27,871 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.

Multi Infrastructure Control and Optimization Toolkit, Resilient Design Module (MICOT-RDT), version 2.X

Russell Bent, Harsha Nagarajan, Emre Yamangil & Carleton Coffrin
MICOT is a tool for optimizing and controlling infrastructure systems. In includes modules for optimizing the operations of an infrastructure structure (for example optimal dispatch), designing infrastructure systems, restoring infrastructures systems, resiliency, preparing for natural disasters, interdicting networks, state estimation, sensor placement, and simulation of infrastructure systems. It implements algorithms developed at LANL that have been published in the academic community. This is a release of the of resilient design module of the MICOT.

evaleev/libint: 2.6.0-beta.3

Eduard Valeyev, Drew Lewis, Patrick Seewald, Justus Calvin, Jonathan Dullea, Chong Peng, Katsuhiko Nishimra, Mclement1, Jfermann, Michael F. Herbst, James D Whitfield, Ondřej Čertík, Soohaeng Yoo Willow & David Williams-Young
Release 2.6.0-beta.3 amended the CMake build of the exported lib to work out-of-source.

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".

The structure and organisation of housing production : a background paper and literature review

Alastair Whyte Greig
To be added after scanning

proycon/folia: v2.1.0

Maarten Van Gompel, Ko Van Der Sloot, Martinreynaert & Lars
Set definitions can now define constraints on the combination of classes/subsets used. #50 Added a t-ref element as a text markup counterpart to ref Added flexibility for structure elements (more nesting options)

pitthsls/pycounter: non-UTF-8-system friendly alpha

Geoffrey Spear, Fvieites, James Fournie & Pyup.Io Bot
Appveyor was having trouble with earlier prereleases because of a unicode handling problem in the poetry library. Pinning pendulum (which itself uses poetry) to an earlier version that installs cleanly, mostly to make Appveyor's build system happy.

JGCRI/hector: Hector version 2.3.0

Robert Link, Ben Bond-Lamberty, Corinne Hartin, Alexey Shiklomanov, Bvegawe, Pralit Patel, Sven Willner, Kalyn R. Dorheim, Robert Gieseke, Steve Smith & Cary Lynch
Hector 2.3.0 Constrain atmospheric CO2 concentration to be equal to the preindustrial concentration during the model spinup. The result of this is that the concentration at the beginning of the simulation will be equal to the value specified in the PREINDUSTRIAL_CO2 parameter, which was not the case previously.

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.

chriskbach/Extended-Hill-type-Muscle-Model-for-LS-DYNA: Release v2.0

FaBike & Christian Kleinbach
This Release includes new features: Muscle controller (Equilibrium Point control, reflex control) Part_Averaged routing Ringbuffer using history variables

Build and Execute Environment

Qiang Guan
At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will...

Generalized Rational Variable Projection with Application in ECG Compression

Péter Kovács, Sándor Fridli & Ferenc Schipp
We develop an adaptive transform-domain technique based on rational function systems. Although these systems have been widely and successfully used in system and control theories, they have been applied in signal processing only recently. The construction of the proposed method is discussed in the framework of a general mathematical model called variable projection. First we generalize this method by adding dimension type free parameters. Then we deal with the optimization problem of the free parameters....

Graph Topic Model (GTM) Sampling Demo

Junyu Xuan, Jie Lu & Guangquan Zhang
A Markov chain Monte Carlo (MCMC) algorithm is developed and implemented to inference the Graph Topic Model (GTM). GTM is a probabilistic graphical model for the data represented by graph structure, e.g., chemical formulas or documents. The enclosed codes are written by Matlab. 'text_gs.m' is the test program in which a synthetic dataset is simulated to demonstrate the procedure of the MCMC algorithm. When you want to use this code, you can format your data...

STEllAR-GROUP/hpx: HPX V1.3.0: The C++ Standards Library for Parallelism and Concurrency

Hartmut Kaiser, Bryce Adelstein Lelbach Aka Wash, Thomas Heller, Agustín Bergé, Mikael Simberg, John Biddiscombe, Anton Bikineev, Grant Mercer, Andreas Schäfer, Adrian Serio, Taeguk Kwon, Kevin Huck, Jeroen Habraken, Matthew Anderson, Marcin Copik, Steven R. Brandt, Martin Stumpf, Daniel Bourgeois, Denis Blank, Shoshana Jakobovits, Vinay Amatya, Lars Viklund, Zahra Khatami, Devang Bacharwar, Shuangyang Yang … & Christopher
The C++ Standard Library for Parallelism and Concurrency

PKPass

Ryan Adamson
Password management solutions exist, but few are designed for enterprise systems administrators sharing oncall rotations. Due to the Multi-Factor Level of Assurance 4 effort, DOE is now distributing PIV cards with cryptographically signed certificate and private key pairs to administrators and other security-significant users. We utilize this public key infrastructure (PKI) to encrypt passwords for other recipients in a secure way. This is cross platform (works on OSX and Linux systems), and has already been...

cdanielmachado/framed: Bug fix release

Daniel Machado, Sergej Andrejev, Kaizhuang, Marta Matos, Sara Correia & Nikolaus Sonnenschein
framed: a metabolic modeling package for python

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.

The Datatype Compare Library v.1.0

A. Moody
The Datatype Compare (DTCMP) library provides routines that sort, search, merge, partition, rank, and select items using operations that compare MPI datatypes. Such routines are needed im MPI applications dealing with large distributed latasets, where the amount of data is too large to gather to a single process.

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