Codefest to focus on collaboration and results

Here’s a concept: a conference where people get real work done.

I’m not attempting to be snarky or to criticize the many worthwhile conferences offered to professionals every year; I’m simply paraphrasing a statement on the Open Science Codefest website. OSCodefest will bring together scientists and programmers involved in developing scientific software who think their work could benefit from collaboration with other researchers, software engineers and developers.

The conference will be held Sept. 2 – 4 in Santa Barbara, CA, and is sponsored by the Institute for Sustainable Earth and Environmental Software (ISEES) at UC Santa Barbara’s National Center for Ecological Analysis and Synthesis (NCEAS) with support from the Water Science Software Institute (WSSI) project led by RENCI. Both ISEES and WSSI are early-stage efforts to create institutes to sustain scientific software, funded by the National Science Foundation. The conference planners, including conference co-chair Chris Lenhardt, RENCI’s expert on environmental data science and systems, plan to build on their experience conducting hackathons, where programmers and scientists sit down face-to-face for several days and leave with a product: better software capable of making the process of scientific discovery less tedious and more productive.

This hands-on, unconference-style gathering is a chance to turn ideas into tangible results in real time. It draws on successful open source development models used in business and elsewhere, where developers are constantly taking input from the user community, refining and improving code, and introducing new versions that incorporate that feedback.

In addition to Lenhardt, RENCI’s presence will include the HydroShare team, led by Ray Idaszak, director of collaborative environments. HydroShare is an NSF-funded web-based system being developed to enable easy sharing of hydrologic data and models. When completed, HydroShare will allow scientists to retrieve data and models to their desktops, use grid and cloud-based computing resources from their desktops, and publish their research results (including raw data) to the system.

Among the Codefest activities, developers and scientists will focus on improving one of the key HydroShare software resources, the Regional Hydro-Ecologic Simulation System (RHESSys), a modeling framework that simulates carbon, water and nutrient fluxes. Co-developed by Larry Band, a Hydroshare co-PI and director of UNC-Chapel Hill’s Institute for the Environment, RHESSys seeks to understand the behavior of water at the watershed level and its impact on humans and natural and built environments.

Improving RHESSys during a three-day conference certainly qualifies as getting real work done—work that could have much broader impacts. So, roll up your sleeves Codefest participants, and good luck. This will not be your typical conference.

-Karen Green

In science, software matters

Outer Banks flooding from Hurricane Irene (2011). Modeling software used to understand high-impact events will benefit from software development best practices.

Outer Banks flooding from Hurricane Irene (2011). Modeling software used to understand high-impact events will benefit from software development best practices.

In the 21st century, it’s impossible to separate science from the software scientists use to collect data, run computer models and analyze model outputs.

Several RENCI experts make the case for sustainable software development practices in scientific research in two articles recently published in the Journal of Open Research Software.  In the first article, written by RENCI Senior Scientist and Oceanographer Brian Blanton and Chris Lenhardt, domain scientist for environmental data sciences and systems, the authors point out that developing scientific software that is sustainable, accessible, and transparent is especially important when policy decisions and public safety are at stake.

For example, climate models can inform policies about development and energy use, and models of hurricanes, storm surge and coastal flooding often help government officials make decisions about evacuations, search and rescue, road closures and more. It’s in the interest of scientists, policy makers and the general public to use modeling software developed by following best practices. And although today’s scientific software is better than ever in its ability to accurately model the natural environment and provide insights into problems, few guidelines exist to ensure that software is easy to use and sustained for the long haul.

Blanton and Lenhardt note that efforts such as the Water Science Software Institute (WSSI) led by RENCI, and the Institute for Sustainable Earth and Environmental Software (ISEES), led by National Center for Ecological Analysis and Synthesis at the University of California Santa Barbara, are leading the push to develop scientific software that is sustainable and reusable while meeting the research needs of scientists. Both WSSI and ISEES are funded through the National Science Foundation’s Software Infrastructure for Sustained Innovation (S2I2) program and both take inspiration from the NSF report  Cyberinfrastructure Framework for 21st Century Science and Engineering (CIF21).

Another article in the same journal makes a case for using well-documented and accepted data lifecycle management best practices as a blueprint for developing best practices for a scientific software development lifecycle. Linking the data management lifecycle, designed to ensure long-term data preservation and enable reuse and repurposing of research data, with a software development lifecycle in which software is continually tested and improved based on community input, is one path to achieving reproducible science, say the authors. In addition to Blanton and Lenhardt, authors of the article are RENCI Director Stan Ahalt, Ray Idaszak, who manages the WSSI effort, and Laura Christopherson, a senior research writer involved in the WSSI effort.

Both articles are interesting reads and illustrate the wide impact of scientific software. Both are also also included in a special collection published by the Journal of Open Research Software called Working towards Sustainable Software for Science: Practice and Experiences. Kudos to the scientists, developers, and funding agencies working to transfer open source software development best practices into the realm of scientific research. The benefits of this paradigm shift will be far reaching and long lasting.

Coming soon: A “Facebook for hydrologists”

After two years of work, HydroShare, a “Facebook for hydrologists,” will go live in July as an open source website. The HydroShare research team, which includes collaborators from RENCI, Brigham Young University, the University of South Carolina, Purdue University, Tufts University, the University of Texas at Austin, and the University of California at San Diego, received a $4.5 million grant from the National Science Foundation in July 2012 for this project.

HydroShare will give hydrologists the technology infrastructure they need to address critical issues related to water quality, accessibility, and management. The open website will be similar to YouTube in that it will allow users to simply drag and drop their models and data to upload to the site, and similar to Amazon, with a message board and rating system. It will provide an online collaborative environment for discovering, accessing and sharing water science research.

Ray Idaszak, collaborative environments director at RENCI and one of the project leaders, said the team plans to announce the first production release of HydroShare at the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Biennial Colloquium, to be held July 28-30 at the National Conservation Training Center in Shepherdstown, WV. CUAHSI is a nonprofit research organization representing more than 110 U.S. universities and international research organizations that work to advance water science research.

The project’s lead Principal Investigator (PI), David Tarboton of Utah State University, will also attend the Colloquium, as will RENCI’s Jeff Heard, the lead architect of the Hydroshare website.

“Scientific problems related to water—how to maintain quality, manage scarce water resources, and ensure accessibility—are fundamental to the health of our planet and its societies,” said Idaszak. “Hydroshare will help water scientists share and publish their data and make it easier for them to collaborate and address these critical challenges.”

Yes, social media bombards us with a lot of trivial information every day (cutest baby animal photo of the day, anyone?). But HydroShare proves that Facebook-like functionality can also help scientists solve crucial environmental problems.

Big data innovation explodes at RENCI

Claire McPherson of Deloitte closes out a great Innovation Summit.
Claire McPherson of Deloitte closes out a great Innovation Summit.

 

The creative vibes were buzzing at the First NCDS Data Innovation Showcase, held at RENCI on Wednesday, May 21, 2014. The Showcase, centered around innovative strategies for the rapidly-expanding big data field, brought together NCDS members, faculty and students to share data-related projects, activities and ideas.

The Showcase began with a student poster session during breakfast, where students from NCDS academic institutions showcased their submitted posters on data-related projects and networked with industry and university professionals. The group then gathered to hear short presentations from each of the NCDS Data Science Faculty Fellows on the background, goals, and intended results of their research.

More presentations followed, as researchers and leaders from NCDS member institutions, including RTI, SAS Institute Inc., Deloitte, Cisco and GE, gave brief talks about innovative data technologies, novel approaches to data challenges, and useful lessons about integrating the emerging field of big data into their businesses. Faculty members from NCDS member universities, such as the University of North Carolina at Chapel Hill and Duke University, also spoke.

During lunch there was another student poster session and in the afternoon, the five top student posters, as selected by an NCDS committee, gave short presentations on their research. This was a great opportunity for undergraduate and graduate students to expand their own networks and receive feedback from real-life successful industry professionals.

The event showcased the true mission of the NCDS: to explore and generate important dialogues about the future of big data and connect a variety of people at different levels in the field.

See more photos of the event here.

Girl Power in the Programming World

Though their numbers are expanding, women are still the minority in the computer development and website coding community, which remains about 90 percent male. A group of women in the Triangle, Girl Develop It (GDI), formed to provide a comfortable environment where women can learn about coding, website development and new technology and strategies at their own pace. As an institution that believes in diversifying STEM career fields and fully supports broadening the coding community, RENCI recently opened its doors to GDI to provide a space to host its “Python for Beginners” course.

The course, held at RENCI’s Europa Center headquarters on Saturday, April 26, consisted of an all-day workshop on Python, a software program that powers some of the most popular websites and apps, including Pinterest and Instagram. It can be used to build websites, program robots, visualize data and run servers.

The workshop was offered to women and girls with very limited or no programming experience and allowed them to explore functions, built-in data types such as lists and dictionaries, and utilize Python to tackle real problems. The course began with basic concepts such as “what is programming?,” variables and arithmetic, and statements and error messages. By the end of the class, the women were able to create a simple interactive game using Python software.

The class was taught by Caleb Smith, a Python expert at the Carrboro-based website development group Caktus Group Consulting, LLC.

Check out the GDI group or sign up for an event or class here.

Creating the universe in a Social Computing Room

photoStudents in a communications class at UNC Chapel Hill have been using the recently opened Social Computing Room (SCR) in the Odum Institute to create their own universe.

The SCR provides an immersive 360-degree view of any visual content, allowing users to interact with and explore data in groups. The original SCR, built in 2007, is located in the RENCI space in ITS Manning on the UNC campus. Similar versions based off the original have recently opened at NC State University and in Odum’s offices in Davis Library. RENCI assisted in the technical design and implementation of the room, helping to install all the hardware, baseline operating system, and projectors and supported part of the cost of outfitting the room.

Since the Odum SCR is so new, this project was one of the first chances for students and faculty to test the room’s capabilities. The students in the project-based research class Communications 566, Media and Performance, were divided into teams and given nine days to execute some type of mixed live and digital performance using the SCR.

Each team came up with very different performance methods including dance, acting, music, and even puppetry.

One team was able to showcase their final product to an audience that included RENCI staff, some of whom helped design and implement the SCR space.

Juniors Trevor Phillips, Elliot Darrow, and Kevin Spellman, and senior Ben Elling used their knowledge of dramatic arts, music composition, technical software and information science to create a performance piece that acted out the creation of the universe. Three walls of the SCR served as an interactive stage that the performers could touch, play with, and eventually turn into a panorama of the stars and galaxies in space, all to an original soundtrack of orchestral music.

Spellman, a dramatic arts and information science double major, explained how the team came up with the idea for the project.

“The two main things that we had to consider with this project were the functionality and limitations of the space and the music,” Spellman said. “We were all just shooting off ideas about what would be really cool to do in a space like this that truly could only be done in a space like this. This vision of something as great as space—it literally turned out to be space—was something we wanted to do from the very beginning.”

Spellman said they also thought about the small size of the room, and how that would impact the audience experience.

“[The SCR] is very up close and the audience is right here. So there was this tactile experience that we thought of: What would happen if we created this virtual, tactile experience with the performers touching the wall and the media reacting with touch?

Spellman did much of the programming for the digital portion of the piece, while Philips provided the self-composed music and Darrow and Elling acted as the performers.

Joseph Megel, a visiting artist with the UNC Chapel Hill department of communication studies and one of the professors teaching the course, said he plans to utilize the SCR space with classes in the future.

Hacking for the public good

It’s one thing to say that the explosion of digital data can be used for public good. It’s quite another to sit down in a room for four hours, access open data files and create an application with practical uses.

Terra-Hub-1-500x270

View of the Wake County Parks Finder app created using the TerraHub platform.

That’s what Jeff Heard did when he attended the Triangle Open Data Day (TODD) a few weeks ago. TODD, organized by TechnologyTank.org, was a daylong event to promote open data—the idea that digital information from sources such as government agencies should be easy to access and that if it is, smart, innovative techies will use it in interesting ways.

Heard, a RENCI senior research software developer and co-founder of the startup TerraHub, is one such smart, innovative techie. He attended TODD’s hackathon activity with the goal of taking a public data set and creating an application that could transform that raw data into useful knowledge.  And he succeeded.

Heard grabbed data on Wake County parks and recreation facilities and loaded it into the TerraHub software framework that allows users to create, share, and interact with geo-referenced documents, including layers of maps and data associated with locations on the maps. In one sitting, he built a “parks finder” mobile application.

The app allows users to search for parks based on the amenities they offer. For example, if you want to entertain the kids for an afternoon, you might look for a park that offers a playground, restrooms, and picnic tables.

Heard’s work was recognized as a TODD success story. It’s also a RENCI success story by extension because TerraHub grew out of a RENCI effort to create a geoanalytics platform—essentially a system for working with geo-referenced data in an intuitive, map-based format.

Congratulations to all those who participated in TODD and to the open data movement, which shows us that the big data revolution isn’t all about loss of privacy and information overload. In good hands, hacking the vast stores of open data can benefit us all.

-Karen Green

The Human Impact of Genetic Research

Jim Evans

Jim Evans of the UNC School of Medicine leads the NCGENES research team.

It’s been about a year and a half since I sat down with Jim Evans, MD, PhD, and Bryson Professor of Genetics and Medicine at the UNC School of Medicine, to learn about NCGENES, a research project to develop processes and a supporting cyberinfrastructure that will allow researchers, clinicians and patients to take full advantage of whole genome and whole exome sequencing. The project is funded by the National Human Genome Research Institute, one of the National Institutes of Health.

The patients enrolled in NCGENES – about 750 of them over four years – have undiagnosed conditions that likely have genetic causes. Through sequencing and an innovative, streamlined analysis process, the researchers hope to find genetic markers for their conditions, make diagnoses, and if possible, treat them.

Elizabeth Davis was one such patient, and her remarkable story illustrates the impact that routine genome and exome analysis can have on ordinary people. According to a story in Cosmopolitan, Davis’ undiagnosed condition had limited her ability to walk for 30 years and confined her to a wheelchair in recent years. After having her genome sequenced as an NCGENES participant, researchers determined she suffered from dopa responsive dystonia, a condition caused by a mutation that leaves the body unable to produce the chemical dopa and the nervous system unable to function properly. The condition is easily treatable with medication, and today, 11 months after her diagnosis, Davis has shed wheelchair and crutches and walks on her own. She is also now free of painful and debilitating leg spasms that had occurred daily for the prior 30 years.

According to Dr. Evans, RENCI plays an “indispensible and fundamental” role in the NCGENES project, developing the technical infrastructure that tracks, categorizes, and helps to analyze genetic material as it makes its way through multiple laboratories. Congratulations to Jim Evans, Co-PI Jonathan Berg of the UNC School of Medicine, the NCGENES team at RENCI (Kirk Wilhelmsen, also with the UNC School of Medicine, Chris Bizon, Dan Gillis, Phil Owen, Jason Reilly, Charles Schmitt, Erik Scott, and Dylan Young) and, of course, to Elizabeth Davis.

Perhaps this is a glimpse at how genetic research can revolutionize medical diagnostics and healthcare in the years to come.

To read the Cosmopolitan story, click here. To read the RENCI story on NCGENES, click here.

-Karen Green

TEDxUNC flies high with new ideas

Chancellor Carol L. Folt talks with a student during a TEDxUNC breakout session. (Courtesy of Connelly Crowe, TEDxUNC.)

Chancellor Carol L. Folt talks with a student during a TEDxUNC breakout session. (Courtesy of Connelly Crowe, TEDxUNC.)

It’s been more than a week since the successful conclusion of TEDxUNC 2014, our local version of a TED conference. The event took place Saturday, Feb, 15, only a few days after a winter storm, which closed the university for the previous two and half days and kept most people hunkered down at home.

Despite flight delays and cancellations, all 20 speakers and performers made it to Chapel Hill to perform to a packed house. Another 1,800 viewers from 10 countries watched the events using the conference’s live stream.

TED launched in California a couple decades ago as a way to inspire and motivate people by spreading the most innovative, potentially world changing ideas. Since then, TED events have spread around the U.S. and the world through the TEDx initiative, and this year’s TEDxUNC was the third annual event held at UNC Chapel Hill.

Congratulations to the students, speakers, performers and sponsors who thumbed their noses at a little bad weather and orchestrated a day full of thought provoking ideas and inspiring performances. RENCI is proud to have pitched in as a sponsor.

For a recap of the day’s events, click here. For a recording of the live stream, visit the TEDxUNC website.

RENCI Sponsors TEDxUNC Conference

RENCI is serving as one of the sponsors of the Third TEDxUNC 2014 conference, an annual conference at UNC-Chapel Hill that brings together innovative thinkers from the university, community and state to explore ideas for the future. This year’s conference will be held at Memorial Hall from February 15-25 and the theme will be “Taking Flight”.

This year’s diverse group of speakers includes an astronaut, a beekeeper, social innovators, and several artists including an opera singer, a multimedia artist, and a composer. There will also be two UNC students speaking, who earned this prestigious honor after going through several rounds of a rigorous public speaking competition.

These thinkers will discuss their approaches to some of humanity’s fundamental concerns by explore varied disciplines, transgressing cultural boundaries, and seeking simple, tangible solutions. The conference is always a completely free event, and tickets were all taken by the day after they were released. You can also view the talks via live stream or after the event through online video recordings. For more information, see the conference website.