This release has a number of bug fixes and added functionality. All can be seen listed here. The VM can be downloaded here.

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.

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

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

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

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.

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

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

The PEcAn project has been selected to participate in Google Summer of Code(GSoC) once again for 2018. We are excited to work with more great developers. Information about our project and how to apply can be found on our GSoC page.

The application period is from March 12th-27th, but we welcome all interested developers to contact us to discuss projects and/or the application process and start coding!

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

The Event will be held at the Hilton next to the New Orleans convention center:

Hilton New Orleans Riverside, 2 Poydras St., New Orleans, LA 70140 Third Floor - Parish Room

The demonstration will entail a general overview of the project and breakout groups in which members of the PEcAn team will lead hands-on tutorials and take questions. Attendance is free and open to whomever shows up, so please encourage your colleagues and collaborators to come.

The Science Team meeting will focus on high-level development goals and user needs for the coming year. This will be the first year we’re opening up the Science Team meeting to beyond the core development team. The meeting is open to all, but we’re particularly interested in touching base with projects that are funded to use PEcAn or are otherwise invested in setting up PEcAn-based projects. Confirmation of attendance is appreciated but not required.

Istem attended the FIA Stakeholder Science Meeting this year in Park City, Utah. She presented her work on assimilating demographical data into model and validating model against FIA data.

Alexey and Betsy attended the Google Summer of Code Mentor Summit as a result of our project's successful participation in the Google Summer of Code Program. We look forward to participating again next year and having more developers successful contribute to our project.

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 (pun intended)."

Many of PEcAn and Dietze Lab members will be attending and presenting at this year's Ecological Society of America's conference in Portland Oregon.

Added

Changed

Mike Dietze, Ankur Desai, Betsy Cowdery, and James Simkins are all returning to teach at this year's Flux Course.

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, in the online dating domain. Shubham is currently enrolled in the one year, Masters (MSIAM) Data Science specialization program offered jointly by Universite Grenoble Alpes and Grenoble INP, Grenoble, France. He will be working on our GSoC project 'Scientific Visualization' over the summer, specifically responsible for our Shiny Dashboard visualization of our model endpoints.

Aman Kumar

Aman Kumar graduated with a Bachelor of Engineering from BMS Institute of Technology & Management Bangalore, India. He has always been a tech enthusiast and web technologies, Offensive security, Distributed technologies, Big data interest him the most. Currently, he is working on replacing the current VM distributions technique with docker containers and modularizing it into smaller independent parts like PEcAn-Core, PEcAn-web, Postgresql & Bety so it will become easy to maintain.

Anne Thomas

This summer, Anne Thomas will be contributing to the benchmarking module of PEcAn, putting together multi-model benchmarks for semi-arid and arid ecosystems as well as working on the overall benchmarking workflow. A lifelong nature lover and a growing programming nerd, Anne is studying Conservation Biology and Bioinformatics at Brigham Young University. After she completes her undergraduate degree she plans to pursue a PhD in computational ecology with the goal of addressing conservation challenges like climate change with programming power.

Google Summer of Code ,BU RECS ,BU UROP , and other programs have afforded us the opportunity to have number of undergradaute and graduate researchers contribute to the project over the Summer of 2017. Please stay tuned for individual profiles.

Mike Dietze attended the 3rd PROFOUND Spring School: Baysian calibrartion, forecasting and multi-model prediction of process-base vegetation models in Rencurel/Grenoble, France as a lecturer.

A report fom the course can be found by clicking on this link.

Three PEcAn team members participated in the American Association of Geographers (AAG) Annual Meeting in Boston this year.

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

Elizabeth Cowdery - Accessible tools for Multi-Model Benchmarking: Evaluating Productivity Predictions Under Elevated CO2 Conditions

Tess McCabe - Validating the Ecosystem Demography Model Version2 for Southern Pine Forests

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

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

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.

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!

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.

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.

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

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

Additional information about the course can be found here

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"

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 onYouTube. Slides from the workshop are available here.

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 hereand 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

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.

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 hereand 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

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.

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.

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.

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

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 hereand 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

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.

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

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 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" .

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.

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

Just in time for Flux CoursePEcAn 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

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.

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!

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.

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.

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.

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.

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.

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!

Summary

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

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

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.

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.

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

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

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

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

Overview

pecan.xml Changes

web changes

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

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!

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!

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.

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.

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

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

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.

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.

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.

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"

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.

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

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.

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.