Search Results for "using"
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Showing 61 open source projects for "using"
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1
BioXTAS RAW
Processing and 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 (EFA) or the regularized alternating least squares (REGALS) methods. Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. ... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In 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 -... -
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luscus
molecular editor and viewer
...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 interface for MOLCAS program package, however it's adaptive nature makes possible using luscus with other computational program packages and chemical formats. If you use this program, please cite: G. Kovačević, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z -
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Charmol
Program for molecular graphics
...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) - surfaces using gaussian cube files (also color-mapped surfaces according to potential) - schematic representation of vibrations using arrows - user-defined arrows representing vectorial properties - measuring gauges - combinations of these features (more orbitals together, orbitals and arrows together etc.) ... -
Retool your internal operationsBuild internal software that meets enterprise security standards without waiting on engineering resources. Retool connects to your databases, APIs, and data sources while maintaining the permissions and controls you need. Create custom dashboards, admin tools, and workflows from natural language prompts—all deployed in your cloud with security baked in. Stop duct-taping operations together, start building in Retool.
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GrowthRates
Calculate growth rates from microplate reader output
...GrowthRates completely analyzes growth parameters in all 384 wells in under 5 minutes. CGR2 (Compare Growth Rates) is a statistical program specifically designed to assess the results of a growth rate experiment that has been analyzed using the program GrowthRates. The purpose of a statistical analysis is to establish our level of trust in both the data and in the conclusions we draw from that data. Both the GrowthRate and CGR2 packages are -
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relax
Molecular dynamics by NMR data analysis
...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 anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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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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MSCC Applications Support
Materials and Computational Chemistry applications on HPC platform
...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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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
...There are also instructions provided in case you are running these analyses via a computing cluster/Slurm workload manager. You can choose to go through the workflow using either an Rmd script, an html file, or a PDF, or via the homepage link provided. If you have questions or concerns, please don't hesitate to reach out. Thanks! -
Say goodbye to broken revenue funnels and poor customer experiencesLeanData is a Demand Management solution that supports all go-to-market strategies such as account-based sales development, geo-based territories, and more. LeanData features a visual, intuitive workflow native to Salesforce that enables users to view their entire lead flow in one interface. LeanData allows users to access the drag-and-drop feature to route their leads. LeanData also features an algorithms match that uses multiple fields in Salesforce.
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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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hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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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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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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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...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 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. ... -
15
easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
This package of MATLAB routines with accompanying GUI allows scientific users to measure the 3D location of single molecules when using the double-helix point spread function (DH-PSF) widefield microscope. Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) - DH localization is performed through template matching and subsequent double Gaussian fitting - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions - Two spectral channels are registered by generating a locally-weighted quadratic mapping function from control point pairs -
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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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The Wily DNA Editor
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section. -
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
...Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviors recorded at different beamlines. If you use DATASW in your work, please, cite: Shkumatov A.V. & Strelkov S.V. (2015) Acta Cryst. ... -
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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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ISVASE
identification of sequence variant associated with splicing event
...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. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time. -
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orthos
Simulation of EPR spectra of nitroxide biradicals
...NB: Please note that now (as of Nov 2016) the distribution is being updated so that to improve reliability, OS-universality, and the quality of documentation. If you have any troubles installing/compiling/using the software, please contact me. I would be glad to help. -
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
...However, in developing PDBManip, I have customized scripting language, by adding predefined PDB related variables and functions, in such a way that a user with a very basic knowledge of programming can easily write very eligible scripts, even for very complicated editing and manipulating tasks. In this way, proficiency in computer programming, that is a must in using Awk or Perl, is not a barrier. -
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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... -
25
ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. ...
