diff --git a/src/pages/about.module.css b/src/pages/about.module.css index 74440f4..e3a9bae 100644 --- a/src/pages/about.module.css +++ b/src/pages/about.module.css @@ -21,3 +21,8 @@ padding: 2rem; } } + +.workshopimages { + width: 600px; + height: 400px; +} diff --git a/src/pages/news.js b/src/pages/news.js index 953e755..476ca9a 100644 --- a/src/pages/news.js +++ b/src/pages/news.js @@ -3,623 +3,183 @@ import Layout from "@theme/Layout"; import "./News.css"; // Import your CSS file for styling function News() { - return ( - -
-

News

-
-

PEcAn 1.6.0 Released

- - October 2018 - - - - - - - -
- -

- - 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.
    • -
- -

-

-

-
-
- -
-

1oth World Dendro Conference Program

- - June 2018 - - - - - - - -
-

- -

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

- -

- -
- -
- -
-

AMS 33rd Conference

- - May 2018 - - - - - - - -
-

- -

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

- -

-
- -
- - -
-

Drought-Net Steering Committee Meeting

- - May 2018 - - - - - - - -
-

- -

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

- -

-
- -
- - -
-

Graduate Student Talk at LBL

- - April 2018 - - - - - - - -
-

- -

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

- -

-
- -
-
-

NASA Biodiversity and Ecological Forecasting Team Meeting

- - April 2018 - - - - - - - -
-

- -

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

- -

-

-
- -
- - - - - - - - -
-

qBio Seminar

- - April 2018 - - - - - - - -
-

- -

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

- -

-

-
- -
- - -
-

PEcAn Google Summer of Code 2018

- - March 2018 - - - - - - - -
-

- -

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!

- -

-

-
- -
- - -
-

PEcAn AGU Workshop

- - December 2017 - - - - - - - -
-

-

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. -

+ return ( + +
+

News

+
+

PEcAn 1.6.0 Released

+ + October 2018 + + + + + - - -
-

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.

+

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

-

-
- -
- - -
-
-

PEcAn Team at AGU 2017

- - December 11-15, 2016 - - - - - + + +
-

+

Major additions include: +

    +
  • A data ingest SHINY app that allows users to upload and register data from their own + local machine or from the DataOne.
    • +
  • Preliminary containerized modules of PEcAn using Docker.
    • +
  • Preliminary automated, Daily Forecasting using NOAA GEFS and the Sipnet model.
    • +
-
The PEcAn Team will be at the 2017 American Geophysical Union (AGU) Conference and will be - presenting the following talks and Posters:
+

+

+

+
+
-
Tuesday
+
+

1oth World Dendro Conference Program

+ + June 2018 + + + + + + + +
+

-

ORAL PP21D-06: Istem Fer "Paleoclimate reconstruction through Bayesian data assimilation", - 9:15 Room 343

+

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

-

ORAL Poster Hall D-F: Cristine Rollinson "Impacts of weather versus climate and driver - uncertainty on multi-centennial ecosystem model simulations", 10:35 Room 343

+

-

ORAL PP22A-05: Ann Raiho " Estimating the ecology of extinct species with paleoecological - data assimilation", 11:20 Room 343

+
-

ORAL B22C-07: Alexey Shiklomanov "Leaf optical properties shed light on foliar trait - variability at individual to global scales ", 11:50 Room 383-385

+
-
Wednesday
+
+

AMS 33rd Conference

+ + May 2018 + + + + + + + +
+

-

POSTER IN31A-0063: Rob Kooper "Data Flow for the TERRA-REF project", 8:00 Poster Hall D-F -

+

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"

-

PANEL B31H-04: Michael Dietze "Integration of Ecosystem Research Infrastructures for - Multiscale Analysis II", 8 - 10 am Rooms 383-385

+

+
-

Poster B31A-1979: Eugenie Euskirchen "Predicting Changes in Arctic Tundra Vegetation: Towards - an Understanding of Plant Trait Uncertainty", 08:00 - 12:20 Poster Hall D-F

+
-
Thursday
+
+

Drought-Net Steering Committee Meeting

+ + May 2018 + + + + + + + +
+

-

ORAL David LeBauer: "TERRA REF: Advancing phenomics with high resolution, open access sensor - and genomics data", 10:40 Room 383-385

+

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

-

ORAL Tony Gardella: "A multi-model assessment of terrestrial biosphere model data needs", - 2:25 Room 356-357

+

+
-
FRIDAY
-

Poster B51G-1893 Anne Thomas: "Assessing Ecosystem Model Performance in Semiarid Systems", - 8am Poster Hall D-F

+
-

Poster B53B-1953 Molly Aufforth "Constraining Agricultural Irrigation Surface Energy Budget - Feedbacks in Atmospheric Models", 1:40 pm Poster Hall D-F

-

ORAL H54D-01: Betsy Cowdery: "Looking Past Primary Productivity: Benchmarking System - Processes that Drive Ecosystem Level Responses in Models", 4 pm Room 298-299

+
+

Graduate Student Talk at LBL

+ + April 2018 + + + + + + + +
+

-

ORAL H54D-05: Shawn Serbin: "Evaluation of Multiple Mechanistic Hypotheses of Leaf - Photosynthesis and Stomatal Conductance against Diurnal and Seasonal Data from Two - Contrasting Panamanian Tropical Forests ", 5 pm Room 298-299

+

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.

-

ORAL B54B-07: Tess McCabe: "Integrating invasive grasses into carbon cycle projections: - Cogongrass spread in southern pine forests", 5:30 pm Room 388-390

+

+
-

-

-
- -
- -
- - -
-

FIA Annual Meeting

- - October 2017 - - - - - - - -
-

- 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. -

-

-
- -
- - -
-

GSOC Mentor Summit

- - October 2017 - - - - - - - -
-

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

-

-
- -
- -
-

COST-PROFOUND Final Conference

- - October 2017 - - - - - - - -
-

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

-

-
- -
-
-

PEcAn at ESA 2017

- - August 2017 - - - - - - - -
-

- 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. -

-
- -
- - -
-

PEcAn v1.5.0

- - July 2017 - - - - - - - -
- -

Added

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

    Changed

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

    -
    - -
    - -
    -

    PEcAn at Flux Course 2017

    - - July 2017 - - - - - - - -
    -

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

    -

    -
    - -
    -
    -

    Summer Developers

    - - May2017 - - - - - - - -
    -

    + +

    +

    NASA Biodiversity and Ecological Forecasting Team Meeting

    + + April 2018 + + + + + + + +
    +

    -

    Shubham Agarwal
    +

    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".

    -

    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. -

    -

    -

    -
    -
    - - - - - - -
    -

    Summer 2017 PEcAn developers

    - - May-August, 2017 - - - - - - - -
    -

    - 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. -

    -

    -
    -
    - - - -
    -

    PROFOUND Summer Course 2017

    - - May 5-10, 2017 - - - - - - - -
    -

    - 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. -

    - -

    -

    -
    -
    -

    PEcAn Team at AAG

    +

    qBio Seminar

    - April 5-9, 2017 + April 2018 @@ -627,57 +187,26 @@ function News() { +
    -

    PEcAn at NACP 2017

    +

    PEcAn Google Summer of Code 2018

    - March 26th-30th, 2017 + March 2018

    - 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

    +

    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?"

    -

    +

    @@ -686,3033 +215,3504 @@ function News() { +
    -

    DIBBS NSF Meeting

    +

    PEcAn AGU Workshop

    - January 11-12, 2017 + December 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.

    +

    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.

    -

    Agenda of the meeting - can be found here.

    +

    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!

    +

    -

    - 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

    -

    +

    +

    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.

    + + +

    +

    -
    -

    PEcAn v1.4.7 Release

    - - July 13, 2016 - - - - - - - -
    -

    CMIP5, Shiny, FLUXNET2015, Global Sensitivity

    -

    CMIP5:

    +
    +
    +

    PEcAn Team at AGU 2017

    + + December 11-15, 2016 + + + + + - - -
    +

    -

    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.

    +
    The PEcAn Team will be at the 2017 American Geophysical Union (AGU) Conference and will be + presenting the following talks and Posters:
    -

    Advanced Visualizations:

    +
    Tuesday
    -

    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:

    +

    ORAL PP21D-06: Istem Fer "Paleoclimate reconstruction through Bayesian data assimilation", + 9:15 Room 343

    -

    workflowPlot:

    +

    ORAL Poster Hall D-F: Cristine Rollinson "Impacts of weather versus climate and driver + uncertainty on multi-centennial ecosystem model simulations", 10:35 Room 343

    -

    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.

    +

    ORAL PP22A-05: Ann Raiho " Estimating the ecology of extinct species with paleoecological + data assimilation", 11:20 Room 343

    -

    global-sensitivity:

    +

    ORAL B22C-07: Alexey Shiklomanov "Leaf optical properties shed light on foliar trait + variability at individual to global scales ", 11:50 Room 383-385

    -

    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.

    +
    Wednesday
    -

    FLUXNET2015 and Ameriflux LBL:

    +

    POSTER IN31A-0063: Rob Kooper "Data Flow for the TERRA-REF project", 8:00 Poster Hall D-F +

    -

    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.

    +

    PANEL B31H-04: Michael Dietze "Integration of Ecosystem Research Infrastructures for + Multiscale Analysis II", 8 - 10 am Rooms 383-385

    -

    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.

    +

    Poster B31A-1979: Eugenie Euskirchen "Predicting Changes in Arctic Tundra Vegetation: Towards + an Understanding of Plant Trait Uncertainty", 08:00 - 12:20 Poster Hall D-F

    -

    Known issues:

    -

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

    +
    Thursday
    -

    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).

    +

    ORAL David LeBauer: "TERRA REF: Advancing phenomics with high resolution, open access sensor + and genomics data", 10:40 Room 383-385

    -

    In the pipeline:

    +

    ORAL Tony Gardella: "A multi-model assessment of terrestrial biosphere model data needs", + 2:25 Room 356-357

    -

    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.

    +
    FRIDAY
    +

    Poster B51G-1893 Anne Thomas: "Assessing Ecosystem Model Performance in Semiarid Systems", + 8am Poster Hall D-F

    -

    -
    - -
    -
    -

    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 -

    +

    Poster B53B-1953 Molly Aufforth "Constraining Agricultural Irrigation Surface Energy Budget + Feedbacks in Atmospheric Models", 1:40 pm Poster Hall D-F

    -

    -

    -
    - -
    - - -
    -

    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: -

    +

    ORAL H54D-01: Betsy Cowdery: "Looking Past Primary Productivity: Benchmarking System + Processes that Drive Ecosystem Level Responses in Models", 4 pm Room 298-299

    -
      -
    • 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
      • -
    +

    ORAL H54D-05: Shawn Serbin: "Evaluation of Multiple Mechanistic Hypotheses of Leaf + Photosynthesis and Stomatal Conductance against Diurnal and Seasonal Data from Two + Contrasting Panamanian Tropical Forests ", 5 pm Room 298-299

    -

    - 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. -

    +

    ORAL B54B-07: Tess McCabe: "Integrating invasive grasses into carbon cycle projections: + Cogongrass spread in southern pine forests", 5:30 pm Room 388-390

    + +

    +

    +
    + +
    + +
    + + +
    +

    FIA Annual Meeting

    + + October 2017 + + + + + + + +
    +

    + 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. +

    +

    +
    + +
    + + +
    +

    GSOC Mentor Summit

    + + October 2017 + + + + + + + +
    +

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

    +

    +
    + +
    + +
    +

    COST-PROFOUND Final Conference

    + + October 2017 + + + + + + + +
    +

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

    +

    +
    + +
    +
    +

    PEcAn at ESA 2017

    + + August 2017 + + + + + + + +
    +

    + 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. +

    +
    + +
    + + +
    +

    PEcAn v1.5.0

    + + July 2017 + + + + + + + +
    + +

    Added

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

    Changed

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

    +
    + +
    + +
    +

    PEcAn at Flux Course 2017

    + + July 2017 + + + + + + + +
    +

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

    +

    +
    + +
    +
    +

    Summer Developers

    + + May2017 + + + + + + + +
    +

    + +

    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. +

    + +

    +

    +
    +
    + + + + + + +
    +

    Summer 2017 PEcAn developers

    + + May-August, 2017 + + + + + + + +
    +

    + 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. +

    +

    +
    +
    + + + +
    +

    PROFOUND Summer Course 2017

    + + May 5-10, 2017 + + + + + + + +
    +

    + 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. +

    + +

    +

    +
    + +
    + + + +
    +

    PEcAn Team at AAG

    + + April 5-9, 2017 + + + + + + + +
    +

    + 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

    + +

    +

    +
    + +
    + +
    +

    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, 2017 + + + + + + + +
    +

    + 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 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 news-container + + +

    +
    + +
    + + + +
    +

    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

    -

    -

    -
    - -

    - - -
    -

    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
      • +
    • 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
    -

    -

    -

    -
    - -
    - -
    -

    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. +

    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. +
    2. The need to assess, track, and analyze model skill, + structure, and uncertainty;
      3. +
    3. The need to increase the accessibility of modeling tools +
      4. +
    +

    +
    +

    + +
    + +
    +

    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. https://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.

    +

    +
    +

    + +
    -

    -

    -
    - -
    - -
    -

    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. +

    +

    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 +

    +

    +
    +

    -

    -

    -
    - -
    - -
    -

    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. +

    +

    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. +

    +

    +
    +

    -

    -

    -
    - -
    - - -
    - -

    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" . +

    +

    LeBauer hosts forecasting software workshop

    + - - - -

    -

    -
    - -
    - -
    -

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

    - - July 2015 by David LeBauer - - - - - - - -
    -

    + posted Mar 25, 2014, 2:04 PM by Michael Dietze - 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 news-container - - -

    -
    - -
    - - - -
    -

    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. -

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

    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.

    + Meeting + webpage

    +

    + Mike Dietze was also in attendance -

    - 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 - -

    - - - - - - -
    -

    +

    +

    PEcAn synthesis paper across North America

    + - 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

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

    - 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

    + +

    + + + + + + +
    +

    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 + +
    +

    - 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

    +
    +

    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. +

    +

    +
    +

    -
      -
    • 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 -
    • +
    +

    Serbin NASA project recommended: Assimilating hyperspectral data

    + + December 2013 by Michael Dietze -
  • Maintain project webpage, wiki, email lists, and social - media
    • -
  • Design and improvement of user interfaces
    • +     +

    + + + + + + +
    +

    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 + +
    +

    -
  • 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
    • +
    +

    Presentations at AGU + 2013

    + + December 2013 by Michael Dietze -
  • Coordination of weekly developers meeting
    • - -

    Required Education, Training, and Skills

    +     +

    + + + + + + +
    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"
    + +
    +

    -
      -
    • BS/BA in a related field (e.g. ecology, environmental - science/analysis/policy, computer science, engineering)
      • +
    -
  • Previous programming experience
    • +
    +

    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 -
  • Quick to learn new skills, hard working, highly organized -
    • -
  • Excellent writing and communication skills
    • +
    +

    -
  • Able to travel
    • - +
    +
    +

    Dietze teaches + course in Ecological Forecasting

    + + Fall 2013 by Michael Dietze -

    Preferred Experience

    -
      -
    • Previous experience with open-source collaborative software - development
      • + +

      + + + + + + +
      +

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

      +
      The course materials are available on GitHub
      -
    • 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

    -

    -

    -
    -

    -
    +
    +

    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 + +
    +

    +
    -
    -

    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. -

    -

    -
    -

    -
    +
    +

    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 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 highlighted in + Faculty of 1000 review

    + -
    -
    -

    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

    -

    -
    -

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

    Presentations at AGU - Fall Meeting 2014

    - - posted Dec 12, 2014, 5:00 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
    +
    +

    - -

    - - - - - - -
    -

    - 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

    -

    -
    -

    -
    +
    +

    Undergrads exposed to + model-data fusion

    + -
    -

    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! -

    -

    -
    -

    -
    + 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.”
    +
    + +
    +

    +
    -
    -

    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.

    - -

    -
    -

    -
    +
    +

    Spring Semester 2013 Talks

    + -
    -

    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. -
    2. The need to assess, track, and analyze model skill, - structure, and uncertainty;
      3. -
    3. The need to increase the accessibility of modeling tools -
      4. -
    -

    -
    -

    -
    -
    -

    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 -

    -

    -
    -

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

    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.

    -

    -
    -

    + +

    + + + + + + +
    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). - +
    +

    -
    -

    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"

    -

    -
    -

    +
    +

    Student PEcAn Programming + Positions

    + -
    -
    -

    Concepts paper on ecological forecasting

    - - May, 2014 by Michael Dietze + posted Mar 27, 2013, 6:48 PM by David LeBauer - -

    - - - - + + + +

    +

    -

    -
    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. https://doi.org/10.1890/ES13-00273.1 - -
    + + + - -
    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.
    + +
    -

    -
    -

    -

    -
    -
    - -
    -

    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 - -

    - - Meeting - webpage

    -

    - 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 - -

    + +

    +

    PEcAn at NACP AIM4

    + + + + + posted Dec 21, 2012, 6:41 AM 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 - -
    + 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.
    + + + + +

    - +
    -

    PEcAn Seminar at Woods Hole

    +

    Toni Viskari joins PEcAn team +

    - January 28, 2014 by Michael Dietze + + + + posted Dec 21, 2012, 6:25 AM 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. -

    -

    -
    + + + + + + +

    +
    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".
    + +

    - -
    -

    Serbin NASA project recommended: Assimilating hyperspectral data

    +

    PEcAn at AGU 2012

    - December 2013 by Michael Dietze + + + posted Dec 21, 2012, 6:16 AM 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 - -
    -

    - -
    - + + + + + + +
    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
    +
    +

    +

    + +
    +

    -
    -

    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.”
    -
    + + + +
    +

    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. https://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.
    + +
    +

    +
    -
    -

    Spring Semester 2013 Talks

    - +
    +

    PEcAn 1.2.6 Released

    + - posted Jul 12, 2013, 7:11 PM by Michael Dietze + posted Sep 10, 2012, 7:03 PM by David LeBauer - -

    - - - - - - -
    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

    - + +

    + + + + + + +
    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 Mar 27, 2013, 6:48 PM by David LeBauer + posted Sep 10, 2012, 5:41 PM by David LeBauer - - -

    - - - - - - -
    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.
    -
    -

    -
    -
    -

    PEcAn at NACP AIM4

    - + +

    + + + + + + +
    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. +
    + +
    +

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

    PEcAn at FORECAST RCN 2012

    + - -

    - - - - - - -
    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.
    -
    -

    -
    + posted Aug 22, 2012, 7:59 PM by Michael Dietze -
    -

    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
    -
    -

    -

    - -
    -

    - -
    +     +

    + + + + + + +

    +
    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 used to - assess biofuel potential of hybrid Poplar

    - +
    +
    +

    PEcAn at ForestSAT 2012

    + - posted Dec 21, 2012, 5:56 AM by Michael Dietze + posted Aug 22, 2012, 7:56 PM 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. https://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 - - - - - - - - - -

    - - - - - - -
    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 - - - - - - - - - -

    - - - - - - -
    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. -
    -
    -

    -
    -
    -

    PEcAn at FORECAST RCN 2012

    - + +

    + + + + + + +

    +
    Shawn Serbin will be presenting a talk “From + 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 +
    + +
    +

    - posted Aug 22, 2012, 7:59 PM by Michael Dietze +
    +
    +

    PEcAn manuscript: + Ecological Monographs

    + - + posted Aug 22, 2012, 7:51 PM by Michael Dietze - - - -

    - - - - - - -

    -
    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 + +

    + + + + + + +
    +

    +
    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

    + - - - -

    - - - - - - -

    -
    Shawn Serbin will be presenting a talk “From - 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 -
    + posted Aug 22, 2012, 7:44 PM by Michael Dietze -
    -

    -
    -
    -

    PEcAn manuscript: - Ecological Monographs

    - - posted Aug 22, 2012, 7:51 PM by Michael Dietze + +

    + + + + + + +

    +
    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

    + - - -

    - - - - - - -
    -

    -
    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! -
    -
    -

    -
    + posted Aug 22, 2012, 7:39 PM by Michael Dietze -
    -

    PEcAn at ChEAS meeting 2012

    - - posted Aug 22, 2012, 7:44 PM by Michael Dietze - + +

    + + + + + + +
    +
    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
    + +
    +

    +
    - - - -

    - - - - - - -

    -
    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.
    -

    - -

    +
    +

    PEcAn at PalEON summer course + 2012

    + -
    -

    -
    -
    -

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

    - + posted Aug 22, 2012, 7:28 PM by Michael Dietze - posted Aug 22, 2012, 7:39 PM by Michael Dietze - + +

    + + + + + + +

    +
    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.
    + +
    +

    - - -

    - - - - - - -
    -
    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 - - - - - - - - -

    - - - - - - -

    -
    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.
    - -
    -

    - -
    -
    -     - ); + + + + ); } export default News; diff --git a/src/pages/workshops.js b/src/pages/workshops.js index b2693f5..147c98c 100644 --- a/src/pages/workshops.js +++ b/src/pages/workshops.js @@ -1,13 +1,82 @@ import React from "react"; import Layout from "@theme/Layout"; -function News() { +import styles from "./about.module.css"; +function Workshops() { return ( - -
    -

    Workshops

    + +
    +

    PEcAn 2 Terrestial Model Informatics Workshop 2016

    + +

    Information

    +

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

    +

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

    + +

    The goals of the meeting were to:

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

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

    + +

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

    + + +

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

    +
    +
    + Big Picture
    + +
    + Cyber-infrastructure Foundations
    +
    Provenance, Standards, Repeatability, Accessibility, Sharing & Communication, Transparency, Support for clusters, cloud, etc., Portability
    + +
    + Data Ingest
    +
    Drivers, Constraints, Initial Conditions, Traits, Data uncertainty
    + + +
    + Validation, Benchmarking & Visualization
    + +
    + Analysis
    +
    Model sensitivity, uncertainty, ensemble,etc.
    +
    + Tools for analyzing specific data types
    + +
    + Calibration
    +
    Trait meta-analysis, parameter data assimilation
    + +
    State Data Assimilation
    + +
    + Multi-model Synthesis
    +
    Adding Models
    +
    Growing the PEcAn community
    +
    Challenges with running multiple models, tools for MIPs
    + +
    +

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

    + +
    ); } -export default News; +export default Workshops;