The 2025 cohort continued this tradition with three contributions that improve functionality and user experience.

2025 GSoC Projects​

Akash B V: Ensemble-based Uncertainty Propagation Workflows​

Akash developed ensemble-based data preparation workflows for soils, weather, and vegetation initial conditions. This work enables PEcAn’s ability to represent uncertainty in ecosystem models and directly supports applications in NASA CMS and California Air Resources Board (CARB) carbon monitoring efforts.

Read Akash’s report →

Aritra Dey: Interactive Quarto Notebooks for PEcAn Workflows​

Aritra created interactive Quarto notebooks that provide lightweight, reproducible introductions to PEcAn, replacing the previous introductory workflows that relied heavily on databases and the web User Interface. As more scientists become familiar with notebooks, these offer more flexible, direct, and extensible introductions to PEcAn workflows. These notebooks lower the barrier to entry for students and researchers, making it easier to run PEcAn models, explore uncertainty, and learn ecological forecasting through hands-on examples.

Read Aritra’s post →

Harsh Agrawal: Decoupling PEcAn Workflows from BETYdb​

Harsh addressed a long-standing architectural challenge by reducing PEcAn’s reliance on its central database. By decoupling key workflows from BETYdb, his work improves portability, simplifies development, and makes the system more accessible to new users and contributors.

Read Harsh’s post →

Beyond Software: Community and Mentorship​

GSoC projects reflect more than individual effort. They are the result of sustained mentorship, active code review, and an engaged open-source community. We thank the mentors and contributors who guided students, reviewed pull requests, and helped shape these projects into lasting improvements. And we thank Google for supporting open-source software and community development through GSoC.

We invite proposals for small grants to support activities that advance and promote PEcAn-related work.

Supported Activities​

The objective of this funding is to build and support the PEcAn community. A broad scope of activities could be supported. Examples include:

• Community Engagement: PEcAn-related swag or outreach activities that enhance community visibility and engagement.
• Workshops: Funding to help coordinate in-person PEcAn-related meetups.
• Conference Participation: Support for presenting PEcAn-related work at conferences.
• Publications: Assistance with publication costs for PEcAn-related papers.
• Other Uses: We are open to creative proposals that support the PEcAn community.

Expected Award Size​

All proposals will be considered contingent on available funds. We anticipate typical awards between $500-$3000 USD.

Eligibility​

• Open to all PEcAn community members.

Out of Scope / Excluded Activities​

• Activities that already have funding.
• PEcAn Software Development.
• Travel expenses for PEcAn workshops.

How to Apply​

Applicants are encouraged to discuss ideas with the community in the #pecan channel on Slack. Join PEcAn Slack here. Submit a brief proposal (1-2 pages) to pecanproj@gmail.com that includes:

1. Your Name & Affiliation
2. Description of Proposed Activity

• Scope of work
• Deliverables
• How it benefits the PEcAn community

3. Estimated Itemized Budget
4. Timeline (when funds will be used)

Submission​

Proposals will be reviewed on a rolling basis. Prior to formal submission, post ideas and ask questions on the #pecan Slack channel.

This year we had four exciting new projects:

1. Pratik Prakhale's project "Adopting Data Schema for Field Management Events" defined a JSON schema and integrated it into the FieldActivity R Shiny App. This JSON schema allows for more flexible and standardized data storage of field management events, and makes it easier to expand the FieldActivity App as well as build other robust applications that depend on the Schema. Pratik posted his final report as a a pull request to the Field Activity repository PecanProject/fieldactivity#79.

2. Abhinav Pandey's "Optimize PEcAn for freestanding use of single packages" project helped to make PEcAn packages more standalone and thus easier for use by the broader community. Many PEcAn R packages depend on each other and to a Postgres database. Abhinav's work refactored code to reduced these dependencies. Abinav posted about hhis "My GSOC experience: PEcAn Project" on DEV.

3. Sambhav Dixit: "Machine Learning Downscaling of PEcAn Outputs" used Convolutional Neural Networks to enable downscaling of ecosystem model output to high spatial resolution while retaining information contained in ensemble based uncertainty estimates. His final report "Linking Earth System Modeling and Machine Learning: My GSoC Journey with PEcAn" is on Medium.

4. Meet Agrawal worked on "PEcAn Code Hardening by Integration Tests", a project that enhanced the reliability of PEcAn's codebase by improving integration tests. His final report "GSoC 2024 : Final Report" is on Medium.

These projects helped advance PEcAn's code, provided valuable experiences to both mentees and mentors. We are grateful to the participants, mentors, and everyone in the PEcAn community who continue to make the project and our GSOC experiences a success.

What is Google Summer of Code?​

Google Summer of Code (GSoC) is a global program that pairs students with open source organizations to produce code and contribute to these communities while making some money. The whole idea behind this program is to encourage students to get involved in open source contributions.

As part of the program, organizations provide mentors to assist the student throughout the whole process, from learning about the community to contributing code

About PEcAn​

The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox that consists of a scientific workflow system to manage the immense amounts of publicly available environmental data and a Bayesian data assimilation system to synthesize this information within state-of-the-art ecosystems models. It has

• An application program interface (API) that encapsulates an ecosystem model and provides a standard interface, inputs, and outputs.

• Core utilities for handling and tracking model run and the flows of information and uncertainties into and out of models and analyses.

• An accessible web-based user interface and visualization tools.

• An extensible collection of modules to handle specific types of analyses (sensitivity, uncertainty, ensemble), model-data syntheses (benchmarking, parameter data assimilation, state data assimilation), and data processing (model inputs and data constraints).

If you want to contribute and know more about PEcAn Project, then do join the slack channel.

👉 Project Details:​

• Project Title: GitHub Actions

• Mentor: Rob Kooper

• Student: Rohan Sasne

• Organization: PEcAn Project

• Project Link: GitHub Gist

In this blog post, I’ll be discussing my journey of Google Summer of Code 2023 with PEcAn Project.

Pull Requests and Issues opened in the GSoC period​

All my technical contributions across all the repositories of the PEcAn project can be found below:

Google Summer of Code 2023 Work Product Submission

Student: Rohan Sasne (@RohanSasne)
Organisation: PEcAn Project
Project: GitHub Actions - Optimizing CI Pipeline and Utilizing the Whole Docker Stack for Testing

Brief Notes along with weekly progess and learnings can be found here

Overview of Work Done​

(Click on the title for link to PR)

The Project:

GitHub Actions is a powerful tool that enables developers to automate their workflows and streamline their software development process. Our project aimed and successfully achieved the following goals:

• Optimized package version checks in GitHub Actions to limit the number of checks.

• Utilized the full Docker stack for testing SIPNET.

• Created a test that runs tests using the develop stack and writes the results to a file in a special branch.

• Updated the dashboard to fetch data from the special branch and display the results.

Weekly Progress:​

Week 1

• Discussed with mentor the project goals

• Successfully created first PR and waiting for mentor/ community review

• Helped the community on slack to find article to solve a issue

Week 2

• CI time reduction PR finally merged, after a lot of reviews and feedback 🥳

• Also created another PR to fix a small documentation redirect bug in the readme

Week 3

• The PR for testing against the Docker stack using Docker-Compose is UP and in review, hopefully it’ll get merged by this weekend

• Created Another PR which was fixing the Documentation in DEV-INTRO.md and it got merged

• Created an Issue in the Repository for code cleanup to restrict trigger of workflows in certain less necessary cases

Week 4

• Created Pull request in the rpecanapi repository to add a API function which takes custom headers as inputs which was missing till now

• Created an Issue in the Repository for creating an extra function in API to pass on custom headers

• Opened a draft PR in the PEcAn status board repository

Week 5

• Created *an Issue in the Repository for reporting a bug in the POST API request of the rpecanapi repository*

Week 6 & 7

• Created a Pull Request optimizing the code in CI pipeline, thereby reducing the repeatability of code.

• Created an issue, elaborating discussion i had with one of the repository maintainer regarding setting up matrix to reduce the repeatability

• Created another Pull Request to clean the unnecessary extra condition to check the Pull request on only the main branch

Week 8 & 9

• Created an Issue in the Repository for Labeling the PR on the basis of type of changes it makes

• Created an Issue in the Repository for running the docker workflow only after the successful completion of the CI workflow

Week 10 & 11

• Created a PR to fix the Post API failure issue

• Created a PR to auto label the PR for better visual clarity in the repository and to keep track of the type of PR’s made in the long run

• Tested a false PR, to test why we hit the GitHub API rate limit :_

Week 12

• Completed the documentation part of my work submission to google :)

Wrapping Up​

Google Summer of Code is an excellent opportunity for students to work on a project that matters while also significantly improving their coding skills and teamwork abilities.

Working on this GSoC’23 project with PEcAn Project was an enjoyable experience. I want to express my gratitude to my mentor, **Rob Kooper** for his constant support and guidance throughout this program. Thank you so much! Working with you was a really fantastic experience, and I look forward to work with you on more open source projects in the future!

Finally, thanks to the GSoC program for providing this wonderful opportunity to work in such a great open source community, I was able to work on such a large real-world project, and I learned a lot throughout this program. I can confidently say that my coding abilities have improved over the ten weeks of GSoC.

The project aims at creating and deploying a user friendly, interactive and accessible website for PEcAn Project. PEcAn Project's website consisted of html pages, bookdown and pkgdown pages being rendered separately. In this project, all separate sections have been integrated as a consistent, modern website with elegant UI with the help of Docusaurus 2, a static site generator. This project has been created as a part of GSoC'21.

Useful Links​

• Github Repository- https://github.com/PecanProject/web
• Hosted Link- https://pecanproject.github.io/web/
• Documentation- https://github.com/PecanProject/web/blob/main/README.md

Preparations​

After my proposal was selected for the project I started interacting with the mentors and asked them about their expectation about design. I also studied the codebase of the existing website. Since I was familiar with ReactJs, I found it much better to have a static site generator for the project. I studied the official docusaurus docs and got familiar with its ecosystem. Using figma I prepared wireframes for the website. After the first GSoC meeting, I got valuable suggestions from the mentors, which were used to improvise the designs and development of the working model of website began.

Coding Period​

To develop the working model on the website it was required to keep in mind the best practices and modular design, so that changes could be made easily in the future. I have tried to maintain this approach. In this period following goals have been accomplished:

• Revamped the website and converted it into a ReactJs based single page application.
• Added a blog for posting blogs.
• Integrated PEcAn's documentation as part of the website.
• Automated build process of the website with the help of GitHub actions. This helps to deploy the website automatically to GitHub pages, as soon as changes are pushed.
• Documented steps for PEcAn team to add and modify content.

Challenges​

Since the documentation is maintained as bookdown specific Rmarkdown format, it is difficult to parse it using docusaurus's native parser, which supports markdown. The bookdown doesn't offer a native way of converting into md, with relative directory structure to reference different files. I tried converting each Rmd file into md, one by one using RStudio's built-in knit function, but it wasn't feasible. The only optimal solution seemed was temporarily editing MakeFile, but it couldn't achieve desired results. This is also the exact challenge with tutorials section.

Next Steps​

At present we have an iframe which helps us load the documentation inside the website, though it looks like a part of the website, it is the website which is being rendered by bookdown. It can be found on this repo- https://github.com/PecanProject/pecan-documentation. An example of how this is achieved is shown in below codeblock-

<Layout title="Develop" style={{ height: "100%" }}>
  <Foot>
    <body className="documentation"></body>
  </Foot>
  <iframe
    src="https://pecanproject.github.io/pecan-documentation/develop/"
    style={{ border: "none" }}
    width="100%"
    height="100%"
    allowFullScreen
    id="iFrame1"
  >
    <p>
      <a href="/en-US/docs/Glossary">
        Fallback link for browsers that don't support iframes
      </a>
    </p>
  </iframe>
</Layout>

The main issue is that if we had docs already natively on the repository, they would have been much faster to load and would have offered the users a much better experience. So it is essential and recommended to figure out a way for achieving this. Further priorities would be-

• Adding the tutorials section
• Adding a search bar that used scraping to find matches all across website.

Acknowledgements​

Finally, I'd like to say that this summer of 2021 has been the most amazing experience I've ever had. I learnt a lot of technical and non technical skills. Dlebauer and ImPrakher have been awesome mentors and their feedback and suggestions were a key to accomplishing the project.

The year featured conference presentations, invited talks, and another round of community-building through Google Summer of Code and related outreach.

Conferences and Presentations​

10th World Dendro Conference (June 2018)​

Anne Raiho attended the 10th World Dendro Conference and gave a talk on "Improving predictions of forest succession with data assimilation".

AMS 33rd Conference (May 2018)​

Ankur Desai gave a talk at the American Meteorological Society 33rd Conference on Agricultural and Forest Meteorology on "Bringing Forest Management into Earth System Models: Insights from Observations and Theory".

Drought-Net Steering Committee Meeting (May 2018)​

Elizabeth Cowdery gave a presentation on "The PEcAn Project: Tools for Ecosystem Model-Data Fusion" at the Drought-Net Steering Committee Meeting.

Graduate Student Talk at LBL (April 2018)​

Elizabeth Cowdery gave a presentation on "The New PEcAn Project Benchmarking System: Accessible Tools for On-demand Multi-Model Evaluation" at the Lawrence Berkeley Lab graduate student seminar.

NASA Biodiversity and Ecological Forecasting Team Meeting (April 2018)​

Alexey Shiklomanov gave a talk at the NASA Biodiversity and Ecological Forecasting Team Meeting in Washington D.C. titled: "Cutting out the middle man: Calibrating and validating an ecosystem model with remotely sensed surface reflectance".

qBio Seminar (April 2018)​

Ankur Desai gave a talk at the qBio seminar series at the University of Wisconsin - Madison titled, "Move over weatherperson: Can we actually forecast ecology?"

Google Summer of Code 2018 (March 2018)​

The PEcAn project was selected to participate in Google Summer of Code (GSoC) once again for 2018. We were excited to work with more great developers. The application period ran from March 12th-27th.

Key additions included new tools for data ingest, preliminary containerized modules, and early support for automated daily forecasting workflows.

Major additions include:​

• A data ingest SHINY app that allows users to upload and register data from their own local machine or from the DataOne
• Preliminary containerized modules of PEcAn using Docker
• Preliminary automated, Daily Forecasting using NOAA GEFS and the Sipnet model

The VM can be downloaded at https://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN (note: VM has been deprecated, so this link may no longer work).

This was a year of visible community engagement, from AGU and ESA events to training activities, student projects, and continued development of forecasting and data-assimilation workflows.

Major Events​

PEcAn AGU Workshop (December 2017)​

The PEcAn project held a two-part event at the 2017 AGU Fall meeting on Tuesday December 12th, 2017 from 4-7pm. The meeting included an open demonstration (4:00-5:30) followed by a focused science team collaborator meeting (5:30-7:00).

The event was held at the Hilton New Orleans Riverside, Third Floor - Parish Room.

The demonstration entailed a general overview of the project and breakout groups in which members of the PEcAn team led hands-on tutorials and took questions. The Science Team meeting focused on high-level development goals and user needs for the coming year.

PEcAn Team at AGU 2017 (December 11-15)​

The PEcAn Team presented multiple talks and posters at the 2017 American Geophysical Union (AGU) Conference:

Tuesday:

• Istem Fer: "Paleoclimate reconstruction through Bayesian data assimilation" (ORAL PP21D-06, 9:15 Room 343)
• Cristine Rollinson: "Impacts of weather versus climate and driver uncertainty on multi-centennial ecosystem model simulations" (ORAL Poster Hall D-F, 10:35 Room 343)
• Ann Raiho: "Estimating the ecology of extinct species with paleoecological data assimilation" (ORAL PP22A-05, 11:20 Room 343)
• Alexey Shiklomanov: "Leaf optical properties shed light on foliar trait variability at individual to global scales" (ORAL B22C-07, 11:50 Room 383-385)

Wednesday:

• Rob Kooper: "Data Flow for the TERRA-REF project" (POSTER IN31A-0063, 8:00 Poster Hall D-F)
• Michael Dietze: "Integration of Ecosystem Research Infrastructures for Multiscale Analysis II" (PANEL B31H-04, 8-10 am Rooms 383-385)
• Eugenie Euskirchen: "Predicting Changes in Arctic Tundra Vegetation: Towards an Understanding of Plant Trait Uncertainty" (Poster B31A-1979, 08:00-12:20 Poster Hall D-F)

Thursday:

• David LeBauer: "TERRA REF: Advancing phenomics with high resolution, open access sensor and genomics data" (ORAL, 10:40 Room 383-385)
• Tony Gardella: "A multi-model assessment of terrestrial biosphere model data needs" (ORAL, 2:25 Room 356-357)

Friday:

• Anne Thomas: "Assessing Ecosystem Model Performance in Semiarid Systems" (Poster B51G-1893, 8am Poster Hall D-F)
• Molly Aufforth: "Constraining Agricultural Irrigation Surface Energy Budget Feedbacks in Atmospheric Models" (Poster B53B-1953, 1:40 pm Poster Hall D-F)
• Betsy Cowdery: "Looking Past Primary Productivity: Benchmarking System Processes that Drive Ecosystem Level Responses in Models" (ORAL H54D-01, 4 pm Room 298-299)
• Shawn Serbin: "Evaluation of Multiple Mechanistic Hypotheses of Leaf Photosynthesis and Stomatal Conductance against Diurnal and Seasonal Data from Two Contrasting Panamanian Tropical Forests" (ORAL H54D-05, 5 pm Room 298-299)
• Tess McCabe: "Integrating invasive grasses into carbon cycle projections: Cogongrass spread in southern pine forests" (ORAL B54B-07, 5:30 pm Room 388-390)

Conferences and Meetings​

FIA Annual Meeting (October 2017)​

Istem attended the FIA Stakeholder Science Meeting in Park City, Utah, presenting work on assimilating demographical data into models and validating models against FIA data.

GSOC Mentor Summit (October 2017)​

Alexey and Betsy attended the Google Summer of Code Mentor Summit as a result of our project's successful participation in the GSoC Program.

COST-PROFOUND Final Conference (October 2017)​

Mike Dietze attended and presented at the 2017 Cost-Profound FP1304 Final Meeting. His presentation was about his "PROFOUND thoughts on Model-Data Integration & Forecasting".

PEcAn at ESA 2017 (August 2017)​

Many PEcAn and Dietze Lab members attended and presented at the Ecological Society of America's conference in Portland, Oregon.

PEcAn at Flux Course 2017 (July 2017)​

Mike Dietze, Ankur Desai, Betsy Cowdery, and James Simkins returned to teach at the Flux Course.

Summer Developers (May 2017)​

Shubham Agarwal​

Shubham graduated with an Integrated M.Tech in Mathematics and Computing'15 from IIT Delhi. He then worked as a Data Scientist for a year (2015-16) at TrulyMadly Matchmakers Pvt. Ltd. Shubham was enrolled in the one-year Masters (MSIAM) Data Science specialization program offered jointly by Université Grenoble Alpes and Grenoble INP, Grenoble, France, and worked on our GSoC project 'Scientific Workflows'.

Other Events​

PROFOUND Summer Course 2017​

The team participated in the PROFOUND Summer Course.

PEcAn Team at AAG​

Team members presented at the American Association of Geographers meeting.

PEcAn at NACP 2017​

The project had a presence at the North American Carbon Program meeting.

DIBBS NSF Meeting​

Team members participated in the DIBBS NSF meeting.

The release bundled updates across data ingest, Docker-based workflows, configuration editing, and meteorological processing to make the platform easier to operate and extend.

Added​

• PEcAn.utils::download.file() to allow for use of alternative FTP programs
• downloadAmeriflux and downloadNARR to make use of PEcAn.utils::download.file()
• -w flag to load.bety.sh script to specify the URL to fetch the data from
• New table sites_cultivars to betydb sync scripts (dump and load)
• Docker container scripts (.yml) to create docker container for PEcAn
• The configuration edit page to allow easy modification of config via web interface
• Thredds server documentation and catalog generating script

Changed​

• upscale_met now accepts ~any valid CF file (not just full years), retains correct time units, and respects the previously ignored overwrite parameter
• Better date handling in BioCro functions

Across the year, the project combined regular software releases with workshops, invited talks, and hands-on collaborations that broadened both the platform and its user community.

Releases and Major Updates​

PEcAn 1.4.7 Release (January 2017)​

This release included significant updates and improvements to the PEcAn platform.

PEcAn 1.4.6 Released (March 2016)​

This version brought various bug fixes and enhancements to the system.

PEcAn 1.4.5 Released (February 2016)​

Another incremental release with important improvements and bug fixes.

Workshops and Courses​

PEcAn at Flux Course (July 2016)​

The team returned to teach at the annual Flux Course, providing hands-on training in ecosystem modeling and data analysis.

PEcAn at Harvard Forest REU (July 2016)​

The team presented PEcAn to Research Experience for Undergraduates participants at Harvard Forest.

PEcAn Workshop May 2016​

A dedicated PEcAn workshop was held in May 2016 to train new users and gather feedback from the community.

Conferences and Presentations​

Ecological Forecasting book accepted! (June 2016)​

A major milestone - the ecological forecasting textbook was accepted for publication.

PEcAn at ESA Sustaining Biological Infrastructure Workshop (May 2016)​

The team participated in this important workshop focused on sustaining scientific infrastructure.

PEcAn at PROFOUND spring course (April 2016)​

Team members contributed to the PROFOUND spring training course.

PEcAn at ILAMB meeting (April 2016)​

The project was represented at the International Land Model Benchmarking (ILAMB) meeting.

PEcAn at NACP workshop (March 2016)​

Participation in the North American Carbon Program workshop.

PEcAn at the 2016 INTERFACE meeting (February 2016)​

The team presented at this statistical computing conference.

PEcAn at the ED Community meeting (January 2016)​

Engagement with the Ecosystem Demography (ED) model community.

PEcAn Presentation at NEON Workshop "Operationalizing Ecological Forecasting" (January 2016)​

An important presentation on how PEcAn enables operational ecological forecasting, aligning with NEON's goals.

The PEcAn 2 Terrestrial Model Informatics Workshop took place from May 9th-11th 2016 at Boston University.

The big picture of this workshop was to discuss how new and emerging tools and technologies can accelerate the pace of progress in ecosystem and land surface modeling and allow us to better respond to the needs of the community, policy makers, and the general public. This workshop specifically targeted the modeling community.

The goals of the meeting were to:

• Identify informatic, analysis, and cyberinfrastructure bottlenecks in the current workflows of the terrestrial ecosystem/land surface modeling community
• Identify redundancies and opportunities for interoperability of tools/methods
• Develop a roadmap for improving modeling cyberinfrastructure
• Provide training in PEcAn tools
• Present and solicit feedback on PEcAn development plan
• Identify bottlenecks in PEcAn usability/adoption

The full agenda of the workshop can be found here: link

The workshop will produce a paper outlining cyberinfrastructure bottelnecks, opportunities, and a roadmap. An updated PEcAn workplan will be produces as well.

To facilitate discussion, themes and subthemes were created to focus discussion (links lead to slides for each theme):

Big Picture

Cyber-infrastructure Foundations

Provenance, Standards, Repeatability, Accessibility, Sharing & Communication, Transparency, Support for clusters, cloud, etc., Portability

Data Ingest

Drivers, Constraints, Initial Conditions, Traits, Data uncertainty

Validation, Benchmarking & Visualization

Analysis

Model sensitivity, uncertainty, ensemble,etc.

Tools for analyzing specific data types

Calibration

Trait meta-analysis, parameter data assimilation

State Data Assimilation

Multi-model Synthesis

Adding Models

Growing the PEcAn community

Challenges with running multiple models, tools for MIPs

Thank you to everyone that attended. The PEcAn Team looks forward to working with you all!​

The year brought new team members, community-building efforts, and steady advances in releases, grants, and research applications across the PEcAn ecosystem.

Team Updates​

New PEcAn Project Manager (June 2015)​

The project welcomed a new Project Manager to help coordinate development and community engagement.

Workshops and Training​

Flux Course 2015 (July 2015)​

The PEcAn team returned to teach at the Niwot Ridge Flux Course, providing hands-on training in eddy covariance and ecosystem modeling.

PEcAn presentation for Harvard Forest REU's (June 2015)​

Mike Dietze presented to the Harvard Forest Research Experience for Undergraduates program.

Building Global Ecological Understanding Workshop (May 2015)​

Team participation in this important workshop on global ecology.

COST PROFOUND Spring School (April 2015)​

The team contributed to the COST PROFOUND training activities.

Conferences and Presentations​

PEcAn Team at AGU 2015 (December 2015)​

Multiple team members presented at the American Geophysical Union Fall Meeting with various talks and posters.

PEcAn at ESA Centennial (August 2015)​

The team had a significant presence at the Ecological Society of America's 100th anniversary meeting.

PEcAn at IALE 2015 (July 2015)​

Presentations at the International Association for Landscape Ecology conference.

PEcAn at NACP 2015 (January 2015)​

The PEcAn team had a large presence at the North American Carbon Program's 5th All Investigator's Meeting in Washington DC, January 26-29, 2015.

On Tuesday, Mike Dietze presented "The PEcAn Project: a scalable, multi-model platform for uncertainty quantification, analysis, and propagation" in the Uncertainty session. The team organized a hands-on PEcAn workshop at 7pm on Tuesday.

Poster presentations were given by Betsy Cowdery, Josh Mantooth, Afshin Pourmokhtarian, Christine Rollinson, and Alexey Shiklomanov.

Seminars and Invited Talks​

PEcAn talk at University of New Hampshire (March 2015)​

Mike Dietze gave an invited seminar at UNH.

PEcAn talk at Stony Brook University (February 2015)​

Another invited seminar showcasing the PEcAn project.

PEcAn at Montana State (January 2015)​

Presentation of PEcAn capabilities and applications.

Job Postings and Opportunities​

Now Hiring! PEcAn Project Manager (February 2015)​

The project advertised for a new Project Manager position.

Project Activities​

PEcAn at NASA Carbon Cycle & Ecosystems Joint Science Workshop (January 2015)​

Participation in this important NASA science workshop.

Brown Dog @ NSF HQ (January 2015)​

Presentation of the Brown Dog cyberinfrastructure project (related to PEcAn) at NSF headquarters.

PEcAn Allometries at Harvard Forest 2015 (January 2015)​

Work on allometric relationships for ecosystem modeling.

Grants and Funding​

Two DOE ARPA-E grants will support high throughput plant phenotyping (July 2015)​

Important funding announcements for related phenotyping research.

Publications and Media​

NCSA features PEcAn 1.4.3 in news (August 2015)​

The National Center for Supercomputing Applications featured the PEcAn 1.4.3 release in their news.

Help Build rOpensci interface to BETYdb and PEcAn (July 2015)​

Call for community contributions to develop R package interfaces.

Software Releases​

PEcAn 1.4.3 Released (July 2015)​

Major software release with new features and improvements.

It continued the project's emphasis on improving the reliability and usability of ecosystem modeling and data-assimilation workflows.

This release continues to improve the PEcAn platform's capabilities for ecosystem modeling and data assimilation. For detailed release notes and download information, please visit the PEcAn GitHub repository.

The project continued to grow through major conference activity, software development, publications, and related cyberinfrastructure efforts such as Brown Dog.

Major Conferences​

Presentations at AGU Fall Meeting 2014 (December 2014)​

The PEcAn team presented the following at the 2014 Fall meeting of the American Geophysical Union in San Francisco:

• B13C-0202 "The PEcAn Project: Accessible Tools for On-demand Ecosystem Modeling" (Poster)
• B13C-0192 "Constraining carbon budgets at a regional scale: fusing forest inventory data with a cohort-based biosphere model" (Poster)
• B13C-0198 "A Hierarchical Analysis of Tree Growth and Environmental Drivers Across Eastern US Temperate Forests" (Poster)
• B52A-04 "Caught in the flux net: disentangling error, uncertainty, heterogeneity, and spatial process in biogeochemical scaling" (Invited Talk)
• B51G-0101 "Scaling Forest Management Practices in Earth System Models: Case Study of Southeast and Pacific Northwest Forests" (Poster)
• B53D-0218 "Measured and modelled carbon and water fluxes in hybrid willows grown for biofuel production" (Poster)
• B53I-07 "Integrating satellite and tower phenology: a case-study in real-time ecological forecasting" (Talk)

PEcAn Team at ESA 2014 (August 2014)​

David LeBauer presented "Combining heterogeneous data and process understanding using the Predictive Ecosystem Analyzer" on Wednesday, August 13, 2014 in Symposium 11: Challenges and Advances in Statistical Software For Ecology. Shawn Serbin and Mike Dietze were co-authors.

Mike Dietze also presented "Predicting phenology: A case-study in real-time ecological forecasting" on Monday, August 11, 2014 in Organized Oral Session 4: The National Ecological Observatory (NEON): Opportunities and models for building synergistic partnerships with the community to advance continental scale ecology.

Workshops and Training​

COST PROFOUND 2014 (November 11-13, 2014)​

Mike Dietze gave the keynote address, "Models and Data", at the inaugural meeting of PROFOUND (FP 1304 Towards robust projections of European forests under climate change), a new EU COST Action.

Mike participated in several COST PROFOUND working groups and task groups. In particular, Mike Dietze and David Cameron (UK) co-organized Task Group 15 - Statistical problems in fitting models to heterogeneous data.

Brown Dog Early User Workshop (July 22, 2014)​

Kenton McHenry (Brown Dog PI, PEcAn co-PI) hosted the Brown Dog Early User Workshop from July 22-23, 2014 at NCSA in Urbana, Illinois.

Mike Dietze (PEcAn PI, Brown Dog co-PI) gave a presentation (pdf, YouTube) on how Brown Dog will be used to access and harmonize vegetation and meteorological data, and how it will be incorporated into PEcAn.

Rob Kooper (NCSA Senior Programmer on both Brown Dog and PEcAn) presented on how Brown Dog will interact with other NSF computational resources. David LeBauer (PEcAn) presented a lightning talk on how Brown Dog might benefit BETYdb.

PEcAn Summer Courses 2014 (August 2014)​

Hands-on tutorials on using PEcAn were presented at the 2014 editions of the Niwot Ridge Flux Course and the PalEON summer course Assimilating Long Term Data into Ecosystem Models.

PEcAn Seminar for Harvard Forest REU program (July 2, 2014)​

Mike Dietze was invited back to the Harvard Forest Summer REU program to present an evening seminar "The PEcAn Project: Carbon-Cycle Reanalysis Facilitated by Model-Data Ecoinformatics".

Seminars and Invited Talks​

PEcAn seminar at Columbia University (October 7, 2014)​

Mike Dietze gave a seminar "The PEcAn Project: A Community Platform for Synthesis & Forecasting of Ecosystems" in the Department of Ecology, Evolution & Environmental Biology (E3B) at Columbia University.

PEcAn Workshop and Seminar at Kent State (September 26, 2014)​

Mike Dietze gave a seminar in the Biology Department at Kent State titled "Terrestrial Ecosystems: Past, Present, & Future". While at Kent, Mike also ran a two-hour PEcAn workshop for departmental grad students and faculty.

Dietze Tenure Talk (September 22, 2014)​

Mike Dietze presented his tenure seminar "Terrestrial Ecosystems: Past, Present, & Future" to the Department of Earth and Environment at Boston University. This talk focused on the PalEON and PEcAn projects and laid out the vision for PEcAn's future direction.

Grants and Proposals​

PEcAn 2 Proposal Submitted (August 12, 2014)​

Mike Dietze, Ankur Desai, and Kenton McHenry submitted the PEcAn renewal proposal "Collaborative Research: ABI Development: The PEcAn Project: A Community Platform for Ecological Forecasting" to the NSF program Advances in Biological Informatics (ABI).

The PEcAn 2 proposal focuses on three additional challenges:

1. The need for a scalable solution to improving models, both in the cyberinfrastructure and the involvement of the research community
2. The need to assess, track, and analyze model skill, structure, and uncertainty
3. The need to increase the accessibility of modeling tools

Publications​

Concepts paper on ecological forecasting (May 2014)​

Niu S, Y Luo, M Dietze, T Keenan, Z Shi, J Li, FS Chapin III. 2014. The role of data assimilation in predictive ecology. Ecosphere 5:art65. https://doi.org/10.1890/ES13-00273.1

PEcAn synthesis paper across North America (March 19, 2014)​

Dietze M, S Serbin, C Davidson, A Desai, X Feng, R Kelly, R Kooper, D LeBauer, J Mantooth, K McHenry, D Wang. 2014. A quantitative assessment of a terrestrial biosphere model's data needs across North American biomes. Journal of Geophysical Research Biogeosciences DOI: 10.1002/2013JG002392 link

Dietze paper on modeling photosynthesis (February 2014)​

Dietze M. 2013. Gaps in knowledge and data driving uncertainty in models of photosynthesis. Photosynthesis Research 19:3-14 DOI: 10.1007/s11120-013-9836-z

Workshops Hosted​

LeBauer hosts forecasting software workshop (February 2014)​

FORECAST RCN workshop, "Advancing Software for Ecological Forecasting", March 25-27 2014, Urbana, IL. Meeting webpage. Mike Dietze was also in attendance.

Meetings and Other Events​

New Phytologist meeting on modeling photosynthesis (April 22-25, 2014)​

Mike Dietze participated in the New Phytologist workshop "Improving Representation of Photosynthesis in Earth System Models" in Montauk, NY organized by Alistair Rogers, Belinda Medlyn, and Jeff Dukes. Mike presented on how PEcAn can help constrain photosynthetic traits in Earth System Models and assess the uncertainty in model projections. A meeting report was published in New Phytologist and can be found here.

Sunny Feng defends PhD (April 8, 2014)​

Xiaohui "Sunny" Feng successfully defended her PhD dissertation "PRODUCTIVITY, PHYSIOLOGY, COMMUNITY DYNAMICS, AND ECOLOGICAL IMPACTS OF A GRASSLAND AGRO-ECOSYSTEM" at the University of Illinois, Urbana-Champaign.

Software Releases​

PEcAn 1.3.6 Released (July 28, 2014)​

This version focused on more database updates, including improved site/data management and support for meteorology conversion from netCDF CF standard to SipNET's .clim driver files.

PEcAn 1.3.5 Released (May 2014)​

Major update switching to PostgreSQL, enabling distributed instances of BETYdb and maintaining local database changes. This enabled multiple installations to run BETYdb and exchange local changes across databases.

The update focused on making met forcing data easier to download, standardize, gap fill, and convert into model-ready formats for PEcAn runs.

Overview​

This version supports conversion of met files. The code can now download and convert the met data to CF standard and to model specific format. The met data will along the way be gap filled. This allows any researchers to pick any Ameriflux site and run the SIPNET model on this site.

The latest VM can be downloaded from NCSA.

pecan.xml Changes​

The met tag can now support a special notation that lets it download and convert the met data. The met tag can have an input="Ameriflux" and output="sipnet" attribute. Currently these are the only supported conversion but more will be added in future releases of PEcAn.

Web Interface Changes​

When running in the web interface you now have the ability to edit the pecan.xml before the software runs. This allows you to change the number of ensemble runs done, as well as any other changes to the pecan.xml.

After the run finishes, you can now download the sipnet clim file used for a particular run. You can now also plot different variables against each other instead of time vs one of the variables.

This release expanded the platform's flexibility for model integration and made it easier to configure the inputs needed for different workflows.

Overview​

This version supports new model types better. BETY now allows you to add new model types to the database. You can associate these model types with PFTs. Each model type will have a list of required and optional inputs associated. These inputs will be listed in the <run><inputs> tag.

The latest VM can be downloaded from http://isda.ncsa.illinois.edu/download/index.php?project=PEcAn&sort=version

Support for DALEC​

A new model has been added to this release, DALEC. BETY already has a modeltype DALEC in the database to support this model.

pecan.xml Changes​

Using the new modeltypes we can now check the inputs specified in the pecan.xml file. All inputs should now be listed under the <run><inputs>. The code will try and update your pecan.xml file to this new format. Any missing inputs that are required will quit the run, allowing you to quickly fix your pecan.xml file.

For updated information see the PEcAn Configuration wiki.

Database Changes​

The database requires updates for the model types table. You will need to update BETY to be able to see this. This requires version 3.2 of BETYdb (https://github.com/PecanProject/bety/releases/tag/betydb_3.2).

Sites now store their information as geometry objects. If you have custom queries that use the site.lat and site.lon information you will need to change this to ST_X(ST_CENTROID(geometry)) AS lon, ST_Y(ST_CENTROID(geometry)) AS lat.

Code Changes​

One major change is to the function called get.trait.data(). This function now requires a model type as the second parameter. The model type is used to make sure we get the right PFT. This allows multiple PFTs to have the same name, but be distinguishable by the combination of name and model type.

Highlights from the year include conference presentations, new collaborations, and continued progress in connecting ecosystem models with observations and data synthesis workflows.

Conferences and Presentations​

Presentations at AGU 2013 (December 2013)​

The following PEcAn presentations occurred at the American Geophysical Union Fall Meeting:

• Viskari, Dietze, Desai: "Model-data assimilation of multiple phenological observations to constrain and forecast leaf area"
• Serbin, Dietze, Desai, LeBauer, Viskari, Kooper, McHenry, Townsend: "Assimilation of Leaf and Canopy Spectroscopic Data to Improve the Representation of Vegetation Dynamics in Terrestrial Ecosystem Models"

Presentations at ESA 2013 (August 2013)​

LeBauer and Dietze hosted a lunch-time workshop: "Combining Field Measurements and Ecosystem Models"

Additional PEcAn presentations at the Ecological Society of America Annual Meeting in Minneapolis, MN:

• Dietze: "Assimilating forest inventory data into models"
• LeBauer, Dietze, Jaiswal, Kooper, Long, Serbin, Wang: "Reducing uncertainty through data-driven model development"
• Hardiman, Serbin, Mantooth, Kennedy, Dietze: "Assimilating PALSAR remote sensing data to reduce uncertainty in ED2 predictions of forest biomass dynamics following disturbance"

Kooper presents PEcAn at XSEDE13 (July 2013)​

Kooper R, K McHenry, M Dietze, D LeBauer, S Serbin, A. Desai. 2013. Ecological Cyberinfrastructure and HPC Towards More Accurately Predicting Future Levels of Greenhouse Gases. Proceedings of XSEDE13: Extreme Science and Engineering Discovery Environment

Publications​

PEcAn highlighted in Faculty of 1000 review (July 2013)​

LeBauer et al. 2013 was recommended in two different reviews on F1000. You can read the reviews at http://f1000.com/prime/718024607

LeBauer article in R Journal (June 2013)​

LeBauer D, M. Dietze, B. Bolker. 2013. Translating Probability Density Functions: From R to BUGS and Back Again. R Journal Vol. 5/1, June, 207-209

Feng paper on photosynthesis module (December 2013)​

Feng X, M Dietze. 2013. Scale-dependence in the effects of leaf economic traits on photosynthesis: Bayesian parameterization of photosynthesis models. New Phytologist 200(4): 1132–1144 DOI: 10.1111/nph.12454 link

This paper describes the statistical model underlying the PEcAn photosynthesis module.

Grants and Projects​

Serbin NASA project recommended: Assimilating hyperspectral data (December 2013)​

The proposal "Assimilation of imaging spectroscopy data to improve the representation of vegetation dynamics in ecosystem models" led by Shawn Serbin, with Mike Dietze and Phil Townsend as co-PIs, was recommended for funding by NASA. This project focuses on assimilating hyperspectral data in the PEcAn framework by building a Radiative Transfer Model into the Ecosystem Demography model.

Teaching and Outreach​

Dietze teaches course in Ecological Forecasting (Fall 2013)​

GE585 – Ecological Forecasting and Informatics was taught by Mike Dietze at Boston University in Fall of 2013. The course materials are available on GitHub.

Undergrads exposed to model-data fusion (June 2013)​

Mike Dietze was invited back to Harvard Forest to present PEcAn to the summer REU students (June 12). Student feedback highlighted their newfound appreciation for how data and models can work together iteratively and how modeling is useful to scientific progress.

Spring Semester 2013 Talks (Spring 2013)​

Mike Dietze presented talks on the PEcAn project at the Boston University EBE Seminar series (April 1), Harvard University's ClimateTEA (April 2), and at Harvard Forest (May 2).

Community Building​

Student PEcAn Programming Positions (March 2013)​

The project advertised for web programmers to develop PEcAn and BETYdb front-end and back-end features, seeking skills in PHP, SQL, Ruby, R, C, or Fortran.

This year included foundational publications, software releases, training activities, and conference presentations that helped establish PEcAn's early scientific and community footprint.

Major Milestones​

PEcAn manuscript: Ecological Monographs (August 2012)​

The first manuscript describing the initial components of the PEcAn project was accepted for publication:

LeBauer, D.S., D. Wang, K.T. Richter, C.C. Davidson, M.C. Dietze. Feedbacks between measurements and ecosystem models. Ecological Monographs in press

PEcAn used to assess biofuel potential of hybrid Poplar (December 2012)​

Wang, Dan, David LeBauer, and Michael C. Dietze. In press. Predicting yields of short-rotation hybrid poplar (Populus spp.) for the contiguous US through model-data synthesis. Ecological Applications. https://doi.org/10.1890/12-0854.1

In this paper the PEcAn workflow was used to calibrate the Ecosystem Demography model (ED2) for hybrid poplar using a combination of trait data and yield data. The validated model was used to make projections of potential poplar yields and optimal rotation periods across the continental US. The most promising regions for poplar production were identified as the Northeast, upper Midwest, and northern California.

Software Releases​

PEcAn 1.2.6 Released (September 2012)​

As of September 2012, PEcAn version 1.2.6 became the latest stable version. This version was released for the August 2012 summer course "Assimilating long-term data into ecosystem models" that taught methods advanced by the PalEON project. Available at: http://isda.ncsa.illinois.edu/download/index.php?project=PEcAn&sort=category

PEcAn 1.1 Source Code Released (September 2012)​

The PEcAn version 1.1 source code was released, including an R package with functions and R scripts used to run the PEcAn workflow. The PEcAn 1.1 Virtual Machine can reproduce all of the computational steps used in the manuscript "Facilitating feedbacks between field measurements and ecosystem models" (LeBauer et al in press).

Conferences and Presentations​

PEcAn at AGU 2012 (December 3-7, 2012)​

The following PEcAn related talks and posters were presented at the 2012 meeting of the American Geophysical Union:

• B22B-08: "The modeled effects of fire on carbon balance and vegetation abundance in Alaskan tundra" - Michael C. Dietze; Carl D. Davidson; Ryan Kelly; Philip E. Higuera; Fengsheng Hu
• B34B-04: "What do we need to measure, how much, and where? A quantitative assessment of terrestrial data needs across North American biomes through data-model fusion and sampling optimization" (Invited) - Michael C. Dietze; Carl D. Davidson; Ankur R. Desai; Xiaohui Feng; Ryan Kelly; Rob Kooper; David S. LeBauer; Joshua Mantooth; Kenton McHenry; Shawn P. Serbin; Dan Wang
• B41C-0296: "A Web Interface for Eco System Modeling" - Kenton McHenry; Rob Kooper; Shawn P. Serbin; David S. LeBauer; Ankur R. Desai; Michael C. Dietze
• B41C-0306: "The use of informed priors in ecosystem model-data fusion" - David S. LeBauer; Michael C. Dietze

PEcAn at FORECAST RCN 2012 (October 9-11, 2012)​

Mike Dietze presented an invited talk on the PEcAn project at the FORECAST RCN meeting in Woods Hole, MA.

PEcAn at ForestSAT 2012 (September 11-14, 2012)​

Shawn Serbin presented a talk "From multiple datasets to predictive ecology: The PEcAn workflow and model-data assimilation" at the ForestSAT 2012 meeting in Corvallis, OR.

PEcAn at ChEAS meeting 2012 (June 27-29, 2012)​

Mike Dietze, Shawn Serbin, and Ankur Desai each presented a number of short talks on the PEcAn project at the annual investigator's meeting for the Chequamegon Ecosystem Atmosphere Study (ChEAS) held at the Kemp Biological Station, WI. Agenda and slides: http://flux.aos.wisc.edu/twiki/bin/view/Main/ChEASMeeting2012

Training and Education​

PEcAn at PalEON summer course 2012 (August 2012)​

PEcAn was used for all aspects of the modeling and data assimilation activities in the week-long summer course "Assimilating Long-Term Data into Ecosystem Models" offered at the University of Notre Dame Environmental Research Center (UNDERC), Land O' Lakes, WI.

Mike Dietze presented 12 hours of lecture, tutorial, and hands-on demos using PEcAn, covering workflows for model calibration and analysis, parameter data assimilation at the Sylvania flux tower, and state-variable data assimilation of tree ring data.

PEcAn allowed students to go from coring trees Monday, mounting them Tuesday, and analyzing them Wednesday, to calibrating SIPNET Thursday using trait databases and flux tower data and assimilating the tree ring data on Friday.

Student Achievements​

Carl Davidson defends Master's Thesis applying PEcAn to Alaskan Tundra (June 11, 2012)​

Carl Davidson successfully defended his Master's thesis on "The modeled effects of fire on carbon balance and vegetation abundance in Alaskan tundra".

Carl's thesis represents an incredible case-study in the application of the PEcAn system, using meta-analysis, sensitivity analysis, and variance decomposition to develop tundra PFTs, designing field campaigns based on model analysis, and assimilating field and flux data.

Team Updates​

Toni Viskari joins PEcAn team (December 21, 2012)​

Dr. Toni Viskari joined the PEcAn team as a postdoctoral fellow in the Dietze lab starting January 1, 2013. Toni worked on the NSF ABI project using the northern Wisconsin "ChEAS" project as a testbed for regional-scale multi-proxy data assimilation. Toni joined from the Finnish Meteorological Institute and the University of Helsinki.

Upcoming Events​

PEcAn at NACP AIM4 (February 4-7, 2013)​

The PEcAn team announced their planned participation at the 4th North American Carbon Program All-Investigators Meeting in Albuquerque, New Mexico. Mike Dietze, Ankur Desai, Trevor Keenan, and Quinn Thomas planned to chair a breakout session on "Harnessing the 'long tail' of ecosystem carbon cycle observations: Approaches and challenges in synthesizing and assimilating non-automated and experimental data".