Search Results for "alpha"
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Showing 86 open source projects for "alpha"
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EMC: Enhanced Monte Carlo; A multi-purpose modular and easy extendable solution to molecular and mesoscale simulations
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QTPN
Visualization, electronic structure and multicomponent calculations
C/C++ code with GUI, supported on QT library for handling of windows and OpenGL/GLU for display of graphics. It is capable of dealing with plotting, electronic structure calculation and multicomponent calculations. Current version reads XYZ and deMon output files. Displays image of geometry, atomic orbitals, molecular orbitals, density and Fukui functions in a few different formats. In situ SCF Hartree-Fock calculations available. -
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WavePacket (C++/Python)
Time-dependent simulation of open and closed quantum systems
Note: This package has been superseded by a Python-only package. See https://github.com/ulflor/wavepacket for the follow-up project. WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations. Optionally accounting for the interaction with external electric fields within the semiclassical... -
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ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.
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ClusterAlign
Alignment of tilt-series TEM images based on faint fiducial markers
Tracking markers shown faintly in projections of rotating rigid body with translational jitter based on uniqueness of structures -
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SpectralWorks
View, manipulate, analyze (LS fit, SVD, FT), and make figs of, spectra
Program for viewing, editing, manipulating, and analyzing absorbance spectra. Simple arithnetic includes making linear combinatins of up to 10 spectra. Advanced functions include fitting spectra as LC of standard basis spectra, singular value decomposition, Fourier transform, differentiation, integration, global fitting of 3D titration and kinetic data. Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into photoshop for... -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the... -
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AnharmoniCAOS
Cagliari-Orsay model for anharmonic molecular spectra in 2nd order PT
Given dynamical coefficients and/or derivatives of the ionic potential with respect to normal (harmonic) vibrational modes, compute anharmonic energies and electric dipole-permitted transitions and intensities using nearly-degenerate perturbation theory (i.e. properly accounting for Fermi and Darling-Dennison resonances). -
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MolDynSim
TrajLab subproject: Molecular dynamics simulations in MATLAB
...AMBER, GROMACS, NAMD, etc.), the MATLAB environment offers easy access to manipulating the codes, testing novel algorithms, non-standard force fields and performing all kinds of numerical experiments. To be used mainly in research and teaching! Started early 2010, MolDynSim is still in an early (alpha) stage, and any help in further development is highly appreciated. Developed mainly by B. Schmidt (FUB) -
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MetaStable
TrajLab subproject: Metastability analysis of molecular conformations
...AMBER, GROMACS, NAMD, etc.), the MATLAB environment offers easy access to manipulating the codes, testing novel algorithms, non-standard force fields and performing all kinds of numerical experiments. To be used mainly in research and teaching! Started early 2010, MetaStable is still in an early (alpha) stage, and any help in further development is highly appreciated. Developed by B. Schmidt (FUB), F. Haack, S. Röblitz, and M. Weber (ZIB) -
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data.... -
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pyxaid
PYthon eXtension for Ab Initio Dynamics
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in... -
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LUNUS software for generating 3D maps of diffuse scattering from macromolecular X-ray crystallography diffraction images. Also see http://lunus.sourceforge.net
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RErun
Create virtual DNA/RNA agarose gels
RERun is a software tool for creating virtual agarose electrophoresis gels of nucleic acid fragments (restriction digests, PCR amplicons, etc). It is written in Perl and developed on Linux, although it can be made to run on Windows with some work (undocumented). -
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VSViewer3D
3D Virtual Screening Viewer
This project is an interactive viewer for 3D virtual screening data. -
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Magnetic Drug Targeting (MDT) simulation and visualization in traversal and longtitudinal mode.
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The Diffraction Image Experiment Repository (DIMER) is an online archive for diffraction experiments, providing secure storage during analysis and publishing of experiments so they can be linked to, searched, and integrated into other databases.
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Project for develop force fields with using ab-initio calculations
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allink
Software for data analysis, image processing, simulations, solver.
Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the... -
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Quantum Chemistry Import Tool is a django application that parses the output file of quantum chemistry software as NWChem, Octopus, Gaussian, etc. The result can be saved in relational database.
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