OpenScience / Software



NWChem

Posted on June 27, 2014 by Dan Gezelter

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional … Continue reading →

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Posted in Ab Initio Quantum Chemistry | Leave a comment

Gephi

Posted on June 27, 2014 by Dan Gezelter

Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. Gephi is a tool for people that have to explore and understand graphs. Like Photoshop but for data, the user … Continue reading →

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Posted in Mathematics | Leave a comment

codenode

Posted on June 27, 2014 by Dan Gezelter

Codenode is a notebook-style browser based interface to Python and Sage. It lets you write and run code, create plots, and organize your work into sections. You can manage many notebooks – add, delete, sort, and create folders. You can … Continue reading →

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Posted in Tools | Leave a comment

DUNE

Posted on June 27, 2014 by Dan Gezelter

DUNE, the Distributed and Unified Numerics Environment is a modular toolbox for solving partial differential equations (PDEs) with grid-based methods. It supports the easy implementation of methods like Finite Elements (FE), Finite Volumes (FV), and also Finite Differences (FD). Find … Continue reading →

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Posted in Partial | Leave a comment

Unipro UGENE

Posted on June 27, 2014 by Dan Gezelter

A free open-source cross-platform bioinformatics tool. It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces. Using UGENE Workflow Designer, one can arrange the required tools and algorithms into a workflow schema. Find … Continue reading →

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Posted in Bioinformatics | Leave a comment

tonatiuh

Posted on June 27, 2014 by Dan Gezelter

A Monte Carlo ray tracer for the optical simulation of solar concentrating systems. Find tonatiuh at: http://code.google.com/p/tonatiuh/

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Posted in Energy | Leave a comment

fOOm-d

Posted on June 20, 2014 by Dan Gezelter

fOOm-d (framework for Object Oriented molecular dynamics) is a molecular dynamics framework with an emphasis on methods that require coupling of separate trajectories – e.g., EVB methods and a range of classical-trajectory guided quantum dynamics methods Find fOOm-d at: http://foom-d.sourceforge.net/

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Posted in Molecular Dynamics | Leave a comment

MESMER

Posted on June 20, 2014 by Dan Gezelter

MESMER (Master Equation Solver for Multi Energy-well Reactions) models the interaction between collisional energy transfer and chemical reaction for dissociation, isomerisation, association, and non-adiabatic hopping processes. Find MESMER at: http://www.chem.leeds.ac.uk/mesmer.html

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Posted in Theoretical and Computational | Leave a comment

Stripe’s Open Source Retreat

Posted on April 29, 2014 by Dan Gezelter

The Open-Source Retreat that is being sponsored by stripe looks quite intriguing.  Stripe relies on a lot of open source software, and they’ve announced a program to give a grant to a small number of developers to come to San Francisco to work … Continue reading →

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TeraPy

Posted on April 6, 2014 by Dan Gezelter

TeraPy is a graphical user interface for terahertz time-domain spectroscopy and other sequential measurements processes. Find TeraPy at: http://pythonhosted.org/terapy/

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Posted in Condensed Matter, Spectroscopy | Leave a comment