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The massXpert project aims at providing (bio)chemists with a software package allowing the following: * User-specific atom definitions and polymer chemistry definitions; * Powerful sequence editing with user-defined glyphs for each monomer and monomer chemical modification. Multi-region selections; * Polymer sequence chemical/enzymatic cleavage; * Intramolecular cross-linking, like disulfide bonds with total resolution of the peptides generated upon enzymatic cleavage; * Gas-phase fragmentation of oligomers; * Mass-to-charge ratio calculations with inline change of ionization agent; * Calculation of net electrical charge and of isoelectric point (even by taking into account monomer modifications if polymer is a protein); * Simulation of isotopic patterns for any chemical formula and z charge; * A number of plugins allow 1) translation of the sequence from one format to another (using a dictionary, like between the 1-letter code and the 3-letter code of proteins) 2) conversion of number format according to any localized number format 3) sort mass lists.

* What MBDyn is o a command-line, direct initial-value problem solver with a large, flexible multifield element library o a research tool o a community developed, research driven open-source software * What MBDyn is not o a complete out-of-the-box ``bells and whistles'' GUI for solid modeling o a commercial tool o a completely supported software

McStas - Monte Carlo ray tracing simulations of neutron experiments. McStas is a tool for simulating neutron instrumentation and experiments using a ray-tracing formalism. Currently the main use of McStas is in the field of instrument design. This port contains the McStas component library.

McStas - Monte Carlo ray tracing simulations of neutron experiments. McStas is a tool for simulating neutron instrumentation and experiments using a ray-tracing formalism. Currently the main use of McStas is in the field of instrument design.

Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry. Features currently include: * A huge variety of common chemical file formats * Recognition of file type based on filename extension * SMARTS matcher * Flexible atom typer * Gasteiger partial charge calculation * Hydrogen addition and deletion * Automatic feature perception (rings, hybridization, aromaticity) * Multiple conformer storage within molecules * Command line interface development class * Bitvector class * Open-source/Free Software under the GNU General Public License * Cross platform (Windows, Linux, Mac OS X, SGI, Solaris, Dreamcast...)

ObsPy is an open-source project dedicated to provide a Python framework for processing seismological data. It provides parsers for common file formats, clients to access data centers and seismological signal processing routines which allow the manipulation of seismological time series (see Beyreuther et al. 2010, Megies et al. 2011). The goal of the ObsPy project is to facilitate rapid application development for seismology.

McStas perl tools to aid in running neutron ray tracing simulations. McStas is a tool for simulating neutron instrumentation and experiments using a ray-tracing formalism. Currently the main use of McStas is in the field of instrumentation design. This port contains a few perl-based helper tools (including a GUI) to aid the user in setting up and running simulations. The tools are: mcgui: A Tk/Perl based GUI. mcrun: A Script that makes it easy to run sims and perform point scans and simple optimizations. mcdoc: Script for viewing inline component documentation. mcplot: Tool for plotting McXtrace-generated results. mcdisplay: Visual ray-tracing displaying neutron trajectories. mcformatgui: Front-end to mxformat to help reformat data-files (obsolescent). mcdaemon: Deamon to dynamically monitor and plot results (obsolescent). mcstas2vitess: Tool to transfer a McStas simulation to ViTESS. mcresplot: Script to help plotting resolution functions.

ParaView is a powerful scientific visualization application, designed with the need to visualize large data sets in mind.

PsychoPy is an open-source package for creating psychology stimuli in Python (A real and free alternative to Matlab). PsychoPy combines the graphical strengths of OpenGL with the easy Python syntax to give psychophysics a free and simple stimulus presentation and control package. The goal is to provide, for the busy scientist, tools to control timing and windowing and a simple set of pre-packaged stimuli and methods. The code is platform independent, using Python and C libraries that are widely available.

The sigrok project aims at creating a portable, cross-platform, Free/Libre/Open-Source signal analysis software suite that supports various device types, such as logic analyzers, MSOs, oscilloscopes, multimeters, LCR meters, sound level meters, thermometers, hygrometers, anemometers, light meters, DAQs, dataloggers, function generators, spectrum analyzers, power supplies, GPIB interfaces, and more.