DAMASK the Dsseldorf Advanced Material Simulation Kit

DAMASK is a flexible and hierarchically structured model of material point behavior for the solution of (thermo-) elastoplastic boundary value problems. Its main purpose is the simulation of crystal plasticity within a finite-strain continuum mechanical framework. DAMASK is currently coupled to the commercial FEM solvers Abaqus and MSC.Marc and additionally provides an spectral method based solver.
Find DAMASK the Dsseldorf Advanced Material Simulation Kit at: http://damask.mpie.de

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rOpenSci

At rOpenSci we are creating packages that allow access to data repositories through the R statistical programming environment that is already a familiar part of the workflow of many scientists. Our tools not only facilitate drawing data into an environment where it can readily be manipulated, but also one in which those analyses and methods can be easily shared, replicated, and extended by other researchers. We develop open source R packages that provide programmatic access to a variety of scientific data, full-text of journal articles, and repositories that provide real-time metrics of scholarly impact. Visit our packages section for a full list of production and development versions of packages.
Find rOpenSci at: http://ropensci.org

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GitHub Science Showcase

Scientists around the world are working together to solve some of the biggest questions in research. Take a look at some of the examples featured here to find out more.
Find GitHub Science Showcase at: https://github.com/showcases/science

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A modest proposal

OALogoDear Professor X,

Thank you for the invitation to review for the Journal of X.  I appreciate the work you do and have done for the X community.

That said, I have decided not to review for Elsevier journals unless the journal making the request is willing to convert one mutually agreed-upon article in the same journal to Gold Open Access status.  If that condition can be met, I would be happy to review this paper, but if not, I’m afraid I must decline.

With best regards,

 –Dan Gezelter

Posted in Open Access, open science | 1 Comment

Open Science Codefest

Open Science CodefestThe National Center for Ecological Analysis and Synthesis (NCEAS) at UCSB is co-sponsoring the Open Science Codefest 2014, which aims to bring together researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate on coding projects of mutual interest.

Do you have a coding project that could benefit from collaboration, or software skills you’d like to share? The codefest will be held from September 2-4 in Santa Barbara, CA.

Inspired by hack-a-thons and organized in the participant-driven, unconference style, the Open Science Codefest is for anyone with an interesting problem, solution, or idea that intersects environmental science and computer programming. This is the conference where you will actually get stuff done — whether that’s coding up a new R module, developing an ontology, working on a data repository, creating data visualizations, dreaming up an interactive eco-game, discussing an idea, or any other concrete collaborative goal that interests a group of people.

Looks like a great program!

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Energy system modelling with ASCEND

This a major release of the program. It introduces major modifications on the usage of Tonatiuh from previous versions of the program. In this new release, the user must decide what ray tracing results to save and how to save them before starting the ray tracing. The results saving options are:
Find Energy system modelling with ASCEND at: http://ascend4.org/Energy_system_modelling_with_ASCEND

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compute_fep

Free energy perturbation for LAMMPS, with soft-core pair potentials. Uses FEP, Thermodynamic Integration (TI), Mezei FDTI, and Bennet Acceptance Ratio methods. It can be used for alchemical transformations of pair potentials or charges in selected atoms.
Find compute_fep at: https://github.com/agiliopadua/compute_fep

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SciDraw

SciDraw is a system for preparing publication-quality scientific figures with Mathematica. SciDraw provides both a framework for structuring figures and tools for generating their content. SciDraw helps with generating figures involving mathematical plots, data plots, and diagrams. The package allows extensive manual fine tuning of the styling of text and graphics.
Find SciDraw at: http://scidraw.nd.edu/

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MUSCLE

MUSCLE 2 – The Multiscale Coupling Library and Environment is a portable framework to do multiscale modeling and simulation on distributed computing resources. The generic coupling mechanism of MUSCLE is suitable for many types of multiscale applications, notably for multiscale models as defined by the MAPPER project or complex automata as defined in the COAST project.
Find MUSCLE at: http://apps.man.poznan.pl/trac/muscle

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Dendrimer Builder Toolkit (DBT)

DBT can be used to build polymers (linear or hyperbranched) for use in AMBER depending upon multiplicity of joining residues. DBT sequences and calculates the number of residues required for building dendrimer (or polymer), which further depends on core multiplicity and generation of dendrimer.
Find Dendrimer Builder Toolkit (DBT) at: http://www.physics.iisc.ernet.in/~maiti/dbt/home.html

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