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Data Carpentry – Geospatial Analysis

Workshop dates: Thursday and Friday, March 26-27, 9 a.m. – 5 p.m.

Instructors: Erich Seamon and Travis Seaborn

Description: This hands-on workshop will focus on managing and understanding spatial data formats, understanding coordinate reference systems, and working with raster and vector data in R for analysis and visualization. An introductory knowledge to R is helpful, but not required. Participants will be encouraged to help one another and to apply what they have learned to their own research problems, and will be aimed towards graduate students and other researchers.

Attendees must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. More details can be found at https://erichseamon.github.io/2020-03-26-uidaho-geospatial

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Introduction to R for Reproducible Science

Workshop dates: Thursday and Friday, February 27-28, 9 a.m. – 5 p.m.

Instructors: Lihong  Zhao and Amanda Culley

Description: This introductory course will showcase reproducible research through simple analysis examples. The goal is to teach novice programmers to write modular code and best practices for using R for data analysis. This 2-day hands-on short course will give participants a strong foundation in the fundamentals of R, and to teach best practices for scientific computing: breaking down analyses into modular units, task automation, and encapsulation. Note that this workshop will focus on teaching basic programming in R, and will not teach statistical analysis. No prior knowledge of R or RStudio is needed. More details can be found at https://dearmint.github.io/2020-02-27-uidaho/.

Requirements:Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). Please ensure you have the latest version of R and RStudio installed on your machine.

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Software Carpentry: Unix, Git, and Python for Novices

Workshop dates: Thursday and Friday, January 30-31, 9 a.m. – 5 p.m.

Instructors: Amanda Stahlke, Breanna Sipley, Salvador (Chava) Castaneda Barba, and Clint Elg

Description: Software Carpentry  aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation in Unix, GitHub, and Python. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The course is aimed at graduate students and other researchers. You don’t need to have any previous knowledge of the tools that will be presented at the workshop.  Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. More details can be found at https://astahlke.github.io/2020-01-30-uidaho/.

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Dynamic Virtual Protein Project Wins International Award

Last week a University of Idaho team presented at the 25th VRST Symposium in Sydney, Australia, and won the Best Demo Award for their project “Dynamic Virtual Proteins: Visualization, Interaction and Collaboration in Virtual Reality.” In the world of virtual reality, the Symposium on Virtual Reality Software and Technology (VRST) is among the top ten virtual reality conferences in the world.

The Dynamic Virtual Proteins project team consists of Jean-Marc Gauthier, Virtual Technology and Design Associate Professor, Jagdish Suresh Patel, Department of Biological Sciences Research Assistant Professor, and Ian McGrath, 2019 graduate of the College of Art and Architecture. The interdisciplinary research is part of a $6 million EPSCoR Track-2 grant from NSF and supported by the Institute for Modeling Collaboration and Innovation (IMCI).

In addition to presenting at VRST 2019, the U of I team was one of six projects selected by Real Time Live, a world-wide, peer-reviewed event of SIGGRAPH Asia 2019. SIGGRRAPH is an annual conference and exhibition that attracts the most respected technical and creative people from all over the world to present cutting-edge projects on computer graphics and interactive techniques. The U of I team demonstrated their most recent project, the Virtual Protein Builder, in real time in front of an audience of more than 1200 people in Brisbane. The presentation showed the visualization of and interaction with two proteins in virtual reality. One of them, beta-lactamase, which provides resistance to antibiotics, was built in real-time in front of the live audience using virtual agents.

“The demo was very well received,” said Gauthier. “We made strong connections for future collaborations with research labs in New Zealand, Germany and Hong Kong. This was a wonderful opportunity to promote some of the research being done at the U of I.”

U of I’s newest institute is IMCI: Institute for Modeling Collaboration and Innovation

U of I’s newest institute is IMCI: Institute for Modeling Collaboration and Innovation

The Institute for Modeling Collaboration and Innovation (IMCI) is the university’s newest Level III Institute. Housed within the Office of Research and Economic Development (ORED), IMCI plays a pivotal role in advancing U of I’s strategic plan to be a leader in addressing large, complex problems.

Modeling improves research at every stage: making predictions, generating hypotheses, exploring scenarios, and guiding empirical work. It is a highly interactive process and often used when it is impossible or impractical to create experimental conditions in which scientists can directly measure outcomes.

A specific focus on modeling started on the U of I campus in 2015 with the Center for Modeling Complex Interactions (CMCI) – a five-year, $10.6M Center of Biomedical Research Excellence (COBRE) grant from the National Institutes of Health. Housed in the College of Science and supported by the COBRE grant, the center flourished.

The institute grew out of the center’s success. Now the organization is able to offer modeling support beyond the biomedical sciences. CMCI remains intact. It is the cornerstone grant and will continue advancing biomedical research and infrastructure under the institute’s supervision.

IMCI is the new face of the organization but most aspects of the unit remain the same.

Most importantly, IMCI continues to be a highly collaborative, service-based organization led by accomplished researchers: Holly Wichman, Director; Marty Ytreberg, Associate Director; Tanya Miura, Assistant Director; and Craig Miller, Modeling Core Director. It serves as a resource for any U of I researcher in need of modeling support, no matter which U of I college they are affiliated with. IMCI has systems and programs in place to guide and support interdisciplinary research at all levels.

For example, IMCI’s Modeling Core is a “brain core” populated by talented and collaborative postdoctoral fellows who provide modeling services to the community. Current modeling expertise spans molecular modeling, genomics, mathematical modeling, population genetics, machine learning, and geospatial modeling; and will soon include proficiency in statistical modeling.

Located on the third floor of the IRIC building, the institute’s staff also provides exceptional service to the IMCI community. This includes proposal submission, grant management, reporting, event management, communications support and financial processing.

Level III entities like IMCI are focal points for cross-disciplinary research at U of I and can draw on resources from multiple U of I units, external agencies and institutions. Sister U of I institutes under ORED’s supervision include the Aquaculture Research Institute (ARI), the Institute for Bioinformatics and Evolutionary Studies (IBEST), and the Idaho Water Resources Research Institute (IWRRI). Learn more about IMCI at www.imci.uidaho.edu or email imci@uidaho.edu to get involved.