This program converts several Cufflinks output files into easily readable Microsoft Excel tables using Apache's POI library. Only the "cuffdiff" output format currently is supported, but future versions may include other output formats.

Maps and Multimedia


The Russian-English Agricultural Atlas is the world’s most comprehensive source of information on the geographic distribution of plant-based agriculture in Russia and neighboring countries. The Atlas contains 1500 maps that illustrate the distribution of 100 crops, 560 wild crop relatives, 640 diseases, pests and weeds, and 200 environmental parameters. Additionally, the Atlas provides detailed biological descriptions, illustrations, metadata and reference lists. Currently, individual maps can be downloaded and viewed using freely available AgroAtlas GIS Utility software, which can also be downloaded at this site.

Agroecosystems & Environment


Geopack is a comprehensive, user-friendly software package containing several computer programs for carrying out geostatistical analyses of spatially correlated data. The programs were written so that they can be used by scientists, engineers or regulators with little experience in geostatistical techniques and still satisfy the requirements of more advanced users. Using the programs, and spending a little time becoming familiar with geostatistics, the end-user should be able to include the geostatistical techniques in their work and research environment.

Agroecosystems & Environment

Stream Temperature Modeling and Monitoring: Air Temperature Based Thermal Stream Habitat Model

The Air Temperature Based Thermal Stream Habitat Model was originally developed from weather station information across the Columbia River basin in the Pacific Northwest. Multiple regression was used to predict mean annual air temperatures from elevation, latitude, and longitude with good success R^2 ~ 0.89). The model was developed as an alternative to PRISM data interpolations based on spline surface smoothing and should more accurately represent thermal conditions in stream valleys.

Stream Temperature Modeling and Monitoring: Multiple Regression Stream Temperature Model

This simple Stream Temperature Modeling and Monitoring approach uses thermograph data and geomorphic predictor variables from GIS software and digital elevation models (DEM). Multiple regression models are used to predict stream temperature metrics throughout a stream network with moderate accuracy (R^2 ~ 0.65). The models can provide basic descriptions of spatial patterns in stream temperatures, suitable habitat distributions for aquatic species, or be used to assess temporal trends related to climate or management activities if multiple years of temperature data are available.

2017 Census of Agriculture - Census Data Query Tool (CDQT)

The Census Data Query Tool (CDQT) is a web-based tool that is available to access and download table level data from the Census of Agriculture Volume 1 publication. The data found via the CDQT may also be accessed in the NASS Quick Stats database. The CDQT is unique in that it automatically displays data from the past five Census of Agriculture publications.

2017 Census of Agriculture

Code from: Using cameras for precise measurement of two-dimensional plant features

Images are used frequently in plant phenotyping to capture measurements. This chapter offers a repeatable method for capturing two-dimensional measurements of plant parts in field or laboratory settings using a variety of camera styles (cellular phone, DSLR), with the addition of a printed calibration pattern. The method is based on calibrating the camera using information available from the EXIF tags from the image, as well as visual information from the pattern. Code is provided to implement the method, as well as a dataset for testing. We include steps to verify protocol correctness by imaging an artifact. The use of this protocol for two-dimensional plant phenotypoing will allow data capture from different cameras and environments, with comparison on the same physical scale.

NorWeST Stream Temperature Regional Database and Model

The NorWeST webpage hosts stream temperature data and climate scenarios in a variety of user-friendly digital formats for streams and rivers across the western U.S. Temperature data and model outputs, registered to NHDPlus stream lines, are posted to the website after QA/QC procedures and development of the final temperature model within a river basin.

Agroecosystems & Environment

The National Stream Internet project

National Stream Internet (NSI) project was developed as a means of providing a consistent, flexible analytical infrastructure that can be applied with many types of stream data anywhere in the country. A key part of that infrastructure is the NSI network, a digital GIS layer which has a specific topological structure that was designed to work effectively with SSNMs. The NSI network was derived from the National Hydrography Dataset Plus, Version 2 (NHDPlusV2) following technical procedures that ensure compatibility with SSNMs.

Agroecosystems & Environment