OpenScience / Software



cb2bib – From clipboard to BibTeX: A tool for extracting bibliographic references

Posted on November 17, 2008 by Dan Gezelter

From clipboard to BibTeX: A tool for rapidly extracting unformatted bibliographic references from email alerts, journal web pages, and PDF files. The cb2Bib facilitates the capture of single references from unformatted and non standard sources. Output references are written in … Continue reading →

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FELLA (Free Electron Laser Atomic, Molecular, and Optical Physics Program Package)

Posted on November 6, 2008 by Dan Gezelter

The software package FELLA has been written for basic research in atomic, molecular, and optical physics. The atomic physics programs treat the atomic electronic structure in Hartree-Fock-Slater approximation and the interaction of electrons with light of up to two colors. … Continue reading →

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View3D: calculation of radiation view factors in 2D and 3D

Posted on October 21, 2008 by Dan Gezelter

View3D is a command-line tool for evaluating radiation view factors for scenes with complex 2D and 3D geometry. It uses an adaptive integration method to calculate the view factors between faces where there is partial obstruction from inbetween faces. This … Continue reading →

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Posted in Engineering | 1 Comment

Open Source Image Velocimetry

Posted on October 10, 2008 by Dan Gezelter

OSIV is a program written to perform cross-correlation analysis of particle image velocimetry (PIV) images. The program was designed to be both very modular and quite efficient. It incorporates most of the tried-and-true algorithms and some of the more recent … Continue reading →

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Exhibit: make your data web-accessible

Posted on September 18, 2008 by Dan Gezelter

David Karger‘s lab at MIT has developed some neat web software called exhibit, which is designed to let non-ultra-sophisticated individuals publish data in ways that make it immediately accessible and interactive for people encountering it on the web. With exhibit, … Continue reading →

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Posted in Open Data, open science, Software | 2 Comments

OpenFVM

Posted on September 4, 2008 by Dan Gezelter

OpenFVM is a general open source three-dimensional CFD solver (for Linux and Windows). It uses the unstructured finite volume method to simulate non-isothermal transient flow. Gmsh is used for pre- and post- processing. Find OpenFVM at: http://openfvm.sourceforge.net/

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New Software: Data Mining

Posted on August 7, 2008 by Dan Gezelter

Some new software is in our Knowledge Discovery and Data Mining section. I can remember a time when “data mining” was a bit of an epithet in science (like “fishing expedition”), but now it has become an established way of … Continue reading →

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Posted in Science, Software | Tagged | 6 Comments

Automated out-of-plane finder?

Posted on July 1, 2008 by Dan Gezelter

The code I’ve been working on has some cool features. If you give it a list of atoms and bonds, it automatically figures out bend and dihedral interactions using simple graph concepts. That is, if the molecule has a bond … Continue reading →

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Cool finds at the NCCB2008 workshop

Posted on June 27, 2008 by Dan Gezelter

Some of the cooler online resources that have been discussed at the NCCB2008 workshop: OpenWetWare The international genetically engineered machines competition (IGEM) Registry of Standard Biological Parts Nature Precedings Proteopedia The Open Protein Structure Annotation Network (TOPSAN) SciVee.tv FriendFeed

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Posted in Policy, Science, Software | Tagged , | 1 Comment

Praat: doing Phonetics by Computer

Posted on June 18, 2008 by Dan Gezelter

Praat is an integrated software workbench for studying phonetics on real-life sound data. Find Praat: doing Phonetics by Computer at: http://www.fon.hum.uva.nl/praat/

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Posted in Linguistics | Leave a comment