Search Results for "sequence scaffold, java"
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97 programs for "sequence scaffold, java" with 1 filter applied:
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This means every device on your network, and every interface on every device is automatically analyzed for performance, errors, QoS, and configuration.
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Our robust pre-built connectors and our no-code, drag-and-drop interface makes it easy and fast to automatically sync vendors, invoices, and invoice payment data between Tipalti and your ERP or accounting software.
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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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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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Managing your therapy and rehab practice is a time-consuming process. You spend hours on paperwork, billing, scheduling, and more. Raintree’s Therapy & Rehab EHR is here to help you manage your practice more efficiently. With our all-in-one solution, you’ll get the tools you need to streamline your therapy and rehab practice, improve patient care, and get back to doing what you love.
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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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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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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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BeigeUML
UML diagram editor
BeigeUML is an UML diagram editor. It has two user interfaces - ordinary desktop SWING and Android. Features: 1. Supports UML 2.4.1 compliant class diagram, package diagram, object diagram, sequence diagram and use case diagram. 2. It generates UML class diagram from Java source. 3. It's a doclet that generates standard Javadoc with UML class diagram. This application you can download from Central Maven Repository: https://search.maven.org/#search%7Cga%7C1%7Cg%3A%22org.beigesoft%22... -
Exact Payments delivers easy-to-integrate embedded payment solutions enabling you to rapidly onboard merchants, instantly activate a variety of payment methods and accelerate your revenue — delivering an end-to-end payment processing platform for SaaS businesses.
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
... for the entire scaffold, taking into account the taxonomic ontology. Scaffolds that exclusively match potential contaminants may be safely removed while sequences matching partially contaminants and partially the target organism may constitute horizontal transfers or assembly artifacts and need to be examined manually. -
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The Wily DNA Editor
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section. -
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KAnalyze
DNA/RNA Sequence K-mer Toolkit
KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API. -
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Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit
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Generic REST Fetcher
Execute a cascading sequence of REST calls to a common end-point
REST API's often require multiple calls to achieve a business objective. Eg get a list of objects, then get data for each object. This application allows you to transform data received from one REST call to determine other methods to call. All this is configured via an XML file. A simple example is fetching data for all respondents to a Survey Monkey survey. You need to get the set of respondent ids, then call the API passing in the list of respondent ids. See the README.md file on... -
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The Panini Language
Better Modularity, Better Concurrency
This project makes the compiler and tools for the Panini language available. A central goal of the Panini language is to make concurrent programming easier and less error-prone. The main new feature in Panini is called a capsule. A capsule is like an actor but better because it largely retains the traditional approach for reasoning about programs as a sequence of operations, abstracts away all details of thread creation and locking, and supports fully-automatic compile-time analysis of common... -
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xorlisp
Bit level lambda continuations and nothing else - Queue automata
... of stack and queue. The stack is a linked list of pair of true or false and object pushed on the stack. The queue is also such a linked list but is paired oppositely so previous queue state goes on the left and next object queued on the right of the new pair, so when the queue is navigated in sequence of that astronomically long bitstring (thats exponential of reusing objects in the acyclicNet), the Nav32 (using linearForward and treeForward for random access) first sees the oldest object queued -
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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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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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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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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... -
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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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FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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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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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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ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.