Protocols

Steady-state groundwater solution with particle tracking to determine flow paths and residence times. Particles released to water table surface in each model cell excluding stream cells, with cumulati...

Used Maximum Entropy machine learning algorithm to predict species occurrence based on known presence locations and environmental variables, followed by independent field validation of model predictio...

Computational approach for constructing phylogenetic trees of viral protein sequences using maximum likelihood methods with various substitution models and statistical support assessment.

Mathematical modeling approach extending classic Levins metapopulation models to incorporate both consumptive and nonconsumptive effects of generalist predators on prey colonization and extinction dyn...

Systematic feature selection using six complementary statistical methods to identify key environmental drivers of chemodiversity while reducing bias from any single technique.

Comparative simulation study using five different soil organic carbon models (DAYCENT, CORPSE, MIMICS, MEND, RESOM) to project responses to warming and litter addition manipulations. Models were run u...

A systematic approach to test climate change impacts at multiple model resolutions by running the same scenarios at both coarse (1 km) and fine (100 m) spatial resolution. Climate scenarios are develo...

Synthesis of climate records from five different sources (resident observer, NOAA, USGS, USDA, and PRISM) with standardized protocols for handling missing data and format inconsistencies. Includes cal...

Novel ensemble learning approach combining XGBoost, CatBoost, and Random Forest algorithms with SHAP interpretability analysis to predict cloud condensation nuclei from aerosol optical properties.

Simulates trait data with hierarchical genetic structure where genotypes are nested within species, allowing comparison of nested vs non-nested statistical approaches. Uses allele matrices to generate...

Offline land surface model simulation using Noah-MP at high spatial resolution (250m) with terrain-corrected meteorological forcing from WRF model output. Model estimates snow accumulation, ablation, ...

Numerical solution of the one-dimensional Richards equation using PFLOTRAN software to simulate soil water flow and generate synthetic soil moisture data for method testing.

Geochemical modeling using PHREEQC code for initial evaluations of column effluent for potential mineral dissolution/precipitation and calculating carbon dioxide concentrations. Used generalized surfa...

Calculation of multiple phylogenetic distance metrics (NND, MPD, INND, MIPD) using PHYDIST procedure to quantify relatedness of focal species to native community members.

Spatial averaging of gridded precipitation data over selected headwater basins to create seasonal and annual precipitation totals for water balance analysis.

Simulation model that estimates climate sensitivity using first event dates and mean dates for systems with different degrees of correlation between slopes and intercepts of individual reaction norms.

Construction of phylogenetic-like trees based on DNA methylation patterns rather than sequence data. Uses correlation-based dissimilarity measures applied to methylation profiles.

Construction of phylogenetic trees using Phylomatic web service with APG III megatree, followed by branch length assignment using BLADJ algorithm in Phylocom.

Computational approach to estimate phylogenetic relationships and distances using the Phylomatic web service with standardized angiosperm phylogenies and fossil-calibrated branch lengths.

A novel theoretical model that couples leaf physiology to climate variables through water balance principles, using vein density as a predictor of transpiration rate and linking it to growing season t...

Numerical modeling approach combining energy-mass balance calculations with ice-flow modeling to reconstruct past glacier extents and determine paleoclimate conditions. Uses digital elevation models a...

Simulates alternating H and V polarized radar pulses with controlled time separation to overcome decorrelation limitations in spaceborne Doppler radar measurements. Incorporates realistic crosstalk co...

Comparative analysis of genome assembly improvement using pooled vs individual Illumina short reads for polishing long-read assemblies, assessed using BUSCO completeness metrics.

Development of a mathematical framework to predict when animals should integrate multisensory stimuli based on uncertainty, predator probability, and cost-benefit ratios. Uses signal detection theory ...

Bioinformatics pipeline for processing RNA-seq reads including quality control, mapping to reference genome, and statistical analysis of differential gene expression using mixed models.

T-matrix and DDA computational methods to simulate radar scattering properties of ice particles with various shapes and orientations. Used to interpret observed radar signatures and constrain particle...

A methodology using random forest algorithms to fill missing values in sub-hourly groundwater monitoring data with entropy-based uncertainty quantification.

Machine learning approach using Random Forest algorithms to downscale coarse resolution climate data to higher spatial resolution using topographic predictors. Models are trained on relationships betw...

Rapid Radiative Transfer Model for GCMs used to calculate clear-sky broadband radiation fluxes. Uses atmospheric profile inputs to estimate what radiation would be in absence of clouds for comparison ...

A custom ray tracing algorithm that generates shade masks for hyperspectral imagery by calculating paths between the sun, ground points, and sensor using solar geometry, sensor view angles, and digita...

High-resolution regional climate modeling using RegCM_4.4.5 to simulate North American Monsoon dynamics under different Last Interglacial orbital configurations. Uses MIT-Emanuel convection scheme wit...

A method for generating field sampling locations using multiple remote sensing datasets to ensure environmental similarity between study and reference areas. Combines elevation, vegetation indices, an...

Bayesian clustering analysis using STRUCTURE software to infer population structure and individual ancestry coefficients (Q values) from multilocus genotype data, incorporating reference populations t...

Simulation experiment using skew-normal density distributions to quantify the potential impact of skewness differences on species overlap. Parameter space is systematically explored to find maximum po...

Radiocarbon-based modeling of soil organic carbon transit times and system ages using three parallel pools (LF, OF, HF) with different turnover rates and petrogenic carbon corrections.

A three-step approach that combines regional occurrence data, species distribution modeling, and phenological filtering to create targeted candidate species lists for improved metabarcoding accuracy.

Dynamic programming model incorporating energy balance, predation risk, and body condition to predict optimal hiding decisions across different demographic categories and environmental scenarios. Uses...

Neural network-based artistic interpretation of landscape photographs using generative adversarial networks to create data sculptures.

Using synteny analysis with a closely related reference genome to arrange contigs into chromosome-level scaffolds using MUMmer alignment and RagTag scaffolding.

Established methods for quantifying wind transport and redistribution of snow from cleared areas into avalanche starting zones.

Systematic variation of hillslope angle using synthetic regular topography to isolate topographic effects on weathering dynamics and carbon partitioning from other environmental variables.

Computational pipeline using VirSorter2 and CheckV for viral sequence identification, followed by clustering into viral operational taxonomic units and taxonomic/host prediction.

Computer simulation modeling bird foraging behavior and responses to human pedestrian disturbance in a virtual park environment with manipulated detection distances, flight initiation distances, and p...

Weighted Gene Co-expression Network Analysis adapted for methylation data to identify co-methylated CpG modules and their associations with phenotypic traits.

Combined XANES fitting and Simplex Volume Maximization analysis to identify and quantify redox microsites while eliminating false positives.

Population genetic simulations using coalescent theory to test whether observed allele frequency similarities between species are compatible with neutral genetic drift versus natural selection.

Three-dimensional protein structure prediction using homology modeling to assess the structural impacts of amino acid polymorphisms on PEPCK protein structure and bonding interactions.

A systematic search and review of published literature on ecological drivers and consequences of body size variation in bumble bees using standardized database queries and inclusion criteria.

Gas diffusion model used to convert CO2 concentration data to estimates of soil CO2 production.

Climate modeling to support archaeological interpretation of past environmental conditions.