OpenScience / Software



OpenMD

Posted on April 4, 2014 by Dan Gezelter

OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. sticky atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, … Continue reading →

Share
Posted in Molecular Dynamics | Leave a comment

SPINA: Structure parameter inference approach

Posted on April 3, 2014 by Dan Gezelter

SPINA (structure parameter inference approach) is a method that allows for calculating constant structure parameters of endocrine feedback control systems in vivo from hormone levels obtained from serum or plasma. A first successful implementation applies to evaluation of thyroid function. … Continue reading →

Share
Posted in Medical Sciences | Leave a comment

New PLOS Open data policy

Posted on February 25, 2014 by Dan Gezelter

PLOS has announced some changes to their publishing policies, and these changes are great news.  The new PLOS policies will go a significant way towards encouraging open data and open source.  Although the announcement itself is somewhat vague on the … Continue reading →

Share
Posted in Open Access, Open Data, open science, Software | Tagged , | Leave a comment

CloudSim

Posted on October 31, 2013 by Dan Gezelter

A Java Framework For Modeling And Simulation Of Cloud Computing Infrastructures And Services. Find CloudSim at: http://www.cloudbus.org/cloudsim/

Share
Posted in Computer Science | Leave a comment

GENtle2

Posted on October 21, 2013 by Dan Gezelter

An updated, open source (MPL 2.0), web-based version of GENtle. Find GENtle2 at: http://gentledna.org

Share
Posted in Bioinformatics | Leave a comment

EPANET

Posted on October 7, 2013 by Dan Gezelter

EPANET is software that models water distribution piping systems. EPANET is public domain software that may be freely copied and distributed. It is a Windows 95/98/NT/XP program. EPANET performs extended period simulation of the water movement and quality behavior within … Continue reading →

Share
Posted in Engineering | Leave a comment

A simple-r Linux command line R environment for statistical analysis

Posted on October 2, 2013 by Dan Gezelter

The program is a simple wrapper to use R functions on a single text file from the command line; useful for quick data plotting or statistical analysis. The program generates and runs R script that: (a) loads up data from … Continue reading →

Share
Posted in Statistics | Leave a comment

HEALPix

Posted on October 1, 2013 by Dan Gezelter

HEALPix (Hierarchical Equal Area isoLatitude Pixelation of a 2-sphere), can refer to either an algorithm for pixelation of the 2-sphere, or the associated software package available under the GNU GPLv2 license. Among other features, the HEALPix software implements extremely efficient … Continue reading →

Share
Posted in Astrophysics | Leave a comment

Bio-Linux 7 – NEBC

Posted on September 18, 2013 by Dan Gezelter

Bio-Linux 7 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs … Find Bio-Linux 7 – NEBC at: http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info

Share
Posted in Bioinformatics | Leave a comment

PredictionIO: An Machine Learning Server

Posted on August 25, 2013 by Dan Gezelter

PredictionIO is an open-source Machine Learning server. It enables developers and data engineers to build smarter web and mobile applications through a simple set of APIs. Admin UI is provided for developers to select and tune algorithms. Find PredictionIO: An … Continue reading →

Share
Posted in Artificial Intelligence | 1 Comment