Source code of DESTINY, a 2D and 3D SRAM/eDRAM/NVM Cache Modeling Tool

Posted on February 20, 2015 by Dan Gezelter

DESTINY models both 2D and 3D caches designed with SRAM, eDRAM, PCM, STT-RAM and ReRAM, thus covering both conventional and emerging technologies. In its purpose, it is similar to CACTI. Accompanying paper available at http://goo.gl/qzyWFE Category should be: Computer Science > Architecture
Find Source code of DESTINY, a 2D and 3D SRAM/eDRAM/NVM Cache Modeling Tool at: https://code.ornl.gov/3d_cache_modeling_tool/destiny

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Posted in Linear Algebra | Leave a comment

Source code of Parallel and Serial Red-Black SOR in Chapel, D and Go Languages

Posted on January 7, 2015 by Dan Gezelter

Successive over-relaxation (SOR) is a computationally intensive, yet extremely important iterative solver for linear systems. Due to recent growth in amount of data generated and increasing problem sizes, serial platforms have proved to be insufficient in providing the required computational power. This code provides parallel implementations of red-black SOR method using three modern programming languages: Chapel, D and Go.
Find Source code of Parallel and Serial Red-Black SOR in Chapel, D and Go Languages at: http://www.academia.edu/9709444/Source_code_of_Parallel_and_Serial_Red-Black_SOR_Implementation_in_Chapel_D_and_Go_Languages

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Posted in Linear Algebra | Leave a comment

Pathomx

Posted on November 19, 2014 by Dan Gezelter

Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis. The software functions as a hybrid of workflow and script-based approaches to analysis. Using workflows it is possible to construct rapid, reproducible analysis constructs for experimental data. By combining this with custom inline scripting it is possible to perform any analysis imaginable. Workflows can be dynamically re-arranged to test different approaches and saved to track the development of your approach. Saved workflows can also be shared with other users or groups, allowing instant reproduction of results and methods. Tools can export images as publication-ready high resolution images in common formats.
Find Pathomx at: http://pathomx.org

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Posted in Bioinformatics | Leave a comment

Quantum GIS

Posted on November 19, 2014 by Dan Gezelter

A Free and Open Source Geographic Information System QGIS is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, Windows and Android and supports numerous vector, raster, and database formats and functionalities.
Find Quantum GIS at: http://qgis.org/

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Posted in Geography | Leave a comment

DAMASK the Dsseldorf Advanced Material Simulation Kit

Posted on November 18, 2014 by Dan Gezelter

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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Posted in Engineering, Materials | Leave a comment

rOpenSci

Posted on September 14, 2014 by Dan Gezelter

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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Posted in Required Reading and Other Sites | Leave a comment

GitHub Science Showcase

Posted on September 14, 2014 by Dan Gezelter

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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Posted in Required Reading and Other Sites | Leave a comment

A modest proposal

Posted on August 20, 2014 by Dan Gezelter

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

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Posted in Open Access, open science | 1 Comment

Open Science Codefest

Posted on July 12, 2014 by Dan Gezelter

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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Posted in Conferences, open science, Science, Software | Tagged | Leave a comment

Energy system modelling with ASCEND

Posted on July 12, 2014 by Dan Gezelter

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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Posted in Energy | Leave a comment