Search Results for "throughput" - Page 2
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Showing 82 open source projects for "throughput"
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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. ... -
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CAT
CAT is the basic component of the server project
CAT is a distributed application performance monitoring and alerting system that specializes in tracking request flows, exceptions, and metrics across microservice ecosystems. It offers real-time dashboards showing throughput, response times, error rates, and service dependency graphs to help operations and development collaborate on reliability issues. In addition to metrics, it enables tracing—propagating context across RPC boundaries so problems like latency spikes or failed calls can be traced end-to-end. Alert rules and anomaly detection can be defined to notify teams proactively. ... -
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sRNAWorkbench
The UEA sRNA Workbench
...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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sirius signing server
Centralized signing and verification
Sirius-Sign is a signing and verification server with it's focus on high throughput and easy integration into an existinig landscape. For signature creation smartcards with OCF and PKCS11 interfaces are supported. An EJB container is required. -
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Apache Dubbo Spring Boot Project
Spring Boot project for Apache Dubbo
...Dubbo provides high performance interface based RPC, which is transparent to users. Dubbo supports multiple load balancing strategies out of the box, which perceives downstream service status to reduce overall latency and improve system throughput. Dubbo supports multiple service registries, which can detect service online/offline instantly. Dubbo’s micro-kernel and plugin design ensures that it can easily be extended by third party implementation across core features like protocol, transport, and serialization. -
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exchange-core
Ultra-fast matching engine written in Java based on LMAX Disruptor
Exchange-core is an open-source market exchange core based on LMAX Disruptor, Eclipse Collections (ex. Goldman Sachs GS Collections), Real Logic Agrona, OpenHFT Chronicle-Wire, LZ4 Java, and Adaptive Radix Trees. Designed for high scalability and pauseless 24/7 operation under high-load conditions and providing low-latency responses. Single order book configuration is capable to process 5M operations per second on 10-years old hardware (Intel® Xeon® X5690) with moderate latency degradation.... -
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GraalVM
Run programs faster anywhere
...It is designed to accelerate the execution of applications written in Java and other JVM languages while also providing runtimes for JavaScript, Ruby, Python, etc. Increase application throughput and reduce latency. Compile applications into small self-contained native binaries. Seamlessly use multiple languages and libraries. Advanced optimizing compiler that generates fast lean code which requires fewer compute resources. Native binaries start up instantly and deliver peak performance with no warm up time. Leverage the best features and libraries of popular languages in a single app with no overhead. ... -
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AhoCorasickDoubleArrayTrie
An extremely fast implementation of Aho Corasick algorithm
...By using a double-array trie representation, the project emphasizes performance and memory efficiency compared to simpler pointer-heavy trie structures, which can matter a lot for large dictionaries or latency-sensitive services. This makes it a strong fit for tasks like content filtering, entity/term spotting, dictionary-based annotation, or high-throughput log/text processing. In short, it’s a specialized, speed-focused library for industrial-strength multi-keyword matching in Java. -
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Miaosha
Design and implementation of flash sale system
...The code showcases a typical Spring Boot stack that cleanly separates controllers, services, and persistence, making bottlenecks and optimization points easy to identify. As a study case, it provides a practical blueprint for building resilient sale/booking endpoints where fairness and correctness matter as much as raw throughput. -
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PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions and canonically spliced transcripts. ... -
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The Elvira project is a suite of tools to perform high-throughput genomic assemblies of repetitive, structured samples such as viruses or targeted regions of larger genomes.
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JPPF
The open source grid computing solution
JPPF makes it easy to parallelize computationally intensive tasks and execute them on a Grid. -
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets.
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PCAPAnalyzer
Network traffic analysis from PCAP format
PCAP Analyzer is a tool that helps analyzing network traffic captured in a PCAP format (standard of tcpdump). It has extensible Filters in charge of dissecting packets and printing information like throughput or anything that can be analyzed by Filters (e.g. packet loss, reordering, ...). It comes with several built-in Filters but can be expanded by adding custom-made Filters to the classpath. It was developped to help understanding complex network routing problems, where packets could arrive out-of-order, some were lost, or duplicated. ... -
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DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.
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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... -
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Hyperic is application monitoring and performance management for virtual, physical, and cloud infrastructures. Auto-discover resources of 75+ technologies, including vSphere, and collect availability, performance, utilization, and throughput metrics.
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Bamformatics
Toolkit and GUI for sequencing data analysis
The Bamformatics project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data. Its toolkit includes, among others, programs to identify variants and to compute various types genomic tracks. It also provides a graphical user interface to facilitate general bioinformatic workflows. The project wiki contains further details. -
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Apache Kafka
Mirror of Apache Kafka
Apache Kafka is a distributed streaming platform built around durable, partitioned logs called topics, enabling high-throughput, fault-tolerant event pipelines. Producers append records to partitions, brokers replicate them for durability, and consumer groups read them at their own pace while balancing work across instances. The commit/offset model and retention policies support patterns from real-time processing to event sourcing and audit trails. Exactly-once processing semantics, idempotent producers, and transactions help prevent duplicates across complex dataflows. ... -
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Network Analyzer
Analyze the network carateristics like Delay, Jitter, Packet loss etc.
...(The receiving host is then required to echo all the packets back to the sender, which can be easily done via iptables rule under linux). Once the eched packets arrives back to the sender, the analyzer will calculate all the related statistics like, packet loss, jitter throughput etc... NOTE: in order to receive the echo packets you must configure the receiving host to echo the incoming packets. In the next release i will provide another java application that just echo on an UDP port. -
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. ... -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. Information on this and other projects can be found on: http://www.altmann.eu
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JPerf
Java Performance and Scalability Testing
JPerf is a simple framework for writing and running automated performance and scalability tests. It's like JUnit but for performance. Simple write a class that implements PerfTest then create a PerfTestRunner instance to run the test. *** JPerf has moved! Please go to https://github.com/andygrove/jperf for the current version *** -
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TriageTools
Tools for partitioning and prioritizing fastq data
TriageTools is a collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. The project wiki contains usage information.
