Search Results for "java open source"
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Showing 407 open source projects for "java open source"
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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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APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.
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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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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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STORIS provides ERP software solutions for the home furnishings and appliance industryFor over 35 years, it has delivered tools designed to meet the specific needs of retailers in this sector. STORIS’ ERP platform integrates core retail operations, including Point of Sale, Inventory Management, Logistics and Distribution, Buying Tools, Customer Service, Accounting, Financing, Reporting, Business Intelligence, and System Tools.
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ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.
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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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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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Subread
High-performance read alignment, quantification and mutation discovery
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in... -
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The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
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Haystack is a modern, engaging, and intuitive intranet platform that employees actually use.With customizable iOS and Android mobile apps, Slack and Microsoft Teams integrations, and an intuitive design employees love, Haystack brings an outstanding digital employee experience to your entire workforce, no matter where their work takes them.
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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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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
... - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us - kabeermuzammil614@gmail.com MzDOCK Development - Available on WindowsOS and Linux ubuntu 22.04 and more - Software Authorship - Muzammil Kabier -
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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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Molsketch
2D molecule editor
Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats. -
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JRC QSAR Model Database
(Q)SAR Model Reporting Format Inventory
In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf... -
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ShelXle
ShelXle is a Qt GUI for SHELXL
ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details. -
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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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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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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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bmrblib
The BMRB library
Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format. -
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Nest-o-Patch
Software for analysis of patch-clamp recordings and other wave data
This program was designed mainly for preconditioning and analysis of electrophysiological data, including patch-clamp and 2-electrode voltage clamp recordings. The program includes tools both for basic analysis of whole-cell recordings or analysis of single channel properties. Program can display and analyse long traces incuding many sweeps, series and even groups simultaneously. Current amplitudes or time intervals are easily measured. Single channel conductance, kinetics, NPo, as well as... -
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pharmit
Open-source online virtual screening tools for large databases
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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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ERmod
Approximate solvation free energy calculator
ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation software, such as LAMMPS, GROMACS and/or AMBER. -
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RetroScheme- Get Your Retrosynthesis
- RetroScheme is used for molecule sketching and retrosynthesis
RetroScheme was specifically designed to help Chemists in knowing potential starting material through retrosynthetic analysis. The App is basically a GUI wrapper for the library Aizynthfinder from Astrazeneca.. - The App is coupled with molecular sketching tool to sketch your compound - This was made to be easy for the user and can be used endlessly to assist in potential new drug synthesis
