News
Current News
Welcome back!
For those who are new to the University, we welcome you and hope that we’ll be able to assist you with your research and course questions. For the returning Hoos out there, we look forward to continuing to work with you! We hope that you will familiarize yourself with the assortment of research computing support services that are freely available to you here in the Research Computing Lab. For your convenience, we have included recent changes below.
Software Distribution and Support
The Research Computing Lab continues to be the place to go for specialized scientific software support. We offer access to some of the most popular research and instructional software in the sciences and distribute the installation media and licenses for many of these packages (Matlab, Mathematica, LabView, SAS, SPSS, IDL, ArcGIS, etc.). Please see the following url for our full listing: http://www2.lib.virginia.edu/brown/rescomp/distributions.html . In addition to these packages, we offer technical and methodological support around statistics, quantitative methods, programming, data management, visualization, scientific publishing, and a number of other areas. Let us know if we can be of assistance.
Short Courses and Training:
This Fall we are happy to offer an assortment of short courses and training opportunities that will help you boost your skills. Our selection of courses this Fall include: STATA / R, Intro to Quantitative Stats, Regression, etc., Logistic Regression, SAS, Managing the Research Data Lifecycle, Data, Databases, LaTeX, Image Integrity, Image Data Management for sciences. We are also expecting to have visits from National Instruments (maker of LabView) and other vendors. Please visit our website at http://www.lib.virginia.edu/brown/rescomp for a complete listing and schedule. All courses offered by the Research Computing Lab are free and open to all.
Software Solutions Beyond Labs Pilot:
As many of you know, ITC is in the process of transitioning student computing labs at the University. Over the next two years, the current physical computer lab environment will transition to a virtualized computing environment (background documentation on this change at ( http://itc.virginia.edu/org/reports/labstransition.html ). In preparation for this transition, the Software Solutions Beyond Labs (SSBL) Community, comprised of ITC and members of the U.Va. community including students, has committed to administering a pilot this Fall to test two virtualized software delivery platforms, VMware Virtual Desktop Infrastructure and Microsoft Terminal Services. The scope is relatively small in size, as this pilot is to test “proof of concept.” Participants in this pilot include two groups: 1) students whose faculty members have volunteered to have their students access course software using the virtualized solutions during their Fall 2009 classes; and 2) independent testers made up of faculty, staff, and students throughout the University. This pilot will run during Fall 2009 courses, from mid-September to December 1, 2009. The goal of the pilot is to document how well virtualized software delivery works on both laptop and desktop machines, in both wired and wireless environments, and on PC, Mac, and Linux platforms. The average experience in a current ITC student computing lab will be the benchmark for this pilot. Proposed applications to be tested are: 1. Civil 3D (AutoCAD), 2. Inventor, 3. Excel with VBA, 4. Matlab, 5. Heat Transfer, 6. Aspen Tech, 7. Maple, 8. Mathematica. As public computing labs decrease in size and number, the Research Computing Lab will continue to be available as a location for access to specialized research software and support. Keep an eye on the ITC website for further updates on the Software Solutions Beyond Labs effort.
Centers and Labs Union Small Grants:
On behalf of the VP/CIO’s office, the Centers and Labs Union, an informal alliance of technology support units around Grounds, administers small, $1,000 technology-focused grants for U.Va. faculty and faculty-sponsored graduate students. This program, known as the CLU Grants, aims to provide, with minimal administrative overhead, a small amount of money that will remove an impediment to an ongoing project in research, scholarship, or pedagogy. This funding is earmarked for technology (typically hardware, software, or electronic resources) and may not be used for travel. It is also not a “starter grant,” but is instead meant to smooth bumps in the road for existing digital projects. CLU Grants have a ceiling of $1000 and are limited to two awards per project, per year. They are meant as a funding source of last resort, after you have sought the assistance of your department and other administrative units. Applications will be evaluated by the CLU community and are accepted on a rolling basis until funding is exhausted. You should expect to be contacted within two business days of making your application. CLU Grant Application: http://spreadsheets.google.com/viewform?formkey=cFdNUFZ0WGo4UHFNdTlMdGlTb29NVkE6MA Contact Andrew Sallans (als9q@virginia.edu), Librarian for Digital Services, with questions.
Facebook and Twitter:
You can now follow the news and events of the Research Computing Lab on Facebook and Twitter. Become a fan of the “Research Computing Lab” on Facebook, and follow us on Twitter @UVA_RCL.
The Research Computing Lab Team:
The RCL team is unusual for a library. The team is a hybrid of IT and Library staff, and consists of specialists in statistics, data, web technologies, scientific publishing, and a variety of other areas. It also includes student staff members, who bring experience in science, engineering, and technology, and prove to be an invaluable asset to helping meet your support needs. The team approaches problems from a consulting perspective, and aims to help you learn through the process. This integration of scientific support into the academic research library has become a model that other academic science and engineering libraries are now adopting.
When We’re Available This Fall:
The Research Computing Lab space will be open for use during all times that the Brown Science and Engineering Library is open. Our staff will be available for assistance on the following schedule: Monday – Thursday from 10am to 8 pm, Friday from 10am to 5 pm, Saturday closed, and Sunday from 12pm to 8pm. We are also available by appointment for more in-depth consulting questions. We can be reached by phone at 243-8799, in person at the East Wing of the Brown Science and Engineering Library, or online via our ticket system at http://www.lib.virginia.edu/brown/rescomp Please visit our website for more information and updates regarding any schedule changes.
Feedback:
We’re always looking to improve our services and better support your needs. Please let us know if you have questions, would like assistance with something that we don’t currently offer, or would like to simply let us know how we are doing. We greatly value your input.
Are you on Twitter? Keep up with what’s happening in the RCL by following our Twitter feed. We are @UVA_RCL.
Return to top of pageFrom the Chronicle for Higher Education…
“Amazon, the online retailing giant, is now offering educators, researchers, and students the chance to apply for free access to its hosted computing, or “cloud,” services, the company announced this week. The services can be used to work with massive amounts of data that would jam a regular desktop computer.
The company is offering computer-usage credits, worth up to $100 per student, to instructors who wish to utilize its cloud services in the classroom. Grant applications are available through Amazon’s Web site. Amazon says its hosted services are already being used at institutions such as Harvard University and the University of Oxford.
For example, Oxford scientists at the Malaria Atlas Project—an effort to map the geography of the disease in order to drive prevention strategies—use Amazon’s hosted services to store, share, and analyze data.”
-Steve Kolowich
Original article: http://chronicle.com/wiredcampus/article/3748/amazon-offers-educational-grants-for-cloud-computing-access
Return to top of pageCheck out the Library’s newly released mobile website that is optimized for handheld, web-enabled mobile phones and devices. The current version is specifically geared toward Apple iPhones and iPod Touch, but in May 2009 will be updated for RIM Blackberry, Motorola, Palm, and Samsung. Read more at www.lib.virginia.edu/mobile .
((2009-06-01T22:00:00))
Return to top of pageThe Research Computing Lab staff congratulates our fourth-year student staff on their accomplishments and graduation.
Jonah Lee graduated in December 2008 with a degree in Mechanical Engineering. After transferring to U.Va. from Tulane University, Jonah spent 2 1/2 years working for the Research Computing Lab. Following a summer internship in the industry and leveraging his strong technical skills, Jonah began working with the Exxon Mobil Corporation in Louisiana in March 2009.
Yiding Li will be graduating with a degree in Biomedical Engineering and Economics. Yiding will pursue graduate study in biomedical engineering at U.Va. specializing in nanoparticle medicine. He will continue research around ways in which viruses may be able to detect pancreatic cancer. This summer he will be traveling to East and Southeast Asia.
Kevin Meehan will be graduating with a degree in Systems and Information Engineering. He will be joining the IT team at Booz-Allen-Hamilton near DC in August. Over the summer he will put his knowledge of Portuguese to use while working on a farm in Brazil. Kevin also has plans to spend a few weeks hiking the Appalachian Trail.
Rachel Miller will be graduating with a degree in Computer Science and Physics. She will complete her Masters degree in Mathematics over the summer and has been awarded a National Defense Science and Engineering Graduate (NDSEG) Fellowship which she will use to continue studies in Computer Science at MIT in the Fall. Rachel also has been awarded a NSF Graduate Fellowship and is a 2009 recipient of the McShane Prize awarded by the Mathematics Department.
We wish you the best of luck in your future endeavors!
Return to top of pageUniversity of Virginia: Imagine continuously zooming into an image from your personal photo collection. Unlike with modern image processing software, however, this zoom operation would reveal details missing from the original image. For example, zooming into someone’s shirt would eventually show a high-resolution image of the threads that compose it. A research team in the Department of Computer Science at the University of Virginia plans to develop techniques for intelligently enlarging a digital image that use a database of millions of on-line images to find examples of what its components look like at a higher spatial resolution. (From NSF Press Release)
Full press release: http://nsf.gov/news/news_summ.jsp?cntn_id=114686
Return to top of pageGoogle just announced a new program called Google FUSE and is seeking first-years in computer science as participants. It looks like a great opportunity to gain experience and awareness in the field.
Google FUSE will provide an opportunity for successful and invested freshmen computer science students who are historically underrepresented in the field to connect with one another and with Google. Up to 50 aspiring computer scientists will be invited to an all-expenses paid retreat that will run Wednesday evening through Friday afternoon on July 15–17 in New York, NY. The weekend will include networking and learning opportunities.
Program Goals:
* To form a network among the top young students from underrepresented backgrounds in CS that will allow them to learn about research, academic, and industry opportunities in the years to come.
* To make connections between students and Googlers that will allow students to discover career paths, create meaningful academic experiences, and take advantage of the college years in CS.
* To give students an insight in to careers in CS and show how rewarding, challenging, and fun they can be.
* To learn more about the program and apply, visit http://www.google.com/jobs/fuse/ . The deadline to apply is May 1, 2009.
For more announcements about student opportunities with Google, see: http://www.googleforstudents.blogspot.com/
Return to top of pageCYBERINFRASTRUCTURE SUMMER TRAINEESHIPS 2009
VIRTUAL DATA CENTER FOR
BIODIVERSITY, EARTH, ECOLOGICAL, AND EVOLUTIONARY SCIENCE DATA
http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009
Summer traineeships are available for up to four students and postdocs
interested in informatics as applied to scientific data ranging from the
fields of biodiversity, ecology, and evolutionary biology. The program
provides a unique opportunity for undergraduate, masters, and PhD students
as well as postdocs to obtain hands-on experience writing and extending
open-source software as part of a distributed collaborative software
development team building a Virtual Data Center (VDC) that includes major
data and metadata repositories in those fields.
Trainees accepted into the program will receive a stipend ($4,500), and
with the exception of attending one meeting near the beginning and one near
the end of the 3-month program period may work from their home, or home
institution. Travel costs incurred in connection with the meetings will be
reimbursed. Each student will have at least one dedicated mentor to show
them the ropes and help them complete their project.
Initial project ideas are listed on the website. These range from
validation of metadata and identifier resolution, to supporting LSID and
semantic-web compliant PURLs for digital data objects, to implementing
modern web-service APIs, to cataloging the diversity of metadata schemas.
The project ideas are flexible and can be adjusted in scope to match the
skills of the student. We also welcome novel project ideas that dovetail
with student interests.
The traineeships are supported by a National Science Foundation (NSF) grant
to a consortium of major repositories for biodiversity, earth and
environmental, ecological, and evolutionary science. The consortium
includes the LTER Network Office, the U.S. Geological Survey, NASA and Oak
Ridge National Laboratory, the Global Biodiversity Information Facility
(GBIF), the National Evolutionary Synthesis Center(NESCent), and the
National Center for Ecological Analysis and Synthesis (NCEAS). It aims to
develop the cyberinfrastructure and technologies necessary to build a
Virtual Data Center (VDC) based on a network of existing and new physical
repositories (“nodes”) that interoperate using open standards and
protocols. The network will enable discovery of as well as open, stable, and
secure access to data in any of its member nodes.
TO APPLY: Students apply online. Instructions for applying are at the
website (see “When you apply”), along with program rules and eligibility
requirements. The 15-day application period for students opens on Monday
March 30th and runs through Monday, April 13th, 2009.
INQUIRIES: vdc-twg {at} ecoinformatics {dot} org. We strongly encourage all
interested students to get in touch with us with their ideas as early as
possible.
Cyberinfrastructure Traineeships Website:
http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009
2009 NESCent Phyloinformatics Summer of Code (NESCent’s participation in the
Google Summer of Code; managed separately; postdocs not eligible; ***student
application period ends April 3rd***)
http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009
To sign up for quarterly NESCent newsletters:
http://www.nescent.org/about/contact.php
On behalf of the VP/CIO’s office, the Centers and Labs Union, an informal alliance of technology support units around Grounds, administers small, $1,000 technology-focused grants for U.Va. faculty and faculty-sponsored graduate students. This program, known as the CLU Grants, aims to provide, with minimal administrative overhead, a small amount of money that will remove an impediment to an ongoing project in research, scholarship, or pedagogy. This funding is earmarked for technology (typically hardware, software, or electronic resources) and may not be used for travel. It is also not a “starter grant,” but is instead meant to smooth bumps in the road for existing digital projects.
CLU Grants have a ceiling of $1000 and are limited to two awards per project, per year. They are meant as a funding source of last resort, after you have sought the assistance of your department and other administrative units. Applications will be evaluated by the CLU community and are accepted on a rolling basis until funding is exhausted. You should expect to be contacted within two business days of making your application.
CLU Grant Application: http://spreadsheets.google.com/viewform?formkey=cFdNUFZ0WGo4UHFNdTlMdGlTb29NVkE6MA
Contact Andrew Sallans (als9q@virginia.edu), Librarian for Digital Services, with questions.
Return to top of pageInterested in what Open Science might offer your research? Have you considered what kind of competitive advantage this might bring to your work and your career in science? How might this improve the quality and credibility of your work? What might this mean in terms of new grant regulations (ie. NIH)? This is a rapidly expanding area of interest right now, and the staff in the Research Computing Lab can offer you guidance as you begin to explore the possibilities. For more information, take a look at the following video from a recent panel on Open Science held at Columbia University.
Columbia University Libraries held a panel on February 19, 2009 on the topic of Open Science. The panel description is as follows: “Open science refers to information-sharing among researchers and encompasses a number of initiatives to remove access barriers to data and published papers, and to use digital technology to more efficiently disseminate research results. Advocates for this approach argue that openly sharing information among researchers is fundamental to good science, speeds the progress of research, and increases recognition of researchers. Panelists: Jean-Claude Bradley, Associate Professor of Chemistry and Coordinator of E-Learning for the School of Arts and Sciences at Drexel University; Barry Canton, founder of Gingko BioWorks and the OpenWetWare wiki, an online community of life science researchers committed to open science that has over 5,300 users; Bora Zivkovic, Online Discussion Expert for the Public Library of Science (PLoS) and author of “A Blog Around the Clock.” “
Url: http://scholcomm.columbia.edu/open-science-good-research-good-researchers
Return to top of pageWant to keep in the loop on what short courses and events we have coming up? Add them directly into your Outlook, Entourage, iCal, or Google Calendar quickly and easily via our feeds on our Events page: http://www2.lib.virginia.edu/brown/rescomp/events.html All it takes is a click of the mouse!
Return to top of pageDue to inclement weather, the Tuesday, January 27th LabView User’s Group meeting has been cancelled. Please see our events called for rescheduling information.
Return to top of pageSanborn will be presenting a seminar on the Virginia Base Mapping Program (VBMP) 2009-2012 imagery acquisition for Virginia, focusing on land use and forestry applications.
Date: Monday, January 26, 2009, 1 p.m. – 3 p.m.
Location: Board Room Virginia Department of Forestry Central Office, Fontaine Research Park 900 Natural Resources Drive, Suite 800, Charlottesville, VA 22903
Who’s Invited: All are welcome.
The Commonwealth of Virginia has contracted with Sanborn for the VBMP for the period of 2009 to 2012. The 2009-2012 Virginia Base Mapping Program (VBMP) fulfills VGIN’s charge of developing a statewide orthophotography base map and managing it as an ongoing, four year program that is a resource for state and local government entities, both public and private. This product is the basis that enables consistency for the development of geospatial products and data that are produced in the Commonwealth.
Return to top of pageYou can now keep up with the latest happenings in the Research Computing Lab by becoming a friend of the RCL on Facebook. The Research Computing Lab’s Facebook id is for a page and is titled “Research Computing Lab”. Become a fan and show your support!
Return to top of pageFollowing on a series of successful High-Performance Computing (HPC) bootcamps, ITC is working with UVACSE in exploring the feasibility of creating a “tiger team program” to help researchers at the University of Virginia move their science to the next level using advanced computational techniques. The tiger teams will work with researchers with existing research codes on code optimization, parallelization, workflow, checkpointing, and data management issues, as well as assisting with taking problems from conceptualization to code.
Tiger teams are not targeted at help desk problems, e.g., how do I login, or which queue should I use. Rather they are focused on problems that require a creative partnership and may take days to months to design, develop, and test a solution. There is no charge for work by a tiger team, though longer term funded collaborations are possible.
The proposed tiger team program is part of a wider effort to realize the goals for computational science as outlined by the Commission on the Future of the University.
For more information, please see the May 2008 ITC Research Computer Support Newsletter .
Return to top of pagePerry Roland, Information Technologist in Alderman Library’s Digital Library Production Service was recently invited by the Center for Computer-Assisted Research in the Humanities (CCARH) at Stanford University to consult on uses of the Music Encoding Initiative (MEI) in medieval chant and Japanese koto repertoires.
Stefan Morent, from Eberhard Karls Universit’t in T’bingen, Germany, is creating a digital edition of the works of Hildegard von Bingen utilizing MEI. Craig Sapp, from CCARH, will employ MEI as the native format for a collection of koto scores. The meeting in Palo Alto provided an opportunity for spirited, face-to-face discussions and exchange of ideas and data. CCARH shared approximately 300 encoded musical works for MEI testing.
The May 08, 2008 article in HPCWire online news article titled “High Performance Humanities” by John E. West, reports
…On April 21, the National Endowment for the Humanities (NEH) announced something new: they would be teaming up with the U.S. Department of Energy to offer one million CPU hours on supercomputers at NERSC for use by researchers in the humanities. The effort is managed out of the NEH’s new Office of Digital Humanities…
…The recognition of this shift in research methodology was the genesis for the creation of the ODH as the nation’s leading humanities research funding organization. The NEH sponsored the “Supercomputing and the Humanities” workshop in July of 2007 to explore some of the research already going on at that time, and to get a glimpse at the potential for the future. There were many presenters, including David Koller from the Institute for Advanced Technology in the Humanities at the University of Virginia, who presented results of efforts to computationally reassemble fragmentary artifacts; essentially, using a computer to put together the pieces of ancient, broken puzzles. In another example, David Bamman at Tufts University presented efforts by the Perseus Project to use computational methods for syntactic parsing of document stores to create a distilled understanding of an entire library’s contents…
Read the entire article .
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