Search Results for "open source assembly software source code" - Page 15
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Showing 613 open source projects for "open source assembly software source code"
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SeqAnt is an open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform.
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Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
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Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.
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Stop Storing Third-Party Tokens in Your DatabaseRolling your own OAuth token storage can be a security liability. Token Vault securely stores access and refresh tokens from federated providers and handles exchange and renewal automatically. Connected accounts, refresh exchange, and privileged worker flows included.
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Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)
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VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.
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BioSpring is a molecular simulation software based on a spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics. It incorporates MyPal for locating ion binding sites and IMPALA for interactive placement of membrane proteins in a membrane environment.
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A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
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This software computes likelihoods for infinitely-many-sites sequence data under multiple merger coalescents. The likelihood can be computed exactly or approximated via importance sampling.
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PyMOL Plugins aims to provide many plugins for the PyMOL software. You can find further informations about PyMOL on this website: http://www.pymol.org/
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Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
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The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html
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This software is a Perl Catalyst based electronic lab notebook (ELN) aiming for small biologic laboratories, that have no funding to invest into a closed source ELN.
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GenoGUARD is a DNA sequence screening software that implements the best match method recommended by the federal government to detect the presence of biosecurity threats in synthetic DNA orders.
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NeuroBees
Multi-agent algorithm
Software tool (NEURON, Python, C++) based on the multi-agent Bee algorithm and aiming at multi-parametric optimization. 2 versions : - Link with NEURON (need download and install NEURON and NEURON-python) - Autonomous, with two types of neurones (Izhikevich and hodgkin huxley) -
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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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The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
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The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
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TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
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""" E-Cell's source code repository has moved to GitHub! https://github.com/ecell The development of E-Cell now continues on GitHub. The Subversion repository was abandoned. """ E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model.
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MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
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This software is developed by Kalidas (http://openwetware.org/wiki/Kalidas_Y) as part of his Ph.D. thesis. The method enables alignment of ligand molecules considered molecular graphs. It is useful in the domain of drug discovery and bioinformatics.
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Foad is an open source software which receive an EKG Signal from scanner, WFDB database or heart sensors. Finding patient disease started by taking Fourier transform (FFT) from input signal and extract a single cycle. Based on some heuristic algorithm the most important feature like P , Q , R , S , T captured and feed to trained neural network. and so the final decision made by CNN library.
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FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.