Search Results for "throughput" - Page 12
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Showing 502 open source projects for "throughput"
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OncoBase
A platform for decoding regulatory somatic mutations in human cancers
...The vast majority of identified somatic mutations are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput chromosome conformation capture (3C)-based technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn), an integrated database for annotating regulatory noncoding somatic mutations in human cancers by exploring their roles in distal interactions between target genes and regulatory elements. ... -
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De_Lux
Deconvolution of luminescence cross-talk in microplate reader data
An algorithm to deconvolve the luminescence cross-talk in high-throughput gene expression profiling to recover the true luminescence activity of a microplate. -
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CONDEL is a method for detecting CNVs and deletion types from single samples using high-throughput sequence data. It can be used for analyzing genomes from tumor cells or normal cells with an input of genome reference, reference index, SAM file, and read counts.
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Root Phenotyping Suite
Three different software tools for phenotyping plant root images
RootAnalyzer is a fully automated tool, for efficiently extracting and analyzing anatomical traits from root-cross section images. RootAnalyzer segments the plant root from the image's background, classifies and characterizes the cortex, stele, endodermis and metaxylem, and produces statistics about the morphological properties of the root cells and tissues. RTipC is a system for the fully automated detection and classification of root tips in root images obtained either by 2d flat bed... -
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UDPStressTest
A Desktop app for network stress testing, TCP-Ping and icmp ping.
... * You can ping any ip address you want and get measure of TTL. * It gets the available range of IP's in your local network. * When you start the test you see testing throughput as a graph against time also total size of packet sent in (MB). *You can use it as DOS attack tool. *Every action done on the app is logged in XML file as data source (only stress test + ping). *TCP-Ping is a perfect way to discover network devices which active firewall to ignore ping packets or you can use it as TCP port scanner to check your network security. ... -
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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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D-Tailor
D-Tailor: automated analysis and design of DNA sequences
Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. -
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gain
Asyncio-based Python framework for building fast web crawling spiders
Gain is a Python web crawling framework designed to simplify the process of building efficient and scalable web scrapers. It is built on top of asynchronous technologies such as asyncio, aiohttp, and uvloop to support high-performance crawling with concurrent network requests. It provides a structured framework for creating spiders that can navigate websites, extract structured data, and process the collected results. Developers define crawlers using components such as spiders, parsers, and... -
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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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FBENCH
FBENCH is TCP and UDP throughput-measurement and stress-test tool.
FBENCH is the throughput benchmark tool for measuring TCP and UDP performance between two systems. It also used as the networking stress tool. Originally it was developed as part of the FNET TCP/IP stack project. -
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Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).
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An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)
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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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CRISPRamplicon
A tool for analysis of Genome editing outcomes from sequencing data
CRISPR-Cas9 is a unique technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding or altering sections of the DNA sequence. It is faster, cheaper and more accurate than previous techniques of editing DNA and has a wide range of potential applications. Here, a cost-effective and high-throughput strategy was developed for identifying CRISPR/Cas-induced mutations via CRISPR Amplicon Sequencing (Xie’s lab, http://www.biootools.com/). In particular, we have developed a new bioinformatics tool named CRISPRamplicon, which can be used for analysis of CRISPR/Cas9 genome editing outcomes for high-throughput sequencing data with fast speed. -
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...Audience for this tool: * Advanced system administrators trying to analyze on process level what is going on in a production server; * Software developers analyzing the troughput of their process: e.g. TCP throughput, memory usage, memory leaks; The most advanced feature is the monitoring of TCP/IP traffic figures, for each SINGLE process (actual connections and throughput). As far as known no other tool has this capability. In the process tree, use the right mouse button to monitor process details.
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rDock
A Fast, OpenSource Program for Docking Ligands to Proteins and N.Acids
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages. The full rDock software package requires less than 50 MB of hard disk space and it is compilable in all Linux computers. Thanks to its design and implementation, it can be installed on a computation cluster and deployed on an unlimited number of CPUs, allowing HTVS campaigns to be carried out in a matter of days. ... -
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GlycoPAT
Comprehensive, open-source tool for glycoproteomics MS data analysis
GlycoPAT is a modular, open-source MATLAB based toolbox for shotgun mass spectrometry based glycoproteomics data analysis. This program provides a novel platform for the streamlined analysis of traditional LC-MSn based high-throughput experimental data for the identification of site-specific N- and O-linked glycosylation on various proteins. More details are available at https://www.VirtualGlycome.org/glycopat Source code also available at https://github.com/kaichengub/GlycoPAT If you use this software please cite: Gang Liu, Kai Cheng, Chi Y. Lo, Jun Li, Jun Qu and Sriram Neelamegham. " A comprehensive, open-source platform for mass spectrometry based glycoproteomics data analysis", Molecular Cell Proteomics, 2017 Sep 8, in press. https://doi.org/10.1074/mcp.M117.068239 -
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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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HTSFinder
High-Throughput DNA Signature Finder
HTSFinder consists of three computational phases. This pipeline generates all the possibilities of k-mers for every genome individually and then determines their frequency in the entire database. Finally, DNA signatures of every species or strain are obtained in the database or multiple databases that have been involved in the pipeline. HTSFinder implements the parallel and distributed computational tool Hadoop for the second and third phases. -
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tiedot
A rudimentary implementation of a basic document database in Go
...It runs on *nix and Windows operating systems. tiedot has fault-tolerant data structures that put your data safety first, while easily scales to 4+ CPU cores. tiedot has very stable performance, even with millions of records! It consistently achieves high throughput, swallow more than 120k records or 80k complicated queries per second with confidence. The newest version 3.4 comes with general performance and compatibility improvements. tiedot is a very small project in the large open source community, it is growing fast thanks to the 800+ stars and watchers, as well as many contributors for their feedback, comments, ideas and code. -
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
...Sensitivity is gained by repeatedly running the HMM gene predictor Augustus with varied input parameters, and selectivity by choosing the models with best homology to known proteins and best agreement to the RNA-Seq data. SnowyOwl has successfully predicted genes in 26 novel fungal genomes. The pipeline can be installed locally for high throughput and control over configuration. It can also be run on a remote server through a convenient web interface for occasional use. -
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MaxInfo
Transcriptome assembler for RNA-seq
MaxInfo is an automated transcript discovery and quantification software designing for high-throughput RNA sequencing (RNA-seq). Assembling transcripts from reads are challenging because of the unpredictable uncertainties arising from completing full genome structure with very partial observations. MaxInfo tackles this problem by explicitly reducing the inherent uncertainties in the biological system caused by missing information. -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
.... ** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. ... -
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We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. License: The DSS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. ...
