Search Results for "sandbox:/mnt/data/project_plan.pod" - Page 3
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Showing 151 open source projects for "sandbox:/mnt/data/project_plan.pod"
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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/ -
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LOOS
Analyze molecular simulation data
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods. THIS PAGE IS NO LONGER UPDATED. Please see https://github.com/GrossfieldLab/loos for all recent developments -
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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, please cite it as follows: Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, and Axel Schild, "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data", J. ... -
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RDKit
Open-Source Cheminformatics and Machine Learning
A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches. -
GoAnywhere Managed File Transfer (MFT)GoAnywhere MFT provides secure managed file transfer for enterprises. Deployable on-premise, in the cloud, or in hybrid environments, GoAnywhere MFT software enables organizations to exchange data among employees, customers, and trading partners, as well as between systems, securely. GoAnywhere MFT was a recipient of the Cybersecurity Excellence Award for Secure File Transfer.
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Tigris is an open source suite of classes and programs implemented in C++ for single particle electron microscopic image processing.
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Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.
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A toolkit in C++ and python to process both experimental and simulation data of colloidal particles. Includes among others * a multiscale particle tracking algorithm [1] whose C++ implementation is optimised for 3D confocal data. Python implementation is more versatile (2D and 3D data). * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H.
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ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.
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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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MZmine 2
A framework for differential analysis of mass spectrometry data
MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data. -
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
...To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs. -
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gMol
gMol molecular graphics
We've moved to https://github.com/tjod/gMol/wiki gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces. -
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Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.
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[OBSOLETE, check Github repository: https://github.com/LBT-CNRS/MDDriver) MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time.
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BAIT
Software to help analyse Strand-Seq data
Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. -
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Larch: Data Analysis for X-ray Spectra
Data Processing and Analysis for X-ray Spectroscopy and More
Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. ... -
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VSViewer3D
3D Virtual Screening Viewer
This project is an interactive viewer for 3D virtual screening data. -
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the... -
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The CCP1GUI
An extensible GUI for computational chemistry codes
The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes. -
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
...Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. Thus we need to standardize data management and tracking systems, built on a scalable, flexible structure with an easily accessible and web based interface, what is usually called Laboratory Information Management System (LIMS). -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
...IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/". -
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SIMtoEXP
For comparison of simulation and experimental scattering data
SIMulation to EXPeriment is software that allows the direct comparison of simulation density information with that obtained from X-ray and neutron scattering experiments, by converting the simulation data to form factors. It also calculates volume probability distributions according to a space filling volumetric model. Written in C++ and Qt, SIMtoEXP has a very simple and easy to use GUI with interactive plotting. The software was originally developed by Norbert Kucerka. The code has been tested on OpenSUSE and Ubuntu (both binary and compilation); Windows and Mac are not officially supported, see the 'Notes' in the tar. ... -
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allink
Software for data analysis, image processing, simulations, solver.
...Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the operation of Matematica on different sets of data visualized on a Qt graphical interface. DrImage) image manipulation on the Matematica filters. The program is intended to use as less as possible external libs (optional: openGL, gsl, fftw, cgal, png, tiff, boost, MPI, Qt...).
