Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
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.

Events on September 21, 2018

SCI Seminar
Carsten Burstedde

Carsten Burstedde, University of Bonn Presents:

Parallel Tree Partitions and their Role in Scalable Computing

September 21, 2018 at 12:00pm for 1hr
Evans Conference Room, WEB 3780
Warnock Engineering Building, 3rd floor.


In this talk, we illustrate a specific encoding of forest-of-octrees meshes that enables particularly elegant and highly scalable recursive algorithms for many common tasks. These algorithms solve local/near problems, which are often symmetric between sender and receiver processes, as well as non-local/far and asymmetric problems. Assembling the ghost layer of a mesh, for example, classifies as near since direct neighbor processes communicate. Reassigning moving objects between processes, on the other hand, links processes whose partitions may be far from each other in space, and a sender to some process does not necessarily receive from that process. Another prominent non-local/far problem arises in parallel visualization, when we match the subdomain of a data process with the subimage of a compositing process. We are inspired by large-scale applications and exemplify how the above algorithms translate into compelling parallel scalability.

Posted by: Nathan Galli

SCI Distinguished Lecture Series
Anna Michalak

Anna Michalak, Carnegie Science Presents:

Exploring climate impacts on inland and coastal water quality

September 21, 2018 at 2:00pm for 1hr
Evans Conference Room, WEB 3780
Warnock Engineering Building, 3rd floor.


Questions surrounding water sustainability, climate change, and extreme events are often framed around water quantity – whether too much or too little. The massive impacts of water quality impairments are equally compelling, however, and recent years have provided a host of compelling examples of unprecedented harmful algal blooms and hypoxic dead zones, including in Utah Lake. Linkages between climate change and water quality impacts are not well understood, however. Several factors explain this lack of understanding, including the relative complexity of underlying processes, the spatial and temporal scale mismatch between hydrologists and climatologists, and observational uncertainty leading to ambiguities in the historical record. Here, we draw on a number of recent studies that aim to quantitatively link meteorological variability and water quality impacts. Focusing on eutrophication, harmful algal blooms, and hypoxic dead zones, this talk will frame challenges and opportunities related to characterizing water quality, bridging from local to global scales, identifying key drivers, and understanding the role of climate. In each case, the availability of new scientific computing and visualization tools makes it possible to develop and test novel hypotheses about the role of climate and what the future may hold.

Dr. Anna M. Michalak is a faculty member in the Department of Global Ecology of the Carnegie Institution for Science and a Professor in the Department of Earth System Science at Stanford University. She holds a Ph.D. and M.S. in Civil and Environmental Engineering from Stanford University, and a B.Sc.(Eng.) in Environmental Engineering from the University of Guelph, Canada. Dr. Michalak studies the cycling and emissions of greenhouse gases at urban to global scales – scales directly relevant to informing climate and policy – primarily through the use of atmospheric observations. She also explores climate change impacts on freshwater and coastal water quality via influences on nutrient delivery to, and on conditions within, water bodies. Her approach is focused on the development of spatiotemporal statistical data fusion methods that optimize the use of limited in situ and satellite data. She is the lead author of the U.S. Carbon Cycle Science Plan, a former Editor of the journal Water Resources Research, and Chair of the scientific advisory board for the European Integrated Carbon Observation System. She is the recipient of the Presidential Early Career Award for Scientists and Engineers (nominated by NASA), the NSF CAREER award, and the Leopold Fellowship in environmental leadership.

Posted by: Nathan Galli