Search Results for "sequence scaffold, java" - Page 4
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Showing 219 open source projects for "sequence scaffold, java"
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MSCViewer
A tool for visualization and analysis of logs as sequence diagrams
MSCViewer is a tool intended for debugging of control flows in concurrent, distributed systems. The tool loads logs generated by various entities in the system and visualize a sequence diagram chart for events and interactions. The diagram is fully interactive: entity can be added/removed from the diagram and shuffled; events can be filtered, searched, highlighted and annotated with comments. MSCViewer features integration with a Python interpreter which allows writing Python scripts... -
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xorlisp
Bit level lambda continuations and nothing else - Queue automata
Not working yet. To deal with the Halting Problem, computing and data are navigated using debugger ops: linearForward and treeForward, which navigate an astronomically large bit string where 1 is ( and 0 is ). All pairs are derived from (). For example, true is represented as ((()())()), and false is (()(()())). It appears related to the church encoding of lambda where T chooses first parameter and F chooses second, of a pair. Continuations are nearly finished code and are represented as a... -
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jSimpleTools
A simple tool box to assist in coding tests in Java.
This is a simple library to help with writing tests in java. SimpleContext: a lightweight (and fast!) IoC container to quickly create test contexts. StringGenerator: a random string generator using a regex as input. Sequence: a convenience wrap around a simple long to help convey meaning to the sequence. Even minor revisions will have the stable/released code base. Use it in your projects without fear. -
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GESPA
Accurately predicts disease association of single nucleotide mutations
...The software can be used clinically to determine if observed nsSNPs are associated with disease. A host of annotations are provided: orthologous and paralogous multiple sequence alignments, UCSC annotations, reports detailing conservation of a nsSNP in alignments, and links to external nsSNP and gene information such as relevant publications. GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. ... -
Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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TE-locate
a tool for calling transposons
TE-locate is a tool to locate all copies of sequences in a reference sequence using read-pairs. TE = Transposable Element Input is NGS-data. Please download all files first (including the demo data) and make your first run then. -
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DomainMath IDE
An open source gui frontend application for GNU Octave
DomainMath IDE is an open source GUI front-end application for GNU Octave -
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ALTER is a web-based tool to transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation and several recessive disease genes have been discovered with the help of this technique in consanguineous families. The researchers typically use SNP arrays to determine the... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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NGSbinningpytools
Python tools for binning NGS scaffolds to various genomes.
Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation please refer to the link below: https://sourceforge.net/p/ngsscaffolds/wiki/Documentation/ -
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NOTE: developement of this project has moved to GitHub http://github.org/matthuska/biasviz/ BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments.
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Fluent NHibernate Generator
Fluent NHibernate Generator coded by Java
I design this Fluent NHibernate Generator just because that I need this kind tool in my work. As to Fluent NHibernator, you can find other tools such as NMG. However, it can only generate C# code but and some bugs. Although it says that it can generate VB.NET code, there are many errors. For that reason, I need to develop another tool to generate correct C# and VB.NET code. I am not a professional programmer. So please forgive me if you think that my code style is very poor -
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MNCubes
Research project to compute repeating patterns in discrete planes
A 2D line can be rasterized into a 8-connected sequence of pixels which exhibit repeating patterns of connected pixels. Likewise, a 3D plane can be rasterized into connected cubes. A 'rectangular' cut of m x n cubes is a (m,n)-cube. Given m and n, the goal of this project is to generate all the (m,n)-cubes for all the (integer) discrete planes, based on the intersection vertices on a Farey diagram. -
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vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. Information on this and other projects can be found on: http://www.altmann.eu
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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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JSIP2
SIP2 Library for Java.
3M Standard Interchange Protocol (SIP) is an industry standard protocol by 3M to allow automatec check out terminals communicate with library systems. JSIP2 is an Open Source (MIT) library that implements the 3M SIP version 2 protocol including the 3M SIP2 Extensions for SIP2 clients. The library contains the necessary functionality for SIP2 client socket based implementation supporting all the SIP2 messages and fields, including also the fields defined in the the 3M SIP2 Extensions. -
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x2fasta
Tools for reformatting common sequence formats into fasta
A collection of tools to transform common biosequence formats (e.g. EMBL, SWISS-PROT, UniProtKB, GenBank and RefSeq) into the fasta sequence format. -
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Aspose for Hadoop
This project holds source code for Aspose for Hadoop project.
Aspose for Hadoop project enables Apache Hadoop / MapReduce developers to work with various binary file formats. The developers can create and convert binary sequence files into text sequence files. -
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A tool to compare microbial genomes by their sequence fragments. We redistributed the Bioperl package in our software for convenience purpose. The latest Bioperl package can be downloaded from: http://www.bioperl.org. System Requirement: Java Runtime Environment 1.6.0 or above; Perl 5.0 or above If you have any difficulties to run this tool, just let me know by chenh12@nyumc.org.
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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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NSIT
Novel Sequence Identification Tool
...It requires about 2 GB of RAM. NSIT comes with a JAVA graphical viewer which can be used to view how the identified novel sequences compare with other sequence sets. -
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EDNA
Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. http://www.ncbi.nlm.nih.gov/pubmed/23990411 -
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Genome Microsatellite Analyzing Tool
GMATO : Microsatellite Analyzing Tool for Huge Genome at any size
The increasing sequence availability of more and more huge whole genomes (>1G) defeated currently existing SSR analyzing tools. Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel powerful program for faster SSR mining at any length, any size,and comprehensive statistical analysis at genome aspect, especially designed for huge genome based on Perl scripts. -
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DimerRemover
Remove adapter dimers from NGS data
This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment. -
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Midi Player Tool
Java Piano GUI
Piano function Tonality settings Play scales PC keyboard can be used or mouse Play MIDI files Metronome Pitch Trainer Karaoke function Playlists Timer for wake up USB support SF2 support Show midi sequence Implements Java accessibility API
