Research Triangle Analysts at RENCI: Topological Data Analysis

Research Triangle Analysts met at RENCI for their first monthly meeting of the new year on January 19. Research Triangle Analysts meet at RENCI every third month and elsewhere around the Triangle during other months. The group, a 501(c)(3) non-profit and all-volunteer organization, promotes the advancement of data science throughout the Triangle’s collaborative communities of analysts, mathematicians, statisticians, and scientists.

Research Triangle Analysts participants learn about topological data analysis at RENCI.

Research Triangle Analysts participants learn about topological data analysis at RENCI.

Hamza Ghadyali, a PhD candidate in mathematics at Duke University, featured as the speaker for the meeting. Ghadyali develops new topological data analysts (TDA) tools, particularly for the analysis of electroencephalogram (EEG) data. Topology is the mathematical study of shape. TDA tools analyze large, noisy, complex datasets from disciplines such as, but not limited to, oncology, astronomy, meteorology, and neuroscience. Analysis of the shapes and changes in shape represented by data yield information about the data.

Ghadyali outlined the topological methods of homology which describes shapes by their holes. By representing data as graphs, networks of nodes connected by edges, the homology of data emerges. Ghadyali described building a higher-dimensional generalization of a graph known as a simplicial complex. By building a family of simplicial complexes called a filtration, the data can be examined at multiple scales. Tracking how the homology of the simplicial complexes changes across multiple scales, that is, quantifying how holes persist over multiple scales, identifies a phenomenon known as persistent homology. Ghadyali also detailed one method of constructing a filtration, known as a Morse filtration, as a particular way of building the family of simplicial complexes from a function or a signal such as an EEG time series.

Hamza Ghadyali presents topological data analysis to the Research Triangle Analysts meeting at RENCI.

Hamza Ghadyali presents topological data analysis to the Research Triangle Analysts meeting at RENCI.

EEGs are signals obtained from electrodes placed on the brain measuring electrical activity. Epilepsy is characterized by abnormal electrical activity. Ghadyali’s research creates and adapts TDA methods to understand EEGs of epileptic patients. His work characterizes epileptic abnormalities using topological signatures and also uses machine learning to build seizure detection and localization algorithms. Machine learning in the form of supervised learning plays a role in the discovery of the seizure detection algorithms by automatically identifying which topological features are most relevant to characterizing seizures.

View video of Ghadyali’s talk here as well as the illustrations in his presentation here.

-Chris Calloway

Crossing the pond in the name of better data management

iRODS Chief Technologist Jason Coposky offers guidance to iRODS users at the University of Utrecht.

iRODS Chief Technologist Jason Coposky offers guidance to iRODS users at the University of Utrecht.

The iRODS data management platform and the iRODS Consortium that works to sustain it are making waves well beyond their home base in Chapel Hill, NC.

This week, three of the smart, savvy people behind iRODS and the Consortium (iRODS originator Reagan Moore, Consortium Executive Director Dan Bedard, and Chief Technologist Jason Coposky) traveled to France, the United Kingdom, and the Netherlands to talk about the benefits of iRODS as a data management solution for large distributed research projects, to provide training for those interested in becoming iRODS power users, and generally to evangelize about software that is now being used far and wide in Europe, the U.S., Asia, South America, Australia, and South Africa.  Read more…

Coffee and Viz series brings teaching in a Social Computing Room to life

Professors at NC State University and UNC-Chapel Hill have access to a tool that can bring both excitement and exploration into their curriculum – the Social Computing Room (SCR). While the resource is available on both campuses, educators can be unsure about how it effectively fits into their course plans.

NC State’s Coffee and Viz series hopes to provide ideas for instructors of all disciplines by highlighting those already using SCRs and other visualization spaces and by providing speakers with novel ideas for the use of visualization in education and research.

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DataNet presentations lead to invigorating discussion at ESA annual meeting

ESAlogoDataNet Tools and Services was the topic of a session at the recent Ecological Society of
America Annual Meeting, held last month in Baltimore.

Chris Lenhardt and Mike Conway presented in the session representing the UNC Chapel Hill-based DataNet Federation Consortium (DFC). Chris is lead of the DFC Facilities and Operations team and is active in RENCI’s environmental sciences group; Mike is a senior developer with DFC.

Organized by Amber Budden of the DataONE DataNet project, the session used the IGNITE format: a series of 5-minute, 20-slide talks followed by Q & A. The fast-paced IGNITE talks present forward-looking, unconventional, and/or controversial ideas to spur the audience into questioning their usual assumptions and thinking creatively about the topic. Both of the DFC IGNITE talks challenged the audience to consider how a data management system can provide tools and services for scientists that go beyond simply storing, indexing discovering, and accessing data files. Read more…

Three keys to work-life balance

Last week, I was asked to speak to young professionals about work-life balance, so I have been pondering this topic a lot. How do you juggle both a full-time, demanding and exacting career and the often-contradictory demands of raising little human beings to become productive members of society? To be honest, I think the “secret” is that all of us are just winging it, really, and we are creating and maintaining balance as we go – even if it doesn’t appear that way to others from the outside. Parenting and careers are all about change. Just when you think you have achieved the perfect balance, something changes – your child starts potty training, enters puberty, adjusts to a new school, or gets chosen for a school team. You earn a promotion and gain new responsibilities, move offices (which affects your commute), or start a new job. Your spouse has to travel more or has a change in health condition. Older family members need care and help in a way they haven’t before.

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Software to accelerate science

In three years, the WSSI shows that software best practices can make a difference in water science.

Ask any elementary school student and they will tell you that water is a renewable resource.

Unfortunately, this “fact” comes with a few complications, like the truth that if we are not careful stewards of our water, it will run out. According to the United Nations Department of Economic and Social Affairs (UNDESA), “more than 1.7 billion people live in river basins where depletion through use exceeds natural recharge.”

This trend could see two-thirds of the world’s population living in water-stressed countries by 2025.

Understanding and sustaining water resources depends on using the best scientific modeling and software development practices, which is why RENCI has been part of the Water Science Software Institute (WSSI) planning grant for the past three years.   Read more…

Collaborations in coastal resilience

New funding for DHS Center of Excellence means continued collaboration with RENCI on coastal issues

The U.S. Department of Homeland Security (DHS) recently announced it will provide $20 million over five years to fund the Coastal Resilience Center of Excellence (COE) at UNC-Chapel Hill. That’s a good thing for people in coastal areas who each year must cope with hurricanes, erosion, flooding, and storm surge.

Aftermath of Hurricane Sandy. RENCI and the DHS Coastal Resilience Center work together to improve hurricane storm surge prediction.

Aftermath of Hurricane Sandy. RENCI and the DHS Coastal Resilience Center work together to improve hurricane storm surge prediction.

The new grant acknowledges the effectiveness of a longtime partnership between the Coastal Resilience COE (formerly the Coastal Hazards Center of Excellence) and RENCI. For more than five years, Brian Blanton, RENCI’s director of environmental programs and a coastal oceanographer, has worked closely with Rick Luettich, lead investigator for the Coastal Resilience COE and director of UNC’s Institute of Marine Sciences, to enhance the ADCIRC storm surge modeling system and put it to use as a tool to help coastal communities understand, predict, and mitigate the impacts of coastal storms.

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Webinar to put the spotlight on metadata

Need your data to remain useful and discoverable over its entire lifespan? Metadata is the key.

metadata-loveMetadata—or data about data—and its importance in life sciences research will be the discussion topic at an upcoming webinar featuring RENCI’s Dan Bedard, Interim Executive Director of the iRODS Consortium, Stephen Worth, director of Global New Business Development Operations at EMC, and Patrick Combes, Principal Life Sciences Solutions Architect in EMC’s Emerging Technologies Division.

The webinar—titled Expanding the Face of Metadata in Next Generation Sequencing—takes place Wednesday, May 13 at 2 p.m. and should offer insights for life sciences researchers, bioinformatics specialists, software developers, and IT and research computing experts. To register, click here.

Read more…

Pearl Hacks draws female coders from across the nation

“Every single one of you are makers.”

These words from Dona Sarkar kicked off UNC Chapel Hill’s recent Pearl Hacks event. Sarkar is an engineer manager at Microsoft, author, and fashion designer, and this past weekend she was in Chapel Hill inspiring an audience of over 600 high school and college-age women gathered to create through hacking.

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NC FIRST Robotics program grooms science and tech heroes of the future

There has been a growing buzz in the media about the importance of STEM (Science, Technology, Engineering, and Math) education and the struggle to ensure students receive enough of it in public schools. Part of the reason for this intense focus is that the U.S. Department of Labor expects there will be 1.2 million job openings in STEM related fields by 2018, but there won’t be enough qualified graduates to fill those jobs.

According to a Harris Interactive survey, many students who choose a math or science career interacted with a teacher or participated in a program that inspired them and helped launch their STEM career path. NC FIRST Robotics, which was created to help students acquire the knowledge and skills needed to compete in our technologically-driven society, is one such program.  Read more…

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