Research Technology Services Tufts Lionel H Zupan October

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/

Research Technology Services “It is hard to use a service when 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 GNU), Maple, Materials Studio, Matlab, Mathematica, R, Stata. • Website: 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, f. MRI, particle physics, DNA sequencing, astronomy, …). • • April 2007: 20 TB April 2008: 40 TB Now: 53 TB April 2009: 80 TB 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 FY 012. • Self-Serve Webform: http: //researchstorage. uit. tufts. edu/

Research Storage (3) • • Medford - Psychology: f. MRI 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 GB of memory.

Bioinformatics Server: Emboss (2) • Tufts UIT Bioinformatics Server supports open-source research codes and Em. Boss/w. Emboss 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/

Bioinformatics Server: Carma. Web (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 Gene. Chip, ABI microarrays and two color microarrays. • The analysis includes normalization and data preprocessing, 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 Bio. Conductor 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 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: uit-tlr@tufts. edu • 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 (1080 i) 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/

Spark. Labs project 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

Geographical Information Services • GIS Consultation & Specialized Services • GIS Education & Outreach • GIS Data Services • GIS Computing & Technology Services Website: http: //gis. tufts. edu

Pathways to Technology • 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. Website: http: //it. tufts. edu

Faculty IT Liaison Program • 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 Website: http: //go. tufts. edu/itliaison/

Contact Info Lionel Zupan Associate Director for Research Technology 16 Dearborn Rd, Somerville MA 02144 617 -627 -4933 lionel. zupan@tufts. edu