Search Results for "bio-bwa"
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Showing 31 open source projects for "bio-bwa"
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.
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SpectralWorks
View, manipulate, analyze (LS fit, SVD, FT), and make figs of, spectra
Program for viewing, editing, manipulating, and analyzing absorbance spectra. Simple arithnetic includes making linear combinatins of up to 10 spectra. Advanced functions include fitting spectra as LC of standard basis spectra, singular value decomposition, Fourier transform, differentiation, integration, global fitting of 3D titration and kinetic data. Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into photoshop for... -
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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DBSolveOptimum
The software for systems biology/pharmacology modeling
DBSolveOptimum is a stand-alone software tool for the construction and analysis of mathematical models of biological systems. It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling... -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
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PSICOV
The unofficial binary for PSICOV: Protein Sparse Inverse COVariance
PSICOV (Protein Sparse Inverse Covariance estimation program) is a coevoultion algorithm applied to very large (typically >=1000 sequences) multiple sequence alignments for precise protein structural contact prediction. This is the unofficial precompiled Windows binary for PSICOV compiled by Chengxin Zhang at Fudan University. The source code is copyrighted by David T. Jones, University College London. -
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**** This page is not used for this project any longer. *** Please update your bookmarks and go to https://github.com/UUPharmacometrics/PsN
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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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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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
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Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.
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WHATCH'EM
WHATCH’EM simulates mosquito container water temperature
WHATCH’EM simulates the highly non-linear manner in which atmospheric conditions and container characteristics determine water temperature and height, leading to results that are not always intuitive and likely not simulated by simpler empirical models. WHATCH’EM has the capacity to be utilized for other mosquitoes and other container-inhabiting arthropods. -
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BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.
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ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.
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Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
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PGenome, created in C++, contains several tools to analyze genotype frequencies, linkage disequilibrium, association of individual nucleotides and of genotypes and power calculations of minimal allelic and genotypic effects.
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cifget is a DDLm dictionary import expansion utility, which generates expanded dictionaries that could be used when reading, writing, or validating CIF files
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ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
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Simple console program intended for factor or principal components analysis. It calculates the optimal number of factors using the Horn's parallel analysis, computes the Kaiser-Meyer-Olkin and a few other measures of sampling adequacy.
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RPowr is a simple calculator for planning correlational research. It computes the power of the Pearson correlation coefficient allowing adjustment for unreliability and range restriction of the variables (e.g. predictor and criterion measures).
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The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.