Search Results for "open source assembly software source code" - Page 22
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Showing 1558 open source projects for "open source assembly software source code"
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samsn
A tool to handle multi-stage mass spectrometry data
The source code for SAMSN can be found in github at https://github.com/miquelrojascherto/samsn -
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Linking Yabi with RDA
This software system enables publication of YABI workflows to the RDA.
Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror... -
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CallSim
low-volume read processing base corrector
CallSim is a software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. CallSim provides a final classification or rescue of a base/indel in reads, where putative variants have been identified via typical SNP/indel workflows. plots rendered by: JFreeChart library http://sourceforge.net/projects/jfreechart/ -
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The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.
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TiffToDicom
A converter from Tiffs to Dicoms
This is not a final version but a work in progress. I am releasing the code only in the hopes that it will be helpful. There will be further updates in the future as the project is being actively developed. -
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The Aglets Software Development Kit (ASDK) is a framework and environment for developing and running mobile agents. Mobile Agents are a type of software agents that have the unique ability to transport themselves from one system to another. Doing so, an
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jPeriodic
jPeriodic is a table of elements written in Java
jPeriodic is a simple table of elements coded in Java providing the user with the most common informations about each known chemical element. By clicking an element a popup will apear containing the selected elements attributes. Additionaly jPeriodic offers a small temperature converter which is able to convert between Celcius and Kelvin. Because jPeriodic is coded in Java the software is platform-independent, meaning you can run jPeriodic on Windows, Mac OS, Linux and many other... -
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Cherokee is a fully extensible and scriptable automation engine for any and all java applets. To make it work for your favorite java applet the most you have to do is write is two classes.
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Galois sub-hierarchy builder
Visualize Galois sub-hierarchy of 2d matrix
GSH builder is a free Galois Sub-Hierarchy visualization tool. The algorithm for calculating GSH is called Pluton and the present Java realization is based on two articles. "Efficiently computing a linear extension of the sub-hierarchy of a Concept Lattice" by Anne Berry, Marianne Huchard, Ross M. McConnell, Alain Sigayret and Jeremy P. Spinrad. "Performances of Galois Sub-hierarchy-building algorithms" by Gabriela Arevalo, Anne Berry, Marianne Huchard, Guillaume Perrot and... -
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Linking BPA with RDA
This software system enables publication of ISA-Tab files to RDA.
BioPlatforms Australia (BPA) has funded a number of datasets generation initiatives around important research themes and scientific challenges faced by Australian researchers to provide a unique public resource for the benefit of Australian life sciences research. These large scale genomic, proteomic and metabolomic datasets are being generated and centrally managed by Bioplatforms Australia in collaboration with leading scientists, research institutes and government agencies. With the... -
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iLastic
Query, integrate and manipulate data using natural languages.
iLastic is an open-source framework to query, integrate and manipulate any type of data in English. Extract, transform and merge information from the web, databases, files or any other data repository using a language you already know... English -
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Bracer
Repository has been moved to: http://dtitov.github.com/bracer
Java library for parsing and evaluating math expressions. Javadoc is available at http://bracer.sourceforge.net/javadoc/ P.S. This library depends on Apache Commons Math, so don't forget to include commons-math-2.2.jar to your project. -
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and... -
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TRMSim-WSN (Trust and Reputation Models Simulator for Wireless Sensor Networks) is a Java-based simulator aimed to test Trust and Reputation models for WSNs. It provides several Trust and Reputation models and new ones can be easily added.
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The software is related to the PhD thesis of Zoltán Farkas, used to simulate work distribution and processing in hierarchical desktop grid systems.
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SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.
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JSpoor is a utility software for logging and recording of user interface events and actions during working sessions of users with a Java/Swing Software. It captures and records both high level (semantic) actions and low level actions such as mouse moves.
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This project is about stochastic simulation methods and their applications to physical systems. We develop interactive books, which can be used by students to study physics using free resources. The books contain text and Java source code.
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OpenMCD
Eclipse debugging tools for ecu development
OpenMCD wants to become a top-class collection of open source, eclipse based development and debugging tools for the development of electronic control units (ECUs). MCD stands for measurement, calibration and diagnostics: three activities often performed during the development of software for embedded and mechatronic systems. -
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Nen
neural network implementation in java
3-layer neural network for regression and classification with sigmoid activation function and command line interface similar to LibSVM. Quick Start: "java -jar nen.jar" -
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The Unified Modeling Language (UML) is used for designing software. ArgoUML is an open source UML editor. This plugin integrates the "Context-Based Constraint Language (CCL) for Components" into ArgoUML. On Berlios we speak german - check www.cocons.or
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Modelio-Open is a project hosting a set of open source extensions (SoaML, SysML and UML Testing Profile) for a previous version (1.2) of the Modelio Free tool . Currently, the lastest version (2.x) of Modelio modeling and generation tool is available at http://modelio.org/downloads/download-modelio.html. All extensions are downloadable at http://forge.modelio.org/projects.
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A cross platform GUI for several code formatter, beautifier and indenter like AStyle, GNU Indent, GreatCode, HTML Tidy, Uncrustify and many more. Main feature is a live preview to directly see how the selected formatting option affects the source code.
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A software toolkit that implements the CoSy Architecture Schema for developing integrated intelligent robotic systems. The toolkit focuses on supporting on a space of information-processing architectures based on shared working memories.