1,348 Works

Jsim Downloads And Models

Erik Butterworth, Bartholomew E. Jardine, Gary M. Raymond, Maxwell L. Neal & James B. Bassingthwaighte
Jsim/ directory contents: Jsim_license.html - this license applies to all files in the jsim/ directory JSim_linux_2_12.zip - binary Linux distribution JSim_macos_2_12.zip - binary MacOS distribution JSim_src_2_12.zip - source distribution JSim_win32_2_12.zip - binary Windows distribution linux.html - Linux binary distribution installation instructions macos.html - MacOS binary distribution installation instructions source.html - Source distribution build instructions win32.html - Windows binary distribution installation instructions models/ directory contents: BTEX20simple.mod - model code BTEX20simple.proj - JSim project for model figure...

Benchmark For: A Comparison Of The Influence Of Different Multi-Core Processors On The Runtime Overhead For Application-Level Monitoring

Jan Waller & Wilhelm Hasselbring
Application-level monitoring is required for continuously operating software systems to maintain their performance and availability at runtime. Performance monitoring of software systems requires storing time series data in a monitoring log or stream. Such monitoring may cause a significant runtime overhead to the monitored system. In this paper, we evaluate the influence of multi-core processors on the overhead of the Kieker application-level monitoring framework. We present a breakdown of the monitoring overhead into three portions...

Panfunpro

Oksana Lukjancenko, Martin Christen Thomsen, Mette Voldby Larsen & David Wayne Ussery
PanFunPro stands for PAN-genome analysis based on FUNctional PROfiles. PanFunPro is a tool for pan-genome analysis. It has several following functionalities – (1) homology detection and genome functional characterization by three HMM-collections, (2) pan-/core genome calculation within the set of proteomes, (3) pairwise pan-/core-genome analysis, (4) specific genome calculation for different subsets of genomes as well as pairwise analysis of specific proteomes, (5) basic statistics for the output genes from the pan-/core-/specific-genome calculation, (6) analysis...

Benchmark For: A Benchmark Engineering Methodology To Measure The Overhead Of Application-Level Monitoring

Jan Waller & Wilhelm Hasselbring
Application-level monitoring frameworks, such as Kieker, provide insight into the inner workings and the dynamic behavior of software systems. However, depending on the number of monitoring probes used, these frameworks may introduce significant runtime overhead. Consequently, planning the instrumentation of continuously operating software systems requires detailed knowledge of the performance impact of each monitoring probe. In this paper, we present our benchmark engineering approach to quantify the monitoring overhead caused by each probe under controlled...

Illuminaio Version 0.5.4

Mike Smith, Keith Baggerly, Henrik Bengtsson, Matthew Ritchie & Kasper Hansen
illuminaio version 0.5.4 as an R package tarball. A library for parsing Illumina IDAT files.

Statsdb: Platform-Agnostic Storage And Understanding Of Next Generation Sequencing Run Metrics

Ricardo H. Ramirez-Gonzalez, Richard M. Leggett, Darren Waite, Anil Thanki, Nizar Drou, Mario Caccamo & Robert Davey
StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, allowing consolidated multi-faceted querying and visualisation of QC and primary analysis data via concise APIs in Java and Perl.

Integrative Genomics Viewer Modified To Work With The Application Programming Interface Of Intrepid Bioinformatics

Yuri Morozov & Ted Kalbfleisch
Integrative Genomics Viewer developed by the Broad Institute modified to work with the application programming interface of Intrepid Bioinformatics (http://server1.intrepidbio.com/).

Protein Sequence To Gene Ontology Translation System

Wang Liang & Zhao KaiYong
Based on Mose translation system, we build a protein sequence to Gene ontology translation system for protein function

N-Back Task Code (D Prime Version For Probing 3-Back).

Níall Lally
Description: N-back task code (d prime version for probing 3-back, including training). Coded in Matlab (release 2008b for Windows; Mathworks, Natick, MA, USA) using the Cogent Toolbox (http://www.vislab.ucl.ac.uk/cogent_2000.php).

Computational Model Of Arterial Blood Pressure

Daniel A. Beard, Klas H. Pettersen, Brian E. Carlson, Stig W. Omholt & Scott M. Bugenhagen
A computational model was developed and identified to serve as a phenomenological representation of the major physiological processes controlling arterial blood pressure.

Methylextract

Guillermo Barturen, Antonio Rueda, José L Oliver & Michael Hackenberg
MethylExtract main script (MethylExtract_version.pl)
The main script of MethylExtract performs methylation profiling and SNV (Single Nucleotide Variant) calling from previously aligned bisulfite-treated reads. The script includes multiple quality-control related features. to. Estimation of the bisulfite conversion rate (MethylExtractBSCR_version.pl) The script calculates the bisulfite conversion rate from an unmethylated genome. In the case of plants, the script can be run with the reads aligned to the chloroplast genome, while in other organisms an unmethylated genome (as...

Thousands Of Exon Skipping Events Differentiate Among Splicing Patterns In Sixteen Human Tissues

Liliana Florea, Li Song & Steven L Salzberg
Software and associated data from the paper, including: ASprofile software (ASprofile.tar.gz); Exon skipping events with annotations (BodyMap.exon_skipping.tbl); Concatenated GTF transcript file for the 16 tissues (BodyMap.ens61.0.0.gtf.gz); (All) Events extracted from pairwise transcript comparisons (BodyMap.ens61.0.0.as.gz); Expression (FPKM) values for exon skipping events in the 16 tissues (BodyMap.fpkms.tar.gz); and Supporting summary data (Excel) for the alternative splicing analyses (BodyMap.xls).

Codes And Manuals For Proquad And Escapist

Sandeep Chakraborty, Ravindra Venkatramani, Basuthkar J. Rao, Bjarni _Asgeirsson & Abhaya M. Dandekar
manualescapist.pdf: Manual for ESCAPIST. Manual for using the ESCAPIST program (includes installation instructions) manualproquad.pdf: Manual for PROQUAD. Manual for using the PROQUAD program (includes installation instructions) pd.CB.score.full: Potential difference for CBeta atom. Distribution of Cbeta values in different amino acid pairs, learnt from the PISCES database. perl_scripts: Source code. Contains the perl source code for PROQUAD and ESCAPIST

VEDA 2.0 (Virtual Environment for Dynamic AFM)

John Melcher, Daniel Kiracofe, Shuiqing Hu & Arvind Raman
There is a new version of this tool which can be found here: https://nanohub.org/tools/veda . Please use that tool instead

Bertini: a software package for numerical algebraic geometry

Bates, Daniel J.; Hauenstein, Jonathan D.; Sommese, Andrew J.; Wampler, Charles W.

Quamc2D

Shaikh Ahmed & Dragica Vasileska
Quantum-corrected Monte-Carlo transport simulator for two-dimensional MOSFET devices.

Drift-Diffusion Lab

Saumitra Mehrotra, Abhijeet Paul, Gerhard Klimeck & Gloria Budiman
Simulate single semiconductor characteristics

DFT calculations with Quantum ESPRESSO

Janam Jhaveri, Ravi Vedula, Alejandro Strachan & Benjamin Haley
DFT calculations of molecules and solids

NanoGromacsDemo

Dairui Chen, Jay Mashl, Nahil Sobh & Eric Jakobsson
Implementation of the popular molecular dynamics software suite GROMACS

1D Heterostructure Tool

Arun Akkala, Sebastian Steiger, Jean Sellier, Sunhee Lee, Michael Povolotskyi, Tillmann Kubis, Hong-Hyun Park, Samarth Agarwal & Gerhard Klimeck
Poisson Schrödinger Solver for 1D Heterostructures

BioSensorLab

Pradeep Nair, Jonghyun Go, Graeme Landells, Tejas Pandit & Muhammad Alam
BioSensorLab is a tool to evaluate and predict the performance parameters of Biosensors.

KP Nanowire/UTB FET

Mincheol Shin
Simulate Nanowire/UTB FETs Using KP method

PETE : Purdue Emerging Technology Evaluator

Arijit Raychowdhury, Charles Augustine, Yunfei Gao, Mark Lundstrom & Kaushik Roy
Using PETE one can evaluate any MOSFET like devices or any New Devices in terms of performance on Benchmark circuits. The input to the tool can be in terms of typical MOSFET parameters or in terms of I-V and C-V tables. The Benchmark circuits include minim

nicktest title update3334

Alissa Nedossekina, Xufeng Wang, Steven Clark, Arun Akkala & Nicholas Kisseberth
testing contribtool again

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