skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: cluster trials v. 1.0

Abstract

This software contains a set of python modules – input, search, cluster, analysis; these modules read input files containing spatial coordinates and associated attributes which can be used to perform nearest neighbor search (spatial indexing via kdtree), cluster analysis/identification, and calculation of spatial statistics for analysis.

Authors:
 [1];  [1]
  1. Sandia National Laboratories
Publication Date:
Research Org.:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1327534
Report Number(s):
CT app v.1.0; 004949MLTPL00
SCR #2151
DOE Contract Number:
AC04-94AL85000
Resource Type:
Software
Software Revision:
00
Software Package Number:
004949
Software CPU:
MLTPL
Open Source:
Yes
Source Code Available:
Yes
Related Software:
This software makes use of python 3, numpy, scipy, and mpi4py which are all open source and freely available. These auxiliary packages are not distributed with CT App and must be seperately installed in order to use CT App.
Country of Publication:
United States

Citation Formats

Mitchell, John, and Castillo, Andrew. cluster trials v. 1.0. Computer software. https://www.osti.gov//servlets/purl/1327534. Vers. 00. USDOE. 21 Sep. 2016. Web.
Mitchell, John, & Castillo, Andrew. (2016, September 21). cluster trials v. 1.0 (Version 00) [Computer software]. https://www.osti.gov//servlets/purl/1327534.
Mitchell, John, and Castillo, Andrew. cluster trials v. 1.0. Computer software. Version 00. September 21, 2016. https://www.osti.gov//servlets/purl/1327534.
@misc{osti_1327534,
title = {cluster trials v. 1.0, Version 00},
author = {Mitchell, John and Castillo, Andrew},
abstractNote = {This software contains a set of python modules – input, search, cluster, analysis; these modules read input files containing spatial coordinates and associated attributes which can be used to perform nearest neighbor search (spatial indexing via kdtree), cluster analysis/identification, and calculation of spatial statistics for analysis.},
url = {https://www.osti.gov//servlets/purl/1327534},
doi = {},
year = {Wed Sep 21 00:00:00 EDT 2016},
month = {Wed Sep 21 00:00:00 EDT 2016},
note =
}

Software:
To order this software, request consultation services, or receive further information, please fill out the following request.

Save / Share:
  • Genomic islands are key mobile DNA elements in bacterial evolution, that can distinguish pathogenic strains from each other, or distinguish pathogenic strains from non-pathogenic strains. Their detection in genomes is a challenging problem. We present 3 main software components that attack the island detection problem on two different bases: 1) the preference of islands to insert in chromosomal tRNA or tmRNA genes (islander.pl), and 2) islands' sporadic occurrence among closely related strains. The latter principle is employed in both an algorithm (learnedPhyloblocks.pl) and a visualization method (panGenome.pl). Component islander.pl finds islands based on their preference for a particular target genemore » type. We annotate each tRNA and tmRNA gene, find fragments of each such gene as candidates for the distal ends of islands, and filter candidates to remove false positives. Component learnedPhyloblocks.pl uses islands found by islander.pl and other methods as a training set to find new islands. Reference genomes are aligned using mugsy, then the "phylotypes" or patterns of occurrence in the reference set are determined for each position in the target genome, and those phylotypes most enriched in the training set of islands are followed to detect yet more islands. Component panGenome.pl produces a big-data visualization of the chromosomally-ordered "pan-genome", that includes every gene of every reference genome (x-axis, pan-genome order; y-axis, reference genomes; color-coding, gene presence/absence etc.), islands appearing as dark patches.« less
  • Generates data for the associated paper and its supplementary data table, which are sets of residues and poles that define rational functions to approximate the Fermi-Dirac distribution.
  • The NIRP Core Software Suite is a core set of code that supports multiple applications. It includes miscellaneous base code for data objects, mathematic equations, and user interface components; and the framework includes several fully-developed software applications that exist as stand-alone tools to compliment other applications. The stand-alone tools are described below. Analyst Manager: An application to manage contact information for people (analysts) that use the software products. This information is often included in generated reports and may be used to identify the owners of calculations. Radionuclide Viewer: An application for viewing the DCFPAK radiological data. Compliments the Mixture Managermore » tool. Mixture Manager: An application to create and manage radionuclides mixtures that are commonly used in other applications. High Explosive Manager: An application to manage explosives and their properties. Chart Viewer: An application to view charts of data (e.g. meteorology charts). Other applications may use this framework to create charts specific to their data needs.« less
  • This software provides onsite analysis of the hyperspectral reflectance data acquired on an outdoor algal pond by a multichannel, fiber-coupled spectroradiometer. The analysis algorithm is based on numerical inversion of a reflectance model, in which the above-water reflectance is expressed as a function of the single backscattering albedo, which is dependent on the backscatter and absorption coefficients of the algal culture, which are in turn related to the algal biomass and pigment optical activity, respectively. Prior to the development of this software, while raw multichannel data were displayed in real time, analysis required a post-processing procedure to extract the relevantmore » parameters. This software provides the capability to track the temporal variation of such culture parameters in real time, as raw data are being acquired, or can be run in a post processing mode. The software allows the user to select between different algal species, incorporate the appropriate calibration data, and observe the quality of the resulting model inversions.« less
  • This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions bymore » either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.« less

To initiate an order for this software, request consultation services, or receive further information, fill out the request form below. You may also reach us by email at: .

OSTI staff will begin to process an order for scientific and technical software once the payment and signed site license agreement are received. If the forms are not in order, OSTI will contact you. No further action will be taken until all required information and/or payment is received. Orders are usually processed within three to five business days.

Software Request

(required)
(required)
(required)
(required)
(required)
(required)
(required)
(required)