dogwood. If you have X11 forwarding enabled in your desktop ssh client, blue.unix will pass this through.Direct access will continue to be available from on-Grounds locations as usual. Only off-Grounds access is affected by this policy.
Please contact ITC Research Computing Support if you have questions by emailing Res-Consult@Virginia.edu or by telephoning or visiting either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).
Mathematica 5.2.2 Available for Intel-Based Macs
ITC is now distributing CDs for Mathematica 5.2.2 for installation on University-owned, Intel-based Macintosh computers from either the Research Computing Lab in the Brown Science and Engineering Library, or the Scholars' Lab in Alderman Library, 4th floor.
Mathematica 5.2 is currently available on ITC's IBM AIX (64-bit), SGI IRIX (64-bit), Sun Solaris (64-bit), and Linux platforms, as well as in the Windows public computing labs. Mathematica 5.2.2 will be available in ITC's Intel-based Macintosh public computers in the Spring 2007 semester.
Detailed information about Mathematica 5.2 can be found at the Wolfram Research website at
http://www.wolfram.com/Further information on how to access and use Mathematica can be found on the Research Computing Services website at
http://www.itc.virginia.edu/research/mathematicaQuestions concerning the use of Mathematica should be directed to ITC Research Computing Support; email us at Res-Consult@virginia.edu or phone 243-8800.
N'Vivo 7 Now Available!
N'Vivo 7 is a popular and powerful qualitative research tool produced by QSR, International. ITC has recently obtained the site license from the Curry School of Education, and the program is available via download from the ITC licensing Web page at
http://www.web.virginia.eduEach license costs $125, and may be paid for using a PTAO or a check made out to The University of Virginia.
Specific questions about N'Vivo should be directed to ITC Research Computing Support; email us at Res-Consult@virginia.edu or telephone or visit either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).Increase in CMS and HDS Quotas
Effective as of October 31, 2006, available disk space quotas on the Central Mail Service (CMS) and the Home Directory Service (HDS) are increased to two gigabytes. This change applies to all faculty, staff, graduate and undergraduate students.
On the CMS, if the attempted delivery of an email message would cause the Inbox to exceed two gigabytes, the delivery of the message will fail and the sender will receive a failed mail notice. Processing of near-quota and over-quota situations will remain unchanged. For more information on these procedures or to check your CMS quota, use your Web browser to go to
http://www.itc.virginia.edu/desktop/email/cms/quota.htmlFor those who read email through unix.mail.virginia.edu, Home Directory storage includes files and email folders, but not the Inbox. Individuals needing more than two gigabytes on the Home Directory Service may also lease additional storage from ITC. For more information and to check your Home Directory quota, use your Web browser to go to
http://www.itc.virginia.edu/homedirWolfram Workbench: A Mathematica Integrated Development Environment
Wolfram Research has released Wolfram Workbench, an integrated development environment that makes it easier to build and maintain software solutions written with Mathematica technologies.
Wolfram Workbench is currently available as a prerelease exclusively to Premier Service customers, which includes Mathematica users at the University of Virginia. You can download a free copy now for any U.Va.-owned computing on-grounds on which you've installed Mathematica through the site license.
Key features in Workbench enable users to:
- Group files, code, and other Mathematica resources into a single project
- Perform source-code editing with syntax highlighting, error reporting, local variable coloring, and many more options
- Study code as it runs to easily detect and fix any problems
- Profile code's execution and develop and run tests, with an array of insightful reporting methods
- Manage multiple versions of files and access their version histories
- Build and deploy Mathematica packages
For more information about Workbench, visit our website at
http://www.wolfram.com/workbenchTo download Wolfram Workbench, go to:
http://www.wolfram.com/services/premiersupport/workbench.cgi?License=26266593Further information on how to access and use Mathematica can be found on the Research Computing Services Web page at
http://www.itc.virginia.edu/research/mathematica/Questions concerning the use of Mathematica should be directed to ITC Research Computing Support; email us at Res-Consult@virginia.edu or telephone or visit either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).
SecureCRT Upgrade Available
ITC announces the upgrade of SecureCRT from version 5.1.1 to version 5.2. SecureCRT is a telnet program from Van Dyke Technologies that provides data encryption and secure login capabilities. This release contains SSL (Secure Sockets Layer) support; protocol support for Telnet over SSL which gives you additional security when the remote machine only supports SSL, or when firewall settings prevent the use of SSH.
To find out more about SecureCRT, please visit ITC's SecureCRT information site at:
http://www.itc.virginia.edu/helpdesk/softwaredocs/securecrt/Contact the ITC Help Desk at 924-3731 or by email to consult@virginia.edu if you have questions about the upgrade.
SecureFX Upgrade Available
ITC announces the upgrade of SecureFX from version 3.1.1 to version 4.0. SecureFX is a secure file transfer client from Van Dyke Technologies. This release, like that of SecureCRT, contains SSL support; protocol support for FTP over SSL (TLS) gives you additional security when the remote machine only supports SSL, or when firewall settings prevent the use of SSH/SFTP.
To find out more about SecureFX, please visit ITC's SecureFX information site at:
http://www.itc.virginia.edu/helpdesk/softwaredocs/securefx/Contact the ITC Help Desk at 924-3731 or by email to consult@virginia.edu if you have questions about the upgrade.
Events and Announcements..........
Technical Session: Using MATLAB & Simulink in Life Sciences on November 16
The MathWorks Company invites you to a free technical session to help university professors, researchers, and students learn how to use MATLAB and Simulink in Life Sciences.
This technical session will show how MATLAB and Simulink products are used as a flexible platform for technical computing and application development in life science and biomedical research. We will also demonstrate the use of several toolboxes including the Statistics, Image Processing, Bioinformatics, Signal Processing Toolboxes and SimBiology to analyze and visualize biosignal data, perform microarray analysis, and customize statistical algorithms in bioinformatics.
Event Details
When: Thursday, November 16, 2006 from 1:00 to 4:00 p.m.
Where: University of Virginia, Old Medical School Building (Health System), First Floor, Classroom C1 Charlottesville, VA
For directions to the Old Medical School Building (#24 on webmap), please visit
http://www.virginia.edu/webmap/BHealthSciences.html
How: Register now at
http://www.mathworks.com/seminars/uva
or call 978-659-6104.
Who Should Attend: Professors, researchers and students.
Topics Covered:For more information contact:
- Data Acquisition and Import
- Pulse Oximetry - Streaming data from hardware
- Gene expression - Importing data from Excel
- Filtering Tumor data - Pulling data from databases, building SQL statements
- Gene Ontology - Importing data from Web databases
- Analysis, Automation, and Visualization
- Mass spectrometry (SELDI-TOF) - Developing user-interfaces for advanced analysis
- Quantification of metastatic lesions - Automating image processing
- Estimating retinal blood flow - Advanced image processing
- Pharmacokinetics - Modeling and estimating parameters in Simulink
- Sharing and Communicating your Research
- Flow cytometry - Publishing HTML reports
- Gene expression - Creating Excel plug-ins and stand-alone executables
- Leveraging Distributed and Parallel Computing
Scott Benway
sbenway at mathworks.com
Account Manager, Education Department
508-647-7741
www.mathworks.comThanksgiving Holiday Schedule for Research Computing Support
For the Thanksgiving Recess (November 18-26) the Scholars' Lab in Alderman Library and the Research Computing Lab in Brown Library will generally be open when that library is open. For the Scholars' Lab, the full Thanksgiving Recess schedule is available at:
http://www.lib.virginia.edu/scholarslab/info/hours/thanks.htmlPlease note the Scholars' Lab will be closed Thursday and Friday, November 23 and 24.
The Research Computing Lab will be open during Brown Library's open hours for the Thanksgiving Recess, but with reduced staffing. For more information, please see the Web page at
http://www.lib.virginia.edu/hours/thanksgiving_recess_2006.htmlRegular hours for both locations will resume on Sunday, November 26.
Fall Research Computing Colloquia
Research Computing Support will be hosting a series of colloquia this Fall semester. Except where noted, the talks will be from 3:30 p.m. to 4:45 p.m. on every other Wednesday in the Scholar's Lab, Alderman Library. Snacks and drinks will be provided. If you have a topic you'd like covered or have any questions about these talks, please contact us by email to Res-Consult@virginia.edu or by calling 243-8800.
Please join us on:
If you cannot make it to a talk, all is not lost. The notes and visual aids from the talk will be available shortly after the talk on our website at:
- Wednesday, November 15: SAS Enterprise Guide, presented by Kathy Gerber.
With SAS Enterprise Guide you can produce great results in just a few minutes, regardless of your SAS knowledge. Enterprise Guide provides the beginner with an easy way to get the most out the powerful SAS environment. Experienced SAS programmers will appreciate the time savings in applying more efficient ways of organizing data and performing tasks through the use of Enterprise Guide projects. Using sample data we'll demonstrate how to perform exploratory data analysis, estimate a regression model, and explore the model fit graphically. We will also demonstrate how code generated automatically by EG can be customized, stored, and reused.
- Wednesday, November 29 (3:30PM): A Picture Says a Thousand Words: Displaying Quantitative Data and Information Effectively, presented by Nancy Kechner.
You've written the proposal, submitted the grant, gotten funded, and successfully performed the research. Now what?! One of the most important aspects of your research is disseminating the results to the academic community for review. How often have you looked at a graph and wondered: what exactly was the researcher trying to get across in the graph?
Join us for an informative and entertaining examination of the do's and don'ts of effective quantitative data presentation. Learn to understand what good graphics contain, and how to create them. We'll also take a look at some truly awful graphics so that you can learn what to avoid when creating your graphs. Think of it as "everything you've wanted to learn about graphing... but didn't know what to ask.
http://www.itc.virginia.edu/research/talks/Immediate Opening for Research Computing Student Consultants
Information Technology and Communication's (ITC) Research Computing Support (RCS) is now accepting applications for student research computing consultant. The positions can start as soon as suitable candidates are found. It is expected that the students hired will start this summer and work at least through this academic year (2006-2007). ITC-RCS provides support for a wide variety of statistical, mathematical, scientific, and visualization software programs across a wide spectrum of computer platforms. Please see our website at
http://www.itc.virginia.edu/researchers/service.htmlfor a listing of the software package and breadth of support and services offered by ITC research computing support.
To qualify for the position you must have a good working knowledge of at least one of the primary statistical, scientific, or mathematical packages we support and familiarity with at least one other software package.
The primary software packages are: SPSS, Matlab, SAS, Mathematica, Maple, S-Plus, and Stata. The most competitive candidates should have some working knowledge with more than one software package. In addition, you should be experienced using at least one of the computer systems below:
- Microsoft Windows
- Apple Macintosh
- UNIX (blue.unix, Linux, or other flavors)
An applicant must be a student who possesses the maturity and social skills needed to work closely with a variety of computer users, ranging from undergraduates to senior faculty and from novice to experienced users and the computer skills to work on a variety of computers and software programs.
The research computing consultant is responsible for helping users successfully run their research software programs and understand the output generated.
The position offers a research or quantitatively oriented graduate student exposure to a wide variety of scientific computing and statistical analysis projects and a broad assortment of research projects from many departments in the University and extensive experience using computers for data analysis and computational science.
Students interested in applying for a position should complete the application online at:
http://web.virginia.edu/labcon/applications/labconapp.asp
Please make sure you check the box "Research/Statistical Computing Support" to indicate you are applying for this consultant position.
If you have questions or concerns about this position, please feel free to contact the ITC Research Computing Support Coordinator, Nancy Kechner, by sending electronic mail to nek8n@Virginia.EDU or by telephone at 243-8800.
Applications will be accepted until the positions are filled. Apply as soon as possible. (AA/EOE)
Mathematica Free Online Seminars
The Wolfram Education Group has begun offering free online seminars to Mathematica customers worldwide. Taught by experienced Wolfram Research staff, presentations are given twice weekly. The seminar series began with S10: A Technical Overview of Mathematica located at
http://www.wolfram.com/weg/seminarsFor a list of dates and to enroll, visit:
http://www.wolfram.com/weg/calendarFurther information on how to access and use Mathematica can be found on the Research Computing Services Web page at
http://www.itc.virginia.edu/research/mathematica/Please contact ITC Research Computing Support if you have questions by emailing Res-Consult@Virginia.edu or by telephoning or visiting either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).
Stay Informed About SAS Users Group Activities!
SAS Institute has many exciting SAS users group events planned for 2006 and beyond - and they want to keep you up-to-date on the activities that will interest you most. To help them do that, please visit and log in with your existing SAS profile or create a new one at
http://sems.sas.com/bess/get?id=559.1:-n81zun:ey2&RZNVY=gswg@ivetvavn.rqh&nccvq=5344Stay informed and enjoy the unique opportunities for networking, learning and professional development that only SAS users group events can offer. Mark your calendar for the SAS Global Forum (formerly SUGI) that will be held April 16-19, 2007, in Orlando. They look forward to seeing you at one of these upcoming events! (Posted by:Michael H. Smith, SAS Users Group Support, Manager, SAS Institute).
SESUG Website Updated with Presentation Lineup and FAQ
The SESUG website has been recently updated with some new details about the conference.
- Click on Presentations to display a list of the more than 120 presentations planned for this year's conference. A PDF is available for download that includes all of the abstracts as well.
http://sems.sas.com/bess/get?id=1175.1:-unwpbd:eym&RZNVY=ggbyfba@ivetvavn.rqh&nccvq=4603- Click on Frequently Asked Questions to get answers to the most common questions the SESUG chairs and registrars are asked by attendees.
http://sems.sas.com/bess/get?id=1176.1:-unwpbd:eym&RZNVY=ggbyfba@ivetvavn.rqh&nccvq=4603But if your question is not answered here, feel free to contact the conference chairs, Marje Fecht at AcademicChair2006 at sesug.org or Deborah Skinner at OperationChair2006 at sesug.org.
Virginia Visualization Group to Meet on November 28 in New Visualization Studio
The Visualization Studio will open and host a meeting of the Virginia Visualization Group on Tuesday, November 28, at 11 a.m. The Visualization Studio is in Jury Room C in Campbell Hall. There will be a talk about the design of the room, a demonstration of how it works, and information on how faculty can use the room for teaching and research. Space for this event is limited to 25 people, so please R.S.V.P. to Joy Shifflette at jbs9q@virginia.edu or by calling 924-3137.
IronPort Spam Tagging for the Central Mail Service
On November 14, 2006, ITC turned on a new spam management system for all accounts on U.Va.'s Central Mail Service (CMS). Due to the ever-increasing volume of spam email and the limited effectiveness of our existing solutions, ITC has bought a commercial anti-spam solution from IronPort Systems. Extensive testing has shown that IronPort is much better at reducing spam than our existing tools, and it generates almost no false positives (legitimate messages that are mis-identified as spam). For that reason, IronPort protection is not only being extended to all email accounts on the CMS, but will also be made available to the administrators of other U.Va. mail systems in the coming months.
For more information, please see the Web page at
http://www.itc.virginia.edu/pubs/ads/ironport/
Now is the time to encourage your colleagues and students to join us and learn about research computing support at U.Va. We only send out an e-mail once or twice a month to this mail list. Anyone can subscribe to this "itc-research" mail list via the Web page at:
http://list.mail.virginia.edu/mailman/listinfo/itc-researchPlease encourage your colleagues to subscribe to our Research Computing mail list today!
