Search Results for "atom-project"
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Showing 68 open source projects for "atom-project"
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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OligoYap Portable
Oligo design and bioinformatic analysis software.
...On some systems (as win8.1) you may also need to check the "run as administrator" option. You can download the Turkish version (OligoYap_tur_portable.exe) from the Project Activity or by clicking on the Files menu. You can download the user manual video (OligoYap_eng_video.avi) from the Project Activity (click See All Activity) or by clicking on the Files menu. -
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DEEP
Differential Evolution Entirely Parallel Method
...The introduced improvements are: (I) allow several oldest individuals to be overwritten by the same number of best ones in the population, (II) new selection rule uses several objective functions in offspring evaluation. RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio This work is supported by RNF Grant 14-14-00302 and by “5-100-2020” Program of the Russian Ministry of Education and Science. The previous funding included SYSPATHO FP7 project №260429, RFBR grants 10-01-00627-a, 11-01-00573-a, 11-04-001162-a and State Contract with Russian Ministry of Science №14.740.11.0166 and №11.519.11.6041 -
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Eleana
Program for the analysis of spectroscopic data, in particular EPR(ESR)
Eleana is a program for manipulating, modifying and analyzing various spectroscopic data, in particular electron paramagnetic resonance spectra. It allows you to import data from Bruker spectrometers such as Elexsys or EMX and data from any ASCII file or imported from the clipboard. The program is under constant development, but already has many functions implemented for spectral analysis. Some of the basic functions include: baseline corrections, filtering, spectral clipping, integration /... -
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rssfiz
Java science library.
Java science library. Project contains modules for physics units, particle and quantum physics, molecule, chemistry and universe definitions, also additional math classes. -
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MSCC Applications Support
Materials and Computational Chemistry applications on HPC platform
Five software i.e. AMDKIIT , ANN-CI, LITESOPH, MTASpec, and µ2mech are developed as an outcome of the Materials and Computational Chemistry (MSCC) project under the National Supercomputing Mission (NSM). These are the set of codes (software) developed by the investigators to perform the computations to study the properties of atoms, molecules, clusters, alloys, bio-molecules, and composite materials using high-performance computing (HPC). For more information on the softwares developed under MSCC please go to: https://sourceforge.net/p/mscc-applications-nsm/wiki/ To download the versions of the MSCC softwares installed on NSM HPC systems please go to: https://github.com/mscc07/mscc To download the test input dataset please go to: https://github.com/mscc07/mscc-testinput For training material please go to: http://www.youtube.com/@mscctraining -
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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 dipole approximation, WavePacket can be used to simulate modern experiments involving ultrashort light pulses in photo-induced physics or chemistry. ... -
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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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FDMNES powered by sparse solvers
The sources and builds history of FDMNES project
The sources and builds history of FDMNES project (http://neel.cnrs.fr/spip.php?rubrique1007&lang=en ) with parallel sparse solvers moved to github: https://github.com/gudasergey/fdmnes -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/ -
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Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.
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The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
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MCTDHTools
A library to easily analyse output of the Heidelberg MCTDH code
This project aims to provide a set of routines to easily read in and manipulate the output of the Heidelberg MCTDH code. The goal is to enable a new user to quickly get started with writing custom analysis programs. Also, it should enable more experienced users (== us) to write small, clean, and testable analysis programs, something that seems incompatible with the Fortran-77 code of the Heidelberg MCTDH package. -
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Collaborative Computing Project for NMR
Collaborative Computing Project for NMR (CCPN)
The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. ... -
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!!! PTEROS DEVELOPMENT MOVED TO GITHUB !!! New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
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TX-TL modeling toolbox
Modeling and analysis tools for the TX-TL cell-free expression system
This project contains tools for using the TX-TL cell-free expression system. These tools include component models for simulating and analyzing biomolecular circuits, as well tools for composing circuits and creating more complex systems. NOTE: This project has been shifted to GitHub: https://github.com/BuildACell/txtlsim -
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
RAtom solves nonlinear Kohn-Sham equation for the neutral atom. The adaptive algorithm based on finite element method (FEM) is implemented. Discretization of the differential eigenvalue problem is done by finite element method with Lobatto polynomials as a basis functions. High order Gauss quadratures are applied in order to obtain the total energy of atom with absolut accuracy of 1E-6 hartree. -
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BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. -
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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. If you use orbkit in your work,... -
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DNA patterns & application
A software for generating DNA patterns
...One of the questions to which an answer was given is: How many types of promoters are out there regulating the genes ? It seems that there are 10 types of promoters. The project also contains 20,000 images (DNA patterns) that can be analyzed in relation to various genetic disorders (if Homo Sapiens) or for understanding the evolutionary mechanisms between species. References: [1] Gagniuc and Ionescu-Tirgoviste: Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics 2012, 13:512... -
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Reference implementation of the Systems Biology Graphical Notation: map exchange format and library handling import/export and validation. Resource of the libSBGN project have been migrated from SourceForge to GitHub. Latest changes can be found on GitHub now. The code repository can be found here now https://github.com/sbgn/libsbgn The files (releases) can be found here now https://github.com/sbgn/libsbgn/releases The bugs and features (issues) can be found here now https://github.com/sbgn/libsbgn/issues
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HYBRYD
Library written in C with Python API for IPv6 networking
This project is a rewritten of an initial project that I've called GLUE and created in 2005. I'm trying to readapt it for Python 2.7.3 and GCC 4.6.3 The library has to be build as a simple Python extension using >python setup.py install and allows to create different kind of servers, clients or hybryds (clients-servers) over (TCP/UDP) using the Ipv6 Protocol. -
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
...We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do not hesitate to contact us in the forum or by email. Please see the original manuscript: Lopes, TJS, et al. (2015) - "Identifying problematic drugs based on the characteristics of their targets" - Frontiers in Pharmacology doi: 10.3389/fphar.2015.00186