Search Results for "sequence scaffold, java" - Page 5
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Showing 219 open source projects for "sequence scaffold, java"
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SecStAnT
Secondary Structure Analysis Tool for data selection and statistics
SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only... -
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DocCO
Non-disjoint groupping of Documents based on word sequence approach
This is a GUI for learning non disjoint groups of documents based on Weka machine learning framework. It offers the possibility to make non disjoint clustering of documents using both vectorial and sequential representation (word sequence approach based on WSK kernel). All data format supported by WEKA could be used in DocCO. Data could be loaded from files, from databases or from specified URL. All the preprocessing techniques implemented in WEKA could be used before performing the learning. -
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(Diver is in the process of being moved to GitHub. Please find us at https://github.com/thechiselgroup/Diver. Support requests & messages sent here may never be seen.) Dynamic Interactive Views For Reverse Engineering. Div/er is a set of Eclipse Plugins that aid developers in understanding software. It uses dynamic analysis and reverse engineering to offer views and filters that aid comprehension and discovery.
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ADOPS
Automatic Detection Of Positively Selected Sites
ADOPS is a bioinformatics tool that automatizes the detection of positively selected sites given a set of unaligned nucleotide sequence data. ADOPS implements a complete workflow that integrates three well-known bioinformatic tools: T-Coffee, MrBayes and Codeml (PAML). -
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SlalomGenerator
Generator of coherent slalom sequence
Slalom Generator is small java tools (cross platform) to generate sequence. Indicate figures you know, number of plot, and expected number of figures in sequence and generate ! -
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JAVA Program to Sequence Diagram Generator. This tool tries to help on analysing and understanding the behavior of the code when developping JAVA applications by generating the respective Sequence Diagram automatically at program execution.
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KTNotes
Speedy formatted advanced note-taking with the Kindle Touch.
KTNotes is a fast, advanced note-taking tool built for the Kindle Touch. With an emphasis on mathematical formulas, fractions and subscripts; the greek alphabet; and other Ǝxtra ∫pecial characters are available right on the main keyboard. Using prebuild binaries for the Kindle Touch of ffmpeg and mplayer, audio recording and playback of lectures are available right in the program. Finally, as KTNotes is built as a Kindlet, KTNotes is launchable right from the main page, with an easy... -
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Bowling Score
Simple Java project to compute the bowling score
A simple Java project meant to compute the score of a bowling game. Currently implemented: - src/ao.bowling: architecture for the bowling game (a Game can be played by multiple Players, each Player has 10 Frames in which to knock down the pins within 1-3 Throws) - test/ao.bowling: JUnit test cases for a few typical scenarios TODO: - parse&sanitize user input (sequence of numbers representing number of pins knocked down at each throw) - simple swing interface where user inserts data and gets the score - documentation -
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Ferox
Ferox - Sequence Alignment with Fuzzy K-mers
Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file. -
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Seurat
A sequence analysis tool for normal/tumor DNA and RNA data.
THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data. -
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Jnomics
Jnomics is a collection of cloud-scale DNA sequence analysis tools
Jnomics is a collection of cloud-scale DNA sequence analysis tools -
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REQ Modeler
Requirement Modeling Tool
REQ Modeler는 공개용 UML을 지원하는 모델링 툴입니다. 2012년 10월 4일 REQ Modeler 0.7 입니다. 이 프로그램은 SW 요구 및 검증공학 기술 연구 센터(Requirement and Validation engineering Technology: ReVeT)에서 지원합니다. <Features> Use Case Diagram - Actor / Use Case - Association / Direct Association - Generalization - Dependency - Include / Exclude Class Diagram - Class / Interface - Association / Direct Association - Aggregation / Composition - Generalization - Dependency - Realization Sequence Diagram - ... -
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JGBA
This project is a genome browser and annotation tool in java.
This project is a genome browser and annotation tool in java. -
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Firefly UML
A free, easy-to-use and user-friendly Java-based UML editor.
Firefly UML is a 100% pure Java application designed to create and edit UML conform diagrams. With class diagrams, sequence and instance diagrams, Firefly UML provides a solid selection from the vast range of existing UML diagram types. Firefly UML is really easy to learn as it provides you multiple ways of access to the same function - be it mouse action, hotkey, context menu or toolbar icon. -
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Pontos
Pontos calculates distance matrices from DNA sequence alignments.
...Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like: - consider ambiguities as always different; - consider ambiguity as partially different (e.g. R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. Pontos was written in Linux, but should run in any system where Java works. -
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video highlighter
A Java Programme to Grab the Highlights from your Video
This programme hunts through a long video for Highlights represented by a short black sequence in the clip. This can be created by putting your hand over the lens for a couple of seconds after something good has happened. -
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mPSQed
Alignment editor and multiplex pyrosequencing assay designer
Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required for confirmation or typing. The design of appropriate PCR-based assays is a complex task, especially when conserved discriminating polymorphisms are rare or if the number of types which need to be... -
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GenLab abbreviation of Genetics Laboratory .It is a user-friendly bioinformatics tool to support your bioinformatics lab work. GenLab creates a software user-friendly environment, which makes users to make a large number of protein, DNA, and RNA sequence analysis and excellent graphical viewing. It also provides powerful environment for simulations of Protein 3D molecular models. GenLab typically provides: •User-friendly graphical tools used for finding and working with relevant...
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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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Index biological data (genbank sheets, Uniprot...) in a Solr indexer, with index shard support and provides a query interface. Project goal is to create a virtual image with indexer and web interface to query and visualize biological data.
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Randomizer
Random sequence generators for Java objects
Random sequence generators for Java objects, which currently provide you with 3 specialized generators. The simplest of them - Randomizer - gives every Object an equal chance to be selected from the group. The useful RandomizerSet - shuffles the provided Objects and returns the next object in queue once needed. The complex RandomizerMap - Writing a MMORPG? -
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The X Project
You will canalize the project and determine what will it become.
Do you know story completion game? Everybody writes a sentence in sequence and nobody knows what will the story be in the end. Would you like to play a code completion game? Write a line of code (or as much as you like) and invite some friends of you to join our game. I started the project with a simple java application produced in Netbeans which does nothing absolutely. I want to learn how much strong the open source comunity is. -
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JSeqUnit enhances Javadoc documentation with UML sequence diagrams that are generated with the help of JUnit tests. It uses JSeq to trace the execution of test executions. It supports re-engineering of components through improved reverse engineering of methods with the help of sequence diagrams.
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FOREVER is an environment to translate UML Sequence Diagrams to Petri Nets and ckeck system properties with SMV. The tool receives as input sequence diagrams of UML and provides the Petri net in three different formats: APNN, PNML and SMV .
