Search Results for "scientific plotting software"
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Showing 74 open source projects for "scientific plotting software"
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes... -
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GrowthRates
Calculate growth rates from microplate reader output
The Bellingham Research Institute (BRI) develops and distributes software that is free of charge to academic and other non-profit organizations. GrowthRates is our software tool that simplifies the analysis of microplate reader output from microbial growth experiments without having to program in Python, R, or MATLAB. It automates the calculation of growth rate parameters, including rates, lag times, maximum population density. Manual calculation of those parameters requires at least 5... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis... -
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and... -
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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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Software and codes created in "Laboratorio de Química Computacional" of "Facultad de Ciencias y Tecnología" of "Universidad de Carabobo"
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WaveTrain (Python)
Quantum dynamics of chain-like systems using tensor train formats
WaveTrain is an open-source software for numerical simulations of chain-like quantum systems with nearest-neighbor (NN) interactions only (with or without periodic boundary conditions). This Python package is centered around tensor train (TT, or matrix product) representations of quantum-mechanical Hamiltonian operators and (stationary or time-evolving) state vectors. WaveTrain builds on the Python tensor train toolbox scikit_tt, which provides efficient construction methods, storage... -
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HostDesigner
General purpose de novo molecular design software
Although many potential applications exist in chemistry and material science, software to allow the general application of de novo structure-based design methods in supramolecular chemistry was non-existent. To address this limitation we created HostDesigner, a code that builds and evaluates millions of molecules in minutes. This command line executable builds 3D molecular structures by covalently connecting user-defined input fragments with pre-computed hydrocarbon fragments from a library.... -
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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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TVscript
Exploration of the removal of count variable transcripts.
> See TVscript wiki: https://sourceforge.net/p/tvscript/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: (See wiki) 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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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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biOP
biOP [bio~ObjectPascal/bio~Delphi] bioinformatics libraries
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Toxmatch
Exploring chemical similarity
Toxmatch is a flexible and user-friendly open-source software application that encodes several chemical similarity indices to facilitate the grouping of chemicals into categories and read-across. The core functionalities include the ability to compare datasets based on various structural and descriptor-based similarity indices as well as the means to calculate pair wise similarity between compounds or aggregated similarity of a compound to a set. -
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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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An open-source software aimed at unsupervised molecular alignment
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An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)
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Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
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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. The 28 partners of... -
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nmr-nessy
NMR relaxation dispersion spectroscopy analysis software
NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models. -
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MELTING is a software to compute, for a nucleic acid duplex, the enthalpy and the entropy of the helix coil transition and then the melting temperature. Four types of hybridization are possible : DNA/DNA, RNA/RNA, RNA/DNA and mRNA/RNA.
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Grid-based Coupled Electron and Electromagnetic field Dynamics (GCEED) is an open-source software package for massively parallel first-principles calculations of electron dynamics in real time and real space. The program codes are written in the Fortran 90/95 language with MPI and OpenMP. Time dependent density functional theory (TD-DFT) calculations can be performed on 100,000 CPU cores of K Computer with high parallel efficiency.
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An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
