27,871 Works

LIME 0.5

None None
LIME 0.5 is an initial version of a Lightweight Integrating Multi-physics Environment for coupling codes. LIME by itself is not a code for doing multiphysics simulations. Instead, LIME provides the key high-level software, a flexible but defined approach, and interface requirements for a collection of (potentially disparate) physics codes to be combined with strong coupling (when needed) though non-linear solution methods (e.g. JFNK, fixed point), thus creating a new multi-physics simulation capability customized for a...

An FPGA-Based Phase Measurement System

Jubin Mitra & Tapan K. Nayak
Phase measurement is required in electronic applications where a synchronous relationship between the signals needs to be preserved. Traditional electronic systems used for time measurement are designed using a classical mixed-signal approach. With the advent of reconfigurable hardware such as field-programmable gate arrays (FPGAs), it is more advantageous for designers to opt for all-digital architecture. Most high-speed serial transceivers of the FPGA circuitry do not ensure the same chip latency after each power cycle, reset...

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.

The Scalable Checkpoint/Restart Library

A. Moody
The Scalable Checkpoint/Restart (SCR) library provides an interface that codes may use to worite our and read in application-level checkpoints in a scalable fashion. In the current implementation, checkpoint files are cached in local storage (hard disk or RAM disk) on the compute nodes. This technique provides scalable aggregate bandwidth and uses storage resources that are fully dedicated to the job. This approach addresses the two common drawbacks of checkpointing a large-scale application to a...

SOFT-IO: SOft attribution using FlexparT and carbon monoxide emission inventories for In-situ Observation database

B. Sauvage, A. Auby & A. Fontaine
SOFT-IO is a tool based on the FLEXPART particle dispersion model (Stohl et al., 2005) coupled on emission inventories provided in the scientific community. It has been developed to quantify source/receptor links for atmospheric trace gases. SOFT-IO simulates the contributions of anthropogenic and biomass burning emissions from the ECCAD emission inventory database for all locations and times corresponding to the measured carbon monoxide mixing ratio along each flight measurements. The main goal is to supply...

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.

Two linear time, low overhead algorithms for graph layout

Brian Wylie & Jeff Baumes
The software comprises two algorithms designed to perform a 2D layout of a graph structure in time linear with respect to the vertices and edges in the graph, whereas most other layout algorithms have a running time that is quadratic with respect to the number of vertices or greater. Although these layout algorithms run in a fraction of the time as their competitors, they provide competitive results when applied to most real-world graphs. These algorithms...

Graphic User Interfaces for the calculation of nanoparticle molecular weight

Lewis MacKenzie
We provide stand-alone graphic user interfaces to calculate UCNP:RE molecular weight as described in our paper 'The molecular weight of NaYF4:RE photonic up-conversion nanoparticles' available as a preprint from the associated link (https://doi.org/10.1101/114744) NOTE: IT IS POSSIBLE THAT FILES ASSOCIATED WITH THIS RECORD MAY CHANGE AS A RESULT OF PEER REVIEW. THE EXECUTABLE FILES WILL REMAIN AVAILABLE.

Taxonlookup: Zenodo Trial

Will Cornwell & Rich FitzJohn
trying to get automatic doi system to work

FireHose Streaming Benchmarks

Steve Karl Anderson
The FireHose Streaming Benchmarks are a suite of stream-processing benchmarks defined to enable comparison of streaming software and hardware, both quantitatively vis-a-vis the rate at which they can process data, and qualitatively by judging the effort involved to implement and run the benchmarks. Each benchmark has two parts. The first is a generator which produces and outputs datums at a high rate in a specific format. The second is an analytic which reads the stream...

Markovian language model of the DNA and its information content

Murilo Da Silva Baptista
Computer codes for paper by S. Srivastava and M. S. Baptista, Markovian language model of the DNA and its information content, Royal Society Open Access, in press

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.

Machine Learning Toolkit for Extreme Scale

None None
Support Vector Machines (SVM) is a popular machine learning technique, which has been applied to a wide range of domains such as science, finance, and social networks for supervised learning. MaTEx undertakes the challenge of designing a scalable parallel SVM training algorithm for large scale systems, which includes commodity multi-core machines, tightly connected supercomputers and cloud computing systems. Several techniques are proposed for improved speed and memory space usage including adaptive and aggressive elimination of...

root-project/root: Patch release of v6.18 series

Fons Rademakers, Philippe Canal, Axel Naumann, Olivier Couet, Lorenzo Moneta, Vassil Vassilev, Danilo Piparo, Sergey Linev, Gerardo GANIS, Bertrand Bellenot, Guilherme Amadio, Wverkerke, Enrico Guiraud, Pere Mato, TimurP, Matevž Tadel, Wlav, Enric Tejedor, Andrei Gheata, Jakob Blomer, Stefan Roiser, Marsupial, Anirudha Bose, CristinaCristescu, Raphael Isemann … & Omar Zapata
See https://root.cern/content/release-61804

Matlab code for "An Efficient Semi-Lagrangian Algorithm for Simulation of Corona Discharges: The Position-State Separation Method"

Lipeng Liu & Marley Becerra
This code was written in MATLAB by Lipeng Liu (lipeng@kth.se) to illustrate how POSS (The Position-State Separation Method) works in the simulation of glow corona discharges. Please refer to the following paper for more information: L. Liu, M. Becerra, "An efficient semi-Lagrangian algorithm for simulation of corona discharges: the position-state separation method, " IEEE Transactions on Plasma Science, volume 44, issue 11 (10 pp), 2016. https://doi.org/10.1109/TPS.2016.2609504

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