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273
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273 results for “Systems biology”
Leaf Area Index on the GLBRC Biofuel Cropping System Experiment at the Kellogg Biological Station, Hickory Corners, MI (2009 to 2017)
Dataset AbstractThe leaf area index was measured to estimate the phenology and growth patterns of the different biofuel crops.original data source http://lter.kbs.msu.edu/datasets/225
BIOLOGICAL DATA in CO2 budget of cultured mussels metabolism in the highly productive Northwest Iberian upwelling system
<p>BIOLOGICAL DATA to estimate the carbon dioxide budget of cultured mussels metabolism in the highly productive Northwest Iberian upwelling system.</p> <p>Álvarez-Salgado et al. (2022) estimate the carbon dioxide and total alkalinity budgets due to the Mediterranean mussels (Mytilus galloprovicialis) growing in suspended culture in a low seston environment such as the Galician Rías (NW Spain). This database contains the biological data needed to estimate the carbon dioxide fluxes and changes in total alkalinity induced by the different biological processes involved in mussel growth. </p> <p>Manuscript available at: <a href="https://doi.org/10.1016/j.scitotenv.2022.157867">https://doi.org/10.1016/j.scitotenv.2022.157867</a></p> <p>Álvarez-Salgado, X.A., Fernández-Reiriz, M.J., Fuentes-Santos, I., Antelo, L.T., Alonso, A.A., Labarta, U., 2022. CO2 budget of cultured mussels metabolism in the highly productive Northwest Iberian upwelling system. Sci. Total Environ. 849, 157867.</p>
Simulation systems for: "Pore formation in complex biological membranes: torn between evolutionary needs"
<p>Simulation systems for the publication:</p> <div> <div> <div> <p>Leonhard J. Starke, Christoph Allolio, and Jochen S. Hub, <em>Pore formation in complex biological membranes: torn between evolutionary needs</em>, BioRxiv (2024), doi: <a href="https://doi.org/10.1101/2024.05.06.592649">10.1101/2024.05.06.592649</a></p> <p>Required software:<br>GROMACS Chain Coordinate, a modified GROMACS variant for pore formation across membranes or stalk formation between membranes: <a href="https://gitlab.com/cbjh/gromacs-chain-coordinate">https://gitlab.com/cbjh/gromacs-chain-coordinate</a></p> <p>See README_small.sh and README_large.sh files for instructions on how to run pulling simulations for inducing pores in the provided complex membrane models.</p> </div> </div> </div>
A Curated Gene and Biological System Annotation of Adverse Outcome Pathways Related to Human Health
<p>Adverse Outcome Pathways (AOPs) are multi-scale models of biological mechanisms connecting molecular initiating events to adverse outcomes through measurable key events. AOPs can guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation in chemical safety assessment. Here, we present a comprehensive molecular annotation of AOPs relevant to human health to embed the AOP framework into molecular data interpretation, which supports the development and application of novel AOP-based approaches in biomedical research.</p> <p>Please cite the following publication alongside this Zenodo entry when using the data:</p> <p>Saarimäki, L.A., Fratello, M., Pavel, A. <em>et al.</em> A curated gene and biological system annotation of adverse outcome pathways related to human health. <em>Sci Data</em> <strong>10</strong>, 409 (2023). https://doi.org/10.1038/s41597-023-02321-w</p>
Trace Gas Fluxes on the Main Cropping System Experiment at the Kellogg Biological Station, Hickory Corners, MI (1991 to 2019)
Dataset Abstract Trace gases (nitrous oxide, methane, and carbon dioxide) have been measured on the LTER Main Site since 1991 and on Successional and Forest sites since 1993. Trace gas fluxes are measured twice monthly or monthly until the ground freezes using permanently-installed, in-situ static chambers. CH4 and N2O are analyzed with gas-chromatography and CO2 with an infrared gas analyzer. Soil moisture and temperature are measured during sampling. original data source http://lter.kbs.msu.edu/datasets/16
Soil Moisture on the Main Cropping System Experiment at the Kellogg Biological Station, Hickory Corners, MI (1989 to 2019)
Dataset Abstract Measurements of soil moisture began in 1989 for all treatments on the LTER main site and in 1993 on the successional and forest sites. Soil moisture is analyzed on the baseline soil samplings which are collected twice monthly or monthly during the growing season. The percent gravimetric moisture content is calculated on a dry weight basis. Other datasets from the baseline soil samplings include Inorganic nitrogen and Total N and Total C. original data source http://lter.kbs.msu.edu/datasets/18
Annual Net Primary Production on the Main Cropping System Experiment at the Kellogg Biological Station, Hickory Corners, MI (1990 to 2018)
Dataset Abstract Aboveground annual net primary production (ANPP) has been measured on the LTER main site since 1990 and on the successional and forested sites since 1993. ANPP is measured at peak biomass for a given treatment. In some systems with multiple harvests or complex communities that have peaks occurring at different times of the year, measurements are taken at multiple times per year. Additional ANPP measurements are made where appropriate using leaf litter traps, estimates of diameter from tree basal diameter and for the poplar treatment occasional destructive harvests. See the ANPP protocol for descriptions of the sampling and measurement methods for each of the treatments. original data source http://lter.kbs.msu.edu/datasets/22
Soil Inorganic Nitrogen on the Main Cropping System Experiment at the Kellogg Biological Station, Hickory Corners, MI (1989 to 2018)
Dataset AbstractMeasurement of soil inorganic nitrogen began in 1989 for all treatments on the LTER Main Site and 1993 on the Successional and Forest sites. Ammonium and nitrate are analyzed twice monthly or monthly during the growing season on baseline soil samplings. Additional datasets from the Baseline Soil Samplings include soil moisture, total N and total C.original data source http://lter.kbs.msu.edu/datasets/24
Insect Population Dynamics on the Main Cropping System Experiment at the Kellogg Biological Station, Hickory Corners, MI (1989 to 2019)
Dataset Abstract Plant dwelling insect occurrence in the LTER main site (all treatments) of the KBS-LTER has been recorded since 1989 and in the successional and forest sites since 1993. The effort has focused on characterizing the temporal and spatial abundance and diversity of a set of insects representative of a higher order insect trophic level, the herbivore predators. The insect database contains more than 400,000 records and consists of counts of adult insects of fourteen species of Coccinellidae, one species of Chrysopidae, and one species of Lampyridae from 30 sample sites in each of the seven treatments in the LTER Main Site. The standard method used to measure these organisms is a yellow sticky trap. Sampling is conducted weekly during the growing season as described in the sampling protocol. original data source http://lter.kbs.msu.edu/datasets/26
Main Cropping System Experiment Field Logs and treatment descriptions at the Kellogg Biological Station, Hickory Corners, MI (1988 to 2020)
Dataset Abstract This dataset includes information about the LTER main site treatments, agronomic practices carried out on the treatments and approved site use requests. Most long-term hypotheses associated with the KBS LTER site are being tested within the context of the main cropping systems study. This study was established on a 48 ha area on which a series of 7 different cropping systems were established in spring 1988, each replicated in one of 6 ha blocks. An eighth never-tilled successional treatment, is located 200 m off-site, replicated as four 0.06 ha plots. Cropping systems include the following treatments: T1. Conventional: standard chemical input corn/soybean/wheat rotation conventionally tilled (corn/soybean prior to 1992) T2. No-till: standard chemical input corn/soybean/wheat rotation no-tilled (corn/soybean prior to 1992) T3. Reduced input: low chemical input corn/soybean/wheat rotation conventionally tilled (ridge till prior to 1994) T4. Biologically based: zero chemical input corn/soybean wheat rotation conventionally tilled (ridge till prior to 1994) T5. Poplar: Populus clones on short-rotation (6-7 year) harvest cycle T6. Alfalfa: continuous alfalfa, replanted every 6-7 years (converted to switchgrass in 2018) T7. Early successional community: historically tilled soil T8. Mown grassland community: never-tilled soil. For specific crops in a given year see the Annual Crops Summary Table. In 1993 a series of forest sites were added to the main cropping system study to provide long-term reference points and to allow hypotheses related to substrate diversity to be tested. These include: TCF. Coniferous forest: three conifer plantations, 40-60 years old TDF. Decidious forest: three deciduous forest stands, two old-growth and one 40-60 years post-cutting TSF. Mid-successional forest: three old-field (mid-successional) sites 40+ years post-abandonment. All share a soil series with the main cropping system treatments, and are within 5 km of all other sit
Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta"
<p>This archive contains the processed source data for the publication by Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe <em>Eggerthella lenta</em>" (2023, in review). Data tables underlying each figure panel are included, except for the following panels:</p> <ul> <li>Figure S1A: Source data is in Table S1 of the publication</li> <li>Figure 6D: Source data can be found at NCBI GEO accession GSE212420 (supplementary counts data matrix)</li> </ul> <p>Raw metabolomics data can also be found at Metabolomics Workbench accession PR001620.</p> <p>Methods used to summarize these data and generate the figures are described in the manuscript Materials and Methods and figure captions. Code to generate all figures is also available at www.github.com/turnbaughlab/2022_Noecker_ElentaMetabolism and 10.5281/zenodo.7779454.</p>
Measurements from CalCOFI cruises in the California Current System, including log of station information, weather, sea conditions as well as physical, chemical and biological measurements including including temperature, salinity, oxygen, density, sigma theta, phosphate, silicate, nitrite, nitrate, ammonia, chlorophyll a, integrated chlorophyll a, primary productivity, and integrated primary production. 1949 - January 2020
Since 1949, hydrographic and biological data of the California Current System have been collected on quarterly CalCOFI cruises. The 59+ year hydrographic time-series includes weather, temperature, salinity, oxygen and phosphate observations. In 1961, nutrient analysis expanded to include silicate, nitrate and nitrite; in 1973, chlorophyll was added; in 1984, C14 primary productivity incubations were added. These data are being provided here in collaboration with CalCOFI-SIO in order to provide an additional queriable interface to the data. The data are updated on a regular basis from the CalCOFI hydrographic database.
Supplementary data to *Benchmarking of numerical integration methods for ODE models of biological systems*
<p>This archive contains supplementary data and code for the manuscript <strong>Benchmarking of numerical integration methods for ODE models of biological systems </strong>by<strong> Städter et al. 2020</strong>. It contains</p> <ul> <li>scripts to automatically download and install all required packages and models,</li> <li>scripts to compile the models and to perform the study,</li> <li>value files containing all data underlying the analyses in the manuscript,</li> <li>scripts to generate the manuscript figures.</li> </ul> <p>There is a <strong>README.md </strong>file with further information, in particular on what scripts to execute to reproduce the study.</p>
Dataset supplementing Lichtenberg et al. (2017) A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes. Global Change Biology
<p>This dataset contains data and scripts that supplement the publication</p> <p>Lichtenberg et al. (2017) A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes. Global Change Biology. DOI: 10.1111/gcb.13714</p> <p> </p> <p>Please cite the above article if you use any of the included data or code.</p> <p> </p> <p>Files are described in README.md.</p>
Dataset to: Terrestrial runoff is an important source of biological ice-nucleating particles in Arctic marine systems
<p>The dataset contains supplementary information to the manuscript "Terrestrial runoff is an important source of biological ice-nucleating particles in Arctic marine systems"</p> <p>The file <a href="https://zenodo.org/api/records/14988900/draft/files/INP_data_all_samples.csv/content" target="_blank" rel="noopener noreferrer">INP_data_all_samples.csv</a> contains information on the ice nucleation measurements for all samples presented.</p> <p>The file "<a href="https://zenodo.org/api/records/14044414/draft/files/Significant_taxa_list_16S.xlsx/content" target="_blank" rel="noopener noreferrer">Significant_taxa_list_16S.xlsx</a>" contains a list of the bacterial taxa that significantly correlated with the concentration of INPs observed in the samples, while the file <a href="https://zenodo.org/api/records/14044414/draft/files/Significant_taxa_list_18S.xlsx/content" target="_blank" rel="noopener noreferrer">Significant_taxa_list_18S.xlsx</a> contains the same information for the microalgae. </p> <p>The relative abundance of the taxa in each sample is indicated in the columns "F" to "T". </p>
Dataset accompanying manuscript "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope"
<p>Raw images and microscope calibration metadata for reconstruction of datasets presented in Fig. 1 and Fig. 3 of "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope". Notebooks demonstrating steps in the label-free and fluorescence anisotropy reconstruction pipelines can be found at https://github.com/mehta-lab/miPolScope.</p>
BRAIN Journal-Brain-Like Artificial Intelligence for Automation-Figure 3. Basic "Components" of Artificial and Biological (Brain-Controlled) Automation Systems
<p>Although basing on different concepts concerning their details, artificial and biological (brain-controlled) automation systems show common points concerning their principal components (see Figure 3).</p>
Fig. 7 in Morphology of the female reproductive system and physiological age-grading of Megamelus scutellaris (Hemiptera: Delphacidae), a biological control agent of water hyacinth
Fig. 7. Number of eggs ovulated by adult females of Megamelus scutellaris correlated by a) age (days) and b) collar length (mm). The solid line represents the linear relationship between variables and the dashed lines is the 95% confidence interval (n = 15; P = 0.001 and r = 0.778).
Fig. 6. The 3 in Morphology of the female reproductive system and physiological age-grading of Megamelus scutellaris (Hemiptera: Delphacidae), a biological control agent of water hyacinth
Fig. 6. The 3 parous classes of Megamelus scutellaris. The P1 class (a and b) is characterized by the presence of follicular relics, which may not be present in some or all ovarioles, may be light in coloration and may or may not encircle the base of the ovariole. The follicular relics do not occur at high enough densities to cause an expansion or bulging. The collar may or may not be visible and does not extend past the follicular relic accumulation area. In the P2 class (c and d) follicular relics are present in all ovarioles and at high enough densities to cause bulging. They are distinctly yellow in coloration and relatively darker in comparison to those found in the P1 class. The collar is easily seen and typically extends past the follicular accumulation area. In the P3 class (e and f) follicular relics are variable, may or may not be in high enough densities to cause bulging, and typically completely encircle the base. The collar length easily surpasses the follicular relic accumulation area.
Fig. 4 in Morphology of the female reproductive system and physiological age-grading of Megamelus scutellaris (Hemiptera: Delphacidae), a biological control agent of water hyacinth
Fig. 4. Follicular relic formation and appearance in the distal area of an ovariole and anterior lateral oviduct (loa) with the germinal vesicle (gv), oocyte with yolk (oy), follicular epithelium (fe) beginning to slough off into the ovariole base (as shown by the arrow), follicular relics (fr), and collar in Megamelus scutellaris. Note the granular appearance of follicular relics having a high enough density to begin to expand or bulge the sides of the lateral oviduct.
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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.