skip to main content

Title: OceanSpy: A Python package to facilitate ocean model data analysis and visualization
OceanSpy is an open-source and user-friendly Python package that enables scientists and interested amateurs to analyze and visualize oceanographic data sets. OceanSpy builds on software packages developed by the Pangeo community, in particular Xarray (Hoyer & Hamman, 2017), Dask (Dask Development Team, 2016), and Xgcm (“Xgcm,” n.d.). The integration of Dask facilitates scalability, which is important for the petabyte-scale simulations that are becoming available. OceanSpy can be used as a standalone package for analysis of local circulation model output, or it can be run on a remote data-analysis cluster, such as the Johns Hopkins University SciServer system (Medvedev, Lemson, & Rippin, 2016), which hosts several simulations and is publicly available. OceanSpy enables extraction, processing, and visualization of model data to (i) compare with oceanographic observations, and (ii) portray the kinematic and dynamic space-time properties of the circulation.  more » « less
Award ID(s):
Author(s) / Creator(s):
Date Published:
Journal Name:
Journal of open source software
Page Range / eLocation ID:
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    The North Equatorial Countercurrent (NECC) simulated by a coupled ocean‐atmosphere model and its oceanic component have been investigated and compared against oceanographic observations. Coupled model simulations using the Community Earth System Model version 2 are compared against ocean‐ice simulations forced by the second phase of the Coordinated Ocean‐ice Reference Experiments (CORE) data set. The modeled circulation biases behave differently to the west of and to the east of 120°W: the CORE‐forced ocean model largely underestimates the NECC transport to the west and the coupled model underestimates it to the east. Further analysis suggests that the surface wind stress and its curl is the most important forcing term for correctly simulating the NECC in both models. West of 120°W, the NECC biases in the ocean model are attributed to the southward movement of the maximum easterly trade winds in the Northern Hemisphere and the associated wind stress curl (WSC) pattern; east of 120°W, the NECC biases in the coupled model are attributed to the weak northward cross‐equatorial winds and southwestward gap winds, which lead to a weak WSC gradient at the latitude of NECC. Further analysis confirms that the WSC biases comes mainly from the zonal wind bias, which may in turn relate to the protocol of CORE‐II of adjusting reanalysis winds toward satellite data, which include the relative wind effect.

    more » « less
  2. Analysis of the time-dependent behavior of the buoyant plume rising above Grotto Vent (Main Endeavour Field, Juan de Fuca Ridge) as imaged by the Cabled Observatory Vent Imaging Sonar (COVIS) between September 2010 and October of 2015 captures long term time-dependent changes in the direction of background bottom currents independent of broader oceanographic processes, indicating a systematic evolution in vent output along the Endeavour Segment of the Juan de Fuca Ridge. The behavior of buoyant plumes can be quantified by describing the volume, velocity, and orientation of the effluent relative to the seafloor, which are a convolved expression of hydrothermal flux from the seafloor and ocean bottom currents in the vicinity of the hydrothermal vent. We looked at the azimuth and inclination of the Grotto plume, which was captured in three-dimensional acoustic images by the COVIS system, at 3-h intervals during October 2010 and between October 2011 and December 2014. The distribution of plume azimuths shifts from bimodal NW and SW to SE in 2010, 2011, and 2012 to single mode NW in 2013 and 2014. Modeling of the distribution of azimuths for each year with a bimodal Gaussian indicates that the prominence of southward bottom currents decreased systematically between 2010 and 2014. Spectral analysis of the azimuthal data showed a strong semi-diurnal peak, a weak or missing diurnal peak, and some energy in the sub-inertial and weather bands. This suggests the dominant current generating processes are either not periodic (such as the entrainment fields generated by the hydrothermal plumes themselves) or are related to tidal processes. This prompted an investigation into the broader oceanographic current patterns. The surface wind patterns in buoy data at two sites in the Northeast Pacific and the incidence of sea-surface height changes related to mesoscale eddies show little systematic change over this time-period. The limited bottom current data for the Main Endeavour Field and other parts of the Endeavour Segment neither confirm nor refute our observation of a change in the bottom currents. We hypothesize that changes in venting either within the Main Endeavour Field or along the Endeavour Segment have resulted in the changes in background currents. Previous numerical simulations (Thomson et al., J. Geophys. Res., 2009, 114 (C9), C09020) showed that background bottom currents were more likely to be controlled by the local (segment-scale) venting than by outside ocean circulation or atmospheric patterns. 
    more » « less
  3. null (Ed.)
    The unique tectonic and paleoceanographic setting of the Naturaliste Plateau (NP) and Mentelle Basin (MB) offers an outstanding opportunity to investigate a range of scientific issues of global importance with particular relevance to climate change. Previous spot-core drilling at Deep Sea Drilling Project Site 258 in the western MB demonstrates the presence of an expanded upper Albian–lower Campanian chalk, marl, and claystone sequence that is nearly complete stratigraphically and yields calcareous microfossils that are mostly well preserved. This sediment package and the underlying Albian volcanic claystone unit extend across most of the MB and are targeted at the primary sites, located between 850 and 3900 m water depth. Coring the Cretaceous MB sequence at different paleodepths will allow recovery of material suitable for generating paleotemperature and biotic records that span the rise and collapse of the Cretaceous hothouse (including oceanic anoxic Events [OAEs] 1d and 2), providing insight to resultant changes in deep-water and surface water circulation that can be used to test predictions from earth system models. The high-paleolatitude (60°–62°S) location of the sites is especially important because of the enhanced sensitivity to changes in vertical gradients and surface water temperatures. Paleotemperature proxies and other data will reveal the timing, magnitude, and duration of peak hothouse temperatures and whether there were any cold snaps that would have allowed growth of a polar ice sheet. The sites are also well-positioned to monitor the mid-Eocene–early Oligocene opening of the Tasman Gateway and the Miocene–Pliocene restriction of the Indonesian Gateway; both passages have important effects on global oceanography and climate. Comparison of the Cenomanian–Turonian OAE 2 interval that will be cored on the Great Australian Bight will establish whether significant changes in ocean circulation were coincident with OAE 2, and over what depth ranges, and whether OAE 2 in the high-latitude Southern Hemisphere was coincident with major changes in sea-surface temperature. Understanding the paleoceanographic changes in a regional context will provide a global test on models of Cenomanian–Turonian oceanographic and climatic evolution related both to extreme Turonian warmth and the evolution of OAE 2. Drilling of Early Cretaceous volcanic rocks and underlying Jurassic(?) sediments in different parts of the MB will provide information on the timing of different stages of the Gondwana breakup and the nature of the various phases of volcanism, which will lead to an improved understanding of the evolution of the NP and MB. 
    more » « less
  4. Abstract Motivation

    The analysis of spatially resolved transcriptome enables the understanding of the spatial interactions between the cellular environment and transcriptional regulation. In particular, the characterization of the gene–gene co-expression at distinct spatial locations or cell types in the tissue enables delineation of spatial co-regulatory patterns as opposed to standard differential single gene analyses. To enhance the ability and potential of spatial transcriptomics technologies to drive biological discovery, we develop a statistical framework to detect gene co-expression patterns in a spatially structured tissue consisting of different clusters in the form of cell classes or tissue domains.


    We develop SpaceX (spatially dependent gene co-expression network), a Bayesian methodology to identify both shared and cluster-specific co-expression network across genes. SpaceX uses an over-dispersed spatial Poisson model coupled with a high-dimensional factor model which is based on a dimension reduction technique for computational efficiency. We show via simulations, accuracy gains in co-expression network estimation and structure by accounting for (increasing) spatial correlation and appropriate noise distributions. In-depth analysis of two spatial transcriptomics datasets in mouse hypothalamus and human breast cancer using SpaceX, detected multiple hub genes which are related to cognitive abilities for the hypothalamus data and multiple cancer genes (e.g. collagen family) from the tumor region for the breast cancer data.

    Availability and implementation

    The SpaceX R-package is available at

    Supplementary information

    Supplementary data are available at Bioinformatics online.

    more » « less
  5. Abstract

    We present a data assimilation package for use with ocean circulation models in analysis, forecasting, and system evaluation applications. The basic functionality of the package is centered on a multivariate linear statistical estimation for a given predicted/background ocean state, observations, and error statistics. Novel features of the package include support for multiple covariance models, and the solution of the least squares normal equations either using the covariance matrix or its inverse—the information matrix. The main focus of this paper, however, is on the solution of the analysis equations using the information matrix, which offers several advantages for solving large problems efficiently. Details of the parameterization of the inverse covariance using Markov random fields are provided and its relationship to finite-difference discretizations of diffusion equations are pointed out. The package can assimilate a variety of observation types from both remote sensing and in situ platforms. The performance of the data assimilation methodology implemented in the package is demonstrated with a yearlong global ocean hindcast with a 1/4° ocean model. The code is implemented in modern Fortran, supports distributed memory, shared memory, multicore architectures, and uses climate and forecasts compliant Network Common Data Form for input/output. The package is freely available with an open source license

    more » « less