Search Results for "software development"
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Showing 24 open source projects for "software development"
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
...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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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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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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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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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 CCPN jointly cover all aspects of biomolecular NMR and together they promote excellence in science in their respective fields. -
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An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
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HYBRYD
Library written in C with Python API for IPv6 networking
This project is a rewritten of an initial project that I've called GLUE and created in 2005. I'm trying to readapt it for Python 2.7.3 and GCC 4.6.3 The library has to be build as a simple Python extension using >python setup.py install and allows to create different kind of servers, clients or hybryds (clients-servers) over (TCP/UDP) using the Ipv6 Protocol. The architecture of the code is based on brain architecture. Will put an IPv6 adress active available as soon as... -
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MDA
Molecular Dynamics Analyzer (MDA)
MDA is a 3D single-particle tracking software that explicitly addresses fluorescence microscopy experiments deep in living specimens. It is capable of minimizing the systematic error that occurs with astigmatism-based 3D techniques owing to the aberrations induced by the refractive index mismatch. In contrast to existing techniques, the method determines the aberration directly from the acquired 2D image stream by exploiting the inherent particle movement and the redundancy introduced by the... -
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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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The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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ISAD
Individual Synaptic Activity Detection (ISAD)
ISAD is a peak detection software that detects individual (pre-)synaptic activity in microscopy images from neuronal cultures transfected with pHluorin. It computes synaptic signals from automatically segmented regions of interest and detects peaks that represent vesicle fusion events, thus, pre-synaptic activity. ISAD is based on MWA, which is a continuous wavelet transform based algorithm that employs multiple wavelets and is published as: Sokoll, S., Tönnies, K., and Heine, M. Detection... -
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Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.
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MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
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Contains various algorithms that maps short reads produced from Illumina (Solexa) Genome Analyzer, or Applied Biosystems' SOLiD System, to a reference sequence or a set of reference sequences.
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Little b is a Lisp-based language which allows scientists to build shareable, reusable mathematical models of complex systems based on shared parts. The initial focus is molecular and multicellular networks. Project web page: http://www.littleb.org
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ChIPOTle 2.0 is a user friendly tool for performing peak detection in ChIP-chip signal. The tool also has functions for probe sorting, signal normalization, replication merging, and multiple correction testing in a windows interface or *nix command line.
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The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.
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FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.
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GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.
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IntiMap is a convenience tool to run the MS-DOS command-line tool MapPop for selective genotyping. It adds facilities to prepare genotyping data files, manage genotype sets and visualize mapping results (genetic marker maps).
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