Search Results for "sequence scaffold, java" - Page 5
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Showing 213 open source projects for "sequence scaffold, java"
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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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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
...It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. ... -
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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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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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Genovar is a JAVA-based stand alone software in order to detect unknown genomic variants, analyze SNP-related copy number variant regions, and comprehensively visualize genomic data such as array CGH and sequence alignments results.
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Simple Java bot, repeat a text sequence using a defined time window. You can load a text file and read it line by line in a specific time window and simulate a conversation.
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sod-builder
Kanji Stroke Order Diagram Builder is a Java GUI Application
Learning stroke-order is the key to remembering Kanji. Stroke Order Diagram Builder allows you to visually record the stroke sequence of Kanji glyphs from specially prepared fonts. -
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IMPACT
Integrated Multiprogram Platform for Analyses in ConTest
Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003 -
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VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.
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MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
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3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
