Search Results for "sequence scaffold, java"
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Showing 209 open source projects for "sequence scaffold, java"
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Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.
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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should... -
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PlantUML
Generate diagrams from textual description
... and intuitive language. (see PlantUML Language Reference Guide). Images can be generated in PNG, in SVG or in LaTeX format. It is also possible to generate ASCII art diagrams (only for sequence diagrams). -
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SequenceDiagram
SequencePlugin for IntelliJ IDEA
Sequence Diagram is a tool to generate simple sequence diagrams (UML) from Java, kotlin, scala(Beta), and Groovy (limited) code. -
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The Ballerina programming language
The Ballerina Programming Language
..., and concurrency safety, combined with a familiar, readable syntax make programs reliable and maintainable. Easy and efficient concurrency with sequence diagrams and language-managed threads without the complexity of asynchronous functions. Programs have both a textual syntax and an equivalent graphical form based on sequence diagrams. -
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Kamon Telemetry
Distributed Tracing, Metrics and Context Propagation for applications
... monitoring with logs because they are there by default. Just connect to your server and start tailing. But logs have a hard time showing you the overall response times for your application, or whether certain calls to the database are happening in sequence or parallel (among a million other things). -
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jDiskMark
Java Disk Benchmark Utility
Cross platform disk benchmark utility written in Java. Measure your storage drive's read and write speeds by creating and accessing sample data files at your chosen location. Results are presented in an easy-to-understand graph, allowing clear characterization of storage device behavior. Customize a benchmark by adjusting the block sequence, sample size and block size. Runs are automatically saved allowing easy review and comparisons. Please try our new new windows installer: https... -
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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Chess Round Robin Manager
Java Schach Turnierverwaltung / Java Chess Tournament Management
Manage chess round robin tournaments with JKlubTV Version 3.0.0-beta This application stores the data belonging to round robin into a SQLite database. It is intended for webmasters who want to easily manage a club tournament in their own chess club. The HTML tables that are to be published for the website will be created easily by the application. Automatically calculate the total points, Sonneborn Berger points of each player, as well as their sequence DWZ, and sorts the HTML table... -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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GETL
ETL engine based on Groovy
P.S. Dear friends. Repository migration to https://github.com/ascrus/getl . You can download jar file from this site or maven. GETL - based package in Groovy, which automates the work of loading and transforming data. His name is an acronym for «Groovy ETL». GETL is a set of libraries of pre-built classes and objects that can be used to solve problems unpacking, transform and load data into programs written in Groovy, or Java, as well as from any software that supports the work with Java... -
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JKlubTV
Java Schach Turnierverwaltung / Java Chess Tournament Management
Manage chess round robin tournaments with JKlubTV Version 3.0.0-beta This application stores the data belonging to round robin into a SQLite database. It is intended for webmasters who want to easily manage a club tournament in their own chess club. The HTML tables that are to be published for the website will be created easily by the application. Automatically calculate the total points, Sonneborn Berger points of each player, as well as their sequence DWZ, and sorts the HTML table... -
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Billiards Covers
This zip jar contains the current coverings of periodic paths.
Researchers, Mathematicians and Enthusiasts. Download "Billiards Covers" to see the most current list of periodic paths in triangles. Download "Billiards Everything" to discover new periodic billiard paths, an unresolved problem from 1775! Follow "The Great Periodic Path Hunt" at gwtokarsky.github.io for the latest news. Email tokarsky@ualberta.ca for feedback. -
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flom
Free Lock Manager
... and transactional sequence. libflom, the library shipped with FLoM, allows you to develop your own application using a simple C, C++, Java, Perl, PHP or Python client API. SSL/TLS security for network communication, X.509 certificates for peer to peer mutual authentication. -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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SpeedGaps
A Java AWT desktop application for Gaps Solitaire (aka "Montana").
A Java AWT desktop application for Gaps Solitaire (aka "Montana"). It uses a reduced card deck to fast play. -
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BitLogic
Simple Java computer algebra calculator
A calculator that solves many types of problems including solving equations computing derivatives and integrals simplifying expressions graphing equations 2d and 3d reverse polish notation, algebraic and word based interpreter infinite writing board for writing out equations requires java 11 or more -
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photogrid
Minimalistic tool to arrange images in a grid, saving the result as a
Minimalistic tool to arrange images in a grid, saving the result as a png image (or sequence of png images). Usage java -cp photogrid-1.0.jar tech.rallen.photogrid.Main This has been tested with OpenJDK 11, and should work with any version of Java from 11 on. The tool takes 5 optional command line parameters 0 : path of input directory (default is ./testimages). 1 : width (in pixels) of each input image in the output image (default 1000) 2 : height (in pixels... -
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NGSpop
NGSpop: identifying & visualizing sequence variation in deepvariant
*NOTICE* The official software(NGSpop) will be updated soon, so please visit us in 2/29. Thank you. -
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Citrus
Citrus: Editing HiC data for de novo genome assembly
juicer and 3D-DNA are two tools that re-arranges HiC data (xxx.hic format) and splits/re-orders super-scaffold data (xxx.assembly) to improve de novo genome assembly. Juicebox was specifically designed to tune or adjust genomic sequences based on HiC data. However, the current Juicebox version does not have a function to save updated HiC data and to summarize chromosome sequences. Thus, we created Citrus which can edit super-scaffolds according to chromatin conformation data captured in xxx.hic... -
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Nexplorer is a web-based phylogenetic browser, used to view and edit comparative data, and ideal for creating publication-quality views in which the tips of a tree are aligned with the rows of a character matrix (e.g., a sequence alignment).
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A fast and reliable tool, written in Java 8, for generating professional UML sequence diagrams from text. Supports actors, con-/destructors, threads, broadcasts, notes, and fragments. Can serve as a Javadoc taglet. Exports PDF, (E)PS, SVG, PNG, ... The source code is hosted at http://github.com/sdedit/sdedit
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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Jack LIRE (Linked Record)
Quantum universal object system with referencing and genetics
Jack LIRE (Linked Record) is a quantum database-backed life-long text record diary with referencing (linking) between records, and a data library for life-long keeping of files such as documents, photographs, music and more. The diary records are fully searchable. Files can be mentioned in diary records to preserve memories, document knowledge and ideas, and more. Massive numbers of diary records and files can be permanently kept. A database located on one computer can be accessed from... -
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ImpressShowRunner
ImpressShowRunner displays a list of Impress shows in a loop.
ImpressShowRunner is a program to chain together multiple LibreOffice impress slide shows. Each show in the sequence is set under Slide Settings so that mouse clicks do not advance the slides. This is important. ImpressShowRunner launches each show in the sequence and then clicks the mouse every few seconds and when the last black screen is shown, the mouse click terminates the show and Impress exits. ImpressShowRunner notices the process exit and then starts the next show. When the last...