Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2021


 C. R. Johnson. “Translational computer science at the scientific computing and imaging institute,” In Journal of Computational Science, Vol. 52, pp. 101217. 2021.
ISSN: 1877-7503
DOI: https://doi.org/10.1016/j.jocs.2020.101217

ABSTRACT

The Scientific Computing and Imaging (SCI) Institute at the University of Utah evolved from the SCI research group, started in 1994 by Professors Chris Johnson and Rob MacLeod. Over time, research centers funded by the National Institutes of Health, Department of Energy, and State of Utah significantly spurred growth, and SCI became a permanent interdisciplinary research institute in 2000. The SCI Institute is now home to more than 150 faculty, students, and staff. The history of the SCI Institute is underpinned by a culture of multidisciplinary, collaborative research, which led to its emergence as an internationally recognized leader in the development and use of visualization, scientific computing, and image analysis research to solve important problems in a broad range of domains in biomedicine, science, and engineering. A particular hallmark of SCI Institute research is the creation of open source software systems, including the SCIRun scientific problem-solving environment, Seg3D, ImageVis3D, Uintah, ViSUS, Nektar++, VisTrails, FluoRender, and FEBio. At this point, the SCI Institute has made more than 50 software packages broadly available to the scientific community under open-source licensing and supports them through web pages, documentation, and user groups. While the vast majority of academic research software is written and maintained by graduate students, the SCI Institute employs several professional software developers to help create, maintain, and document robust, tested, well-engineered open source software. The story of how and why we worked, and often struggled, to make professional software engineers an integral part of an academic research institute is crucial to the larger story of the SCI Institute’s success in translational computer science (TCS).

2015


 Note: VisTrails: A scientific workflow management system. Scientific Computing and Imaging Institute (SCI), Download from: http://www.vistrails.org, 2015.

2011


 J. Mandel, J.D. Beezley, A. Kochanski, V.Y. Kondratenko, L. Zhang, E. Anderson, J. Daniels II, C.T. Silva, C.R. Johnson. “A wildland fire modeling and visualization environment,” In Proceedings of the Ninth Symposium on Fire and Forest Meteorology, pp. (published online). 2011.

2010


 C. Silva, E. Anderson, E. Santos, J. Freire. “Using VisTrails and Provenance for Teaching Scientific Visualization,” In EUROGRAPHICS 2010 Educator Program, Note: Awarded Best Paper!, 2010.

2009


 T. Ellkvist, D. Koop, J. Freire, C.T. Silva, L. Stromback. “Using Mediation to Achieve Provenance Interoperability,” In Proceedings of the IEEE International Workshop on Scientific Workflows, 2009, pp. 291--298. 2009.
ISBN: 978-0-7695-3708-5

2008


 E.W. Anderson, J. Ahrens, K. Heitmann, S. Habib, C.T. Silva. “Provenance in Comparative Analysis: A Study in Cosmology,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 30--37. 2008.


A. Baptista, B. Howe, J. Freire, D. Maier, C.T. Silva. “Scientific Exploration in the Era of Ocean Observatories,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 53--58. 2008.


S.P. Callahan, J. Freire, C.E. Scheidegger, C.T. Silva, and H.T. Vo. “Towards a Provenance-Enabling ParaView,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 120--127. 2008.


S.B. Davidson, J. Freire. “Provenance and Scientific Workflows: Challenges and Opportunities,” In Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data, pp. 1345--1350. 2008.
ISBN: 978-1-60558-102-6


T. Ellkvist, D. Koop, E.W. Anderson, J. Freire, C.T. Silva. “Using Provenance to Support Real-Time Collaborative Design of Workflows,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 266--279. 2008.


T. Ellkvist, D. Koop, J. Freire, C.T. Silva, L. Stromback. “Using Mediation to Achieve Provenance Interoperability,” In Proceedings of the 2008 Fourth IEEE International Conference on eScience, pp. 398--399. 2008.


J. Freire, D. Koop, C.T. Silva. “Provenance for Computational Tasks: A Survey,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 11--21. 2008.


B. Howe, P. Lawson, R. Bellinger, J. Freire, E. Anderson, E. Santos, C.E. Scheidegger, A. Baptista, C.T. Silva. “End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory,” In Proceedings of the 2008 Fourth IEEE International Conference on eScience, pp. 127--134. 2008.


L. Lins, D. Koop, E.W. Anderson, S.P. Callahan, E. Santos, C.E. Scheidegger, J. Freire, C.T. Silva. “Examining Statistics of Workflow Evolution Provenance: A First Study,” In Proceedings of the 20th International Conference on Scientific and Statistical Database Management (SSDBM), pp. 573--579. 2008.
DOI: 10.1007/978-3-540-69497-7_40


L. Moreau, B. Ludäscher, I. Altintas, R. Barga, S. Bowers, S.P. Callahan, G. Chin Jr., B. Clifford, S. Cohen, S. Cohen-Boulakia, S. Davidson, E. Deelman, L. Digiampietri, I. Foster, J. Freire, J. Frew, J. Futrelle, T. Gibson, Y. Gil, C. Goble, J. Golbeck, P. Groth, D. A. Holland, S. Jiang, J. Kim, D. Koop, A. Krenek, T. McPhillips, G. Mehta, S. Miles, D. Metzger, S. Munroe, J. Myers, B. Plale, N. Podhorszki, V. Ratnakar, E. Santos, C.E. Scheidegger, K. Schuchardt, M. Seltzer, Y. L. Simmhan, C.T. Silva, P. Slaughter, E. Stephan, R. Stevens, D. Turi, H.T. Vo, M. Wilde, J. Zhao, Y. Zhao. “The First Provenance Challenge,” In Concurrency and Computation: Practice and Experience, Vol. 20, No. 5, pp. 409--418. April, 2008.


L. Moreau, J. Freire, J. Futrelle, R.E. McGrath, J. Myers, P. Paulson. “The Open Provenance Model: An Overview,” In Provenance and Annotation of Data and Processes, Lecture Notes in Computer Science (LNCS), pp. 323--326. 2008.
ISBN: 978-3-540-89964-8


E. Santos, L. Lins, J.P. Ahrens, J. Freire, C.T. Silva. “A First Study on Clustering Collections of Workflow Graphs,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 160--173. 2008.


C.E. Scheidegger, D. Koop, E. Santos, H.T. Vo, S.P. Callahan, J. Freire, C.T. Silva.. “Tackling the Provenance Challenge One Layer at a Time,” In Concurrency Computat.: Pract. Exper., Vol. 20, No. 5, pp. 473--483. 2008.


C.E. Scheidegger, H.T. Vo, D. Koop, J. Freire, C.T. Silva. “Querying and Re-Using Workflows with VisTrails,” In Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data, pp. 1251--1254. 2008.
DOI: 10.1145/1376616.1376747

2007


 E.W. Anderson, S.P. Callahan, D.A. Koop, E. Santos, C.E. Scheidegger, H.T. Vo, J. Freire, C.T. Silva. “VisTrails: Using Provenance to Streamline Data Exploration,” In Poster Proceedings of the International Workshop on Data Integration in the Life Sciences (DILS) 2007, Note: Poster presentation, 2007.