9,901 Works

Xtract -- Extraction of social interaction functions

Ramón Escobedo, Valentin Lecheval, Vaios Papaspyros, Frank Bonnet, Francesco Mondada, Clement Sire & Guy Theraulaz
This program implements the method presented in
"A data-driven method for modelling and reconstructing social interactions in moving animal groups",with authors
R. Escobedo, V. Lecheval, V. Papaspyros, F. Bonnet, F. Mondada, C. Sire and G. Theraulaz.

We include four files:
- xtract.f: the main program;- pl-2f.gnuplot: a script for gnuplot to visualize the results;- 2hemigr.dat: the data from real fish experiments with pairs of H. rhodostomus,
- 2zebraf.dat: the data from real fish experiments with pairs of D....

aribaReportGen.py

Narender Kumar, Kathy Raven, Beth Blane, Danielle Leek, Nicholas M Brown, Eugene Bragin, Paul A. Rhodes, & Sharon J Peacock
This is a python script that uses default ariba output "report.tsv" and filters the hits based on >90% identity and >90% asssembly of the query sequence.

aribaReportGen.py

Narender Kumar, Kathy Raven, Beth Blane, Danielle Leek, Nicholas M Brown, Eugene Bragin, Paul A. Rhodes, & Sharon J Peacock
This is a python script that uses default ariba output "report.tsv" and filters the hits based on >90% identity and >90% asssembly of the query sequence.

README.txt

Nathan Scales & Peter S. Swain
README for supplementary code and data for "Resolving fluorescent species by their brightness and diffusion using correlated photon-counting histograms" (Scales & Swain).

As this paper is largely focused on theoretical and simulated results, we have provided example code, much of the simulated data used in the main paper, as well as the fitting results for this data.

The simulations and analysis were largely performed in Matlab. However, nearly all of the code and data should run...

NCL script for Fig S3

Mark England
NCL scripts for figures

NCL script for Fig 2

Mark England
NCL scripts for figures

2. Jupyter notebook to analyse gene essentiality

Leopold Parts
Gene essentiality and its reproducibility between replicates, 3'/5' positions, number of gRNAs used, library used, metric used.

Supporting code

Leopold Parts
Scripts that support reading/writing data, processing data, plotting, and simulation.

iFit

Ben Esse
Retrieval of SO2 from volcanic clouds from UV scattered sunlight spectra without a measured reference spectrum.

Hermes-Protocol

Antonios Katsarakis
TLA spec - Hermes: fault-tolerant replication protocol with strong consistency and high performance

Hermes

Antonios Katsarakis
Hermes: a fault-tolerant replication protocol, implemented over RDMA, guaranteeing linearizability and achieving low latency and high throughput.

MOESM6 of Computational modeling of human bone fracture healing affected by different conditions of initial healing stage

Mohammad Ghiasi, Jason Chen, Edward Rodriguez, & Ara Nazarian
Additional file 6. 2D-9-d = 6.py: a python script to handle models when callus thickness was 6 mm. (PY 21kb)

MOESM5 of Computational modeling of human bone fracture healing affected by different conditions of initial healing stage

Mohammad Ghiasi, Jason Chen, Edward Rodriguez, & Ara Nazarian
Additional file 5. 2D-9-d = 5.py: a python script to handle models when callus thickness was 5 mm. (PY 21kb)

2a) RCode used to learn Bayesian network models

Oliver Perkins
This file consists of a set of functions that were used to learn a suite of Bayesian network models of USA agricultural production 1990-2017.
The results generated by this code are provided as 2b). This data was then combined into a single holistic model using the code given in 2c).

4c) R code for overall holistic model of USA agriculture 1990-2017

This code runs a holistic model of USA agricultural production 1990-2017. It is stochastic. The current code is set up to do a run of 125 iterations.
To fully reproduce results produced in the accompanying paper, the model should be run for 125 iterations, setting the seed at 1987, 1988, 1989 and 1990.

Files for Figures

Erik Gjesfjeld
These are files necessary for producing the figures found in the article.

Four code examples for turbulent phase screens simulation

Mikhail Charnotskii
Matlab codes for turbulent phase screens generation.Theory and description in the Preprint
M. Charnotskii "Four methods for generation of turbulent phase screens: comparison"and submitted paper to JOSA A

Agisoft Metashape Python Script to Automate Gradual Selection, Camera Optimization and Error Reduction Steps

Stephen Escarzaga
This following python script was written for the Structure-from-motion protocol pertaining to the gradual selection, error reduction and camera optimization steps. The script is compatible with all current versions of Agisoft Metashape. When ready to run this script, click on "Tools" in the top Metashape menu bar then click on "Run Script". Navigate to where the script is located and select it. While the script runs, pertinent information required by the current SfM protocol will...

Artifact for ASE 20 Pendining Constraints paper

Timotej Kapus, Frank Busse & Cristian Cadar
Docker images and data that should help validate the results presented in Pending Constraints in Symbolic Execution for Better Exploration and Seeding ASE 20 paper.
See the readme for further details

Artifact for ASE 20 Pendining Constraints paper

Timotej Kapus, Frank Busse & Cristian Cadar
Docker images and data that should help validate the results presented in Pending Constraints in Symbolic Execution for Better Exploration and Seeding ASE 20 paper.
See the readme for further details

libpmregion

Florian Heinz
The library "pmregion" for processing polyhedral moving regions, together with a CLI program.

Sperm Gatekeeping: Image Analysis Script

Tania Mendonca, Ashley Cadby & Nicola Hemmings
“Sperm gatekeeping: 3D imaging reveals a constricted entrance to zebra finch sperm storage tubules”
Authors: Tania Mendonca, Ashley J Cadby, Nicola Hemmings Contact: Tania.Mendonca@nottingham.ac.uk
MATLAB (2015b) scripts for extracting SST diameter and length measurements from 3D image stacks taken with a selective plane illumination microscope (SPIM). Please refer to the Methods section of "Sperm Gatekeeping: 3D imaging reveals a constricted entrance to zebra finch sperm storage tubules" for a description of the analysis...

Groundwater recharge, drip water and calcite isotope model

Mark Cuthbert & Andy Baker
Code supporting the paper:Markowska et al (2020), Geochimica et Cosmochimica Acta,"Modern speleothem oxygen isotope hydroclimate records inwater-limited SE Australia" https://doi.org/10.1016/j.gca.2019.12.007

Groundwater recharge, drip water and calcite isotope model

Mark Cuthbert & Andy Baker
Code supporting the paper:Markowska et al (2020), Geochimica et Cosmochimica Acta,"Modern speleothem oxygen isotope hydroclimate records inwater-limited SE Australia" https://doi.org/10.1016/j.gca.2019.12.007

Matlab code for generating model ensembles in real time

Gerardo Chowell, , , Kimberlyn Roosa, & Cecile Viboud
Code for generating model ensembles according to: Real-time forecasting of epidemic trajectories using computational dynamic ensembles G. Chowell1,2,*, R. Luo1, K. Sun2, K. Roosa1, A. Tariq1, C. Viboud2 1 Department of Population Heath Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA 2 Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA * Corresponding author (gchowell@gsu.edu)

Registration Year

  • 2020
    2,272
  • 2019
    2,147
  • 2018
    1,484
  • 2017
    1,254
  • 2016
    1,976
  • 2015
    363
  • 2014
    387
  • 2013
    17
  • 2012
    1

Resource Types

  • Software
    9,901