Migrate news section to blog (fixes #115)

Author: raman976

blog/2012-12-31-year-in-review.md

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+---
+title: 2012 Year in Review
+authors: [david_lebauer]
+tags: [news, conferences, publications, releases]
+---
+
+A roundup of PEcAn project activities and highlights from 2012.
+
+<!--truncate-->
+
+## Major Milestones
+
+### PEcAn manuscript: Ecological Monographs (August 2012)
+
+The first manuscript describing the initial components of the PEcAn project was accepted for publication:
+
+LeBauer, D.S., D. Wang, K.T. Richter, C.C. Davidson, M.C. Dietze. Feedbacks between measurements and ecosystem models. Ecological Monographs _in press_
+
+### PEcAn used to assess biofuel potential of hybrid Poplar (December 2012)
+
+Wang, Dan, David LeBauer, and Michael C. Dietze. _In press._ Predicting yields of short-rotation hybrid poplar (Populus spp.) for the contiguous US through model-data synthesis. Ecological Applications. https://doi.org/10.1890/12-0854.1
+
+In this paper the PEcAn workflow was used to calibrate the Ecosystem Demography model (ED2) for hybrid poplar using a combination of trait data and yield data. The validated model was used to make projections of potential poplar yields and optimal rotation periods across the continental US. The most promising regions for poplar production were identified as the Northeast, upper Midwest, and northern California.
+
+## Software Releases
+
+### PEcAn 1.2.6 Released (September 2012)
+
+As of September 2012, PEcAn version 1.2.6 became the latest stable version. This version was released for the August 2012 summer course "Assimilating long-term data into ecosystem models" that taught methods advanced by the PalEON project. Available at: http://isda.ncsa.illinois.edu/download/index.php?project=PEcAn&sort=category
+
+### PEcAn 1.1 Source Code Released (September 2012)
+
+The PEcAn version 1.1 source code was released, including an R package with functions and R scripts used to run the PEcAn workflow. The PEcAn 1.1 Virtual Machine can reproduce all of the computational steps used in the manuscript "Facilitating feedbacks between field measurements and ecosystem models" (LeBauer et al in press).
+
+## Conferences and Presentations
+
+### PEcAn at AGU 2012 (December 3-7, 2012)
+
+The following PEcAn related talks and posters were presented at the 2012 meeting of the American Geophysical Union:
+
+- B22B-08: "The modeled effects of fire on carbon balance and vegetation abundance in Alaskan tundra" - Michael C. Dietze; Carl D. Davidson; Ryan Kelly; Philip E. Higuera; Fengsheng Hu
+- B34B-04: "What do we need to measure, how much, and where? A quantitative assessment of terrestrial data needs across North American biomes through data-model fusion and sampling optimization" (Invited) - Michael C. Dietze; Carl D. Davidson; Ankur R. Desai; Xiaohui Feng; Ryan Kelly; Rob Kooper; David S. LeBauer; Joshua Mantooth; Kenton McHenry; Shawn P. Serbin; Dan Wang
+- B41C-0296: "A Web Interface for Eco System Modeling" - Kenton McHenry; Rob Kooper; Shawn P. Serbin; David S. LeBauer; Ankur R. Desai; Michael C. Dietze
+- B41C-0306: "The use of informed priors in ecosystem model-data fusion" - David S. LeBauer; Michael C. Dietze
+
+### PEcAn at FORECAST RCN 2012 (October 9-11, 2012)
+
+Mike Dietze presented an invited talk on the PEcAn project at the FORECAST RCN meeting in Woods Hole, MA.
+
+### PEcAn at ForestSAT 2012 (September 11-14, 2012)
+
+Shawn Serbin presented a talk "From multiple datasets to predictive ecology: The PEcAn workflow and model-data assimilation" at the ForestSAT 2012 meeting in Corvallis, OR.
+
+### PEcAn at ChEAS meeting 2012 (June 27-29, 2012)
+
+Mike Dietze, Shawn Serbin, and Ankur Desai each presented a number of short talks on the PEcAn project at the annual investigator's meeting for the Chequamegon Ecosystem Atmosphere Study (ChEAS) held at the Kemp Biological Station, WI. Agenda and slides: http://flux.aos.wisc.edu/twiki/bin/view/Main/ChEASMeeting2012
+
+## Training and Education
+
+### PEcAn at PalEON summer course 2012 (August 2012)
+
+PEcAn was used for all aspects of the modeling and data assimilation activities in the week-long summer course "Assimilating Long-Term Data into Ecosystem Models" offered at the University of Notre Dame Environmental Research Center (UNDERC), Land O' Lakes, WI.
+
+Mike Dietze presented 12 hours of lecture, tutorial, and hands-on demos using PEcAn, covering workflows for model calibration and analysis, parameter data assimilation at the Sylvania flux tower, and state-variable data assimilation of tree ring data.
+
+PEcAn allowed students to go from coring trees Monday, mounting them Tuesday, and analyzing them Wednesday, to calibrating SIPNET Thursday using trait databases and flux tower data and assimilating the tree ring data on Friday.
+
+## Student Achievements
+
+### Carl Davidson defends Master's Thesis applying PEcAn to Alaskan Tundra (June 11, 2012)
+
+Carl Davidson successfully defended his Master's thesis on ["The modeled effects of fire on carbon balance and vegetation abundance in Alaskan tundra"](https://www.ideals.illinois.edu/handle/2142/34234).
+
+Carl's thesis represents an incredible case-study in the application of the PEcAn system, using meta-analysis, sensitivity analysis, and variance decomposition to develop tundra PFTs, designing field campaigns based on model analysis, and assimilating field and flux data.
+
+## Team Updates
+
+### Toni Viskari joins PEcAn team (December 21, 2012)
+
+Dr. Toni Viskari joined the PEcAn team as a postdoctoral fellow in the Dietze lab starting January 1, 2013. Toni worked on the NSF ABI project using the northern Wisconsin "ChEAS" project as a testbed for regional-scale multi-proxy data assimilation. Toni joined from the Finnish Meteorological Institute and the University of Helsinki.
+
+## Upcoming Events
+
+### PEcAn at NACP AIM4 (February 4-7, 2013)
+
+The PEcAn team announced their planned participation at the 4th North American Carbon Program All-Investigators Meeting in Albuquerque, New Mexico. Mike Dietze, Ankur Desai, Trevor Keenan, and Quinn Thomas planned to chair a breakout session on "Harnessing the 'long tail' of ecosystem carbon cycle observations: Approaches and challenges in synthesizing and assimilating non-automated and experimental data".

blog/2013-12-31-year-in-review.md

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+---
+title: 2013 Year in Review
+authors: [david_lebauer]
+tags: [news, conferences, publications]
+---
+
+A roundup of PEcAn project activities and highlights from 2013.
+
+<!--truncate-->
+
+## Conferences and Presentations
+
+### Presentations at AGU 2013 (December 2013)
+
+The following PEcAn presentations occurred at the American Geophysical Union Fall Meeting:
+
+- Viskari, Dietze, Desai: "Model-data assimilation of multiple phenological observations to constrain and forecast leaf area"
+- Serbin, Dietze, Desai, LeBauer, Viskari, Kooper, McHenry, Townsend: "Assimilation of Leaf and Canopy Spectroscopic Data to Improve the Representation of Vegetation Dynamics in Terrestrial Ecosystem Models"
+
+### Presentations at ESA 2013 (August 2013)
+
+LeBauer and Dietze hosted a lunch-time workshop: "Combining Field Measurements and Ecosystem Models"
+
+Additional PEcAn presentations at the Ecological Society of America Annual Meeting in Minneapolis, MN:
+
+- Dietze: "Assimilating forest inventory data into models"
+- LeBauer, Dietze, Jaiswal, Kooper, Long, Serbin, Wang: "Reducing uncertainty through data-driven model development"
+- Hardiman, Serbin, Mantooth, Kennedy, Dietze: "Assimilating PALSAR remote sensing data to reduce uncertainty in ED2 predictions of forest biomass dynamics following disturbance"
+
+### Kooper presents PEcAn at XSEDE13 (July 2013)
+
+Kooper R, K McHenry, M Dietze, D LeBauer, S Serbin, A. Desai. 2013. Ecological Cyberinfrastructure and HPC Towards More Accurately Predicting Future Levels of Greenhouse Gases. Proceedings of XSEDE13: Extreme Science and Engineering Discovery Environment
+
+## Publications
+
+### PEcAn highlighted in Faculty of 1000 review (July 2013)
+
+LeBauer et al. 2013 was recommended in two different reviews on F1000. You can read the reviews at http://f1000.com/prime/718024607
+
+### LeBauer article in R Journal (June 2013)
+
+LeBauer D, M. Dietze, B. Bolker. 2013. Translating Probability Density Functions: From R to BUGS and Back Again. R Journal Vol. 5/1, June, 207-209
+
+### Feng paper on photosynthesis module (December 2013)
+
+Feng X, M Dietze. 2013. Scale-dependence in the effects of leaf economic traits on photosynthesis: Bayesian parameterization of photosynthesis models. New Phytologist 200(4): 1132–1144 DOI: 10.1111/nph.12454 [link](http://onlinelibrary.wiley.com/doi/10.1111/nph.12454/full)
+
+This paper describes the statistical model underlying the PEcAn photosynthesis module.
+
+## Grants and Projects
+
+### Serbin NASA project recommended: Assimilating hyperspectral data (December 2013)
+
+The proposal "Assimilation of imaging spectroscopy data to improve the representation of vegetation dynamics in ecosystem models" led by Shawn Serbin, with Mike Dietze and Phil Townsend as co-PIs, was recommended for funding by NASA. This project focuses on assimilating hyperspectral data in the PEcAn framework by building a Radiative Transfer Model into the Ecosystem Demography model.
+
+## Teaching and Outreach
+
+### Dietze teaches course in Ecological Forecasting (Fall 2013)
+
+GE585 – Ecological Forecasting and Informatics was taught by Mike Dietze at Boston University in Fall of 2013. The course materials are available on [GitHub](https://github.com/EcoForecast).
+
+### Undergrads exposed to model-data fusion (June 2013)
+
+Mike Dietze was invited back to Harvard Forest to present PEcAn to the summer REU students (June 12). Student feedback highlighted their newfound appreciation for how data and models can work together iteratively and how modeling is useful to scientific progress.
+
+### Spring Semester 2013 Talks (Spring 2013)
+
+Mike Dietze presented talks on the PEcAn project at the Boston University EBE Seminar series (April 1), Harvard University's ClimateTEA (April 2), and at Harvard Forest (May 2).
+
+## Community Building
+
+### Student PEcAn Programming Positions (March 2013)
+
+The project advertised for web programmers to develop PEcAn and BETYdb front-end and back-end features, seeking skills in PHP, SQL, Ruby, R, C, or Fortran.

blog/2014-09-09-pecan-1-3-7-released.md

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+---
+title: PEcAn 1.3.7 Released
+authors: [tony_gardella]
+tags: [release, pecan, dalec]
+---
+
+PEcAn version 1.3.7 has been released with better support for new model types and the addition of the DALEC model.
+
+<!--truncate-->
+
+## Overview
+
+This version supports new model types better. BETY now allows you to add new model types to the database. You can associate these model types with PFTs. Each model type will have a list of required and optional inputs associated. These inputs will be listed in the `<run><inputs>` tag.
+
+The latest VM can be downloaded from http://isda.ncsa.illinois.edu/download/index.php?project=PEcAn&sort=version
+
+## Support for DALEC
+
+A new model has been added to this release, DALEC. BETY already has a modeltype DALEC in the database to support this model.
+
+## pecan.xml Changes
+
+Using the new modeltypes we can now check the inputs specified in the pecan.xml file. All inputs should now be listed under the `<run><inputs>`. The code will try and update your pecan.xml file to this new format. Any missing inputs that are required will quit the run, allowing you to quickly fix your pecan.xml file.
+
+For updated information see the [PEcAn Configuration wiki](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.

blog/2014-12-12-pecan-1-4-0-released.md

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+---
+title: PEcAn 1.4.0 Released
+authors: [tony_gardella]
+tags: [release, pecan]
+---
+
+PEcAn version 1.4.0 has been released with major new meteorological data handling capabilities.
+
+<!--truncate-->
+
+## Overview
+
+This version supports conversion of met files. The code can now download and convert the met data to CF standard and to model specific format. The met data will along the way be gap filled. This allows any researchers to pick any Ameriflux site and run the SIPNET model on this site.
+
+The latest VM can be downloaded from [NCSA](http://isda.ncsa.illinois.edu/download/index.php?project=PEcAn&sort=version).
+
+## pecan.xml Changes
+
+The met tag can now support a special notation that lets it download and convert the met data. The met tag can have an `input="Ameriflux"` and `output="sipnet"` attribute. Currently these are the only supported conversion but more will be added in future releases of PEcAn.
+
+## Web Interface Changes
+
+When running in the web interface you now have the ability to edit the pecan.xml before the software runs. This allows you to change the number of ensemble runs done, as well as any other changes to the pecan.xml.
+
+After the run finishes, you can now download the sipnet clim file used for a particular run. You can now also plot different variables against each other instead of time vs one of the variables.