Search Results for "open source assembly software source code" - Page 10
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Showing 613 open source projects for "open source assembly software source code"
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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mitoMaker
mitoMaker - a mitochondria pipeline wrapper script
Mitomaker is a pipeline wrapper, result analyzer and automated annotator, written in Python v2.7, that, with the help of other programs, builds, analyzes, looks for the best build and annotates target genomes (such as mitochondria and cloroplast). It could be used with other targets, such as specific genes, or transcriptomes, even though that is not it's primary goal, nor thoroughly tested. After various attempts to build different mitochondrial genomes in the lab I studied, a general... -
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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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PhaseTank
genome-wide computational identification of phasiRNAs
Phase siRNAs (phasiRNAs) are a class of small RNAs, which triggered by miRNA-targeted cleavage and followed by DCL4-mediated production of small RNAs phased in 21-nt increments. Here, we introduce PhaseTank to systematically characterize 'miRNA → mRNA → tasiRNA → target genes' regulatory casacades in plants. With one command analysis, PhaseTank is an easy-to-use software for users. -
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Java Machine Learning Library is a library of machine learning algorithms and related datasets. Machine learning techniques include: clustering, classification, feature selection, regression, data pre-processing, ensemble learning, voting, ...
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wEMBOSS is a Web interface for the EMBOSS software package for biological sequence analysis. Under wEMBOSS each user has a private workspace (UNIX home directory) on the server, where he can permanently store his data and organize them in projects. The companion suite wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatic software suites as BLAST, CLUSTAL and MRS.
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A Scalable Multicore Code for RNA Secondary Structure Prediction
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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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Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. Tab2MAGE spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.
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EducationalLCS
eLCS - Educational Learning Classifier System
Educational Learning Classifier System (eLCS) is a set of learning classifier system (LCS) educational demos designed to introduce students or researchers to the basics of a modern Michigan-style LCS algorithm. This eLCS package includes 5 different implementations of a basic LCS algorithm, as part of a 6 stage set of demos that will be paired with the first introductory LCS textbook. Each eLCS implementations (from demo 2 up to demo 6) progressively add major components of the entire... -
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ParaBWT - parallel BWT construction
a parallel and space-efficient Burrows-Wheeler transfrom constructor
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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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Percolator, binary downloads
Binary download site for percolator the proteomics post processor
Binary download site for the proteomics data post processor percolator. The source code is hosted on git hub, https://github.com/percolator/percolator -
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GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.
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VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
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provean
Predicting the functional effect of protein sequence variations
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. The prediction is based on the change, caused by a variation, in the similarity of query sequence to closely related sequences collected through BLAST. -
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coalescent
Software tool for Research in Computational Population Genetics
Development of exact and approximate methods (Importance Sampling and MCMC based) for computing likelihoods under the standard population genetic models of mutation,migration & recombination. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/COALESCENT -
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
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Phylogenetic software that implements the algorithms "Fast Computation of Distance Estimators" and "Fast Neighbor Joining".
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WebChemViewer
A simple program for sharing molecular structures with associated data
Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages. WebChem Viewer is released under the FreeBSD license. It was created by Jacob Durrant, a post-doc in the lab of Rommie E. ... -
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mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more
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basecv
BCV is DNA base caller with vocabulary
The Base Calling with Vocabulary (BCV) software package is intended for analysis of direct (population) sequencing chromatograms using known vocabulary sequences similar to the target DNA. The current version of BCV can only process chromatogram files obtained on Applied Biosystems capillary sequencing machines (ABIF file format). -
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AWclust is easy to use non-parametric population structure analysis software written for R with a GUI interface. Just point and click and you will be on your way to discovering the important cluster information in your SNP data sets.
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GraFIX is a software and a method to detect fixations in low and high quality data, consisting of a two-step process in which eye-tracking data is initially parsed by using adaptive velocity-based algorithms, before it is hand-coded using the graphical interface, allowing accurate and rapid adjustments of the algorithms' outcome. GraFIX is released under the GPLv3 public license (http://www.gnu.org/licenses/). Please cite as: Saez de Urabain, I.R., Johnson, M.H., Smith, T.J., (2014)...