+
+ );
+};
+
+const CardList = () => {
+ const half = Math.ceil(contributors.length / 2);
+ const firstHalf = contributors.slice(0, half);
+ const secondHalf = contributors.slice(half);
+ return (
+
+
+
+
+
+
+
+
+ {props.name}
+ {props.role}
+
+ 
+
+
+ {props.profession}
+ {
+ window.location = `mailto:${props.email}`;
+ e.preventDefault();
+ }}
+ >
+ {props.email}
+
+
+
+
+ );
+};
+export default CardList;
diff --git a/src/components/HomepageFeatures.js b/src/components/HomepageFeatures.js
new file mode 100644
index 00000000..89deb2ac
--- /dev/null
+++ b/src/components/HomepageFeatures.js
@@ -0,0 +1,153 @@
+import React, { useEffect, useState } from "react";
+import styles from "./HomepageFeatures.module.css";
+import nsf from "../../static/img/nsf.png";
+import nasa from "../../static/img/nasa-logo.png";
+import dep from "../../static/img/dep-energysvg.png";
+import energy from "../../static/img/energy-bio.png";
+import { Timeline } from "react-twitter-widgets";
+const FeatureList = [
+ {
+ title: "A state-of-the-art ecosystem model",
+ Svg: require("../../static/img/nature.svg").default,
+ description: (
+ <>
+ The Predictive Ecosystem Analyzer (PEcAn) is an integrated informatics
+ toolbox for ecosystem modeling. PEcAn consists of:
+
+ {firstHalf.map((person, index) => (
+
+
+ {secondHalf.map((person, index) => (
+
+ -
+
- + An application program interface (API): + +
- + It encapsulates an ecosystem model, providing a common interface, + inputs, and output. + + +
- + Web-based user interface + +
- + An accessible web-based user interface and visualization tools + + +
- + Extensible collection of modules + +
- + An extensible collection of modules to handle specific types of + analyses , model-data syntheses , and data processing{" "} + +
+
+ );
+ if (index % 2 == 0)
+ return (
+
+ {" "}
+
+
+
+
+ {title}
+{description}
+
+
+ );
+ return (
+
+ {" "}
+
+
+
+
+ {title}
+{description}
+
+
+ );
+}
+
+export default function HomepageFeatures() {
+ const [width, setWidth] = useState(undefined);
+ useEffect(() => {
+ if (typeof window !== "undefined") {
+ function handleResize() {
+ setWidth(window.innerWidth);
+ }
+ window.addEventListener("resize", handleResize);
+ handleResize();
+ return () => window.removeEventListener("resize", handleResize);
+ }
+ }, []);
+ return (
+
+
+ {title}
+{description}
+
+ {" "}
+
+
+
+
+
+
+ );
+}
diff --git a/src/components/HomepageFeatures.module.css b/src/components/HomepageFeatures.module.css
new file mode 100644
index 00000000..d819fdf1
--- /dev/null
+++ b/src/components/HomepageFeatures.module.css
@@ -0,0 +1,110 @@
+/* stylelint-disable docusaurus/copyright-header */
+
+.featureContainer {
+ display: flex;
+ justify-content: space-around;
+ align-items: center;
+ padding: 2rem 0;
+ width: 100%;
+}
+.features {
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ padding: 2rem 2rem;
+}
+.featureSvg {
+ height: 300px;
+ width: 300px;
+ /* margin: 0 2rem; */
+}
+.headContainer {
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ justify-content: center;
+
+ /* max-width: "10px"; */
+}
+.quote {
+ text-align: center;
+ font-size: 1.5rem;
+ font-style: italic;
+}
+.quote::before {
+ content: '"';
+
+ color: #25c2a0;
+}
+.quote::after {
+ content: '"';
+ color: #25c2a0;
+}
+.paragraph {
+ max-width: 50%;
+ margin: 0 1rem;
+ font-weight: 200;
+ /* background-color: var(--ifm-color-emphasis-200); */
+ padding: 10px;
+}
+.cardContainer {
+ max-width: 650px;
+ background-color: var(--ifm-color-emphasis-200);
+ border-radius: 10px;
+ padding: 2rem;
+ height: max-content;
+ margin: 0.25rem;
+ /* margin: 1rem 8rem; */
+}
+/* .cardContainer h1 {
+ font-size: larger;
+} */
+/* .cardContainer p {
+ font-size: 1rem;
+} */
+.foot {
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ flex-direction: column;
+}
+.timeline {
+ margin: 5rem 0 0;
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ flex-direction: column;
+}
+.imageContainer {
+ display: flex;
+ justify-content: space-between;
+}
+.imageContainer .image {
+ width: 5rem;
+ height: 5rem;
+ margin: 0.254rem;
+}
+@media (max-width: 900px) {
+ .paragraph {
+ max-width: 60%;
+ }
+ .featureContainer {
+ display: flex;
+ flex-direction: column;
+ justify-content: center;
+ align-items: center;
+ padding: 4rem 0;
+ width: 100%;
+ }
+ /* .cardContainer{
+ margin: 1rem 4rem;
+ } */
+}
+@media only screen and (max-width: 600px) {
+ .paragraph {
+ max-width: 100%;
+ }
+ .featureContainer {
+ justify-content: center;
+ }
+}
diff --git a/src/components/PeopleCard.js b/src/components/PeopleCard.js
new file mode 100644
index 00000000..e3f7c19c
--- /dev/null
+++ b/src/components/PeopleCard.js
@@ -0,0 +1,37 @@
+import React from "react";
+import clsx from "clsx";
+import { Link } from "react-router-dom";
+import styles from "./people.module.css";
+const PeopleCard = (props) => {
+ console.log(props);
+ return (
+
+
+
+ Our Mission
+
+ {" "}
+
+ + Develop and promote accessible tools for reproducible ecosystem + modeling and forecasting +
+
+
+
+ {FeatureList.map((props, idx) => (
+
+
+
+ Acknowledgements
+
+ 
+ 
+ 
+ 
+
+
+
+
+
+ );
+};
+export default PeopleCard;
diff --git a/src/components/people.module.css b/src/components/people.module.css
new file mode 100644
index 00000000..322639b9
--- /dev/null
+++ b/src/components/people.module.css
@@ -0,0 +1,34 @@
+.card {
+ margin: 2rem;
+ max-width: 400px;
+ flex: 1 1 auto;
+}
+
+.mainContainer {
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ margin: 0;
+ padding: 0 5rem;
+ max-width: 100%;
+}
+
+.column {
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ flex: 1;
+ margin: 0 1rem;
+}
+
+@media (max-width: 768px) {
+ .mainContainer {
+ flex-direction: column;
+ padding: 0;
+ }
+
+ .column {
+ margin: 0;
+ width: 100%;
+ }
+}
\ No newline at end of file
diff --git a/src/css/custom.css b/src/css/custom.css
new file mode 100644
index 00000000..d9804e33
--- /dev/null
+++ b/src/css/custom.css
@@ -0,0 +1,79 @@
+/* stylelint-disable docusaurus/copyright-header */
+/**
+ * Any CSS included here will be global. The classic template
+ * bundles Infima by default. Infima is a CSS framework designed to
+ * work well for content-centric websites.
+ */
+@import url("https://fonts.googleapis.com/css2?family=Montserrat:ital,wght@0,100;0,200;0,300;0,400;1,100;1,200;1,300&display=swap");
+/* You can override the default Infima variables here. */
+:root {
+ --ifm-color-primary: #25c2a0;
+ --ifm-color-primary-dark: rgb(33, 175, 144);
+ --ifm-color-primary-darker: rgb(31, 165, 136);
+ --ifm-color-primary-darkest: rgb(26, 136, 112);
+ --ifm-color-primary-light: rgb(70, 203, 174);
+ --ifm-color-primary-lighter: rgb(102, 212, 189);
+ --ifm-color-primary-lightest: rgb(146, 224, 208);
+ --ifm-code-font-size: 95%;
+ --ifm-font-family-base: "Montserrat", sans-serif;
+ --ifm-font-family-monospace: "Montserrat", sans-serif;
+}
+html[data-theme="dark"] {
+ --ifm-navbar-background-color: #242526;
+}
+.docusaurus-highlight-code-line {
+ background-color: rgb(72, 77, 91);
+ display: block;
+ margin: 0 calc(-1 * var(--ifm-pre-padding));
+ padding: 0 var(--ifm-pre-padding);
+}
+.navbar img {
+ border-radius: 15px !important;
+}
+.footer {
+ --ifm-footer-color: #93a0ac;
+ --ifm-footer-link-color: #93a0ac;
+ --ifm-footer-title-color: #93a0ac;
+}
+.header-github-link:hover {
+ opacity: 0.6;
+}
+
+.header-github-link:before {
+ content: "";
+ width: 24px;
+ height: 24px;
+ display: flex;
+ background: url("data:image/svg+xml,%3Csvg viewBox='0 0 24 24' xmlns='http://www.w3.org/2000/svg'%3E%3Cpath d='M12 .297c-6.63 0-12 5.373-12 12 0 5.303 3.438 9.8 8.205 11.385.6.113.82-.258.82-.577 0-.285-.01-1.04-.015-2.04-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729 1.205.084 1.838 1.236 1.838 1.236 1.07 1.835 2.809 1.305 3.495.998.108-.776.417-1.305.76-1.605-2.665-.3-5.466-1.332-5.466-5.93 0-1.31.465-2.38 1.235-3.22-.135-.303-.54-1.523.105-3.176 0 0 1.005-.322 3.3 1.23.96-.267 1.98-.399 3-.405 1.02.006 2.04.138 3 .405 2.28-1.552 3.285-1.23 3.285-1.23.645 1.653.24 2.873.12 3.176.765.84 1.23 1.91 1.23 3.22 0 4.61-2.805 5.625-5.475 5.92.42.36.81 1.096.81 2.22 0 1.606-.015 2.896-.015 3.286 0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12'/%3E%3C/svg%3E")
+ no-repeat;
+}
+html[data-theme="dark"] .header-github-link:before {
+ background: url("data:image/svg+xml,%3Csvg viewBox='0 0 24 24' xmlns='http://www.w3.org/2000/svg'%3E%3Cpath fill='white' d='M12 .297c-6.63 0-12 5.373-12 12 0 5.303 3.438 9.8 8.205 11.385.6.113.82-.258.82-.577 0-.285-.01-1.04-.015-2.04-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729 1.205.084 1.838 1.236 1.838 1.236 1.07 1.835 2.809 1.305 3.495.998.108-.776.417-1.305.76-1.605-2.665-.3-5.466-1.332-5.466-5.93 0-1.31.465-2.38 1.235-3.22-.135-.303-.54-1.523.105-3.176 0 0 1.005-.322 3.3 1.23.96-.267 1.98-.399 3-.405 1.02.006 2.04.138 3 .405 2.28-1.552 3.285-1.23 3.285-1.23.645 1.653.24 2.873.12 3.176.765.84 1.23 1.91 1.23 3.22 0 4.61-2.805 5.625-5.475 5.92.42.36.81 1.096.81 2.22 0 1.606-.015 2.896-.015 3.286 0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12'/%3E%3C/svg%3E")
+ no-repeat;
+}
+html[data-theme="light"] .card {
+ background: #f5f5f5;
+ transition: all 0.5s ease-in;
+}
+html[data-theme="light"] .card:hover {
+ background: #cfcfcf;
+}
+html[data-theme="dark"] .card:hover {
+ background: #1d1c1c;
+}
+.mdx-page .row {
+ display: flex;
+ flex-direction: column !important;
+ justify-content: center !important;
+ align-items: center !important;
+}
+.documentation .main-wrapper{
+ height: 100vh;
+ width: 100%;
+}
+.documentation iframe {
+ display: block;
+ width: 100%;
+ height: 100%;
+ border: none;
+}
diff --git a/src/pages/News.css b/src/pages/News.css
new file mode 100644
index 00000000..d9b918c1
--- /dev/null
+++ b/src/pages/News.css
@@ -0,0 +1,39 @@
+/* News.css */
+
+.news-container {
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ justify-content: flex-start;
+ margin: 0 auto;
+ padding: 2rem;
+ max-width: 800px; /* Adjust the max-width as needed */
+
+
+ }
+
+.tutorial-container {
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ justify-content: center; /* Change from 'flex-start' to 'center' */
+ margin: 0 auto;
+ padding: 2rem;
+ max-width: 800px; /* Adjust the max-width as needed */
+ }
+
+
+/* Media query for screens with a maximum width of 600px */
+@media (max-width: 600px) {
+ .news-container {
+ padding: 1rem; /* Adjust padding for smaller screens */
+ max-width: 100%; /* Make sure it doesn't exceed the viewport width */
+ }
+}
+
+/* Media query for screens with a maximum width of 1200px */
+@media (max-width: 1200px) {
+ .news-container {
+ max-width: 600px; /* Adjust max-width for medium-sized screens */
+ }
+}
\ No newline at end of file
diff --git a/src/pages/about.js b/src/pages/about.js
new file mode 100644
index 00000000..6ff8683d
--- /dev/null
+++ b/src/pages/about.js
@@ -0,0 +1,97 @@
+import React from "react";
+import Layout from "@theme/Layout";
+import styles from "./about.module.css";
+import clsx from "clsx";
+function Hello() {
+ return (
+
+
+
+
+
+
+
+
+ {props.name}
+ {/* {props.role} */}
+
+
+
+
+ {/* {props.education} */}
+ {/* {
+ window.location = `mailto:${props.email}`;
+ e.preventDefault();
+ }}
+ >
+ {props.email}
+ */}
+
+
+
+ About Us
+
+ {" "}
+
+
+
+
+
+
+
+ Our Vision
+
+
+ + Climate change science has witnessed an explosion in the + amount and types of data that can be brought to bear on the + potential responses of the terrestrial carbon cycle and + biodiversity to global change. Many of the most pressing + questions about global change are not necessarily limited by + the need to collect new data as much as by our ability to + synthesize existing data. This project specifically seeks to + improve this ability. +
+
+
+
+
+
+
+ Our Intuition
+
+
+ + Because no one measurement provides a complete picture, + multiple data sources must be integrated in a sensible manner. + Process-based models represent an ideal framework for + integrating these data streams because they represent multiple + processes at different spatial and temporal scales in ways + that capture our current understanding of the causal + connections across scales and among data types. +
+
+
+
+
+
+
+ Our Solution
+
+
+ + Three components are required to bridge this gap between the + available data and the required level of understanding:{" "} +
-
+
- a state-of-the-art ecosystem model +
- + a workflow management system to handle the numerous + streams of data + +
- + a data assimilation statistical framework in order to + synthesize the data with the model + +
+
+
+
+
+
+ Acknowledgements
+
+
+ + The PEcAn project is supported by the National Science + Foundation (ABI #1062547, ABI #1458021, DIBBS #1261582, ARC + #1023477, EF #1318164, EF #1241894, EF #1241891), NASA + Terrestrial Ecosystems, the Department of Energy (ARPA-E + awards #DE-AR0000594 and DE-AR0000598), the Energy Biosciences + Institute, and an Amazon AWS in Education Grant. PEcAn is + open-source and built using open source software. +
+
+
+ );
+};
+
+const Alumni = () => {
+ // Splitting the projectAlumni array into two
+ const half = Math.ceil(projectAlumni.length / 2);
+ const firstHalf = projectAlumni.slice(0, half);
+ const secondHalf = projectAlumni.slice(half);
+
+ return (
+
+
+
+
+
+
+
+
+ {props.name}
+ {props.role}
+
+
+
+
+ {props.profession}
+ {
+ window.location = `mailto:${props.email}`;
+ e.preventDefault();
+ }}
+ >
+ {props.email}
+
+
+
+
+ + Project Alumni +
+
+
+
+ {firstHalf.map((person, index) => (
+
+
+ {secondHalf.map((person, index) => (
+
+
+
+
+ {" "}
+
+
+
+
+
+
+
+
+
+ Latest Release Documentation
+
+ {" "}
+
+
+
+
+
+
+
+
+
+ Latest Code Documentation
+ +
+ {" "}
+
+
+
+
+
+
+
+
+
+ Release V1.7.1
+ +
+ {" "}
+
+
+
+
+
+
+
+
+
+ Release 1.7.0
+ +
+ {" "}
+
+
+
+
+
+
+
+
+
+ Release V1.6.0
+ +
+ {" "}
+
+
+
+
+
+
+
+
+
+ Release V1.5.3
+ +
+ {" "}
+
+
+
+
+
+
+
+
+
+
+ Release V1.5.1
+ +
+ {" "}
+
+
+
+
+
+
+
+
+
+
+
+ Release V1.5.0
+ +
+ {" "}
+
+
+
+
+
+
+
+
+
+
+
+
+ Release V1.4.10.1
+ +
+
+ Google Summer of Code (GSoC)
+
+ {" "}
+
+
+
+
+
+
+
+
+
+
+
+
+ What is GSoC?
+ For over 10 years Google has sponsored a global program that pairs students with open source software development projects. For three months over the summer students receive real world experience contributing to software development and guidance from mentors. On the other hand, participating organizations are able to bring in new developers to grow their code base. Overall, GSoC helps open source communities grow and thrive. Thousands of student and organization from around the world have participated and now you can too! ++ + +
Project Ideas
+ + Ecosystem science has many components, so does PEcAn! Some Project ideas can be found here on our project ideas list. + ++ +
How to apply?
+ + There are two steps to the application process: + +-
+
- Getting acquainted with the project, mentors and ideas +
- Writing a good proposal +
+ +
Getting acquainted with the project, mentors and ideas
+ + The first step is for you to get acquainted with the PEcAn project, the ideas and to introuduce + yourself with the mentors. This will help you get a significantly better proposal, and will + make it more like for us to rate your propsal higher. + ++ +
-
+
- Choose a project from our project ideas list or come up with your own. +
- Join the #gsoc-2023 channel in our slack workspace and introduce yourself +
- Send message to your project-specific mentors indicating that you are interested in their idea and how you plan to implement the idea +
+ + When talking to the mentors, use the following questions to introuduce yourself: + +
+ +
-
+
- What interests you most about our project? +
- What is your background, and what made you pick the specific idea? +
- What is your familiarity with the recommended technologies? +
- As mentors and project coordinators, how can we get the best out of you? +
- Is there anything that you’ll be studying or working on whilst working alongside us? +
+ +
Writing a good proposal
+ + Next, write and submit your GSoC proposal after discussing this with the mentor. In the proposal make sure to + include a well-defined, weekly schedule with clear milestones and deliverables around it. Make sure to include + in your schedule any time you need to learn new technologies, as well as make sure that before the + evaluations dates, you have a deliverable that we can use to evaluate. We understand that schedules change, but it + would be good to add some must haves to your list of deliverables that will make your project a success as well + as some extra goals in case you have additional time at the end. + ++ + See also Google's proposal guidelines + +
+ + Good Luck + + + +
+
+ GSoC - PEcAn Project Ideas
+
+ {" "}
+
+
+
+
+
+
+
+
+
+
+ Ecosystem science has many components, so does PEcAn! Some of those components where you can contribute. Below is a list of potential ideas. Feel free to contact any of the mentors in slack, or feel free to ask questions in our #gsoc-2023 channel in slack.
+
+
+ +
+ +
+ +
+ +
+ +
+ + +
+ +
+ + +
Project Ideas
+ + Following is a list of project ideas, use this list to contact the appropriate mentors on slack. Feel free to propose your own ideas as well, + in this case contact @kooper on slack so he can put you in contact with the best mentors. + + ++ +
PEcAn packages & CRAN [R package development]
+ + PEcAn is implemented as a set of R packages, but the user must currently download and install all the packages as a single unit. The short-term goal of this project is to focus on fixing warnings in the build process, refactoring to remove unnecessary dependencies, and potentially splitting modules. The medium-term goal is to increase the reliability of PEcAn’s integration tests, and thus this year’s package development will prioritize the packages that are most associated with overall workflow bottlenecks (e.g., PEcAn.data.atmosphere, which is focused on downloading and processing meteorological data). The longer-term goal is to make PEcAn packages available on CRAN (the primary R package archive) which will not only make it easier to install, but also easier to find and easier to use standalone modules. ++ +
-
+
- Expected outcome: +
- PEcAn packages pass checks and integration tests without warnings. Packages are made available in CRAN. +
- Prerequisites: +
- R; experience with R packages is helpful, but most of the process is covered in chapters on R package releases in the book ‘rOpenSci packages’ and the book ‘R packages’ by Hadley Wickham +
- Contact person: +
- Chris Black, @infotroph; Mike @Dietze +
- Duration: +
- Size: 175 hours for proposals that focus on dependency removal, 350 hours for proposals that split modules. +
- Difficulty: +
- Easy, we anticipate the ability for multiple people to work on this project since different individuals can focus on different PEcAn R packages. +
+ +
PEcAn model coupling and development [Data Science]
+ + PEcAn has the capability to interface multiple ecological models. The goal of this project is to improve the coupling of existing models to PEcAn (specifically FATES) and add new models (specifically a simple vegetation model that is under development). It is also possible to contribute to the development of the simple vegetation model which is written in fortran. ++ +
-
+
- Expected outcome: +
- New or improved PEcAn model packages. +
- Prerequisites: +
- R. Fortran is an advantage. +
- Contact person: +
- Hui Tang @Hui Tang, Istem Fer @istfer +
- Duration: +
- Flexible to work as either a Small (175hr) or Large (350 hr) +
- Difficulty: +
- Medium +
+ +
Input Processing / Asynchronous workflow execution [Data Science]
+ + One of the goals of PEcAn is to be able to run different ecological models (which require a range of data inputs) and compare the model outputs with actual measurements (a.k.a. data constraints). The goal of this project is twofold, depending on the specific interests of the GSOC student. +-
+
- The current PEcAn input processing occurs mostly within the primary runtime workflow, but numerous PEcAn applications would benefit from the ability to update near real-time data asynchronously with model execution, handling different data streams in parallel. As part of this we’d also like to make it easier to use PEcAn input processing modules as stand alone tools. This subproject also leverages a joint effort with the Red Hat Collaboratory. +
- Increase the number of input products supported. Students may focus on one or more of the following:
+
-
+
- Add the NMME seasonal weather forecast as an meteorological drivers +
- Add remote sensing data streams: NASA GEDI lidar, solar induced fluorescence e.g., NASA OCO-2, OCO-3, thermal e.g., NASA ECOSTRESS + +
- Extend our existing support for ingesting data from the National Ecological Observatory Network NEON soil moisture and soil respiration data products. This will involve developing integrating NEONSoils code into PEcAn and internal code from the Dietze lab on soil moisture gap-filling and downscaling. +
+
+ +
-
+
- Prerequisites: +
- R. +
- Contact person: +
- @Ankur Desai, Istem Fer @istfer +
- Duration: +
- 1. data workflow update [size: large (350hr)]; 2. Individual data packages: [size: small (175 hr) for one, large for 2-3 data packages] +
- Difficulty: +
- 1 data update [difficulty: hard]; 2. Individual data packages: 2.1 easy, 2.2 easy, 2.3 medium +
+ +
GitHub Actions
+ + Currently GitHub Actions will check to see if there are newer versions of the packages installed. We need to limit these checks since they are limited by GitHub. Additionally we do a simple test of SIPNET, it would be great if that can use the full docker stack to test a full run. ++ + In the past year we have created a dashboard that shows how tests are performing. It would be great to have a test that runs the tests using the develop stack and writes the test results back into a file in a special branch. As part of this task the dashboard will need to be updated to fetch the data from this branch. +
+ +
-
+
- Expected outcome: +
- New GitHub actions that do not take as long to run, and have the ability to do larger tests. +
- Prerequisites: +
- GitHub Actions, Docker +
- Contact person: +
- Rob Kooper @kooper +
- Duration: +
- Flexible to work as either a Small (175hr) or Large (350 hr) +
- Difficulty: +
- Medium, Large if running and updating the integration testing dashboard +
+ + +
SDA Dashboard
+ + This project is primarily focused on the interactive visualization of outputs from our carbon cycle forecast and data assimilation system. This project builds on a previously-developed site-level R Shiny dashboard that is no longer functional, and aims to extend this to a much larger number of sites. We also hope to integrate in functionality from one of our other dashboards (which visualizes spatial interactions) and advances made by external collaborators. If time permits, we’d also like to resurrect our automated email alert system. + ++ +
-
+
- Expected outcome: +
- The aims here are:
+
-
+
- Resurrect a previously-developed R Shiny dashboard for our carbon cycle forecast system , potentially integrating in work done by the Ecological Forecasting Initiative on their dashboard and FMI’s Field Observatory +
- Merge in the functionality from our data assimilation dashboard +
- Resurrect the automated email alert system that sent a subset of visualizations, and links to the full app, to users for the sites they are interested in. +
+ - Prerequisites: +
- R, R Shiny, data visualization +
- Contact person: +
- Mike @Dietze, @HenriKajasilta +
- Duration: +
- Flexible to work as either a Small (175hr) or Large (350 hr) +
- Difficulty: +
- Medium +
+ +
Finish and Deploy New Website
+ + This project includes migrating content and deploying a new version of the PEcAn website. + The code hosted at https://github.com/PecanProject/web was developed during a previous GSOC. + ++ +
-
+
- Expected outcome: +
- The primary aims are to migrate content from the old website and then deploy the new PEcAn website, + as described in + pecanproject/web Issue 11. + Additional ideas may be proposed. +
- Prerequisites: +
- Experience with javascript, git, and web development preferred. +
- Contact person: +
- David LeBauer @dlebauer, Eshan Tripathi @eshan +
- Duration: +
- Small (175hr) +
- Difficulty: +
- Easy +
+
+ {siteConfig.title}
+{siteConfig.tagline}
+
+
+ Get started
+
+
+
+
+ News
+
+
+
+
+
+
+ PEcAn 1.6.0 Released
+ +|
+
+ + + 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: +
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+
+
+
+
+
+
+
+ 1oth World Dendro Conference Program
+ +|
+ + + 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
+ +|
+ + + 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
+ +|
+ + + 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
+ +|
+ + + 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. + + + |
+
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+
+
+
+
+
+
+
+
+
+
+ NASA Biodiversity and Ecological Forecasting Team Meeting
+ +|
+ + + 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
+ +|
+ + + 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
+ +|
+ + + 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
+ +|
+ + 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 Team at AGU 2017
+ +|
+ + + The PEcAn Team will be at the 2017 American Geophysical Union (AGU) Conference and will be + presenting the following talks and Posters:+ +Tuesday+ +ORAL PP21D-06: Istem Fer "Paleoclimate reconstruction through Bayesian data assimilation", + 9:15 Room 343 + +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+ +POSTER IN31A-0063: Rob Kooper "Data Flow for the TERRA-REF project", 8:00 Poster Hall D-F + + +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+ +ORAL David LeBauer: "TERRA REF: Advancing phenomics with high resolution, open access sensor + and genomics data", 10:40 Room 383-385 + +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 + +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 + +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
+ +|
+ + 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
+ +|
+ + 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
+ +|
+ + 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
+ +|
+ + 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
+ +|
+
+ Added + +Changed + + |
+
+
+
+
+
+
+ PEcAn at Flux Course 2017
+ +|
+ + Mike Dietze, Ankur Desai, Betsy Cowdery, and James Simkins are all returning to teach at + this year's Flux Course. + + + |
+
+
+
+
+
+
+
+
+
+
+
+ Summer Developers
+ +|
+ + + 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
+ +|
+ + 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
+ +|
+ + 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
+ +|
+ + 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
+ +|
+ + 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 + + + + + + + |
+
+
+
+
+
+
+ DIBBS NSF Meeting
+ +|
+ + 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". + + + + |
+
+
+
+
+
+
+ PEcAn v1.4.7 Release
+ +
+
+ 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
+ +|
+ + 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! + + + |
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+
+
+
+
+
+ PEcAn at Harvard Forest REU
+ +|
+ + 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. + + + |
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+
+
+
+
+
+ Ecological Forecasting book accepted!
+ +|
+ + 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. + + + |
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+
+
+
+ PEcAn at ESA Sustaining Biological Infrastructure Workshop
+ +|
+ + 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 + |
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+
+
+ PEcAn at PROFOUND spring course
+ +|
+
+ Mike Dietze again taught at PROFOUND spring school on Bayesian model
+ calibration.
+
+ Additional information about the course can be found here + + + + + |
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+
+ PEcAn at ILAMB meeting
+ +|
+ + + 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" + + |
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+
+
+
+
+
+ PEcAn Workshop May 2016
+ +|
+ + + + The PEcAn Workshop was held from May 9th-11th, 2016 at Boston University + with the goals to: + + +
+ 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
+ +|
+ + + 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: +
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+
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+
+
+
+
+
+ PEcAn at NACP workshop
+ +|
+ + + 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. + + + + |
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+
+
+
+
+ PEcAn 1.4.5 Released
+ +|
+ + + 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: +
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+
+
+ PEcAn at the 2016 INTERFACE meeting
+ +|
+ + + 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. + + + + |
+
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+
+ PEcAn at the ED Community meeting
+ +|
+ + + 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. + + + + |
+
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+ PEcAn Presentation at NEON Workshop "Operationalizing Ecological Forecasting" +
+ +|
+ + + 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. + + + + |
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+ PEcAn Team at AGU 2015
+ +|
+ + + 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 + + + + + |
+
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+
+
+
+ PEcAn 1.4.4 Released
+ +|
+ + + 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: +
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+
+
+ PEcAn presentation at DOE workshop "Trait Methods for Representing Ecosystem + Change"
+ +|
+ + + 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. + + + + |
+
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+
+
+
+ PEcAn talk at University of Georgia
+ +|
+ + + 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 + + + + |
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+ PEcAn at ESA Centennial
+ +|
+ + + 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 + + + + |
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+ NCSA features PEcAn 1.4.3 in news
+ +|
+ + + 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" . + + + + + + + |
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+ Two DOE ARPA-E grants will support high throughput plant phenotyping
+ +|
+ + + 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
+ +|
+ + + 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
+ +|
+ + + 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: +
|
+
+
+
+
+
+
+
+
+
+
+ New PEcAn Project Manager
+ ++
|
+ + 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
+ ++
|
+ + + 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
+ + +|
+
+
+ Mike Dietze is presenting the following talk on PEcAn at the
+ International Association for Landscape Ecology (IALE 2015) World Congress in
+ Portland Oregon. |
+
+
+
+
+
+
+
+
+ PEcAn presentation for Harvard Forest REU's
+ ++
|
+ + 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
+ ++
|
+ + + 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
+ ++
|
+
+
+ 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. |
+
+
+
+
+
+
+
+
+ PEcAn talk at University of New Hampshire
+ ++
|
+ + + 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
+ ++
|
+ + + 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
+ ++
|
+ + + 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+ +
Required Education, Training, and Skills+ +
Preferred Experience+ +
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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
+
+ 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
+ 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
+ ++
|
+ + + 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: +
|
+
+
+
+
+
+
+
+
+ PEcAn Summer Courses 2014
+ ++
|
+ Hands-on tutorials on using PEcAn were presented at the 2014 + editions of the Niwot Ridge Flux Course and the PalEON summer course + Assimilating Long Term Data into Ecosystem Models + + + |
+
+
+
+
+
+
+
+
+ PEcAn Team at ESA 2014
+ ++
|
+ + 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
+ ++
|
+ 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
+ ++
|
+ 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
+ ++
|
+ 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
+ ++
|
+ 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
+ ++
+ 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
+ ++
|
+ + 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
+ ++
|
+ + 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
+ ++
+ + 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
+ ++
|
+ |
+
+
+
+
+
+
+
+
+
+ Dietze paper on modeling photosynthesis
+ ++
Dietze M. 2013. Gaps + in knowledge and data driving uncertainty in models of photosynthesis. + Photosynthesis Research 19:3-14 DOI: 10.1007/s11120-013-9836-z + + |
+
+
+
+
+
+
+
+
+
+ PEcAn Seminar at Woods Hole
+ ++
|
+ + Mike Dietze presented the seminar talk "The PEcAn Project: + Accessible ecoinformatic tools for carbon-cycle model-data analysis and + assimilation" at the Ecosystems Center at the Marine Biological Laboratory in + Woods Hole, MA. + + + |
+
+
+
+
+
+
+
+
+
+ Serbin NASA project recommended: Assimilating hyperspectral data
+ ++
|
+ |
+
+
+
+
+
+
+
+
+ Presentations at AGU + 2013
+ ++
| 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
+ ++
|
+ 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
+ ++
|
+ The course materials are available on GitHub
+
+ |
+
+
+
+
+
+
+
+
+
+ Presentations at ESA 2013
+ ++
|
+ 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
+ ++
|
+ |
+
+
+
+
+
+
+
+
+ LeBauer article in R Journal +
+ ++
| 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
+ ++
|
+ 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
+ ++
| Dietze was invited back to Harvard Forest to
+ present PEcAn to the summer REU students (June 12) Some of our favorite quotes:
+
+
+
+ “I learned how data and models can be used to predict the ecological impacts of climate
+ change, and
+ how data can be fed back into models in an iterative process that increases our
+ understanding of the
+ mechanisms behind observed patterns and enables us to make better predictions. I learned
+ about
+ Bayesian statistical analysis and how parameter distributions are constrained by
+ real-world data to
+ reduce uncertainty.”
+ “I learned about ways in which my inquiries as a scientist could be better guided by
+ methods I was
+ previously uninterested in.”
+ “That models should be made more accessible and usable to people other than the engineers
+ of the
+ models. (I’m not going to lie; some of it went over my head a bit, however he was a very
+ interesting
+ speaker.)”
+ “I had no idea before this workshop how useful modeling is to scientific progress.”
+ |
+
+
+
+
+
+
+
+
+
+
+
+ Spring Semester 2013 Talks
+ ++
| 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
+ ++
| 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 PEcAn team will play a number of roles at
+ the upcoming 4th North American Carbon Program All-Investigators Meeting, 4 – 7 February 2013 in
+ Albuquerque, New Mexico. Most directly relevant to the PEcAn mission, Mike Dietze, Ankur Desai, Trevor Keenan, and Quinn
+ Thomas will be chairing a breakout session "Harnessing the 'long tail' of ecosystem carbon
+ cycle observations: Approaches and challenges in synthesizing and assimilating non-automated
+ and experimental data". This session is intended to serve as a call-to-arms for a
+ “community” approach to model calibration, data assimilation, evaluation, and improvement. Tools
+ such as PEcAn play a critical role in achieving this goal but will only be effective if this new
+ approach to the communication between models and data (and between modelers and empiricists) is
+ embraced by the scientific community.
+ In addition, Desai and Dietze will serve as chairs for two of the six presentation sessions,
+ "Theme 1: Diagnosis of the Atmospheric Carbon Cycle" and "Theme 4: Ecosystem Impacts of Change"
+ respectively.
+
+ |
+
+
+
+
+
+
+
+ Toni Viskari joins PEcAn team +
+ ++
+ 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
+ ++
| 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
+ |
+
+
+
+
+
+
+
+
+
+
+ PEcAn used to + assess biofuel potential of hybrid Poplar
+ ++
|
+ 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
+ ++
| 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 +
+ ++
| 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
+ ++
+ 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
+ ++
+ 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
+
+
+ |
+
+
+
+
+
+
+
+
+ PEcAn manuscript: + Ecological Monographs
+ ++
|
+ 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
+ ++
+ 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.
+ Agenda and slides can be found at: http://flux.aos.wisc.edu/twiki/bin/view/Main/ChEASMeeting2012
+ |
+
+
+
+
+
+
+
+
+ Carl Davidson defends Master's Thesis applying PEcAn to Alaskan Tundra
+ ++
|
+ 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
+ ++
+ 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.
+
+ |
+
+
+ + Publications +
+ +- LeBauer, D.S., D. Wang, K. Richter, C. Davidson, and M.C. Dietze (2013). Facilitating feedbacks between field measurements and ecosystem models. Ecological Monographs. [doi:10.1890/12-0137.1](https://doi.org/10.1890/12-0137.1) +- Wang, D, D.S. LeBauer, and M.C. Dietze (2013). Predicting yields of short-rotation hybrid poplar (Populus spp.) for the contiguous US through model-data synthesis. Ecological Applications [doi:10.1890/12-0854.1](https://doi.org/10.1890/12-0854.1) +- Dietze, M.C., D.S LeBauer, and R. Kooper (2013). On improving the communication between models and data. Plant, Cell, & Environment [doi:10.1111/pce.12043](https://doi.org/10.1111/pce.12043) +- Dietze, Michael C., Shawn P. Serbin, Carl Davidson, Ankur R. Desai, Xiaohui Feng, Ryan Kelly, Rob Kooper et al. "A quantitative assessment of a terrestrial biosphere model's data needs across North American biomes." Journal of Geophysical Research: Biogeosciences 119, no. 3 (2014): 286-300. +- Viskari, Toni, Brady Hardiman, Ankur R. Desai, and Michael C. Dietze. "Model-data assimilation of multiple phenological observations to constrain and predict leaf area index." (2015) [doi:10.1890/14-0497.1](https://doi.org/10.1890/14-0497.1) +- Shiklomanov. A, MC Dietze, T Viskari, PA Townsend, SP Serbin. 2016 "Quantifying the influences of spectral resolution on uncertainty in leaf trait estimates through a Bayesian approach to RTM inversion" Remote Sensing of the Environment 183: 226-238 +- LeBauer, David, Rob Kooper, Patrick Mulrooney, Scott Rohde, Dan Wang, Stephen P. Long, and Michael C. Dietze. "BETYdb: a yield, trait, and ecosystem service database applied to second‐generation bioenergy feedstock production." GCB Bioenergy (2017). diff --git a/src/pages/tutorials.js b/src/pages/tutorials.js new file mode 100644 index 00000000..14febedc --- /dev/null +++ b/src/pages/tutorials.js @@ -0,0 +1,139 @@ +import React from "react"; +import Layout from "@theme/Layout"; +import "./News.css"; // Import your CSS file for styling + +function Tutorials() { + return ( +
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ + Hands On Demos:
+ +PEcAn Tutorial v1.5.2
+
+ Tutorial 1
+
+ Tutorial 2
+
+ PEcAn Tutorial v1.5.0
+
+ Tutorial 1
+
+ Tutorial 2
+
+ PEcAn Tutorial v1.4.0
+
+ Survey
+
+ PEcAn Tutorial v1.3.7
+
+ Survey
+
+ PEcAn Tutorial v1.3.0
+ PEcAn Tutorial v1.2.6
+
+ + Vignettes: +
+ +R Packages
+ + + +MCMC - in development
+
+
+
+
+
+
+
+
+
+
+
+