27,874 Works

Softaware from QDMR: a quantitative method for identification of differentially methylated regions by entropy.

Zhang Y, Liu H, Lv J, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F & Cui Y
Allows users to quantify methylation difference and identify differentially methylated regions (DMRs) across multiple samples. QDMR is a quantitative approach genome-wide quantitative comparisons of DNA methylation among multiple samples based on Shannon entropy. The software can be used as an effective tool for the quantification of methylation difference and identification of DMRs across multiple samples.

Pixel-based Adaptive Word Consensus Segmenter (PAWCS)

Pierre-Luc St-Charles, Guillaume-Alexandre Bilodeau & Robert Bergevin
This modified standalone snapshot of the LITIV framework (v1.4.0) is used to evaluate the performance of the PAWCS video segmentation method on the baseline category of the 2014 ChangeDetection.net dataset. The output contains both evaluation reports and segmentation masks.

Maremma: a Ruby library for simplified network calls

Martin Fenner
Ruby utility library for network requests. Based on Faraday and Excon, provides a wrapper for XML/JSON parsing and error handling. All successful responses are returned as hash with key data, all errors in a JSONAPI-friendly hash with key errors.

Software from MEDOC: a Python wrapper to load MEDLINE into a local MySQL database.

Dynomant, Gorieu & Perrin
Allows user to download MEDLINE, a database for scientific text mining, information extraction, natural language processing, algorithm training and reference searches. MEDOC is a Python program designed to download data on an FTP and to load all extracted information into a local mySQL database. The indexed relational database permits user to build complex and rapid queries. All fields can also be searched for desired information.

caltechlibrary/dataset: Preservation Release

Robert Doiel
Testing CaltechDATA integration.

LRSIM: Simulator for Linked Reads

Ruibang Luo
This package simulates whole genome sequencing using 10X Genomics Linked Read technology. We have attempted to realistically capture all of the relevant steps of the 10X protocol so that it can be used to faithfully evaluate linked read sequencing of different genomes, mutation rates, input libraries, and short read sequencing conditions in silico. We have tested the package with LongRanger, SuperNova, HapCUT2, fragScaff and ARCS to confirm that variant identifation, phasing, de novo assembly and...

buddhi1980/mandelbulber2: Continuous build

Krzysztof Marczak, Sebastian Jennen, Mclarekin, Coast77777777777, Rikard Falkeborn, Bernardo Martelli, Orbitcowboy, Biberino, Adrian Meyer, Jeroen Rijckaert, Bruno Duyé, Luchansky, Psyriccio, Probonopd, Danuni, Valera Rozuvan, The Gitter Badger, Martin Herkt & KnifeOfPi
Travis CI build log: https://travis-ci.org/buddhi1980/mandelbulber2/builds/576432598

mrirecon/bart: version 0.5.00

Martin Uecker & Jonathan Tamir
Changes: new tools: moba, looklocker, tgv, extract, fftrot moba: non-linear model-based recon for T1 mapping (Xiaoqing Wang) looklocker: post-processing for moba extract: extract ranges from multi-dim. arrays tgv: a tgv denoiser fftrot: perform rotations using FFTs join: append to non-existing file pics: low-mem flag (-U) pics: efficient basis functions (Sebastian Rosenzweig) pics: pattern for non-Cartesian trajectories nlinv: enlive on the gpu twixread: read multi-raid files twixread: mode for radial traj: custom angle to traj (Aurélien...

GGIR

Vincent van Hees, Zhou Fang, Evgeny Mirkes, Joe Heywood, Jing Hua Zhao, Capdevila Pujol Joan, Séverine Sabia & Jairo H. Migueles
Converts raw data from wearables into insightful reports for researchers investigating human daily physical activity and sleep.

Generation of private sound with a circular loudspeaker array and the Weighted Pressure Matching method

Ferdinando Olivieri, Filippo Maria Fazi, Simone Fontana, Dylan Menzies & Philip Arthur Nelson
MATLAB code and data for the paper "Generation of private sound with a circular loudspeaker array and the Weighted Pressure Matching Method." In this paper, we propose a system for private sound which is based on the weighted pressure matching method (WPMM). The aim is to design the input signals to an array of loudspeakers that allow for the synthesis of a target field defined with large amplitude variations between the so-called dark points and...

Tpetra Next-Generation Templated Petra V1.0

Michael Heroux, Christopher Baker & Paul Sexton
A package of classes for constructing and using distributed sparse and dense matries, vectors and graphs. Templated o the scalar and ordinal types so that any valid floating-point type, as well as any valid integer type can be used with these classes. Other non-standard types, such as 3-by-3 matrices for the scalar type and mod-based integers for ordinal can also be used.

Metropolitan planning : an international perspective

Peter Self
To be added after scanning

Water Evaluation And Planning (WEAP) model for the Cauvery River Basin in Karnataka, India

Ajay Gajanan Bhave, Declan Conway, Suraje Dessai & David Stainforth
This data is a model of the Cauvery River Basin in Karnataka, India used for simulating streamflow changes due to potential future changes in rainfall and water demand. The model is used in the easily available Water Evaluation And Planning software available at http://www.weap21.org/index.asp . The folder has to be copied into the working folder of the software. The model can be viewed by opening the software and clicking on ‘Open’ in the ‘Area’ pull...

Softaware from Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.

Liu H, Liu X, Zhang S, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q & Zhang Y
Detects the cell type-specific methylation marks by integrating multiple methylomes from human cell lines and tissues. SMART is an entropy-based framework focused on integrating of a large number of DNA methylomes for the de novo identification of cell type-specific MethyMarks. To facilitate the specific methylation analysis, this method dynamically integrates multiple methylomes and identifies the cell type-specific methylation marks.

Quasi-geostrophic, two-layer model

Michael Rudko
This is a finite-difference, two-layer, quasi-geosotrophic model. The governing equations are the conservation of potential vorticity in each layer with added viscous terms and forcing (Pedlosky, 1987). This model simulates the dynamics of mesoscale currents. The nonlinear term is discretized with Arakawa energy, enstrophy and symmetry conserving scheme. Doubly-periodic boundary conditions are applied. To compile, please, type "make all".

cairis-platform/cairis: Feature and Maintenance Update

Shamal Faily, Ash-Ley, Nath, Adamrbu, Robin Quetin, D-Dev, Rachel Larcombe, Ben Coleman & AntonP1337
Fixes and enhancements for: Issue #425 Issue #426 Issue #427 Issue #428 Issue #429 Issue #430 Issue #431 Issue #432 Issue #433 Issue #434 Issue #435 Issue #436 Issue #437 Issue #438 Issue #439 Issue #440 Issue #441 Issue #442 Issue #443 Issue #444 Issue #445

Exodiff v. 2.09

R. Drake, G. Sjaardema & D. Hensinger
Exodiff compares the results data from two Exodus II files. By defult, a relative difference is used with a tolerance of 1.-6 (about 6 significant digits). The nodal locations are also compared using an absolute difference with a tolerance of 1.e-6. Time step values are compared using a relative difference with a tolerance of 1.e-6 and a floor of 1.e-15. If a third file [diffile.exo] is given, then it is overwritten with the difference of...

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