LeBauer:Software

From OpenWetWare

Overview

This page is a reference of the programs that I use. This is mostly a log of how I configure the programs on my desktop. Details on my specific use of some of these programs can be found by clicking links.

Useful Links

My notes on installation and Configuration of desktop and server applications

good coding style

Gary King's page on data sharing and replication

Software I am developing

PECAn: The Predictive Ecosystem Carbon Analyzer

PECAn: Overview of steps in PECAn workflow. Orange trapezoids represent data; black rectangles represent the computational modules in PECAn

Project Home Page.

Documentation Wiki

Presentation (pdf).

I am currently leading the development of PECAn, a real-time data assimilation and forecasting system. PECAn is an open source utility that encapsulates 1) acquisition of meteorological inputs, 2) synthesis of physiological trait data as the posterior distribution of a Bayesian meta-analysis, 3) sampling trait meta-analysis posterior distributions to parameterize ensembles of an ecophysiological model, Ecosystem Demography, version 2 (ED2), 4) probabilistic forecasts,5) postprocessing to constrain forecasts and model parameters with field, meterological, eddy flux, and spectral data, and 6) provenance tracking. This system provides a detailed analysis of the past and present ecosystem functioning that seamlessly transitions into forecasts.

As a central component of the new Energy Biosciences Institute Model Integration program, PEcAn will provide the interface between models while BETY will provide the web front end.

Development of Data Assimilation modules in PEcAn is funded by an NSF Advances in Bioinformatics grant.

BETYdb: The Biofuel Ecophysiological Traits and Yields database

BETYdb: Database schema for the BETYdb. The detailed schema with all tables and fields can be downloaded as a pdf Image:Biofuels v7.pdf

BETYdb Web Portal

We use the BETYdb to manage the heterogeneous data sets that we use to parameterize and constrain forecasts made by the ED2 model.

ED2: The Ecosystem Demography Model

ED2 Documentation

The ED2 model (Morecroft 2001, Medvigy 2009) is the first vegetation model used in PECAn. In the Dietze Lab, we are developing ED2 to so that it can model biofuel crops and low input high diversity prairies and support data assimilation and real-time forecasting in these systems. The specific tasks include carbon allocation and phenology schemes for crops, as well as the addition of fertilization, tillage, and harvest events.

Software I use

In Ubuntu, these and other programs (like mysql and lyx) can be installed from the command line:

sudo apt-get install auctex lyx ess r-base grsync bzr bzr-explorer jags texi2html texinfo