Search Results for "sequence scaffold, java" - Page 2
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Showing 244 open source projects for "sequence scaffold, java"
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The only software you need to increase cash flow, optimize resource utilization, and take control of your assets and inventory.
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We design our technology to make workforce management easier. APS offers core HR, payroll, benefits administration, attendance, recruiting, employee onboarding, and more.
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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... -
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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... -
Out-of-the-box scripts. Around-the-clock monitoring. Unmatched automation capabilities. Start doing more with less and exceed service delivery expectations.
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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... -
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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... -
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NGSReadsTreatment
Note: To run the new version use Java version 13.
NGSReadsTreatment, a computational tool for the removal of duplicated reads in paired-end or single-end datasets. NGSReadsTreatment can handle reads from any platform with the same or different sequence lengths. Using the probabilistic structure Cuckoo Filter, the redundant reads are identified and removed by comparing the reads with themselves. Thus, no prerequisite is required beyond the set of reads. NGSReadsTreatment was compared with other redundancy removal tools in analyzing different... -
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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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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. -
When it comes to cybersecurity, what your clients don’t know can really hurt them. And believe it or not, keep them safe starts with asking questions. With ConnectWise Identify Assessment, get access to risk assessment backed by the NIST Cybersecurity Framework to uncover risks across your client’s entire business, not just their networks. With a clearly defined, easy-to-read risk report in hand, you can start having meaningful security conversations that can get you on the path of keeping your clients protected from every angle. Choose from two assessment levels to cover every client’s need, from the Essentials to cover the basics to our Comprehensive Assessment to dive deeper to uncover additional risks. Our intuitive heat map shows you your client’s overall risk level and priority to address risks based on probability and financial impact. Each report includes remediation recommendations to help you create a revenue-generating action plan.
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HF-Sounder Version 1.4 (Beta)
Finds best HF band for site-to-site communications using Fldigi
... station (NCS) listens to each band in the same sequence, starting at the same designated time. In the second half of the ten minute cycle, the remote site becomes the listener and the NCS transmits a text message on the band where the remote site's signal was strongest. Both stations then switch to that frequency and start operating. If more than two stations in the net, the other stations can use the tool in Listener mode, and switch to the band announced by the NCS at the end of the sequence. -
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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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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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HSRA
Hadoop spliced read aligner for RNA-seq data
... is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. Moreover, our tool uses the Hadoop Sequence Parser (HSP) library (link above) to efficiently read the input datasets stored on the Hadoop Distributed File System (HDFS), being able to process datasets compressed with Gzip and BZip2 codecs. -
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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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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... -
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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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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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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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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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Digit Span Tester
A Task / Test of Working Memory for Cognitive / Neurosciece Research
To perform automated digit span tests to evaluate on working memory function, especially in cognitive / neuro research. Hope to reduce practice effects and eliminate the need to use clinical assessments in research settings. Requires Java 7 or newer. Note that this is a research tool, and was not intended (and not evaluated) for clinical assessment. FINAL VERSION: If you want more features, download the source and hack it yourself. Apologies to those who've asked for help and got... -
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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... -
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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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SimpleTAG
Massive audio tagger
SimpleTag is a cross-platform desktop tool, which allows to update the labels of all your music before incorporating it into a musical library or cloud service. Nowadays, the amount of music we have in our equipment is so large, it is no longer possible to manage with the traditional system of filenames and directories. The most convenient is to use the concept of libraries that handle the big market music players: iTunes, Amarok, Windows Media Player, Google Music, ..etc The labels... -
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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... -
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Java bio-informatics library to analyze and convert genomic sequence and assembly data. This library was created and used by the J. Craig Venter Institute (JCVI)