Hunting Invasive Species with HTCondor: High Throughput Computing for Big Data and Next Generation Sequencing

Large amounts of data are being generated that require hours, days, or even weeks to analyze using traditional computing resources. Innovative solutions must be implemented to analyze the data in a reasonable timeframe. The program HTCondor (https://research.cs.wisc.edu/htcondor/) takes advantage of the processing capacity of individual desktop computers and dedicated computing resources as a single, unified pool. This unified pool of computing resources allows HTCondor to quickly process large amounts of data by breaking the data into smaller tasks distributed across many computers. This project team implemented HTCondor at the USGS Upper Midwest Environmental Sciences Center (UMESC) to leverage existing computing...

Categories: Project; Tags: 2016, All Funded Projects, Best Practices, Completed, Computational Tools and Services, All tags... Data and Information Assets, Source Code, Fewer tags

Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA: Data

This data contains environmental DNA (eDNA) sample assay results that were collected from water samples taken from a tank housing Asian carp and placed either on ice or at room temperature. At both treatment temperatures, water samples were left untreated or were treated with an ethanol and sodium acetate solution (EtOH-NaAc). This was done to evaluate an ethanol and sodium acetate solution to maintain the integrity of the DNA samples for the time between collection and lab testing. Every day for 6 days following collection, a subset of the samples was removed from each treatment and DNA was extracted and nuclear and mitochondrial markers were assayed with qPCR. Results showed comparable persistence of DNA between...

Categories: Data; Tags: Asian Carp, La Crosse, WI, USGS Science Data Catalog (SDC), eDNA

Evidence of Asian carp spawning above a key choke point in the Mississippi River: Data

Bighead Carp, Silver Carp and Grass Carp (collectively Asian carp) were introduced to North America in the 1960s and 70s and have established in the lower Mississippi River basin. Previously published evidence for spawning of these species has been limited in the upper Mississippi River to just below Dam 22 (near Saverton, MO). In 2013 and 2014, we sampled ichthyoplankton at 18 locations in the main stem of the upper Mississippi River from Dam 9 through Dam 19 and in four tributary rivers that empty into the Mississippi River (Des Moines, Skunk, Iowa and Wisconsin Rivers). We identified eggs and larvae using morphological techniques and then used genetic tools to confirm species identity. The spawning events we...

Categories: Data; Types: Citation; Tags: Asian carp, Minnesota, Mississippi River, USGS Science Data Catalog (SDC), Upper Mississippi River, All tags... Wisconsin, biological invasion, fish eggs, invasive species, larval fish, Fewer tags