2014-15: ECOL: Developing, Maintaining, and Employing Large Computational Frameworks for the Ecological Sciences: April 13-17, 2015

Location

This workshop was held at SAMSI in Research Triangle Park, NC.

Description

Our ability to simulate and analyze large, complex ecological models is driven, in part, by our ability to construct and maintain computational tools capable of coupling appropriate physical models with accurate and efficient numerical algorithms. In addition, as data analysis and scientific visualization become increasingly more integral to successful ecological-based research, it is imperative for scientists in this discipline to have some fundamental skills in software programming and management to be successful in their work. However, development of fundamental software skills is often insufficient in and of itself to make these problems tractable. Ecosystem problems are true multi-scale and multi-physics problems, and as such ecological research teams require computational scientists as well as mathematical and statistical ecologists to fully utilize computational frameworks in understanding these systems.

Unfortunately, the demands on management of software infrastructure and development also grow significantly as the complexity of the problem and size of the research team increase. Often, models become dependent on several layers of underlying software developed by external groups that may or may not still be active. Maintaining these complex “software stacks” consisting of packages and libraries in multiple languages with multiple configuration and build systems can be non-trivial, particularly when several computational platforms must be supported. Beyond the software itself, managing the development process requires organization and sound software engineering practice. This is particularly imperative as the time frames under which these problems are studied now often span several enumerations of research teams.

In this workshop, participants will learn the basics of effective code construction and management. They will gain experience with software repository tools, which enhance the communication between members of a research team and allow archival of development benchmarks to ease the transition for new members of the development team. They will also learn the basics associated with incorporating third-party software, including building appropriate makefiles and ensuring seamless integration of sometimes conflicting environments. Finally, they will learn basic techniques for navigating between different platforms and developing regression tests for their development efforts.

The target audience will be researchers at the graduate level and beyond who are or will be actively developing code, using complex simulation tools, and/or processing complex data sets to further their efforts in large-system ecological research. Towards that end, the workshop is intended to bring together and foster collaborations between researchers in need of sophisticated simulation tools and those whose work focuses on developing these tools and making them accessible to the community. Each day will begin with a motivating lecture from a member of the computational ecology community. During the late afternoon of the first day, participants will be asked to participate in a round of lightning talks, where they will present their current research problems (in three minutes or less) to the audience. The objective of these lighting talks is to identify possible collaborative teams early as well as to identify needs of participants and adjust lecture content accordingly.

The first three days of the workshop will also consist of interactive tutorials led by instructors who actively work on development of simulation codes for large-scale, physics-based problems. Participants will spend time in break-out groups organized by topic, thus providing a forum for open discussion. The remaining two days will consist of break-out sessions where participants will work on development efforts of common interest. Note that the entire schedule of the workshop is geared towards bringing communities together to resolve complex problems; we expect teams to be coalescing all week, and that collaborations are initiated well before the final two days.

Questions: email eco@samsi.info


Schedule and Supporting Media

Participant List
Posters

Monday, April 13, 2015
at SAMSI

Time Description Speaker Slides Videos
8:00-8:30 Registration
8:30-8:45 Opening Remarks and Introduction Lea Jenkins, Clemson University
8:45-9:15 Verification and Validation of Numerical Models of Coastal Flows Chris Kees, USACE-ERDC pdf
9:15-9:45 Software installation
9:45-10:30 Basics of Shell Scripting David LeBauer, University of Illinois, Urbana/Champaign
10:30-11:00 Break
11:00-12:15 Basics of Shell Scripting David LeBauer, University of Illinois, Urbana/Champaign
12:15-1:30 Lunch
1:30-2:00 Writing, Sharing, and Reusing Scientific Code: An Update for 2015 Aron Ahmadia, USACE-ERDC pdf
2:00-3:15 Python Programming Chris Kees, USACE-ERDC
3:15-3:30 Break
3:30-4:45 Python Programming Chris Kees, USACE-ERDC
4:45-5:30 Lightning Talks
5:30-7:00 Poster Session and Reception
7:00 Shuttle departs

Tuesday, April 14, 2015
at SAMSI

Time Description Speaker Slides Videos
8:45-9:00 Registration and Announcements Lea Jenkins, Clemson University
9:00-9:30 Software for Ecological Inference and Prediction: What We Have and What We Need David LeBauer, University of Illinois, Urbana/Champaign
9:30-10:30 Git and GitHub Aron Ahmadia, USACE-ERDC
10:30-10:45 Break
10:45-12:00 Git and GitHub Aron Ahmadia, USACE-ERDC
12:00-1:30 Lunch
1:30-2:00 Matthew Farthing, USACE-ERDC
2:00-3:15 Topics in R Naupaka Zimmerman, University of Arizona
3:15-3:30 Break
3:30-4:45 Topics in R Kelly Hondula, SESYNC
5:00 Shuttle departs

Wednesday, April 15, 2015
at SAMSI

Time Description Speaker Slides Videos
8:45-9:00 Registration and Announcements Lea Jenkins, Clemson University
9:00-9:30 Computational Modeling of Ecological Species Laura Miller, UNC-Chapel Hill
9:30-10:30 Advanced topics in Python Matthew Farthing, USACE-ERDC
10:30-10:45 Break
10:45-12:00 Advanced topics in Python Matthew Farthing, USACE-ERDC
12:00-1:30 Lunch
1:30-2:15 Infrastructure Impacts on Species Movement and Distributions Andy Goodwin, ERDC Environmental Laboratory
2:15-3:00 Preliminary Collaborative Discussions – Room 150
3:00-3:30 Break
3:30-5:00 Collaborative Discussions – Room 150, Room 219
Advanced Topics in R – Room 203
5:00 Shuttle departs

Thursday, April 16, 2015
at SAMSI

Time Description Speaker Slides Videos
8:45-9:00 Registration and Announcements Lea Jenkins, Clemson University
9:00-10:00 Reports from Collaborative Discussions
10:00-10:30 Break
10:30-12:00 Collaborative Groups Session – Room 150, Room 219
Tutorial – The Predictive Ecosystem Analyzer – Room 203
12:00-1:30 Lunch
1:30-3:30 Collaborative Groups Session – Room 150, Room 219
3:30-3:45 Break
3:45-4:45 Reports from Collaborative Groups
5:00 Shuttle departs

Friday, April 17, 2015
at SAMSI

Time Description Speaker Slides Videos
8:45-9:00 Registration and Announcements Lea Jenkins, Clemson University
9:00-10:00 Wrap-up and Discussion on Future Research Collaborations
10:00-10:15 Break
10:15-12:00 Breakout for Collaborative Groups
12:00 Box Lunch and Adjourn