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30,948 results for “Profile”
September 2002 CTD, PAR, oxygen and chlorophyll profiles for the Georgia Coastal Ecosystems Sapelo River transect
Three hydrographic surveys were performed on September 17, 2002, along a transect from Sapelo Sound up the Sapelo River to Eulonia, Georgia (Sapelo River Transect, GCE-SP). Vertical CTD profiles were collected at approximately 2km intervals from 0km to 36km during low and high tidal regimes. Conductivity, temperature, pressure, optical back scatter, photosynthetically-available radiation, oxygen and chlorophyll a fluorescence were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected during the upcast were deleted. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
September 2002 CTD, PAR, oxygen and chlorophyll profiles for the Georgia Coastal Ecosystems Altamaha River transect
Four hydrographic surveys were performed on September 18, 2002, along an east-to-west transect up the Altamaha River in Georgia (Altamaha River Transect, GCE-AL). Vertical CTD profiles were collected at 1-2km intervals from 2km east of the line of demarcation (station -02) to 28km upriver along the transect during low and high tidal regimes. Conductivity, temperature, pressure, optical back scatter, photosynthetically-available radiation, oxygen and chlorophyll a fluorescence were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected during the upcast were deleted. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
Hubbard Brook Experimental Forest: Soil Profiles (Pedons), 1995-2022
This dataset documents all pedons (soil profiles) that have been located with GPS (2 meter horizontal accuracy) and have been described by genetic horizon for the Hubbard Brook Experimental Forest, within the White Mountain National Forest, NH. Soil profiles were observed between 1995 and 2022 and have been described and sampled at two levels of detail. Soil profiles in the pedon table were dug to bedrock or into the C horizon except where high boulder content limited excavation. The depth of all major soil horizons was measured and most pedons had descriptions written and physical samples collected. The horizon table contains physical observations and chemical analyses for the horizons sampled in the pedon table. Over 2500 of these horizons have had physical samples accessioned into the Hubbard Brook sample archive; the archived mass is included in the horizon table. The reconnaissance table includes pedons observed at a lower level of detail. Small pits were generally dug to a depth of 40 cm or greater, and minimal observations, as needed, were recorded to classify the soil profile by soil map unit (hpu). These data were collected to supplement the detailed observations in the previous two data tables in support of development of a spatial model of soil distribution for the entire Hubbard Brook Experimental Forest. No samples were collected from reconnaissance pits. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE): Soil Profile Rock Characteristics by Bedrock Type in Bartlett and Hubbard Brook, 2004-2018
Soils in our northeastern forests were formed in parent materials deposited by glaciers. The direction and distance of glacial movement can be used to predict the source of glacial till at “downstream” points on the landscape (Bailey 1992). The goal of this project was to identify the rocks excavated from the soil pits in each of the plots and then to use that data to validate the glacial till model. The minority of rocks in the soil pits matched the bedrock, showing the importance of glacial movement. Additional detail on the MELNHE project, including a data table of site descriptions and a pdf file with the project description and diagram of plot configuration can be found in this data package: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=344. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station. Literature cited: Bailey, S.W., 1992. Lithologic composition and rock weathering potential of forested, glacial-till soils (Vol. 662). US Department of Agriculture, Forest Service, Northeastern Forest Experiment Station.
Vegetation profile and canopy height of Tabonuco, Colorado and Cloud Forests
The overall height and the presence of vegetation in different height intervals above ground is recorded above points on a 5 x 5 m grid in three hectare-sized plots in the Luquillo Experimental Forest, Puerto Rico. One plots each is in tabonuco forest (350 m elevation), colorado forest (650 m) and cloud forest (1000 m). The first records were made shortly before Hurricane Hugo, in 1989. Post hurricane measurements have been made five time to six time in each plot, the most recent been in 1998 for all plots. The results show the damage to forest structure wreaked by Hurricane Hugo, steady recovery of forest structure after Hugo, minor damage by Hurricane Hortense in 1996, and resumption of recovery after Hortense. Maximum canopy height and the vertical distribution of vegetation in the forests are returning to pre-hurricane Hugo values. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Canopy height profile starting 1992, 1994 and 1996 of the Luquillo Forest Dynamics Plot (LFDP), Puerto Rico
File LFDP_canopy contain the canopy heights for the Luquillo forest Dynamics plot. The first measurement started in 1992, and it was planned to measure the canopy height profile every 2 years. So far censuses starting in 1992, 1994, and 1996 have been completed. In the 1992 census the canopy height profile at points along the East and North limits of the plot were not included. In 1994 and 1996 these extra points were assessed. The National Science Foundation requires that data from projects it funds are posted on the web two years after any data set has been organized and "cleaned". The data from each census of the LFDP will be updated at intervals as each survey of the LFDP shows errors in the previous data collection. After posting on the web, researchers who are not part of the project are then welcome to use the data. Given the enormous amount of time, effort and resources required to manage the LFDP, obtain these data, and ensure data accuracy, LFDP Principal Investigators request that researchers intending to use this data comply with the requests below. Through complying with these requests we can ensure that the data are interpreted correctly, analyses are not repeated unnecessarily, beneficial collaboration between users is promoted and the Principle Investigators investment in this project is protected. Submit to the LFDP PIs a short (1 page) description of how you intend to use the data; · Invite LFDP PIs to be co-authors on any publication that uses the data in a substantial way (some PIs may decline and other LFDP scientists may need to be included); If the LFDP PIs are not co-authors, send the PIs a draft of any paper using LFDP data, so that the PIs may comment upon it; In the methods section of any publication using LFDP data, describe that data as coming from the "Luquillo Forest Dynamics Plot, part of the Luquillo Experimental Forest Long-Term Ecological Research Program"; Acknowledge in any publication using LFDP data the "The Luquillo Experim
Conductivity, temperature, and depth (CTD) vertical profiles from Lake Joyce, McMurdo Dry Valleys, Antarctica, November 2014
Vertical profiles of conductivity, temperature, and depth (CTD) were collected from Lake Joyce, a perennially ice-covered lake in the McMurdo Dry Valleys of Antarctica. Water column observations were made in November 2014 using a YSI 6600 multiparameter probe in the deepest region of the lake, as identified by Mackey et al. (2018). The water column was accessed by drilling a 10-inch wide hole through the perennial ice cover using a Jiffy drill. This data package includes CTD profiles, as well as measurements of salinity, total dissolved solids (TDS), dissolved oxygen (DO), pH, and pressure.
Lake Fryxell under-ice conductivity, temperature, and depth (CTD) profiles, McMurdo Dry Valleys, Antarctica, January 2025
To characterize the upper ~2 m of the water column beneath the ~3 m ice cover in Lake Fryxell, located in the McMurdo Dry Valleys of Antarctica, 27 CTD (conductivity, temperature, depth) profiles were collected at ~5 m horizontal spacing along a transect spanning the dive hole to the shoreline. Measurements were made using a YSI Castaway CTD mounted on a 1 m mast atop a remotely operated vehicle (ROV), profiling upward from ~2 m below the ice-water interface. Using an ROV rather than drilling a hole through the ice was intended to minimize artifacts associated with ice openings. Sampling late in the austral summer targeted conditions during maximum seasonal ice melt.
Lake Fryxell dissolved oxygen profiles, McMurdo Dry Valleys, Antarctica
Dissolved oxygen (DO) profiles were collected in Lake Fryxell, located in the McMurdo Dry Valleys region of Antarctica, on 18 November 2012 and 6 January 2025 to document decadal changes in water column oxygen structure. In 2012, a 50-µm Unisense oxygen microelectrode (90% response time less than 2 s) coupled to a Richard Brancker Concerto CTD recorded oxygen at 1 Hz and CTD parameters at 6 Hz during ice-penetrating profiling. In 2025, the same microelectrode and picoammeter were paired with an In-Situ Rugged TROLL 100 logger and sampled at 1 Hz. Electrodes were calibrated at ambient temperature using air-saturated and deoxygenated (sodium dithionite) water prior to deployment.
Limno run codes, dates, and locations associated with vertical lake profile data collected in the McMurdo Dry Valleys, Antarctica (1991-2025, ongoing)
This data package provides a summary of "limno runs" performed each season in lakes located throughout the McMurdo Dry Valleys of Antarctica as part of the McMurdo Dry Valleys Long Term Ecological Research program. Each limno run is identified by unique code that allows one to compile a complete set of limnological data from a particular lake and location at specific time points. There are usually two or three limno runs performed per lake per austral summer field season, although the number of runs may vary by lake and by season depending on site access, site conditions, and other external factors.
Elevational Transects (ET): Soil temperature depth profiles from Garwood, Miers, and Taylor Valley, McMurdo Dry Valleys, Antarctica (2019-2024, ongoing)
As part of the McMurdo Dry Valleys Long Term Ecological Research (LTER) project, the Elevational Transects (ET) study was established in 1993 to investigate how elevation and topographic variation influence soil biotic communities and associated soil properties in the McMurdo Dry Valleys of Antarctica. Transects consisting of low-, mid-, and high-elevation sites were initially established in the Bonney, Hoare, and Fryxell basins of Taylor Valley, with additional transects added in Garwood and Miers Valleys during the 2012-2013 austral summer. This data package contains year-round soil temperature measurements recorded at four depths (0, 5, 10, and 20 cm) by HOBO dataloggers installed at the mid-elevation sites of each valley during the 2018–2019 austral summer.
Underwater photosynthetically active radiation (PAR) vertical profiles collected from lakes in the McMurdo Dry Valleys, Antarctica (1993-2025, ongoing)
As part of the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, lakes are monitored for photosynthetic active radiation (PAR) levels. This data set exemplifies the vertical profile of underwater PAR profiles in perennial ice covered lakes and ambient PAR measured at the air-ice interface. Profile data can be used to calculate extinction coefficients for the water column and ice layer.
Ground temperature profiles from DVDP borehole 11 at Explorers Cove, McMurdo Dry Valleys, Antarctica (2020-2025, ongoing)
The Dry Valley Drilling Project (DVDP) drilled multiple boreholes throughout Antarctica’s McMurdo Dry Valleys in the early 1970s, several of which remain open and accessible. DVDP borehole 11, with a total depth of 327.86 m, is located adjacent to the Explorers Cove Meteorological Station (EXEM), operated by the McMurdo Dry Valleys Long Term Ecological Research program (MCM LTER). In January 2020, the MCM LTER instrumented this borehole with a string of thermistors to monitor ground temperatures through the permafrost. Sensors were installed at depths of 1, 2, 3, 4, 5, 10, 20, and 30 m, providing ongoing measurements of subsurface thermal conditions at Explorers Cove.
Conductivity, temperature, and depth (CTD) vertical profiles collected from lakes in the McMurdo Dry Valleys, Antarctica (1993-2025, ongoing)
As part of the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, a series of Taylor Valley lakes have been monitored for conductivity, temperature, and depth (CTD). A Seabird instrument was used to record CTD profiles in these perennial ice covered lakes.
MCR LTER: Coral Reef: Water Column: Nearshore Water Profiles, CTD, Primary Production, and Chemistry ongoing since 2005
This data package contains water chemistry measurements taken 2 to 4 times per year at 6 stations on the north shore of Moorea, French Polynesia: Forereef, Lagoon, Fringing Reef, Cooks Bay, Cooks Bay Stream Mouth, and Offshore (5 km due north). Measurements include standard CTD parameters, nutrients, chlorophyll, phaeopigments, particulate organic carbon and nitrogen, dissolved organic carbon, dissolved inorganic carbon, total alkalinity, water column primary production, and abundance of bacteria. Sampling began in August, 2005. All water samples were collected with Niskin Bottles. CTD data were collected with a SBE19-Plus Seacat Profiler outfitted with WetLabs FLNTURT-221 Flurometer/turbidity sensors. CTD and bottle samples were taken on separate casts at each station. Two additional stations on the Moorea east shore were sampled in August 2005 only: LTER 3 Forereef Water Column, LTER 3 Backreef Water Column. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
MCR LTER: Coral Reef: Water Column: Offshore Ocean Acidification: Water Profiles, CTD, and Chemistry from 2005 to 2012
This data package contains water chemistry measurements taken 2 to 4 times per year at a station 5 km offshore of the north shore of Moorea, French Polynesia. Measurements include standard CTD parameters, phosphate, silicate, total alkalinity (TA) and total dissolved inorganic carbon (DIC). Sampling began in August, 2005. All water samples were collected with Niskin Bottles. This data includes excerpts from CTD data were collected with a SBE19-Plus Seacat Profiler. CTD and bottle samples were taken on separate casts at each station. (For full CTD data refer to knb-lter-mcr.10.) All other parameters were calculated from temperature, pressure, nutrients, TA and DIC with CO2Sys programs available at: http://cdiac.ornl.gov/oceans/co2rprt.html (Lewis E. and D. Wallace Program Developed for CO2 System Calculations) using constants K1, K2 from Mehrbach et al, 1973 refit by Dickson and Millero, 1987, Dickson KHSO4, and the Seawater pH scale (mol/kg-SW). If users wish to use different constants and scales, they will need to recalculate using the emperically collected data (TA and DIC).
Lake Mendota Multiparameter Sonde Profiles: 2017 - current
Intermittent sensor profiling at the deep hole of Lake Mendota began in 2017 with a YSI EXO2 multiparameter sonde. Parameters include water temperature, pH, specific conductivity, dissolved oxygen, chlorophyll, phycocyanin, turbidity, and fDOM. Profiles are nominally 0 - 20 meters in depth in one meter increments, although the depth range and increments vary.
LakeBeD-US: Ecology Edition - a benchmark dataset of lake water quality time series and vertical profiles
LakeBeD-US: Ecology Edition is a harmonized lake water quality dataset containing time series and vertical profiles of 21 lakes in the United States monitored by long-term monitoring institutions. These institutions include the North Temperate Lakes Long-Term Ecological Research program (NTL-LTER), Niwot Ridge Long-Term Ecological Research program (NWT-LTER), National Ecological Observatory Network (NEON), and the Carey Lab at Virginia Tech as part of the Virginia Reservoirs Long-Term Research in Environmental Biology (LTREB) site in collaboration with the Western Virginia Water Authority. The data include depth-discrete observations of 17 water quality variables including temperature, dissolved oxygen, chemical properties, Secchi depth, and more. Observations are divided into data collected by automated sensors at a relatively high temporal frequency and manually sampled data at a relatively low temporal frequency. All data were collected in situ. The data are available as Apache Parquet files, and the included R scripts give guidance on how to utilize and query the dataset in R. LakeBeD-US: Ecology Edition is an ecological science-oriented companion to LakeBeD-US: Computer Science Edition. The Computer Science Edition is available on the Hugging Face Hub.
SBC LTER: Cross-shelf Study 2008-2009: Profiles of CTD, biogeochemistry, primary production, abundance of phytoplankton groups, and abundance and production of bacteria
These data were used by the following papers: Goodman, J., M. A. Brzezinski, E. R. Halewood and C. A. Carlson. 2012. Sources of phytoplankton to the inner continental shelf in the Santa Barbara Channel inferred from cross-shelf gradients in biological, physical and chemical parameters. Continental Shelf Research, 48: 27-39. (DOI: 10.1016/j.csr.2012.08.011) Halewood, E. R., C. A. Carlson, M. A. Brzezinski, D. C. Reed and J. Goodman. 2012. Annual cycle of organic matter partitioning and its availability to bacteria across the Santa Barbara Channel continental shelf. Aquatic Microbial Ecology, 67:189-209. (DOI:10.3354/ame01586) These data were collected on monthly day cruises from January 2008 to April 2009 on the RV Kelp Fish at five stations across the shelf starting at Mohawk Reef in the nearshore area of the Santa Barbara Channel, California, USA. Data were collected with a SBE19-Plus and rosette sampler. Measurements include standard CTD parameters in 1 m bins (e.g. salinity, temperature, density). At selected depths (1, 5, 10, 20 m), rosette bottle samples were collected for nutrients, pigments, particulate and dissolved organic carbon and nitrogen, and bacterial abundance, community structure and productivity. Phytoplankton abundances (to genus) were obtained from the 5 m sample only.
MACREL software benchmark data set: Simulated metagenomes with sequencing quality, errors profile and abundance distributions derived from real samples
<p>These metagenomes were used in the benchmarking of FACS pipeline, and were designed after NGLess benchmark dataset (doi.org/10.5281/zenodo.2560288). Metagenomes were simulated with <a href="https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm">ART-bin-MountRainier-2016.06.05</a> using real abundance profiles (.abund files) available <a href="https://doi.org/10.5281/zenodo.2560288">elsewhere</a>, and <a href="http://progenomes1.embl.de/data/repGenomes/representatives.contigs.fasta.gz">proGenomes' representative contigs</a> as reference genomes. There are available metagenomes with 40, 60 and 80 M (million of reads) based in the reference genomes and abundances of the following samples:</p> <pre><code>SAMEA2466916 SAMEA2466953 SAMEA2466965 SAMEA2621107 SAMEA2621229 SAMEA2621247</code></pre> <p>To convert them from the CRAM format back to fastq files:</p> <pre><code> ## 1. converting from cram to bam format: samtools view -b -T refgenome.fa -o file.bam file.cram ## 2. sorting the bam file: samtools sort -n file.bam -o input_sorted.bam # sort reads by identifier-name (-n) ## 3. converting from bam to fastq format: bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq </code></pre> <p> </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.