View on GitHub

PEcAn

Home News People Tutorials Demo Download Documentation Workshop GSoC Contact Us

PEcAn at NACP 2017

March 26th-30th, 2017

A number of PEcAn team members were in attendance at the Joint North American Carbon Program (NACP) and Ameriflux Principle Investigators Meeting involved in multiple activities.

PEcAn Break-Out Session:

Mike Dietze, Ankur Desai and other members of the team led a break out session, giving a demo of PEcAn's capabilities while discussing the needed tools and goals for the carbon cycle prediction in our community.

Posters:

Mike Dietze: Carbon cycle forecasts need to be closer to real-time: linking theory, data, models, and cyberinfrastructure

Istem Fer: Improving forest carbon sequestration predictions by constraining demographic processes in an ecosystem model

Alexey Shiklomanov:Leaf optical properties shed light on foliar trait variability at individual to global scales

Tempest McCabe: Validating the Ecosystem Demography Model Version2 for Southern Pine Forests

Plenary Talk:

Anthony (Tony) Gardella: Modeling Community Cyber-Infrastructure Needs and Opportunities

Abstracts of the meeting can be found here.

Agenda of the meeting can be found here.

DIBBS NSF Meeting

January 11-12, 2016

Mike Dietze and Kenton HcHenry had a poster at the 1st NSF Data Infrastructure Building Blocks (DIBBS) PI Workshop : "Brown Dog - A Science Driven Data Transformation Service", highlighting BrownDog's capabilities to "access and preserve data transformation tools, track provenance, track information loss, manage data movement, and process jobs in a scalable manner across a diverse set of computational resources".

More information about the meeting can be found here

PEcAn Open House at AGU

Dec 12, 2016

We will be holding an open house & social gathering for the PEcAn project on the Monday night of AGU

When: Mon, Dec 12th from 6:45pm -10:30pm

Where: The Garage SFO- Luxury Live/Work Warehouse. 951 Folsom St, San Francisco, CA 94107 (~2 blocks south of Moscone)

There will not be any formal presentations, so feel free to come and go as it fits your schedule.

We encourage you to:

  • Come meet the PEcAn team
  • Get more information about current tools and training
  • Play with hands-on demos
  • Learn about new developments and what models, tools, and data partnerships are coming down the pipeline
  • Chat with other members of the measurement and modeling communities about ideas for new PEcAn-based analyses
  • Let us know what new tools and features you most want/need

Food and drinks will be provided.

To help us with planning, we encourage you to fill out the following form if you are interested in joining us: RSVP

PEcAn Team at AGU 2016

December 12-16, 2016

The PEcAn Team will be at the 2016 American Geophysical Union (AGU) Conference and will be presenting the following talks and posters:
Monday

B12C-01: Mike Dietze "On the nature of prediction in ecology (Invited) ", 10:20 -10:35 Moscone West - 2004

B12C-02: Betsy Cowdery "Evaluating Productivity Predictions Under Elevated CO2 Conditions: Multi-Model Benchmarking Across FACE Experiments", 10:35 - 10:50 Moscone West - 2004

B12C-06: Istem Fer "Linking big models to big data: efficient ecosystem model calibration through Bayesian model emulation", 11:35 - 11:50 Moscone West - 2004

TUESDAY

B24A-03: Michael Dietze "Show me the data: advances in multi-model benchmarking, assimilation, and forecasting", 16:30 - 16:45 Moscone West - 2004

B21B-0438: James Simkins "Partitioning sources of uncertainty in projecting the impact of future climate extremes on site to regional ecosystem carbon cycling", 08:00 - 12:20 Moscone South - Poster Hall

Wednesday

B31K-01: Alexey Shiklomanov "Synthesizing trait correlations and functional relationships across multiple scales: A Hierarchical Bayes approach", 08:00 - 08:15 Moscone West - 2010

FRIDAY

B51I-05: Alexey Shiklomanov "Leaf optical properties shed light on foliar trait variability at individual to global scales (Invited)", 09:00 - 09:15 Moscone West - 2006

B52A-03: Toni Viskari " Which factors limit constraining ecosystem models with remote sensing observations? ", 10:50 - 11:05 Moscone West- 2006

PEcAn talk at University of Washington

November 7, 2016

Thanks to Abby Swann for having Mike Dietze out to UW to give a talk about PEcAn. It was great to catch up with Abby, Janneke HilleRisLambers, and Lauren Buckley, as well as to meet a diverse set of faculty and students.

PalEON State Data Assimilation Hackathon @ UC Berkeley

November 2-4, 2016

Members of the PEcAn and PalEON modeling teams decendend on UC Berkeley for 3 intensive days of programming aimed at getting state data assimilation (SDA) working for paleoecological data. While some of these models use other data assimilation technology (e.g. CLM-4.5 is already coupled to DART), most attendees were focused on getting models into PEcAn's SDA scheme. Specifically, Alexey Shiklomanov and Tony Gardella worked on coupling ED2 and Istem Fer worked on coupling LPJ-GUESS. At the same time Christy Rollinson worked on generating an ensemble of meteorological inputs while Ann Raiho worked on adjusting the SDA code to handle that ensemble and pass a different met driver to each ensemble member. Mike Dietze helped with system design and started tackling the met workflow's handling of the met ensemble. Everyone found it a productive experience and went home with a lot of home work still left to do before everything's working.

PEcAn data partnership: CTFS/ForestGEO

October 25-27, 2016

We're also excited to report on discussions with Sean McMahon (Smithsonian) about developing the capacity to ingest data from the global CTFS/ForestGEO plot network. This network spans 63 large plots and over 6 million trees from the tropics to the boreal. ForestGEO represents an invaluable benchmark for ecosystem models, especially in the tropics, and we look forward to working with Sean and others on developing innovative multi-model / multi-site analyses. Be aware that not all ForestGEO site data is public, so only a subset of sites will be supported initially, but we'll be developing tools that will allow all sites in the network to easily load their data and leverage PEcAn in their research.

PEcAn data partnership: Hubbard Brook LTER

October 20, 2016

Excited to report on discussions with John Battles about his plans to stream the entirety of the Hubbard Brook data catalog into PEcAn. John is particularly excited about the ability to update models continuously as new data comes online every year. We will be working with John on ingest data this spring during his sabbatical. To meet this demand, we'll be doing a major overhaul of our data ingest documentation and tweaking some of our tools, all of which is aimed at benifiting the larger community (John's just volunteered to be our guinea pig).

PEcAn talk at NASA JPL. Model Farm collaboration

October 13-14, 2016

Thanks to Josh Fisher for having Mike Dietze out to NASA JPL to give a talk about PEcAn and to really dig into the nitty-gritty details of how the JPL Model Farm works. We're excited to report that we see layed out a path forward for incorporating Model Farm technology into PEcAn in order to produce regional and global model runs. We're excited to be collaborating with Josh and his team and will keep everyone posted on progress toward making PEcAn global!

PEcAn talks at UC Irvine

October 12, 2016

Mike Dietze gave a talk about PEcAn to the Earth System Science program at UC Irvine. Thanks to Jim Randerson for having us down and all the useful discussions with students and faculty. Exciting to see progress on ILAMB and talk about ways to work together.

PEcAn talk at LBNL

September 19, 2016

Mike Dietze gave a talk at LBNL on PEcAn, PalEON, and our new forecasting initiative.

Sabbatical at LBNL / NGEE-Tropics

September 7, 2016

PEcAn lead PI, Mike Dietze, is spending the fall at Lawrence Berkeley National Lab working with the NGEE-Tropics team to get CLM-FATES (formerly known as CLM-ED) into PEcAn and get the NGEE-Tropics team set up for using PEcAn in their exciting work bringing together models and data in the tropics. Look for FATES support in the next PEcAn release!

PEcAn at PalEON Summer Course

August 14-20, 2016

Mike Dietze, Ann Raiho, and Christy Rollinson all taught at this year's PalEON summer course on assimilating paleo date into models. PEcAn post-doc Istem Fer was also there as a student. In this one week course students work through an exciting case study in how PEcAn accelerates our ability to assimilate data into models. Students started the week coring trees at the UNDERC field station, then prepped and read the cores. Within PEcAn students then did basic model runs with SIPNET for UNDERC and then sensitivity and uncertainty analyses to determine which parameters had the largest impact on NPP. Next, SIPNET was calibrated against the near-by Sylvania flux tower using PEcAn's parameter data assimilation tools. Finally, the tree ring data were assimilated into SIPNET using PEcAn's state data assimilation tools, accounting for a range of uncertainties estimated by the data.land and allometries modules. It's amazing to see students assimilate data they've just collected -- it's a great demonstration of the possibilities for near-real time model-data synthesis.

PEcAn v1.4.8

August 11, 2016

Camp PEON: Assimilation, multi-site, soil params, Maespa, LPJ-GUESS, improvements to web & tutorials

State Data Assimilation (SDA)

One of the main goals of this release was to re-generalize the EnKF and generalized ensemble filter that @araiho has been using with LINKAGES back to also working with SIPNET and to bring the design one step closer to working with many models. This is working (yeah!), but not yet fully generalized.

The revised SDA tutorial has been migrated to documentation/tutorials/StateAssimilation and the gitbook updated to explain the use of SDA tags in the settings file and the main functions used.

Multisite runs

The basic PEcAn workflow was substantially re-organized to allow PEcAn to more easily run multiple sites at once (see Site Groups below). The core of the design is to split PEcAn’s settings object (what’s read from the XML) into a list of settings objects, one for each run, and applied to existing functions. Both Settings and SettingsList are now R classes. Within the settings file itself, there is now a block that can include any number of individual . Where appropriate, PEcAn gathers information across runs — for example, the meta-analysis is performed on the set of PFTs extracted across all runs, rather than being done run-by-run. This change is the first step in a large plan to re-organize the PEcAn workflow to be more modular and also support multi-model runs.

Note: Multisite/multimodel run SettingLists cannot yet be generated through the web interface.

Parameter data assimilation

Generalized to multiple PFTs

Emulator now supports a range of additional features that can be controlled through the XML settings:

  • multiple chains
  • extending chains (additional samples) starting from their latest state
  • adding additional knots
  • automated burnin detection
The revised PDA tutorial has been migrated to documentation/tutorials/ParameterAssimilation and the PDA vignette contains a more detailed explanation of how to use the new features.

Non-PFT parameter constraint

As an experiment in giving PEcAn control of non-PFT parameters, we've created a 'soil' PFT for SIPNET that contains soil biogeochemical parameters. If successful, we will extend this approach to other models. This change already improves model calibration and validation and has allowed us to assess the relative contribution of plant vs soil parameters to model output uncertainty.

Models

Maespa has basic functionality (thanks @mdekauwe for all the help!) LPJ-GUESS running, but without PEcAn controlling parameters

Drivers

Fluxnet LaThuile

Web Interface

PEcAn landing page updated to be links to tools. Avoids confusion when users forget to add the /pecan, /bety, /rstudio, etc. to the web address.
Site groups has been populated with a number of major research networks: Ameriflux, Fluxnet, Fluxnet 2015 Tier 1 (open), LTER, NEON, ForestGEO, PalEON
Links to documentation, gitter, and bug reports from all pages
Additional mouseover text and links to model and variables tables
Legend in default plot, removed spline from Shiny plot

Camp PalEON

This is a special release for the PalEON summer course, and comes pre-installed with extra libraries and data for the course

Tutorials

In addition to migrating the PDA and SDA tutorials to RMarkdown, the model-data comparison at the end of Demo 1 has also been migrated to documentation/tutorials/AnalyzeOutput

Benchmarking

While still in alpha development, @bcow contributed a large chunk of code bringing us much closer to automated benchmark execution and a first pass at a Shiny page for benchmark visualization.

Bugfixes

C_stack bug in run.sensitivity.analysis: fixed on new VM but older users should upgrade gridExtra R package Units in figures and reading of model output #792 -- downstream applications/code should check for changes.
Can skip meta-analysis in pecan settings. May require updating old pecan.xml, particularly for integration tests.
Interface: met date checking
Misc: #906 #916 #919 #923 #948 #950 #951

Known Issues

This version of PEcAn is misconfigured and is using the wrong server for Brown Dog. The server that is used is the development server for Brown Dog and might result in no data being returned. During the Camp PEON the development server will be using the same code as the production server. If you want to use BrownDog after Camp PEON we highly encourage you to sign up with Brown Dog. We will at that point contact you and send you the instructions to modify your VM to use your new account and the production servers.

PEcAn v1.4.7 Release

July 13, 2016

CMIP5, Shiny, FLUXNET2015, Global Sensitivity

CMIP5:

We’ve add support for running models into the future under climate change scenarios! This release adds support for grabbing GFDL runs for all four RCP scenarios multiple experiments. RCP4.5 is the ‘default’, but Advanced Edit can be used to change the model (CM3, ESM2M, ESM2G), scenario (rcp26, rcp45, rcp60, rcp85), or ensemble member (r1i1p1, r3i1p1, r5i1p1). We are working with Earth System Grid to provide support for other climate models in future PEcAn releases.

Advanced Visualizations:

We’ve added support for R Shiny visualizations in a way that we hope will allow users to easily add new Shiny apps to the catalog of PEcAn visualizations. Simply drop a new app into the pecan/shiny folder and it should go live. We’ve initially populated our Shiny catalog with two visualizations:

workflowPlot:

Similar to our current visualizations, which plots model output timeseries, but now shows output over all years and without a default 1-day time averaging.

global-sensitivity:

Displays results from our new Monte Carlo global sensitivity analysis. Select outputs by model parameter (all model outputs), by output variable (all model parameters), or dig down into individual parameter-by-output relationships.

FLUXNET2015 and Ameriflux LBL:

At the site-level we’ve added support for the new FLUXNET2015 synthesis product, extending PEcAn’s support for flux tower sites globally. For Ameriflux, we’ve also added support for data on the new Lawrence Berkeley server. Past support for data on the ORNL server will also continue so long as that site remains active, but LBL is the preferred server and will contain the most up-do-date data.

Finally, in response to the above changes and feedback from users, we’ve tried to streamline the main PEcAn tutorial. The Parameter Data Assimilation (PDA) tutorial has also been updated to leverage emulator upgrades in the last release.

Known issues:

MAESPA, G’DAY, LPJ-GUESS not yet ready. JULES supported but not installed on VM, need to download and install yourself.

Met processing bugs: code for extending the date range from previous runs has a bug. Current workaround through advanced edit: set new met output directory (See PDA demo). For CRUNCEP and GFDL, workflow gets tripped up when extending to a new model. Currently requires running met process code by hand in R. Bugfixes will be in next release (Aug 12).

In the pipeline:

Next release will focus on PalEON summer course (SDA, tree ring & allometry modules, hopefully alpha support for PalEON met and NEOTOMA database). Also hope to bring Benchmarking up to a functional beta version, add GLDAS & NLDAS met.

PEcAn at Flux Course

July 11-22, 2016

Mike Dietze, Ankur Desai, and Betsy Cowdery are all returning to teach at this year's Flux Course. PEcAn grad students James Simkins (Wisc) and Tess McCabe (BU) are also in attendance. The Flux Course is one of the PEcAn team's big annual deadlines, so look for a bunch of new, cool features in release v1.4.7!

PEcAn at Harvard Forest REU

July 6, 2016

Mike Dietze presented an evening seminar on PEcAn at the Harvard Forest REU summer program, which included a hands-on demo. Dietze enjoyed getting to meet this year's crop of REUs over dinner and we wish them all the best of luck in finishing up their summer projects.

Ecological Forecasting book accepted!

June 27, 2016

Mike Dietze's book "Ecological Forecasting" has been officially accepted for publication by Princeton University Press. Expect the book out Spring 2017. This book captures much of the philosophy and tools of the PEcAn project (check out the PEcAn case study in Chapter 12!), while also looking more broadly at the state of ecological forecasting in many ecological disciplines. This book grew out of the Broader Impacts of our NSF Advances in Biological Informatics (ABI) awards.

PEcAn at ESA Sustaining Biological Infrastructure Workshop

June 2016

Mike Dietze attended the Ecological Society of America's SBI short course for project directors. Thanks to all the great instructors for providing with a lot to think about!

As a result of this experience, the PEcAn team has kicked off it's first ever strategic planning exercise. As a place to start, check out our new Vision and Mission Statements

Vision: Ecosystem science, policy, and management informed by the best available data and models

Mission: Develop and promote accessible tools for reproducible ecosystem modeling and forecasting

PEcAn at PROFOUND spring course

May 2016

Mike Dietze again taught at PROFOUND spring school on Bayesian model calibration.

Additional information about the course can be found here

PEcAn at ILAMB meeting

May 2016

Ankur Desai, James Simkins, and Shawn Serbin represented the PEcAn team at the International Land Model Benchmarking (ILAMB) Workshop in Washington, D.C.

Serbin gave a talk entitled "PEcAn: A community tool to enable synthesis, evaluation & forecasting"

PEcAn Workshop May 2016

May 2016 by Tony Gardella

The PEcAn Workshop was held from May 9th-11th, 2016 at Boston University with the goals 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 PEcAn Team thanks everyone who attended and greatly appreciates all the feedback that was given. Talks were recorded and will be posted on YouTube. Slides from the workshop are available here.

PEcAn 1.4.6 Released

May 2016 by Tony Gardella

This release has the beta release of MAESPA and LPJ-GUESS models, an upgrade to parameter calibration (emulator tools and bayesian sampler tools), and beta release of EnKF generalization. (You can find the VM here and release notes on Github)

Other changes include:

  • Ability to aggregate sites by recognized networks (Ameriflux, Fluxnet, LTER,NEON, etc.) and/or as the user sees fit.
  • Alpha development for benchmarking
  • Code to merge TRY database into BETY instance. TRY is not public, but if you have access this tool will allow easy upload
  • Improvemnets in the RTM package to support stand-level inversion/calibration
  • Bug fixes

PEcAn at NACP workshop

March 7-9, 2016

Mike Dietze presented on the PEcAn project at the North American Carbon Program (NACP) Workshop "Development of Predictive Carbon Cycle Science" in College Park, Maryland.

PEcAn 1.4.5 Released

March 2015 by Tony Gardella

We've coupled another model and meteorological product to PEcAn. The PREdiction of Light use efficiency, Evapotranspiration, and Soil water (PRELES) model comes from our friends at the Natural Resources Institute Finland. The global CRUNCEP met product gives gives us the capability to run any model anywhere around the world! (You can find the VM here and release notes on Github)

Other changes include:

  • The ability to filter runs on the history page by a text search
  • config.php changes that simplify host settings
  • Support for usage of Travis CI continuous integration, allowing for the status of PEcAn builds on anyone's github version of PEcAn
  • A migration of documentation from github wiki to gitbook

PEcAn at the 2016 INTERFACE meeting

January-February 2016 by Tony Gardella

Shawn Serbin and Alexey Shiklomanov attended the Integrated Network for Terrestial Ecosystem Research on Feedbacks to the Atmosphere and ClimatE(INTERFACE) meeting in St.Pete's Beach, FL. Shawn led a working group on Remote sensing and both Alexey and Shawn presented posters.

PEcAn at the ED Community meeting

January 2016 by Tony Gardella

Mike Dietze, Elizabeth Cowdery, and Toni Viskari represented our team at the Ecosystem Demography(ED) meeting in Boulder,CO. Mike gave a presentation on PEcAn and all three participated in various working group discussions. One discussion specifically surrounded the coupling of PEcAn and CLM-ED. It was a productive discussion and we will continue working on this endeavor with our friends at NCAR.

PEcAn Presentation at NEON Workshop "Operationalizing Ecological Forecasting"

January 2016 by Tony Gardella

Mike Dietze and Andy Fox organized a meeting on "Operationalizing Ecological Forecasting" in Ft. Collins, CO during the first week of January. It was hosted by the USGS Powell Center and funded by NEON. Mike gave a talk titled "The PEcAn Project: Putting Ecosystem Model-Data Fusion in your Pocket". More information about the meeting can be found here.

PEcAn Team at AGU 2015

December 2015 by Tony Gardella

The PEcAn Team is gathered at the 2015 American Geophysical Union Conference and will be presenting the following talks and posters:
Monday

B11C-0441: Betsy Cowdery "Assessing model sensitivity and uncertainty across multiple Free-Air CO2 Enrichment experiments", Monday, 14 December 2015 08:00 - 12:20 Moscone South- Poster Hall

B11C-0448: Ann Raiho "Assimilating Paleoecological Data into a Forest Gap Model", Monday, 14 December 2015 08:00 - 12:20 Moscone South- Poster Hall

B11L-02: Josh Mantooth "Tree Nonstructural Carbohydrate Reserves Across Eastern US Temperate Forests", Monday 14, December 12, 2015 8:15-8:30 Moscone West-2004

B11N-06: Ryan Kelly "Widespread Burning of Alaskan Boreal Forests Overcomes Fuel Limitation in the 21st Century", Monday, 14 December 2015 09:15 - 09:30 Moscone West- 2010

B11N-07: Mike Dietze "Fusing data and models to forecast disturbance impacts on ecosystems: past, present, and future", Monday, 14 December 2015 09:30 - 09:45 Moscone West- 2010

B14B-01: Shawn Serbin "Reducing the uncertainty in the projection of the terrestrial carbon cycle by fusing models with remote sensing data", Monday, 14 December 2015 16:00 - 16:15 Moscone West- 2004

TUESDAY

IN21E-07: Mike Dietze "Chasing the long tail of environmental data: PEcAn is nuts about Brown Dog", Tuesday, 15 December 2015 09:30 - 09:45 Moscone West- 2020

Thursday

B42A-04: Ankur Desai "Detection of Extreme Climate Event Impacts to Terrestrial Productivity From Airborne Hyperspectral Imagery", Thursday, 17 December 2015 11:05 - 11:20 Moscone West- 2006

IN43D-08: David LeBauer "Reusable Software and Open Data Incorporate Ecological Understanding To Optimize Agriculture and Improve Crops", Thursday, 17 December 2015 15:25 - 15:40 Moscone West- 2020

FRIDAY

B53D-0594: Alexey Shiklomanov "Applications of spectral inversion to understanding vegetation functional trait relationships", Friday, 18 December 2015 13:40 - 18:00 Moscone South- Poster Hall

B53B-0549: Toni Viskari "Assessing the impact of radiative parameter uncertainty on plant growth simulation", Friday, 18 December 2015 13:40 - 18:00 Moscone South- Poster Hall

B53B-0544: Shawn Serbin "Linking vegetation structure, function and physiology through spectroscopic remote sensing", Friday, 18 December 2015 13:40 - 18:00 Moscone South- Poster Hall

PEcAn 1.4.4 Released

November 2015 by Tony Gardella

Gearing up for a major release before the American Geophysical Union conference, we're bringing in a key new feature: the ability to launch workflows from the web interface and have them executed on remote machines ! (You can find the VM here and release notes on Github)

Other features include:

  • The ability to add notes to a workflow on the web
  • University of Wisconsin – Madison is now part of the PecAn database sync network
  • Updates to RTM package: additional documentation, vignette updates, and support for sensor spectral response functions
  • Updates to Photosynthesis package: added option for TPU limitation and temperature dependence on parameters

PEcAn presentation at DOE workshop "Trait Methods for Representing Ecosystem Change"

November 17-18,2015 by Mike Dietze

Mike Dietze presented an overview of PEcAn's trait modeling research as part of a Department of Energy workshop assessing how trait-based approaches can inform ecosystem and earth system models. Dietze's presentation, can be found here.

PEcAn talk at University of Georgia

October 6,2015 by Mike Dietze

Mike Dietze visited the University of Georgia's Odum School of Ecology on October 5-7 and talked about ongoing work on the PEcAn project in a talk entitled Forecasting Ecosystems: Challenges and Opportunities

PEcAn at ESA Centennial

August 2015 by Mike Dietze

Mike Dietze presented the talk “Breaking the modeling communication gaps: models talking with ecologists, the data, and each other.” at the centennial Ecological Society of America Annual Meeting held August 2015 in Baltimore, MD. This talk was part of an excellent session "Creative Approaches for Addressing Ecological Uncertainty in Earth System Models" organized by Nick Smith and Jeff Dukes

NCSA features PEcAn 1.4.3 in news

August 2015 by Tony Gardella

NCSA has started to pick up on our latest software releases, recently featuring PEcAn 1.4.3 in their newsletter and news section "NCSA Bytes & Pieces" .

Two DOE ARPA-E grants will support high throughput plant phenotyping

July 2015 by David LeBauer

The DOE Advanced Research Projects Agency-Energy (ARPA-E) Transportation Energy Resources from Renewable Agriculture (TERRA) program announced two awards to Illinois and NCSA that will support the further development of PEcAn and BETYdb to support the use and development of a new cyberinfrastructure to synthesize sensor data and develop automated platforms for identifying promising genotypes in breeding trials. Read more about the big data and computing 'reference' platform that will provide a core set of phenotyping data and the development of an all-terrain robot . These projects aim to efficiently quantify plant traits and predict yield potential of individual plants using sensors that can be deployed on robots, tractors, and drones.

Help Build rOpensci interface to BETYdb and PEcAn

July 2015 by David LeBauer

We are looking for help writing an R based interface to the BETYdb API.

A few functions have already been added to the rOpensci traits package that can be found in the file R/betydb.R.

If you can help resolve open issues, implement new functionality, and write vignettes please contact betydb@gmail.com, submit a pull request or review our current short-term job announcement

PEcAn 1.4.3 Released

July 2015 by Rob Kooper & Mike Dietze

Just in time for Flux Course PEcAn 1.4.3 is released. As always you can download the latest VM from and full release notes can be found on Github. The PEcAn VM has also been released on Amazon AWS as a public AMI.

Highlights of this release are:

  • VM now comes with Brown Dog enabled for processing NARR and Ameriflux data
  • Ability to run sensitivity, uncertainty, and ensemble analyses 100% through web interface
  • New vignettes for the RTM, photosynthesis, allometry, and priors modules
  • Brookhaven National Lab now part of PEcAn database sync network

New PEcAn Project Manager

July 2015 by Michael Dietze

We are excited to announce that Tony Gardella will be joining the PEcAn team as Project Manager starting August 1st. He is a recent graduate of Boston University with a Bachelor of Arts degree in Environmental Analysis and Policy. His passion for solving environmental issues and interest in the tools necessary to do so brought him to the PEcAn project. We are confident that his experience in the social sciences, understanding of the natural sciences, and computer science skills will be able to facilitate the growth of the project by engaging a wider user community and improving its accessibility. He cannot wait to work with you all and hopes to do so soon.

Flux Course 2015

July 2015 by Michael Dietze

Mike Dietze, Ankur Desai, and Betsy Cowdery will be representing the PEcAn team at this year's edition of the annual Flux Course at Niwot Ridge, July 20-31.

The PEcAn team is furiously working on new features, tutorials, and R vignettes to show off at the flux course. Because of all this work keep an eye out for PEcAn 1.4.3, the release of which will be timed for the start of camp!

PEcAn at IALE 2015

July 2015 by Michael Dietze

Mike Dietze is presenting the following talk on PEcAn at the International Association for Landscape Ecology (IALE 2015) World Congress in Portland Oregon.

Breaking the modeling communication gaps: models talking with ecologists, the data, and each other.
Monday, July 6, 2015 1:40-2:00

This talk is part of the Symposium S05: Research Priorities in Computational Landscape Ecology organized by Kurt Riitters and Paul Duffy.

PEcAn presentation for Harvard Forest REU's

July 2015 by Michael Dietze

Mike Dietze once again presented the PEcAn project to the Harvard Forest REU (Research Experience for Undergraduates) summer students. In addition to the seminar and a bit of live demo, Mike enjoyed dinner and a wide ranging conversation with this year's crop of students.

Building Global Ecological Understanding Workshop

June 2015 by Michael Dietze

Mike Dietze attended the Building Global Ecological Understanding Workshop at the University of Delaware, June 3-5, 2015. This workshop focused a lot on Big Data in ecology, with considerable discussion on how cyberinfrastructure, such as PEcAn and Brown Dog, can help address cutting edge questions in ecology.

COST PROFOUND Spring School

May 2015 by Michael Dietze

Mike Dietze served as one of the instructors at a week-long spring school Bayesian calibration, forecasting and multi-model predictions of process-based vegetation models organized as part of the COST PROFOUND project. This course ran 12.-16. of May and was located in Rencurel, France, in the foothills of the French Alps near Grenoble. In addition to presenting a hands-on tutorial in PEcAn, Mike also gave lectures on Maximum Likelihood and Bayesian Prediction/Forecasting.

After the Spring School, Mike stayed in Grenoble for the two-day workshop of PROFOUND WG3, focused on larger issues and work surrounding Bayesian model-data fusion in dynamic vegetation models.

PEcAn talk at University of New Hampshire

May 2015 by Michael Dietze

Mike gave a talk in the Biological Sciences Department at the University of New Hampshire on May 1st entitled "The PEcAn Project: A Community Platform for Synthesis & Forecasting of Ecosystems". Mike's host, Kirk Broders, was unfortunately out of town, but Scott Ollinger showed Mike around campus. Mike, Scott, and Scott's lab also enjoyed a long conversation about PEcAn, PNET, and the ongoing forest ecology research across New England.

PEcAn talk at Stony Brook University

April 2015 by Michael Dietze

Mike Dietze gave a seminar in the Ecology and Evolution Department at Stony Brook University on April 29th entitled "The PEcAn Project: A Community Platform for Synthesis & Forecasting of Ecosystems". Thanks to Mike's former Moorcroft Lab labmate, Heather Lynch, for serving as his host and thanks to everyone as SBU for two days of fun conversations and an awesome departmental t-shirt

By sheer coincidence the email from the BU Dean awarding Mike tenure arrived DURING his seminar. This is definately one campus visit that he'll remember for a long time!

Now Hiring! PEcAn Project Manager

April 2015 by Michael Dietze

Summary

The Ecological Forecasting lab at Boston University seeks a full-time software project manager to coordinate phase 2 development, user engagement, outreach, and education on the PEcAn project (Predictive Ecosystem Analyzer, www.pecanproject.org). PEcAn is an ecoinformatics system designed to make ecosystem models more accessible to the research community and managers, to manage the flows of information into and out of such models, and to facilitate analysis, data assimilation, visualization, and forecasting. The project manager would work closely with Prof. Michael Dietze and project collaborators at the University of Wisconsin, the National Center for Supercomputing Applications, and Brookhaven National Lab.

Key Responsibilities

  • Work with modeling teams to couple new models to PEcAn
  • Develop educational and training materials (written, video, web, etc)
  • Organize workshops, hands-on demos, and outreach activities
  • Maintain project webpage, wiki, email lists, and social media
  • Design and improvement of user interfaces
  • Day-to-day oversight of timelines, schedules, budgets, and Github repository
  • Primary point of contact for all project partners and users on project execution status and questions
  • Contribute to reports and scholarly publications
  • Coordination of weekly developers meeting

Required Education, Training, and Skills

  • BS/BA in a related field (e.g. ecology, environmental science/analysis/policy, computer science, engineering)
  • Previous programming experience
  • Quick to learn new skills, hard working, highly organized
  • Excellent writing and communication skills
  • Able to travel

Preferred Experience

  • Previous experience with open-source collaborative software development
  • Familiarity with Linux, cloud, and High Performance Computing technologies
  • Familiarity with ecosystems models, R, C or Fortran, and databases

Compensation

$35k/year salaried Visiting Fellow position with benefits and vacation Annual contract renewable up to 4 years.

To apply send cover letter, CV, and contact info for 3 references to dietze@bu.edu

PEcAn at NASA Carbon Cycle & Ecosystems Joint Science Workshop

April 2015 by Michael Dietze

Shawn Serbin, Toni Viskari, and Alexey Shiklomanov will be presenting posters at the NASA workshop on the work being done in PEcAn to couple ecosystem models to remotely-sensed data. In particular, check out Alexey's awesome work in developing the PEcAn RTM (Radiative Transfer Model) module. This modules is the basis for Alexey's hierarchical Bayes inversion of the PROSPECT leaf-level spectra model and linages between leaf economic and spectral traits.

Brown Dog @ NSF HQ

April 18, 2015 by Michael Dietze

The Brown Dog team is making a big presentation at NSF Headquarters about all the great tools being developed to make data more accessible and make data conversions and extractions easier. Mike Dietze is presenting work done by Betsy Cowdery, Rob Kooper, and others to develop the Brown Dog powered meteorology workflow in PEcAn. Look for more details in the next PEcAn version release (coming soon!). Also presenting some early work by Josh Mantooth on the start of the PEcAn vegetation data standards.

PEcAn at Montana State

March 23, 2015 by Michael Dietze

Mike Dietze presented PEcAn in a departmental seminar at Montana State. Thanks to Paul Stoy for hosting Mike in his visit to Montana State and to all the folks that came out to learn about PEcAn. Particularly exciting was a long discussion with Ben Poulter's lab about ways that PEcAn might contribute to their work with LPJ, LPJ-Guess, and ORCHIDEE

PEcAn Allometries at Harvard Forest 2015

March 17, 2015 by Michael Dietze

Adrien Finzi and Mike Dietze presented work at the Harvard Forest Annual Meeting on work to construct composite allometric equations for the dominant tree species at Harvard Forest using the PEcAn allometry module. This module will sythesize over multiple allometric equations and raw data to generate Hierarchical Bayes estimates of parameters, uncertainties, and site-to-site variability. This module can be applied to any individual species, species grouping, or plant functional type. Look for more from an in prep manuscript from Finzi, Dietze, and graduate student Josh Mantooth

PEcAn at NACP 2015

January 2015 by Michael Dietze

The PEcAn team will have a large presence at the North American Carbon Program's 5th All Investigator's Meeting in Washington DC, January 26-29, 2014.

On Tuesday, 3:12 pm Mike Dietze will be presenting a talk "The PEcAn Project: a scalable, multi-model platform for uncertainty quantification, analysis, and propagation" in the Uncertainty session

We will be organizing a hands-on PEcAn workshop at 7pm on Tuesday. Details here

Also look for poster presentations by Betsy Cowdery, Josh Mantooth, Afshin Pourmokhtarian, Christine Rollinson, and Alexey Shiklomanov

Presentations at AGU Fall Meeting 2014

posted Dec 12, 2014, 5:00 PM by Michael Dietze

The PEcAn team will be presenting the following talks and posters 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" Monday, December 15, 201401:40 PM - 06:00 PM Moscone West Poster Hall

B13C-0192 "Constraining carbon budgets at a regional scale: fusing forest inventory data with a cohort-based biosphere model" Monday, December 15, 2014 01:40 PM - 06:00 PM Moscone West Poster Hall

B13C-0198 "A Hierarchical Analysis of Tree Growth and Environmental Drivers Across Eastern US Temperate Forests" Monday, December 15, 201401:40 PM - 06:00 PM Moscone West Poster Hall

B52A-04 "Caught in the flux net: disentangling error, uncertainty, heterogeneity, and spatial process in biogeochemical scaling (Invited)" Friday, December 19, 2014 11:05 AM - 11:20 AM Moscone West 2002

B51G-0101 "Scaling Forest Management Practices in Earth System Models: Case Study of Southeast and Pacific Northwest Forests" Friday, December 19, 201408:00 AM - 12:20 PM Moscone West Poster Hall

B53D-0218 "Measured and modelled carbon and water fluxes in hybrid willows grown for biofuel production" Friday, December 19, 2014 01:40 PM - 06:00 PM Moscone West Poster Hall

B53I-07 "Integrating satellite and tower phenology: a case-study in real-time ecological forecasting" Friday, December 19, 201403:10 PM - 03:25 PM Moscone West 2002

Release of PEcAN v1.4.0

posted Dec 12, 2014, 5:00 PM by Michael Dietze

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. As always 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 the next release of PEcAn.

web 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 hte variables.

COST PROFOUND 2014

November 11-13, 2014 by Michael Dietze

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. This presentation on challenges in bringing models and data together focused heavily on PEcAn.

Mike will be particpating in a number of COST PROFOUND working groups and task groups. In particular, Mike Dietze and David Cameron (UK) will be co-orginizing Task Group 15 - Statistical problems in fitting models to heterogeneous data

PEcAn seminar at Columbia University

October 7, 2014 by Michael Dietze

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. Thanks to Maria Uriarte for hosting!

PEcAn Workshop and Seminar at Kent State

September 26, 2014 by Michael Dietze

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.

Thanks to Chris Blackwood for being a great host for both the seminar and workshop!

Dietze Tenure Talk

September 22, 2014 by Michael Dietze

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

PEcAn 1.3.7 Released

September 9, 2014 by Michael Dietze

Overview

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

As always 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 https://github.com/PecanProject/pecan/wiki/PEcAn-Configuration.

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.

PEcAn 2 Proposal Submitted

Aug 12, 2014 by Michael Dietze

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

PEcAn Summer Courses 2014

posted Aug 23, 2014, 2:14 PM by Michael Dietze

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 Team at ESA 2014

Aug 2014 by Michael Dietze

David LeBauer presented a talk entitled "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 on the presentation.

Dietze also presented a talk entitled "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.

PEcAn 1.3.6 Released

July 28, 2014 by Michael Dietze

This version focuses on more database updates.

As always you can download the VM from: http://isda.ncsa.illinois.edu/download/index.php?project=PEcAn&sort=category

add sites/data

the script to add sites is now part of PEcAn. To add the sites data you can use pecan/scripts/add.data.sh the script to add models is updated and will setup the binaries and is called pecan/scripts/add.models.sh Both scripts can be called multiple times, but will only add the information to the database once.

pecan.xml:

In pecan.xml the database section now has 2 subsections, bety and fia. Any existing information that was in the database section in pecan.xml will need to be moved to the bety subsection, read.settings() will automatically update your pecan.xml to reflect this. The <bety><write> option in the pecan.xml is now part of the <database><bety> section, read.settings() will automatically update your pecan.xml to reflect this. The ED land use/soil/vegetation/thermal sums data files are now inputs in BETY that need to be specified as inputs.

Action Required: add ED data files to database, see GitHub PEcAn Issue #120

SipNET

Support for meteorology conversion from netCDF CF standard to SipNET's .clim driver files PEcAn Web App

config.php now declares the fully qualified host name ($fqdn)

the config.php in pecan/web will have new database configuration parameters, please see config.example.php. no longer needed to specify vet/soil/ed_inputs in config.php, these are now stored as inputs in BETY. if the fia database is specified in config.php, the user can now select fia2ed from psscss selector. Action Required: update pecan/web/config.php, see pecan/web/config_example for latest settings.

BETY:

To update BETY database either download a new version or update the database.

In the database there is now a link from a model to the dbfiles table. This allows you to have a single model, with binaries located in different places on different systems. Each PFT now stores the model type associated with it, the web application will use this to find the right pfts to display for the user, and read.settings will check to see if the PFT is compatible with the model.

Action Required: add binaries to models, for example using the pecan/scripts/addmodels.sh.

Action Required: the migration of the database will add the appropriate model_type to each PFT based on the prefix of the PFT.

Brown Dog Early User Workshop

July 22, 2014 by Michael Dietze

Kenton McHenry (Brown Dog PI, PEcAn co-PI) hosted the Brown Dog Early User Workshop from July 22-13, 2014 at the National Center for Supercomputing Applications in Urbana, Illinois. Brown Dog is a new, NSF-sponsored cyberinfrastructure initiative to make unstructured, uncurated data more accessible to scientific community and the general public. Brown Dog consists of two key tools, the Data Access Proxy, which converts file formats, and the Data Tilling Service, which extracts useful information and meta-data.

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. Moving forward, Brown Dog will play a key roll in the PEcAn project, helping to manage flows of information into PEcAn and proccessing data into model drivers.

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 benifit BETY-db, the database that underlies PEcAn.

PEcAn Seminar for Harvard Forest REU program

July 2, 2014 by Michael Dietze

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

Concepts paper on ecological forecasting

May, 2014 by Michael Dietze


The following paper has been published

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. http://dx.doi.org/10.1890/ES13-00273.1

PEcAn 1.3.5 Released

Aug 2014 by Michael Dietze

Switch to PostgreSQL, enable distributed instances of BETYdb, maintaining local database changes

This version officially switches to postgreSQL. This allows for the script to enable to keep local changes to the PEcAn database.

This enables multiple instances to run BETYdb, and for local changes to be exchanged across databases. Each installation has a reserved set of foreign key ids (e.g. Boston University has 1,000,000,000-1,999,999,999 reserved. Edits to existing records added on another server will not be preserved.

New Phytologist meeting on modeling photosynthesis

April 22-25, 2014 by Michael Dietze

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 photosynthesic 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 by Michael Dietze

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.

LeBauer hosts forecasting software workshop

posted Mar 25, 2014, 2:04 PM by Michael Dietze


FORECAST RCN workshop, “Advancing Software for Ecological Forecasting”, March 25-27 2014, Urbana, IL


Mike Dietze was also in attendance

PEcAn synthesis paper across North America

posted Mar 19, 2014, 1:55 PM by Michael Dietze


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 by Michael Dietze


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

PEcAn Seminar at Woods Hole

January 28, 2014 by Michael Dietze

Mike Dietze presented the seminar talk "The PEcAn Project: Accessible ecoinformatic tools for carbon-cycle model-data analysis and assimilation" at the Ecosystems Center at the Marine Biological Laboratory in Woods Hole, MA.

Serbin NASA project recommended: Assimilating hyperspectral data

December 2013 by Michael Dietze


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

Presentations at AGU 2013

December 2013 by Michael Dietze

The following PEcAn presentations occurred at the American Geophysical Union Fall Meeting, December 2013, San Francisco

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"

Feng paper on photosynthesis module

December 2013 by Michael Dietze


The following paper describes the statistical model underlying the PEcAn photosynthesis module

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

Dietze teaches course in Ecological Forecasting

Fall 2013 by Michael Dietze


GE585 – Ecological Forecasting and Informatics was taught by Mike Dietze at Boston University in Fall of 2013

The course materials are available on GitHub

Presentations at ESA 2013

August 2013 by Michael Dietze


LeBauer and Dietze hosted a lunch-time workshop

"Combining Field Measurements and Ecosystem Models"


In addition, the following PEcAn presentations occurred at the Ecological Society of America Annual Meeting, 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 by Michael Dietze


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

LeBauer article in R Journal

June 2013 by Michael Dietze

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

PEcAn highlighted in Faculty of 1000 review

posted Jul 12, 2013, 7:32 PM by Michael Dietze

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

Undergrads exposed to model-data fusion

posted Jul 12, 2013, 7:19 PM by Michael Dietze

Dietze was invited back to Harvard Forest to present PEcAn to the summer REU students (June 12)

Some of our favorite quotes:

“I learned how data and models can be used to predict the ecological impacts of climate change, and
how data can be fed back into models in an iterative process that increases our understanding of the
mechanisms behind observed patterns and enables us to make better predictions. I learned about
Bayesian statistical analysis and how parameter distributions are constrained by real-world data to
reduce uncertainty.”

“I learned about ways in which my inquiries as a scientist could be better guided by methods I was
previously uninterested in.”

“That models should be made more accessible and usable to people other than the engineers of the
models. (I’m not going to lie; some of it went over my head a bit, however he was a very interesting
speaker.)”

“I had no idea before this workshop how useful modeling is to scientific progress.”

Spring Semester 2013 Talks

posted Jul 12, 2013, 7:11 PM by Michael Dietze

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).

Student PEcAn Programming Positions

posted Mar 27, 2013, 6:48 PM by David LeBauer [ updated Mar 27, 2013, 6:49 PM ]

Seeking web programmers to develop PEcAn (pecanproject.org), BETYdb (betydb.org) front-end and back-end features. These tools are used to manage information and generate predictions of ecosystem functioning.

Requirements: Strong skills in one or more of: PHP, SQL, Ruby, R, or C, Fortran.

All applicants should review the PEcAn wiki at github.com/pecanproject/pecan/wiki. It is a large project, so don't get overwhelmed with the underlying science or the system design. But take the time to find a piece of code in your preferred programming language that you understand and could contribute to. Also look at 'foreign' language code - R, Ruby, C, Fortran that you would be interested in learning.

Please contact someone on the People page for more information.

Job Opening: Scientific Web Programmer (Urbana, IL)

posted Mar 8, 2013, 1:07 PM by David LeBauer [ updated Mar 8, 2013, 1:13 PM ]

Link to Full Announcement

Energy Biosciences Institute

Institute for Genomic Biology

University of Illinois at Urbana-Champaign

We seek a scientific web application programmer to join the ecosystem modeling program in the Energy Biosciences Institute at the University of Illinois in Urbana Champaign. This is a 12-month non-tenure track Academic Professional position with possibility of renewal. Our group uses data syntheses and ecosystem simulation modeling to provide ecological forecasts to scientists as well as non-specialists. An important objective of our work is the development of user-friendly web interfaces to the computational tools that we are developing.

RESPONSIBILITIES: The programmer will work with our team to develop web resources for ecological data management, modeling, and statistical inference. The programmer will assume responsibility for the design, implementation, and maintenance of front-end and back-end software that will provide into effective interfaces and data visualizations for two software tools that we are developing.


The programmer will be expected to provide leadership in the development of new software and the adoption of best-practices to support development and quality control, to remain current on the latest web technologies, to apply new knowledge to a cutting edge system, and to provide leadership in web-based front-end design and implementation decisions.

Desired Skills:

• Programming experience with web interface/back end design using web framework systems.

• Experience with or willingness to learn Ruby, PHP, R, SQL, Ruby-on-Rails, R, GIS, MVC and REST

To Apply: Please create your candidate profile athttp://jobs.illinois.edu and upload your letter of interest (including email address), resume and contact information for three professional letters of reference by March 18, 2013.

PEcAn at NACP AIM4

posted Dec 21, 2012, 6:41 AM by Michael Dietze

The PEcAn team will play a number of roles at the upcoming 4th North American Carbon Program All-Investigators Meeting, 4 – 7 February 2013 in Albuquerque, New Mexico.

Most directly relevant to the PEcAn mission, Mike Dietze, Ankur Desai, Trevor Keenan, and Quinn Thomas will be chairing a breakout session "Harnessing the 'long tail' of ecosystem carbon cycle observations: Approaches and challenges in synthesizing and assimilating non-automated and experimental data". This session is intended to serve as a call-to-arms for a “community” approach to model calibration, data assimilation, evaluation, and improvement. Tools such as PEcAn play a critical role in achieving this goal but will only be effective if this new approach to the communication between models and data (and between modelers and empiricists) is embraced by the scientific community.

In addition, Desai and Dietze will serve as chairs for two of the six presentation sessions, "Theme 1: Diagnosis of the Atmospheric Carbon Cycle" and "Theme 4: Ecosystem Impacts of Change" respectively.

Toni Viskari joins PEcAn team

posted Dec 21, 2012, 6:25 AM by Michael Dietze


Dr. Toni Viskari will be joining the PEcAn team as a postdoctoral fellow in the Dietze lab starting January 1, 2013. Toni will be working on our NSF ABI project using the northern Wisconsin "ChEAS" project as a testbed for regional-scale multi-proxy data assimilation. Toni joins us from the and the Finnish Meteorological Institute and the University of Helsinki in Finland, where he recently defended his dissertation "Estimating particle number size distributions from multi-instrument observations with Kalman Filtering".

PEcAn at AGU 2012

posted Dec 21, 2012, 6:16 AM by Michael Dietze

The following PEcAn related talks and posters were presented at the 2012 meeting of the American Geophysical Union, December 3-7.

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


On improving the communication between models and data

posted Dec 21, 2012, 6:08 AM by Michael Dietze

Dietze, M.C., D. LeBauer, R. Kooper. On improving the communication between models and data. Plant, Cell, and Environment in press DOI: 10.1111/pce.12043 abstract & pdf

This is a review and perspective piece for a special issue on plant models in PC&E. While it is a review, it highlights PEcAn as an important case study and summarizes much of the motivation for what we are trying to do. The paper is also a call-to-arms for a community-based approach to model-data synthesis that envisions a larger role for experimentalists in assimilating data into models, using models to express non-trivial quantitative hypotheses, and identifying and reducing the dominant sources of uncertainty in their systems.


Abstract

The potential for model-data synthesis is growing in importance as we enter an era of ‘big data’, greater connectivity, and faster computation. Realizing this potential requires that the research community broaden its perspective about how and why they interact with models. Models can be viewed as scaffolds that allow data at different scales to inform each other through our understanding of underlying processes. Perceptions of relevance, accessibility, and informatics are presented as the primary barriers to broader adoption of models by the community, while an inability to fully utilize the breadth of expertise and data from the community is a primary barrier to model improvement. Overall we promote a community-based paradigm to model-data synthesis and highlight some of the tools and techniques that facilitate this approach. Scientific workflows address critical informatics issues in transparency, repeatability, and automation, while intuitive, flexible web-based interfaces make running and visualizing models more accessible. Bayesian statistics provides powerful tools for assimilating a diversity of data types and for the analysis of uncertainty. Uncertainty analyses enable new measurements to target those processes most limiting our predictive ability. Moving forward, tools for information management and data assimilation need to be improved and made more accessible.

PEcAn used to assess biofuel potential of hybrid Poplar

posted Dec 21, 2012, 5:56 AM by Michael Dietze


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. http://dx.doi.org/10.1890/12-0854.1 abstract

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. This analysis involved a trait meta-analysis, the use of sensitivity analysis and variance decomposition to identify dominant parameters, and the assimilation of annual yield data for three planting densities to further constrain these parameters. ED2 was then validated at eight additional sites distributed across the continental US, each with a range of genotypes and planting densities. Finally, the validated model was used to make a 0.5 degree projection of potential poplar yields and optimal rotation periods across the continental US and to make specific site-level projections about the changes in soil carbon relative to native forests and conventional agriculture. The most promising regions for poplar production are the Northeast, upper Midwest, and northern California, where projected poplar yields equal or exceed yields projected for Miscanthus, a highly productive perennial C4 grass being used for biofuel production.

PEcAn 1.2.6 Released

posted Sep 10, 2012, 7:03 PM by David LeBauer [ updated Sep 19, 2012, 8:17 AM by Michael Dietze ]

http://isda.ncsa.illinois.edu/download/index.php?project=PEcAn&sort=category

As of September 2012, PEcAn version 1.2.6 is 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. PEcAn 1.2.6 is being used for ongoing research and applications, while development of PEcAn 1.3 continues. It contains all of the modules described in "version 1.1", with added functionality, improved stability, and improved useability that represents an increasing community of scientists and developers:

PEcAn 1.1 Source Code Released

posted Sep 10, 2012, 5:41 PM by David LeBauer [ updated Sep 10, 2012, 5:41 PM by Michael Dietze ]

The public website is https://ebi-forecast.igb.illinois.edu/redmine/projects/pecan-1-0

The PEcAn version 1.1 source code includes 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 manuscriptFacilitating feedbacks between field measurements and ecosystem models (LeBauer et al in press). These files are provided here as an archived reference and accessibility. For further research, we recommend using the latest stable version available at www.pecanproject.org.

Join PEcAn as a Postdoctoral Fellow

posted Sep 7, 2012, 7:21 AM by David LeBauer [ updated Dec 21, 2012, 5:36 AM by Michael Dietze ]

Postdoctoral Fellow (Ecosystem Model-Data Synthesis & Forecasting), Boston University


[[note: this position has been filled]]

Model-data synthesis and forecasting across the upper Midwest: Partitioning uncertainty and environmental heterogeneity in ecosystem carbon


A post-doctoral position in ecosystem model-data synthesis and ecological forecasting is available in the Dietze lab in the Department of Earth and Environment at Boston University.

This project focuses on integrating eddy-covariance, remote-sensing, forest inventory data, and other ground-based measurements within the Ecosystem Demography 2.2 model to understand and forecast regional-scale ecosystem dynamics across northern Wisconsin. The project is part of the larger PEcAn project (http://pecanproject.org), which aims to make ecosystem models, data assimilation, and forecasting more accessible, automated, and repeatable.

As a test bed for the development and application of the PEcAn informatics tools, this project is focused on the temperate/boreal transition zone in northern Wisconsin, a region that is expected to show large climate change responses and is one of the most data-rich regions in the country. The tools developed here will enable us to partition carbon flux and pool variability in space and time and to attribute the regional-scale responses to specific biotic and abiotic drivers. The data-assimilation framework will partition different sources of uncertainty, which will enable a better understanding of which are limiting our inference, and provide a more complete propagation of uncertainty into model forecasts.

Qualifications:

Minimum qualifications are a doctoral degree in plant ecology or a related ecological or environmental science. Experience with, or interest in learning, Bayesian statistics, ecosystem modeling, remote-sensing, and ecoinformatics tools would be valuable. Salary is commensurate with experience and qualifications. Up to two years and four months of funding is available.

Submit a cover letter, CV, and contact info for 3 references to Dr. Michael Dietze (dietze at bu.edu) For more information visit http://pecanproject.org and MailScanner has detected a possible fraud attempt from "www.life.uiuc.edu" claiming to be http://people.bu.edu/dietze

PEcAn at FORECAST RCN 2012

posted Aug 22, 2012, 7:59 PM by Michael Dietze [ updated Aug 22, 2012, 7:59 PM ]


Mike Dietze will be presenting an invited talk on the PEcAn project at the FORECAST RCN meeting in Woods Hole, MA, October 9-11, 2012.

PEcAn at ForestSAT 2012

posted Aug 22, 2012, 7:56 PM by Michael Dietze [ updated Aug 22, 2012, 8:01 PM ]


Shawn Serbin will be presenting a talkFrom multiple datasets to predictive ecology: The PEcAn workflow and model-data assimilation” at the ForestSAT 2012 meeting in Corvallis, OR, September 11-14th in Corvallis, OR

PEcAn manuscript: Ecological Monographs

posted Aug 22, 2012, 7:51 PM by Michael Dietze [ updated Aug 22, 2012, 7:51 PM ]


The first manuscript describing the initial components of the PEcAn project has been 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

This link will be updated once the preprint manuscript is posted.

Now that this manuscript has been accepted we anticipate releasing v1.1 of the PEcAn software and Virtual Machine very soon, so please stay tuned!

PEcAn at ChEAS meeting 2012

posted Aug 22, 2012, 7:44 PM by Michael Dietze [ updated Aug 22, 2012, 7:44 PM ]


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 on June 27-29th 2012.


Carl Davidson defends Master's Thesis applying PEcAn to Alaskan Tundra

posted Aug 22, 2012, 7:39 PM by Michael Dietze [ updated Mar 8, 2013, 1:01 PM by David LeBauer ]

Carl Davidson successfully defended his Master's thesis on June 11th 2012 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. Carl used the PEcAn meta-analysis, sensitivity analysis, and variance decomposition in an iterative fashion to initially develop three tundra plant functional types (PFTs: graminoid, deciduous shrub, evergreen shrub) for the ED2 model for the tundra based on a literature synthesis. Based on this analysis Carl designed and executed a field campaign in 2011 at the Toolik LTER, a rare example of using model analysis to directly inform field research. Carl then again used PEcAn to assimilate his own field data as well as flux data from two Ameriflux sites. Finally, Carl applied the calibrated ED2 model to run model experiments aimed at disentangling the ecosystem feedbacks involved in post-fire recovery in the tundra.

The thesis is archived at the University of Illinois

PEcAn at PalEON summer course 2012

posted Aug 22, 2012, 7:28 PM by Michael Dietze [ updated Aug 22, 2012, 7:28 PM ]


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

Mike Dietze presented a total of 12 hours of lecture, tutorial, and hands-on demos using PEcAn, covering aspects of 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.