Search Results for "linux operating system"
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Showing 73 open source projects for "linux operating system"
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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luscus
molecular editor and viewer
Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus can also visualize dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to point out a geometrical feature or a physical quantity. The program is developed as a graphical... -
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SeaBreeze
Open-source cross-platform spectrometer device driver
SeaBreeze is a device driver library that provides an interface to select Ocean Optics spectrometers. It is written in C/C++ and builds and runs on Windows (XP/7/8), MacOSX, and Linux (x86/x64/ARM). -
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Web-based Electronic Laboratory Notebook (ELN) with integrated Chemical Inventory by the group of Prof. Goossen (TU Kaiserslautern, Germany), based on PHP/MySQL. Allows (sub-)structure search, reaction planning, management of spectra and literature.
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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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Charmol
Program for molecular graphics
Charmol is a cross-platform GUI/command-line based program for making high-quality pictures of molecular structures, nowadays working on Linux, MacOS and Windows. As output, it produces POV-Ray rendered images or files in VRML format. Charmol is capable of making pictures containing: - from small- to large-size molecules - more molecules together (different settings possible) - orbitals using molden and fchk files (GTO functions up to 'h' angular momentum supported) -... -
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MAF
Bash Framework to combine many preprocessing and alignment tools
DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom... -
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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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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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MSGraph is a program designed for the interactive, fast, qualitative analysis of mass spectrometric (MS) data. It is a tool to provide fast and simple access to all the information contained in an LC/MS analysis run.
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The Chemicals Database
An Open Source "product catalogue" that is customizable and versatile.
The Chemicals Database is a simple yet effective approach to track a stock of products. It provides a "product catalogue" that is accessible from any workplace over Intranet (http) and the server can be operated "in the cloud". Although this documentation deals in particular with a stock of chemicals in a laboratory, it can easily be adapted to any other "items" such as samples, spare parts, tools and other inventory. The software does not rely on a proprietary "solution" but employs... -
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KimBlast
Blast+ the easy way
KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md -
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Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.
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RMGDFT
Real Space Multigrid based electronic structure code.
News: active RMG development has moved to github https://github.com/RMGDFT News: V4.1.0 released on 09/29/2020 News: V4.0.0 released on 09/01/2020 with major updates. News: V3.0.0 released on 06/09/2018 with major updates. News: V2.2.2 released on 10/14/2017 with minor bug fixes. News: V2.2 with performance enhancements, bug fixes and new features released on 06/26/2017. Sources are available with binaries to follow soon. News: V2.1 with many improvements released on... -
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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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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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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chemfiles
Modern library for chemistry file reading and writing
Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with... -
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MethyMer
Design of specific primer combinations for bisulfite sequencing
MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation... -
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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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This package includes a collection of MATLAB files which are designed to: 1. Given a calibration scan of the image of a point emitter with an engineered point spread function (PSF), 2. Perform a phase retrieval algorithm based on maximum likelihood estimation (MLE) of a phase aberration term which is added to the theoretical pupil function of the imaging system. 3. Use the phase-retrieved pupil function to perform single-emitter localization. Accompanying publication available here:...
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Ocean Optics Sample Pack
Sample code for Ocean Optics OmniDriver spectrometer device driver
Sample code demonstrating how to use OmniDriver to drive Ocean Optics full range of spectrometers from C, C++, C#, Java, LabVIEW, Delphi, MATLAB and more. -
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pyxaid
PYthon eXtension for Ab Initio Dynamics
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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. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/
