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Research Technology Services @ Tufts
Lionel H. Zupan
October 2008
Introduction
UIT Academic Technology Services
UIT Academic Technology enables the university and its diverse academic communities to realize their vast potential in teaching, learning, and research through the innovative design and meaningful integration of technology to meet broad and local goals.
http://uit.tufts.edu/at/
UIT Academic Technology Services
UIT Academic Technology enables the university and its diverse academic communities to realize their vast potential in teaching, learning, and research through the innovative design and meaningful integration of technology to meet broad and local goals.
http://uit.tufts.edu/at/
⏏
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Research Technology Services
“It is hard to use a servicewhen one does not even know
it exists !”
Research Technology Services
• Research High Performance Computing (HPC)• Research Storage• Software Licensing• Tools for Visualization• Tools for Communication/Collaboration• Statistical Consulting• Technology Consultation/Planning• Monitoring Emerging Technologies
Research Scientific Computing (1)
• High Performance Computing (HPC) consists in connecting a set of computers together via a high-speed network to provide a single, shared resource.
http://go.tufts.edu/cluster
Research Scientific Computing (2)
• Tufts new UIT Research Cluster went to production on September 15, 2008.
• Tufts UIT Research Cluster is a brand new IBM Blade Center with 40 identical Linux systems (or “compute nodes”) for 320 CPUs interconnected via a high-speed Infiniband network.
• Faculty have access to IBM expertise in High-Performance Computing to help them with their computing needs.
http://go.tufts.edu/cluster
Research Scientific Computing (3)
• Tufts UIT Research Cluster can be used to do “batch” processing via LSF job scheduler and queue management.
• Tufts UIT Research Cluster has also access to ample storage resources (/cluster/home, /scratch, /cluster/shared).
• Available Software: Abaqus, Ansys, Comsol, Deform, Fluent, C, Fortran compilers (Intel, Portland and GNU), Maple, Materials Studio, Matlab, Mathematica, R, Stata.
• Website: http://go.tufts.edu/cluster
http://go.tufts.edu/cluster
Research Scientific Computing (4)
• Physics and Astronomy: simulation of string networks to investigate string theory.
• Mechanical Engineering: simulation of material properties involved in cochlear hydrodynamics.
• Chemical and Biological Engineering: simulation of blood flow in the kidney.
• Mathematics: Fluid dynamics and partial differential equations.
• High-Energy Particle Physics: Analysis of Atlas experiment data from the Large Hadron Collider at CERN. Other projects with Fermilab: Minos.
http://go.tufts.edu/cluster
Research Storage (1)• In addition to the storage available on P: and Q: network
drives, faculty may also request additional research storage space (e.g., Pr. Andrew Hoffman).
• Research storage provides storage resources dedicated to research projects that necessitate large amounts of data (e.g. chemistry, fMRI, particle physics, DNA sequencing, astronomy, …).
• April 2007: 20TB• April 2008: 40TB• Now: 53 TB• April 2009: 80TB
http://researchstorage.uit.tufts.edu/
Research Storage (2)
• With the help of your local support service (ITS, OIT), you can map a connection from your desktop to your research storage to share documents with students, colleagues, and Tufts-affiliated project participants .
• Do not forget that P:, Q: and R: drives are backed-up and that is where crucial data and documents should reside. We have a 1-year back-up cycle policy.
• Over the next years, UIT is dedicated to increase Research Storage as needs grow => 250 TB by end of FY012.
• Self-Serve Webform: http://researchstorage.uit.tufts.edu/
http://researchstorage.uit.tufts.edu/
Research Storage (3)
• Medford - Psychology: fMRI data• Medford - Physics: Particle Accelerator data• Medford - Biology: Soft Robots• Medford - Classics: Perseus Digital Library • Medford - Mathematics: Fluid dynamics, Fractals.• Boston: Spining Disc Confocal Microscopy• Boston - Microbiology: Structural Biology Analysis• Grafton - Clinic Sciences: Respiratory Physiology, Lung
Mechanics• Grafton - Clinic Sciences: Anesthesia
http://researchstorage.uit.tufts.edu/
Bioinformatics Server (1)
• Bioinformatics incorporates techniques from multiple disciplines to solve biological problems in areas that include applied mathematics, informatics, statistics, and computer science.
• Tufts UIT Bioinformatics Server consists of two Intel Quad-Core processors and 16 GBof memory.
Bioinformatics Server: Emboss (2)
• Tufts UIT Bioinformatics Server supports open-source research codes and EmBoss/wEmboss gene sequence analysis tools.
• EMBOSS is "The European Molecular Biology Open Software Suite". It is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
• Tufts UIT Bioinformatics Server is available to Tufts faculty, students and staff engaged in research activities requiring analysis of biological research data.
• Website: http://emboss.uit.tufts.edu/
http://emboss.uit.tufts.edu/
Bioinformatics Server: CarmaWeb (3)• In collaboration with Tufts Medical School, UIT has
launched on October 14, 2008 a new webservice for micro-array analysis: CARMAWeb.
• CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays.
• The analysis includes normalization and data pre-processing, detection for differentially expressed genes, cluster analysis and GO analysis.
• All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages.
• Website: http://carmaweb.uit.tufts.edu
http:/carmaweb.uit.tufts.edu/
Software Licensing• Finite-element analysis: Abaqus, Ansys,
• Multiphysics: Comsol (multiphysics, acoustics, chemical engineering),
• Metal forming: Deform,
• Fluid dynamics: Fluent,
• Coding: C, Fortran compilers (Intel, Portland and GNU),
• Mechanical Engineering: Materials Studio,
• Math: Maple, Matlab, Mathematica.
• Statistics: R, Stata, Sigmaplot.
Statistical Consulting (1)
• UIT Academic Technology can help faculty and students address problems involving the:
– selection of appropriate statistical and mathematical procedures,
– modeling strategies for research designs, – research database management issues, – interpretation of results, – resolution of application error messages.
Statistical Consulting (2)
• UIT Academic Technology can also provide assistance for:– visualizing results, – implementing highly specialized procedures and software
tutorials/introductions for teaching assistants and instructors,– offer suggestions for the best use of a particular software package.
• For assistance, please contact UIT Teaching, Learning and Research: [email protected]
• Please also visit our UIT blog “Statistical Computing Matters”: http://blogs.uit.tufts.edu/statisticalcomputingmatters/
Statistical Consulting (3)
• Medford - Biology (Mike Reed)
• Medford - Child Development (Tama Leventhal)
• Boston - Nutrition (Robert Houser)
• Boston - Nutrition (Parke Wilde)
• Grafton - Centre for Conservation Medicine (Louise Maranda)
• Grafton - Harrington Oncology Program (Chieko Azuma)
Center for Scientific Visualization (1)• The EPDC center in Anderson Hall (Medford campus) was selected
as the location for the new Center for Scientific Visualization at Tufts. A key goal for the Center for Scientific Visualization is to integrate research and education by advancing discovery and understanding while at the same time promoting teaching, training, and learning at both the undergraduate and graduate levels.
• The Tufts Center for Scientific Visualization involves a high-resolution display wall; the display wall is 14' wide and 8' high
(12' deep), and it has far more pixels than conventional computer desktop displays, and far higher than conventional home “High Definition” TV displays: - Viswall resolution is 4096 x 2160, - HD TV (1080i) is 1960 x 1080.
http://sciviz.tufts.edu/
Center for Scientific Visualization (2)
• Stereoscopic vision is included, involving special glasses that separate the left-eye image from the right-eye image.
• The School of Engineering, the School of Arts & Sciences, and UIT collaborated together to provide funding for the construction and remodeling of the space that will house the Visualization Wall.
• Construction began in July and was
completed in December 2007.
Inauguration was on Feb 8, 2008.
• Website: http://sciviz.tufts.edu
http://sciviz.tufts.edu/
By providing Tufts research labs with Spark wiki spaces designed to support their research work and the sharing of their lab's findings, we hope to give research teams a set of tools to facilitate the processes of:– collaborative proposal
writing, – reporting to funding
agencies, – information-sharing both
among lab members and with a public audience.
Visit http://spark.uit.tufts.edu
SparkLabs project
• GIS Consultation & Specialized Services
• GIS Education & Outreach
• GIS Data Services
• GIS Computing & Technology Services
http://gis.tufts.edu
Geographical Information Services
Website: http://gis.tufts.edu
http://it.tufts.edu
•Pathways to Technology is a one-stop, searchable online resource guide supported by a database of information and links to everything related to technology on the Medford campus.
• The Pathways site does not replace any information that is already available on existing university websites, but instead provides a quick, user-friendly way of getting to that information.
•Pathways to Technology is a one-stop, searchable online resource guide supported by a database of information and links to everything related to technology on the Medford campus.
• The Pathways site does not replace any information that is already available on existing university websites, but instead provides a quick, user-friendly way of getting to that information.
Pathways to Technology
Website: http://it.tufts.edu
• Jointly sponsored by UIT and the IT Committee in Arts & Sciences and Engineering
• Creating a robust conduit of communication for sharing information about UIT services and for learning about departmental technology goals
http://go.tufts.edu/itliaison/
Faculty IT Liaison Program
Website: http://go.tufts.edu/itliaison
Contact Info
Lionel ZupanAssociate Director for Research Technology16 Dearborn Rd, Somerville MA [email protected]
