Search Results for "assembly source code" - Page 9
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Showing 246 open source projects for "assembly source code"
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Code for predicting the 2-dimensional folding with minimum energy of a given RNA sequence. The code was written and originally released by Rune Lyngso.
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DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
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Lucy is a program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.
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Next-Gen Scaffolder is a scaffolder for de novo genome assembly projects, taking contigs and paired end libraries to produce high-quality scaffolds. It is compatible with 454 reads.
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BushMan is a web interface and a quality assurance tool for biological sequence assembly. It is a small application that helps process chromatograms, and it assembles using Phred and Phrap. It produces a FASTA formatted consensus sequence.
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Parallel IBDWS is an upgrade from IBDWS that utilizes parallel processing. Also, the incorporation of DNA sequence data has been added since the last code release
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DNPTrapper is a shotgun sequencing assembly editor, specifically designed for analysis and finishing of repeated DNA.
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NOTE: The IntAct package is now hosted at google code: http://intact.googlecode.com IntAct is an open source package to store and manipulate molecular interaction data.
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This software collection is for a DNA sequencing laboratory. It is used to design closure/finishing reactions following a shotgun sequencing experiment. It requires a draft assembly composed of contigs and scaffolds.
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Autoprime
Automated primer design using EnsEMBL
AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression. By connecting to the EnsEMBL database gene structure information is used to find primers spanning exon borders. This way only expressed sequences are captured. Additionally mispriming on repetitive regions can be avoided using information from RepBase. -
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Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.
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CIPTCL is a set of applications for the management of the Tissue Culture Lab at the International Potato Center. It supports handling, tracking and location of clonal plant materials including data logging on hand-held PCs with wireless and bar-code.
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Latronix Regnum Arts - Open Source Faction is an open source and freeware developer for all sorts of goodies. Be it games or applications. This is the home for the Drug Turfs Game (A Drug Wars like game) and the Drug Turfs Library.
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dictyBase is a database application for Dictyostelium genomics. The database software is intended to be of general use and usage of our software by other similar projects is encouraged. Thanks to the Saccharomyces Genome Database (SGD) for lots of code.
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RepeatFinder is a command line tool for generating non-overlapping matches of microsatellite DNA from FASTA format code.
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Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
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The Neural Assembly Simulation Environment (NASE) is a collection of routines written in the Interactive Data Language (IDL) by Research Systems Inc. It provides routines to simulate neural networks and to visualize those networks' behavior.
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Cellular Automata simulator. Native code (fast) and modular design: update rule, topology, time, measurement, initialization are independant. No GUI (for now...): configuration file (commented default automatically generated) overridable by command line.
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The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io
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Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.
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A toolbox for quantitative morphometric analysis of early development in spherical embryos, such as Xenopus laevis (African Clawed Frog). The toolbox is developed for Matlab 6.5 and higher and combines C-Mex code with Matlab functions.
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It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.
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Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)
