Ultrafast Spectroscopy Modelling Toolbox

User-friendly data analysis for multi-pulse spectroscopy. Matlab-based GUI that helps analyze time-dependent spectroscopic data.
Find Ultrafast Spectroscopy Modelling Toolbox at: http://www3.imperial.ac.uk/people/j.vanthor/research/ultrafast_toolbox

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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 workstation clusters. Development is is focused on providing new and essential scientific capabilities to its users in the areas of kinetics and dynamics of chemical transformations, chemistry at interfaces and in the condensed phase.
Find NWChem at: http://www.nwchem-sw.org/index.php/Main_Page

Posted in Ab Initio Quantum Chemistry | Leave a comment


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 interacts with the representation, manipulate the structures, shapes and colors to reveal hidden properties. The goal is to help data analysts to make hypothesis, intuitively discover patterns, isolate structure singularities or faults during data sourcing. It is a complementary tool to traditional statistics, as visual thinking with interactive interfaces is now recognized to facilitate reasoning. This is a software for Exploratory Data Analysis, a paradigm appeared in the Visual Analytics field of research.
Find Gephi at: http://gephi.org

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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 save completed notebooks to share with others.
Find codenode at: http://codenode.org/

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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 DUNE at: http://www.dune-project.org/

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Unipro UGENE

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 Unipro UGENE at: http://ugene.unipro.ru/

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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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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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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

Posted in Theoretical and Computational | Leave a comment

Stripe’s Open Source Retreat

rechargeThe 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 full-time on an open-source project for a period of 3 months. The awardees will have space in Stripe’s SF office, and will be asked to give a couple of internal tech talks over the course of the program, but otherwise it’ll be no-strings-attached.

This is a clever model for supporting open source development, and I hope this idea catches on with other companies that benefit from open source. I can think of a number of academic developers who would love the idea of a sabbatical to work on an open source code project, to meet new people who might use their code, and to get a fresh perspective in new surroundings – an open source sabbatical.  This could be a great way for companies that benefit from open source scientific software to help encourage and influence the development of the tools they use.

The deadline for applying to the Stripe program is May 31st, and the program will run from September 1st through December 1st.

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