get data

NEON infrastructure now available for research

lgoldman — Fri, 28 Oct 2016 20:50:56 +0000

NEON infrastructure now available for research

October 28, 2016

lgoldman Fri, 10/28/2016 - 14:50

Did you know that in addition to free data, the National Ecological Observatory Network (NEON) also provides access to its infrastructure for research? For example, you can now request access to specific field sampling locations or potentially mount your own sensor at a NEON field site. We are excited to announce the Assignable Assets program. This program includes access to four key types of NEON Infrastructure:

Mobile Deployment Platforms (MDPs) by request
Access to Sensor Infrastructure (SI) at field sites
Access to Observational Sampling Infrastructure (OSI) at field sites
Airborne Observation Platform (AOP) by request

Please note that access to NEON field sites is governed by site host policies and permitting requirements. The properties on which NEON infrastructure and observational plots are located are owned by site hosts. Our rights of access and use are defined in formal Land Use Agreements with these landowners and site hosts. Researchers must obtain their own site host permits for their research.

What exactly are these Assignable Assets?

The Mobile Deployment Platform (MDP) is a self-contained suite of sensors, power systems and data logging capabilities for capturing atmospheric, soil, and aquatic based measurements. Central to the concept of the MDP is the ability for rapid deployment to capture stochastic ecological events (e.g. fires, flood events, pest outbreaks) across the landscape. Five MDPs will be available for deployments up to 1 year.

Sensor Infrastructure (SI): At each of NEON’s core and relocatable field sites, there are several distinct physical instrument systems or arrays for collecting environmental data from automated sensors:

An instrument tower for meteorological and eddy flux measurements
An array of soil instruments near the tower
Sensors placed along or in stream or river; or on a buoy in a lake and in the adjacent riparian areas
A small hut that serves various functions including housing instrumentation used for command and control of the sensor infrastructure; and housing of the gas measurement validation system.

Requests may be made through the Assignable Assets program to install additional sensors or instruments on any of these systems or structures.

Observational Sampling Infrastructure (OSI): Researchers may request access to sampling locations at NEON field sites or fresh biological samples before they are archived. As stated above, gaining access to and sampling on NEON observational plots must also be permitted by the landowner and be managed with extreme care so as to not compromise NEON measurements or samples.

To that end, only nondestructive sampling will be permitted and only if it does not negatively impact the integrity of NEON observations.

The Airborne Observation Platform (AOP) is a suite of remote sensing instruments mounted in a Twin Otter airplane for collecting airborne data. The sensor suite consists of a spectroscopic imager operating from 380-nm to 2500-nm, a waveform Lidar, and a high-resolution Digital Camera. The AOP is the only Assignable Asset not yet available for requests. We anticipate the AOP will become available for request in fall 2018.

The details

Researchers must follow a formal process to request Assignable Assets. At this time, requests may be made for MDP, SI and OSI assets.

Standard requests may be made on a quarterly schedule. Ad hoc standard requests outside of this quarterly cycle may be considered, but should be submitted at least 2-3 months prior to the relevant research proposal deadline to ensure adequate time for a feasibility evaluation.

Target of Opportunity requests in response to unexpected events such as might result from a natural or man-made disaster will be handled on an expedited basis

Learn more about how to request an Assignable Asset now!

API and data availability viewer now live on the NEON data portal

lgoldman — Thu, 20 Oct 2016 17:04:01 +0000

API and data availability viewer now live on the NEON data portal

October 20, 2016

lgoldman Thu, 10/20/2016 - 11:04

In response to suggestions from the scientific community, we’ve expedited the production of some new features to the data portal to help you better navigate the data NEON provides! In addition to browsing and downloading data packages on the NEON data portal, you can now use a newly launched prototype Application Programming Interface (API) as well as a compact browser viewer to easily view data availability for each field site by data product.

The NEON Data API

The API is free to use and allows you to retrieve:

Field-based instrument and observational data
Metadata for current and future data products
Field site metadata
More granular location metadata--from towers to measurement plots, observation spots, and more

NEON’s API provides a basic means of constructing URLs that return information in a common machine-readable format, JSON (JavaScript Object Notation).

Explore the API Call examples on the API page on the NEON data portal by selecting an example, clicking GET and then clicking on the Try it button.

Give us your feedback

If you are an API user, we encourage you to test out the API and give us your feedback. We would love to know how you would use the API - ideas and example uses, and/or if you run into any issues. Please visit NEON’s public GitHub repository to share your thoughts!

Wondering what an API is?

If you are unfamiliar with the concept of an API, think of an API as a ‘middleperson' that provides a communication path for a software application to obtain information from a digital data source. APIs are becoming a very common means of sharing digital information. Many of the apps that you use on your computer or mobile device to produce maps, charts, reports, and other useful forms of information pull data from multiple sources using APIs. In the ecological and environmental sciences, many researchers use APIs to programmatically pull data into their analyses.

AG��˰ټ��ֹٷ��վ the Data Availability Feature

Once fully operational, the National Ecological Observatory will provide over 180 data products and will stream data from over 80 field sites. In the interim, while field sites are still being constructed and data products are becoming available, we have created a simple, interactive data availability page to help users determine if and where the data they want are available. Simply select a data product from the dropdown menu to discover its availability across all NEON field sites. Check out the new data availability page now.

Interactive Data Product Catalog

In recent months, we have also launched an interactive data product catalog on the NEON data portal that is powered by the NEON API. The catalog is especially useful for helping you understand what data products NEON produces and if they are available yet.

Have additional ideas and feedback about the NEON data portal? Share your thoughts.

NSF Dear Colleague Letter - Stimulating research using NEON data

Anonymous — Wed, 08 Apr 2015 19:43:57 +0000

NSF Dear Colleague Letter - Stimulating research using NEON data

Apr 8-May 8, 2015

Anonymous (not verified) Wed, 04/08/2015 - 13:43

United States

The National Science Foundation's Directorate for Biological Sciences will consider requests for funding to support conferences (including symposia and workshops) for bringing together a team of researchers with shared research interests to coordinate plans for specific analysis or synthesis of NEON data, and early concept grants for exploratory research (EAGERs) to support innovative research that leverages NEON data and/or samples/specimens. Get more information here.

Interested principal investigators should email a maximum three-page summary of their research ideas and planned activities to [email protected]">[email protected] by close of business on Friday, May 8, 2015.

Language Not specified

Dear Colleague Letter

get data

Sensor Outages and Maintenance

Anonymous — Mon, 09 Feb 2015 21:35:57 +0000

Sensor Outages and Maintenance Anonymous (not verified) Mon, 02/09/2015 - 14:35

NEON field sites occasionally undergo corrective maintenance and infrastructure upgrades that impact the availablility of data products, particularly from sensors. Please see the chart below for more information on sensor outages, including dates and reasons:

Site	Date Down	Date Up	Reason for Outage
Woodworth	8/18/2015	8/19/2015	Electrical Maintenance
North Sterling, CO	8/5/2015	9/20/2015	Sensor Infrastructure Upgrade
Central Plains Experimental Range	8/3/2015	9/18/2015	Sensor Infrastructure Upgrade
Bartlett Experimental Forest	7/2/2015	7/8/2015	Electrical Interference
Lajas Experimental Station	6/12/2015	6/12/2015	Electrical Corrective Maintenance
Oak Ridge	6/1/2015	6/1/2015	Electrical Corrective Maintenance
Dead Lake	5/27/2015	5/29/2015	Electrical Corrective Maintenance
Jones Ecological Research Center	5/23/2015	5/28/2015	Electrical Corrective Maintenance
Harvard Forest	5/15/2015	5/15/2015	Electrical Corrective Maintenance
Smithsonian Conservation Biology Institute	1/30/2015	1/30/2015	Electrical Corrective Maintenance
Ordway-Swisher Biological Station	1/16/2015	1/29/2015	Electrical Infrastructure Upgrade
Blandy Experimental Farm	1/21/2015	1/21/2015	Electrical Corrective Maintenance
Central Plains Experimental Range	1/13/2015	1/29/2015	Electrical Infrastructure Upgrade
North Sterling, CO	1/13/2015	2/19/2015	Electrical Infrastructure Upgrade
Disney Wilderness Preserve	9/9/2014	9/22/2014	Electrical Corrective Maintenance

False

ESA 2015: A Hands-On Primer for Working with Big Data in R: Introduction to Hierarchical Data Formats, Lidar Data & Efficient Data Visualization

Anonymous — Fri, 30 Jan 2015 23:53:22 +0000

ESA 2015: A Hands-On Primer for Working with Big Data in R: Introduction to Hierarchical Data Formats, Lidar Data & Efficient Data Visualization

Aug 9, 2015

Anonymous (not verified) Fri, 01/30/2015 - 16:53

Baltimore, MD
United States

Ecologists working across scales and integrating disparate datasets face new data management and analysis challenges that demand tools beyond the spreadsheet. This workshop will overview three key data formats: ASCII, HDF5 and las and several key data types including temperature data from a tower, vegetation structure data, hyperspectral imagery and lidar data, that are often encountered when working with ‘Big Data��. It will provide an introduction to available tools in R for working with these formats and types.

Things to Do Before the Workshop

To participant in this workshop, you will need a laptop with the most current version of R and, preferably, RStudio loaded on your computer. For details on setting up R & RStudio in Mac, PC, or Linux operating systems please see Additional Set up Resources below.

Install R Libraries

Please install or update each package prior to the start of the workshop.

rgeos: install.packages("rgeos")
maptools: install.packages("maptools")
raster: install.packages("raster")
rgdal: install.packages("rgdal")
ggplot2: install.packages("ggplot2")
rhdf5: source("http://bioconductor.org/biocLite.R") biocLite("rhdf5")
ggplot2: install.packages("ggplot2")
dpylr: install.packages("dplyr"): data manipulation at its finest!

Data to Download

NEON Teaching Data Subset: Field Site Spatial Data

These remote sensing data files provide information on the vegetation at the National Ecological Observatory Network's San Joaquin Experimental Range and Soaproot Saddle field sites. The entire dataset can be accessed by request from the NEON Data Portal.

DOWNLOAD DATASET

Download NEON Teaching Data Subset: Imaging Spectrometer Data - HDF5

These hyperspectral remote sensing data provide information on the National Ecological Observatory Network's San Joaquin Experimental Range field site. The data were collected over the San Joaquin field site located in California (Domain 17) and processed at NEON headquarters. The entire dataset can be accessed by request from the NEON Data Portal.

DOWNLOAD DATASET

NEON Teaching Data Subset: Sample LiDAR Point Cloud Data (.las)

This .las file contains sample LiDAR point cloud data collected by National Ecological Observatory Network's Airborne Observation Platform group. The .las file format is a commonly used file format to store LIDAR point cloud data. NEON data are available on the NEON data portal.

DOWNLOAD NEON TEACHING DATA SUBSET: SAMPLE LIDAR POINT CLOUD DATA (.LAS)

After downloading the data, please uncompress and set your R working directory to the parent directory containing these files. For additional instructions see the bottom of the page. We will be setting up an RStudio project within this working directory. Read more about RStudio projects here.

Background Reading

This workshop will be most useful to those with some basic understanding of spatial & hierarchical data. Please read the following materials if you would like additional background on these topics.

Workshop Instructors

Leah Wasser @leahawasser, Supervising Scientist, NEON, Inc
Natalie Robinson, Staff Scientist, NEON, Inc

Workshop Fearless Instruction Assistants

Claire Lunch @dr_lunch, Staff Scientist
Kate Thibault @fluby, Senior Staff Scientist
Christine Laney @cmlaney, Staff Scientist, NEON, Inc
Mike Smorul @msmorul, Associate Director of Cyberinfrastructure, SESYNC
Philippe Marchand, Scientific Support Specialist, SESYNC

Social Media

Please tweet using the hashtag #WorkWithData during this workshop! Also you can tweet at @NEON_Sci !

Schedule

Location: ESA Annual Meeting, Baltimore, Maryland

The schedule below is subject to change.

Time	Topic	Instructor
8:00	Welcome, Introductions, & Logistics
8:05	Getting Started with Rasters in R	Natalie
9:30	Raster Resolution, Extent & CRS in R	Natalie
10:15	------- BREAK -------
10:30	LiDAR Data Derived Rasters in R	Leah
11:45 - 1:00 PM	Lunch on Your Own
1:00	Introduction to HDF5 in R	Leah
2:30	------- BREAK -------
2:45	Hyperspectral Imagery in R	Leah
	Create Raster Stacks & NDVI in R (if time allows)	Leah
3:45	------- BREAK -------
4:00	Application of Skills with Capstone Project

Additional Set Up Instructions

R & RStudio

Prior to the workshop you should have R and, preferably, RStudio installed on your computer.

Setting Up R & RStudio

Windows R/RStudio Setup

Download R for Windows here
Run the .exe file that was just downloaded
Go to the RStudio Download page
Under Installers select RStudio X.XX.XXX - Windows Vista/7/8/10
Double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Mac R/RStudio Setup

Go to CRAN and click on Download R for (Mac) OS X
Select the .pkg file for the version of OS X that you have and the file will download.
Double click on the file that was downloaded and R will install
Go to the RStudio Download page
Under Installers select RStudio 0.98.1103 - Mac OS X XX.X (64-bit) to download it.
Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Linux R/RStudio Setup

R is available through most Linux package managers. You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R).
To install RStudio, go to the RStudio Download page
Under Installers select the version for your distribution.
Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Set Working Directory to Downloaded Data

1) Download Data

After clicking on the Download Data button, the data will automatically download to the computer.

2) Locate .zip file

Second, find the downloaded .zip file. Many browsers save downloaded files to your computer’s Downloads directory. If you have previously specified a specific directory (folder) for downloaded files, the .zip file will download there.

3) Move to data directory

Third, move the downloaded file to a directory called data within the Documents directory on your computer. You can choose to place the data in other locations, however, you will need to remember to set your R Working Directory to that location and not as we demonstrate in the workshop.

4) Unzip/uncompress

Fourth, we need to unzip/uncompress the file so that the data files can be accessed. Use your favorite tool that can unpackage/open .zip files (e.g., winzip, Archive Utility, etc). The files will now be accessible in three directories:

These directories contain all of the subdirectories and files that we will use in this workshop.

5) Set working directory

Fifth, we need to set the working directory in R to this data directory that is parent to the directories containing the data we want. For complete directions, on how to do that check out the Set A Working Directory in R tutorial.

Install HDFView

The free HDFView application allows you to explore the contents of an HDF5 file.

To install HDFView:

Click to go to the download page.
From the section titled HDF-Java 2.1x Pre-Built Binary Distributions select the HDFView download option that matches the operating system and computer setup (32 bit vs 64 bit) that you have. The download will start automatically.
Open the downloaded file.
- Mac - You may want to add the HDFView application to your Applications directory.
- Windows - Unzip the file, open the folder, run the .exe file, and follow directions to complete installation.
Open HDFView to ensure that the program installed correctly.

Data Tip: The HDFView application requires Java to be up to date. If you are having issues opening HDFView, try to update Java first!

QGIS (Optional)

QGIS is a cross-platform Open Source Geographic Information system.

Online LiDAR Data/las Viewer (Optional)

Plas.io is a open source LiDAR data viewer developed by Martin Isenberg of Las Tools and several of his colleagues.

Language Not specified

work with data

get data

Workshop

get data

NEON infrastructure now available for research

What exactly are these Assignable Assets?

The details

API and data availability viewer now live on the NEON data portal

The NEON Data API

Give us your feedback

Wondering what an API is?

AG���˰ټ��ֹٷ���վ the Data Availability Feature

Interactive Data Product Catalog

NSF Dear Colleague Letter - Stimulating research using NEON data

Sensor Outages and Maintenance

ESA 2015: A Hands-On Primer for Working with Big Data in R: Introduction to Hierarchical Data Formats, Lidar Data & Efficient Data Visualization

Things to Do Before the Workshop

Install R Libraries

Data to Download

NEON Teaching Data Subset: Field Site Spatial Data

Download NEON Teaching Data Subset: Imaging Spectrometer Data - HDF5

NEON Teaching Data Subset: Sample LiDAR Point Cloud Data (.las)

Background Reading

Workshop Instructors

Workshop Fearless Instruction Assistants

Social Media

Schedule

Additional Set Up Instructions

R & RStudio

Setting Up R & RStudio

Windows R/RStudio Setup

Mac R/RStudio Setup

Linux R/RStudio Setup

Set Working Directory to Downloaded Data

1) Download Data

2) Locate .zip file

3) Move to **data** directory

4) Unzip/uncompress

5) Set working directory

Install HDFView

QGIS (Optional)

Online LiDAR Data/las Viewer (Optional)

AG��˰ټ��ֹٷ��վ the Data Availability Feature

3) Move to data directory