Search Results for "sequence scaffold, java" - Page 2
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Showing 219 open source projects for "sequence scaffold, java"
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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) of each input image in the output image (default 1000) (note the image will be scaled maintaining aspect ratio so it fits within both the width and height above) 3 : number of images per row in the output image(s) 4 : number of images per column in the output image(s) (default is to make a square with enough rows/columns to fit all the input images in a single output image) 5 : output path and filename, this will be suffixed by either just '.png' or if there is more than one -
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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... -
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shadow-cljs
ClojureScript compilation made easy
shadow-cljs is a ClojureScript build tool designed with simplicity and modern JavaScript interoperability in mind. Distributed via npm, it handles compilation, hot-reloading, module targets (ESM, Node, Browser), and tight integration with JS tooling. Creating your project can be done quickly using the npx create-cljs-project utility. npx is part of npm and lets us run utility scripts quickly without worrying about installing them first. The installer will create a basic project scaffold and... -
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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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LoopMatcher
Find sequence-specific stem-loops in FASTA and GenBank files.
LoopMatcher is a bioinformatics tool that searches for hairpin structures in cDNA / mRNA sequences (in FASTA, GenBank or Vienna format) with specific consensus sequences in the loop. It uses RNAfold to predict sequence structure and UShuffle to generate random sequences with a defined k nucleotide frequency. Also, sequences in GenBank format can be downloaded directly from NCBI using the NCBI access ID. Requirements JAVA Runtime 8. It's highly recommended to have a multicore processor to process large sequences. * Currently, this version only runs in Windows x64. -
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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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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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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... -
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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Yakoliv Framework
Designed to facilitate Apache CXF based java softwares development
Yakoliv is a framework designed to facilitate the development of Apache CXF based java softwares. It takes advantages on Ibatis and Spring with which it forms a mini-container and facilitates data bases access. Yakoliv Framework is made of a generic DAO artifact and a GUI program that helps developers: - generating the data base schema and enabling sequence management - generating java classes from typed data - mapping generated classes to data base's table using ibatis sql maps - generating configurations for spring security secured web services - generating clients configurations for the generated web services - generating a contract for client-server communication. ... -
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NGSReadsTreatment
Note: To run the new version use Java version 13.
...To execute the multithreaded version adding at the end of command line the number of threads that you will use for processing, it is worth mentioning that this number must be a power of 2. Note: To run the new version use Java version 13. -
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HF-Sounder Version 1.4 (Beta)
Finds best HF band for site-to-site communications using Fldigi
THIS SOFTWARE IS BETA STAGE - PLEASE MONITOR CLOSELY DURING OPERATION & BE PREPARED TO TAKE MANUAL CONTROL OF FLDIGI! When used with Fldigi and a multiband antenna, this tool largely automates the task of testing up to five HF frequencies between two sites. Briefly, one site is configured as a remote site and the other as net control. The remote site transmits a brief text message on each of the five designated frequencies, starting at a prearranged time. The designated net control... -
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Adaptor Logic Sequence Consumer
Client library to asynchronously receive data updates
Open source Java client library to work with Adaptor Logic (tm) DaaS servers and retrieve data asynchronously from the time series database (TSDB). This project is part of the Data as a Service platform implemented by Adaptor Logic. Adaptor Logic (tm) is a product of Interact Computer Services Ltd. -
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MIT Deep Learning Book
MIT Deep Learning Book in PDF format by Ian Goodfellow
The Deep Learning textbook is a resource intended to help students and practitioners enter the field of machine learning in general and deep learning in particular. The online version of the book is now complete and will remain available online for free. MIT Deep Learning Book in PDF format (complete and parts) by Ian Goodfellow, Yoshua Bengio and Aaron Courville. An MIT Press book Ian Goodfellow and Yoshua Bengio and Aaron Courville. Written by three experts in the field, Deep Learning is... -
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inspectIT
inspectIT is the leading Open Source APM
inspectIT is the leading open-source APM (application performance management) tool for monitoring and analyzing your Java(EE) software applications. Various sensors capture end-to-end information for every request from the end user, to the business tier all the way to the backends. inspectIT is based on an application-centric, business-focused approach, where each technical request is mapped to an application and to a business use case. With inspectIT you always know about the health of your... -
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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KaiZen OpenAPI Editor
Eclipse Editor for the Swagger-OpenAPI Description Language
KaiZen OpenAPI Editor is an Eclipse editor for the industry standard API description language, formerly known as Swagger. It now supports both Swagger-OpenAPI version 2.0 and OpenAPI version 3.0. KaiZen Editor is a core component of RepreZen API Studio, a comprehensive solution for API modeling, documentation, visualization, testing and code generation, built on Eclipse. KaiZen OpenAPI Editor is available on Eclipse Marketplace. Drag-and-drop this button into Eclipse Oxygen or later to... -
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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. There beige-uml-swing-[VERSION]-jar-with-dependencies.jar is Swing application and beige-uml-android-[VERSION].apk is Android application. ... -
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
Raw genomic sequences are frequently contaminated with sequences of other organism. Their identification is essential for the interpretation of genomic data. In this context it is essential to distinguish between horizontal gene transfers and contamination. The genomic context of sequences can help distinguish the two scenarios. Taxoblast splits genomic scaffolds into sub-sequences of defined length and for each of them determines the closest related taxon. It then summarizes this... -
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ERMaster is Eclipse plug-in to make ER diagram. Functionally, Import from data base, Making of table definition book on Excel, Image output, DDL output, etc. are being offered.
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Silent Mantis
Event recorder software for animal and human behaviour research.
Silent Mantis is a freely available, cross-platform event recorder software, which integrates the features of a video player, an image viewer and a spreadsheet editor. It can be used in animal or human behavioral research to manually record any animal or human bevavioral states or events from a video file. The results can be exported into text files for statistical evaluation purposes. SM was developed by Peter Szabo at the Institute of Biology of the University of Veterinary Medicine in... -
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Java provides the concurrent library that simplifies concurrent programming, but this is hard to learn and visualize. This project is a series of animations each illustrating the coding and usage of a component in the java concurrent library.
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REHUNT
REHUNT (Restriction Enzymes HUNTing)
REHUNT (Restriction Enzymes HUNTing) is a free and open source package implemented in JAVA for providing many useful methods for biological sequence analysis (especially in SNP genotyping) around restriction enzymes. All academic researchers are encouraged to use REHUNT in their studies or to integrate it into their systems and applications. Non-academic users or commercial needs are also welcome to use it. For further information or additional applications, please contact the author Yu-Huei Cheng <yuhuei.cheng@gmail.com>. -
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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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Kerja Praktek Maret Juni 2017
Kerja Praktek Pengembangan Prototipe dengan Java
Kerja praktek membangun dua buah prototipe dengan menggunakan class diagram - sequence diagram - java. Aplikasi atau prototipe 1 merupakan Sistem Informasi Akademik. Aplikasi atau prototipe 2 merupakan Rent A Car. Mahasiswa menggunakan Net-Beans sebagai Java IDE, Visual Paradigm sebagai UML IDE, dan sourceforge.net sebagai open source software management tool. Mahasiswa mempelajari pengembangan aplikasi dari tingkat abstraksi yang paling abstract (requirement document) hinga merealisasikannya pada tingkat paling detil Java Code). ...
