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Author Archives: Dan Gezelter
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
Posted in Spectroscopy
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NWChem
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
Posted in Ab Initio Quantum Chemistry
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Gephi
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
Posted in Mathematics
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codenode
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
Posted in Tools
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DUNE
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
Posted in Partial
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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 … Continue reading
Posted in Bioinformatics
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tonatiuh
A Monte Carlo ray tracer for the optical simulation of solar concentrating systems. Find tonatiuh at: http://code.google.com/p/tonatiuh/
Posted in Energy
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fOOm-d
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/
Posted in Molecular Dynamics
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MESMER
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
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Stripe’s Open Source Retreat
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
Posted in Software
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