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.

The WSSI conceptualization, funded by the National Science Foundation (NSF), launched with the goal of developing a plan for a center that could transform the software and research cultures of the water science community.

Currently, research software code can be hard to use or incomplete, yet still be valuable to researchers. Graduate students, post-docs, and scientists write software to meet immediate needs, but there is often no formal and repeatable mechanism to ensure the software lives on once the money runs out or the original creator leaves the organization.

In addition, management and funding of research projects tends to remain separate, which often means different organizational silos address the same problem when they could be working on different problems and sharing their results and best practices.

These software and research issues in water science slow the march toward scientific progress and inhibit the ability to address the water crises. The aim of the NSF’s Software Infrastructure for Sustained Innovation (SI2) program, which funded the WSSI, is to create a software development infrastructure that easily scales from small research groups to large collaborations and results in sustainable, reusable software that will enhance productivity and accelerate innovation and discovery.

The WSSI team worked to accomplish this outcome by establishing the Open Community Engagement Process (OCEP), a model for scientific software development that accelerates scientific progress in water science by transforming the software development process and the research culture. The WSSI OCEP process makes progress by: 1) surveying the research community to determine the water science problems that are most dire; 2) training those working on the problems to create quality, sustainable code through established open source practices; and 3) ensuring that valued software and data elements are discoverable and interoperable across disparate projects, programs, centers, and communities.

To implement these best practices, the WSSI team, which includes researchers from RENCI, the Socio Environmental Synthesis Center (SESYNC) at the University of Maryland, and the University of Illinois, organized a series of collaborations and workshops.

  • Two hackathons helped to improve the functionality of the Regional Hydro-Ecological Simulation System (RHESSys), a hydroecological modeling framework designed to simulate the combination of water, carbon, and nutrient cycling among the soils and vegetation of a watershed. The work completed at these hackathons brought RHESSys closer to use by non-experts, an ultimate goal of sustainable software work.
  • The Open Science for Synthesis Workshop offered a bi-coastal training opportunity for early career scientists. The collaboration between UC Santa Barbara’s National Center for Ecological Analysis and Synthesis (NCEAS) and RENCI allowed scientists to work together for three weeks on several core water science and other environmental themes and to receive hands-on guided experience using best practices in the technical aspects that underlie successful open science and synthesis.
  • Most recently, the Open Science Codefest, also done in collaboration with NCEAS, brought together researchers from across the nation to collaborate in “unconference” style on creating more sustainable water science and other scientific software. Attendees from RENCI were able to bring their own water science ideas and concerns to the table and have the group work together to tackle those challenges.

“With the WSSI Open Community Engagement Process, we set out to show that water scientists can adopt sustainable software practices, which in turn will make them more productive scientists,” said Ray Idaszak, project manager for the WSSI and RENCI’s director of collaborative environments. “We’ve made progress in a short time and we believe that our actions and our lessons learned can serve as a blueprint for any discipline looking to improve software development practices.”

For the two-thirds of the world population that could suffer water stress in the next decade, mass adoption of these efficient practices can’t come soon enough.

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.

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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…

Finding common ground in the Social Computing Room

A delegation from Kyrgyzstan views biopsy slides in the RENCI Social Computing Room.

A delegation from Kyrgyzstan views biopsy slides in the RENCI Social Computing Room.

Science, like music, is an international language. No matter their cultural, ethnic, or religious backgrounds, no matter if they conduct fieldwork in the U.S. or run a lab in central Asia, scientists always seem able to find common ground.

It’s a fact all competent science communicators understand, and one I was reminded of when a delegation of science and technology professionals from Kyrgyzstan visited RENCI’s Social Computing Room (SCR) on the UNC-Chapel Hill campus on Feb. 12. The group, comprised primarily of women with backgrounds in mathematics, software engineering, and information science, journeyed half way around the world to participate in the Open World Program, a U.S. exchange program that supports and encourages current and future leaders in post-Soviet block countries.

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TriPython project nights bring community and innovation to RENCI after hours

The Triangle Python Users Group is a local organization that brings together experienced and new enthusiasts of Python, a widely used computer programming language. The group has been active in our area since 2002 but recently had a need for a new meeting space in the Chapel Hill area.

RENCI has opened its doors for a few of the group’s activities. Project nights are now held the second Wednesday of each month at RENCI. The informal project nights bring together new Python users seeking support and assistance with more experienced users. Together, they talk about their projects and potentially create cross collaboration.

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Creekside coders create and engage during “Hour of Code” event

Increasingly, every aspect of society – from education to healthcare – relies on software-driven technology. Even as we rely more often on “smart” devices for all aspects of our daily lives, we may not be producing enough computer scientists and software developers to satisfy our demand for all things tech.

Coding1

Creekside Elementary in Durham hopes students will catch the coding bug at a young age.

According to Code.org, by the year 2020, there will be 1.4 million computer science jobs but only 400,000 computer science students ready to enter the field. Additionally, according to the Computing Research Association, the computer science field suffers from an alarming gender and diversity gap that has not improved over the years – in 2010, less than 14 percent of US and Canadian computer science graduates were women, and only 10 percent were minorities.

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Computer modeling facilitates discussion of coastal hazards

RENCI’s Brian Blanton, PhD, recently gave a talk called “Simulating Storm Surge for Coastal Hazard and Risk Assessment” as part of a Disaster Resilience Symposium held at Virginia Tech.

The goal of the symposium was to facilitate interdisciplinary discussion and collaboration on efforts to reduce the ecological and socioeconomic risks of coastal hazards. Living on a coastline comes with a certain set of risks, and coastal resilience researchers study the most effective ways to ensure coastal communities have the ability to bounce back after events such as tropical cyclones and tsunamis, and the resulting flooding and inundation.

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High performance computing: It really does matter

Better models of coastal storm surge are among  the reasons that HPC matters.

Better models of coastal storm surge are among
the reasons that HPC matters.

Every November thousands of researchers and industry representatives in high performance computing and related fields, such as advanced networking, data storage, and analysis, meet for the annual supercomputing conference.

This year SC14 will bring together computer engineers, software developers, computational scientists, industry CTOs, grad students, and assorted geeks from around the world to New Orleans during the week of November 17. RENCI will be there, sharing information about the iRODS data management platform, the iRODS Consortium, ExoGENI and related projects on Networking Infrastructure as a Service (NIaaS), the National Consortium for Data Science, and other RENCI research projects. Read more…

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