4,995 Works

ABINIT

Amritanshu Palaria, Xufeng Wang, Benjamin Haley, Matteo Mannino & Gerhard Klimeck
Run the community code ABINIT for electronic structure calculations under density functional theory through a convenient graphical user interface

Reference environment for the manuscript [Network link prediction by global silencing of indirect correlations](http://dx.doi.org/10.1038/nbt.2601) Nat. Biotechnol. 31, 720–5 (2013)

DANIEL HURLEY, Baruch Barzel, Albert-Lászlo Barabási, DAVID BUDDEN, Edmund Crampin, JOSEPH CURSONS & Matt Faria
### Overview

This is the reference environment for the manuscript ['Network link prediction by global silencing of indirect correlations'](https://dx.doi.org/10.1038/nbt.2601). It executes code to reproduce specific results described in the manuscript. You can find more information about this research at the GitHub repository for the code(https://github.com/baruchbarzel/NatureBiotech-31-720.git).

To find other versions of this reference environment, see Other Links below. To learn more about reference environments, [see the detailed description here](https://uomsystemsbiology.github.io/reference-environments/).

### Instructions for use

This version of the reference...

A Pattern Calculus for Rule Languages: Expressiveness, Compilation, and Mechanization (Artifact)

Avraham Shinnar, Jérôme Siméon & Martin Hirzel
This artifact contains the accompanying code for the ECOOP 2015 paper: "A Pattern Calculus for Rule Languages: Expressiveness, Compilation, and Mechanization". It contains source files for a full mechanization of the three languages presented in the paper: CAMP (Calculus for Aggregating Matching Patterns), NRA (Nested Relational Algebra) and NNRC (Named Nested Relational Calculus). Translations between all three languages and their attendant proofs of correctness are included. Additionally, a mechanization of a type system for the...

CRAWDAD dataset tools/analyze/802.11/Wit (v. 2006-09-29)

Ratul Mahajan, Maya Rodrig & John Zahorjan
Wit is a non-intrusive tool that builds on passive monitoring to analyze the detailed MAC-level behavior of operational wireless networks.

CRAWDAD dataset tools/collect/location/loctrace (v. 2007-09-14)

Thomas King, Stephan Kopf, Thomas Butter, Hendrik Lemelson, Thomas Haenselmann & Wolfgang Effelsberg
Loctrace is a research tool for 802.11-based positioning systems. Loctrace gathers data offered by Loclib and stores it in a file.

Nanoindentation of Soft Elastic Materials

Taha Goudarzi
Using inverse methods to estimate the Young's Modulus of soft materials for a given nanoindentation force-displacement experimental data.

SugarCube

Jason Clark, Prabhakar Marepalli, Xing Jin & Aarti Chigullapalli
MEMS design, modeling, and simulation

Analysis with the CHAIN-REDS Science Gateway of LEP Data from the ALEPH Collaboration year 2000 datafile ZD4001.85.AL

Roberto Barbera, Bruno Riccardo, Carrubba Carla, Inserra Giuseppina, Maggi Marcello & Ricceri Rita
This is the software of a JSR 286 compliant "portlet" installed on the CHAIN-REDS Science Gateway that allows the analysis of the dataset mentioned in the title. Click on the External link below to be automatically re-directed to the execution page of the portlet on the Science Gateway.

CRAWDAD dataset tools/process/pads/snmp_parser (v. 2006-09-21)

Jihwang Yeo
snmp_parser provides a C library for processing snmp traces, and several tool implementations. Using this library, users can develop their own snmp tools. The PADS system (http://www.padsproj.org) needs to be installed to build and use the library and tools.

ab initio simulations with ORCA

Nicolas Onofrio & Alejandro Strachan
ab initio and density functional theory calculations dedicated to molecular systems

Effects of seal predation on a modelled marine fish community and consequences for a commercial fishery

Francisco De Castro & Jennifer Houle
This file includes all the Matlab scripts required to run the model described in the paper. Main program to run is food_mul.m (program required is MATLAB), The data of the Irish Groundfish Survey is managed by The Marine Institute Ireland (www.marine.ie).

CRAWDAD dataset tools/collect/location/loclib (v. 2007-09-14)

Thomas Butter, Wolfgang Effelsberg, Thomas Haenselmann, Stephan Kopf, Thomas King & Hendrik Lemelson
Loclib is a research tool for 802.11-based positioning systems. Loclib is a connector between applications and sensor hardware. Its task is to collect data from the sensor hardware and pre-process it for further usage.

Unidata THREDDS Data Server

John Caron, Ethan Davis, Marcos Hermida, Dennis Heimbigner, Sean Arms, Christian Ward-Garrison, Ryan May, Lansing Madry, Robb Kambic & Hailey Johnson
The THREDDS Data Server (TDS) is a web server that provides metadata and data access for scientific datasets, using a variety of remote data access protocols. It is built on the netCDF-Java library which implements the Common Data Model (CDM) and provides an interface to data stored in netCDF files and other types of scientific data formats.

CRAWDAD dataset tools/collect/multihop/EXC (v. 2008-09-08)

Wolfgang Kiess, Thomas Ogilvie, Andreas Tarp & Markus Kerper
EXC is a software toolkit to control and steer experiments with wireless multihop networks. EXC enables researchers to evaluate their algorithms in a real-world environment without having to deal with too much thought on how to coordinate an experiment.

Lorentzian fitting tool for phonon spectral energy density

Tianli Feng & Xiulin Ruan
Fit the phonon spectral energy density as Lorentzian function to obtain the phonon frequency and relaxation time.

CRAWDAD dataset tools/process/pcap/wifi_parser (v. 2006-08-10)

Doug Madory
This tool is able to select out header fields/flags from either live or recorded 802.11 traffic. Tcpdump and Tethereal have limited flexibility to tease out specific fields without printing out the entire packet.

Diffusion Calculator: HCP Dilute Solutes

Henry Wu & DANE MORGAN
This tool calculates the diffusivity of a dilute solute in an HCP lattice with the 8-frequency model.

Nanoindentation of Soft Elastic Materials

Taha Goudarzi
Using inverse methods to estimate the Young's Modulus of soft materials for a given nanoindentation force-displacement experimental data.

FiberApp

Ivan Usov

CRAWDAD dataset tools/sanitize/generic/AnonTool (v. 2006-09-26)

D. Koukis, Spiros Antonatos, Demetris Antoniades, E. P. Markatos, P. Trimintzios & Michalis Fukarakis
AnonTool, an open-source implementation of Anonymization API, provides an easy to use, flexible and efficient library of functions that can be used to anonymize live traffic, or packet traces in libpcap file format. Currently, IP, TCP/UDP, HTTP, FTP and Netflow v5 and v9 are supported. Three ready-to-use applications have been implemented on top of this library; one provides basic anonymization functionality for the IP/TCP/UDP protocols, and two more which can perform anonymization on every field...

CRAWDAD dataset tools/analyze/location/loceva (v. 2007-09-14)

Thomas King, Stephan Kopf, Thomas Butter, Hendrik Lemelson, Thomas Haenselmann & Wolfgang Effelsberg
Loceva is an evaluation tool for 802.11-based positioning systems. Loceva uses trace files generated by Loctrace to evaluate different kinds of positioning algorithms. A large number of state-of-the-art positioning algorithms are supported by Loceva. Loceva contains a lot of filters and generators to set up different scenarios and enable emulation.

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