Search Results for "throughput" - Page 13
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Showing 432 open source projects for "throughput"
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JAABA
The Janelia Automated Animal Behavior Annotator
...JAABA uses machine learning techniques to convert these manual labels into behavior detectors that can then be used to automatically classify the behaviors of animals in large data sets with high throughput. JAABA combines an intuitive graphical user interface, a fast and powerful machine learning algorithm, and visualizations of the classifier into an interactive, usable system for creating automatic behavior detectors. Documentation is available at: http://jaaba.sourceforge.net/ -
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HTQC
Quality control and filtration for illumina sequencing data
A toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. -
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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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GUItars
GUItars is designed for the analysis of high throughput RNAi data.
Please refer to the original article published in PLOS ONE at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049386. GUItars's user-friendly graphical interface enables rapid analysis of RNAi and small molecule screens. GUItars uses SSMD for hit selection, which is preferred for its ability to diminish sample size effects and the false hit rate, making it superior to other widely used HTS analysis methods. The program can handle the analysis for screens without... -
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Power Decoder
The Power Decoder simulator for the evaluation of pooled shRNA screen
RNA interference (RNAi) screening using pooled, short hairpin (sh)RNA is a powerful, high-throughput tool for determining the biological relevance of genes for a phenotype. Assessing an shRNA pooled screen’s performance is difficult in practice; one can estimate the performance only by using reproducibility as a proxy for power or by employing a large number of validated positive and negative controls. Here, we develop an open-source software tool, the Power Decoder simulator, for generating shRNA pooled screening experiments in silico that can be used to estimate a screen’s statistical power. ... -
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AmpEx
AmpEx Amplicon Extractor
AmpEx is a tool that aims to extract in silico amplicons from high-throughput data. In particular, AmpEx is able to detect amplicons flanked by primer pairs with homopolymer expansions from 454 pyro-reads. -
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MRelay
Host to Host Network Acceleration and Encryption
MRelay splits and distributes the traffic of a single TCP connection to several connections and merges the data at the other end. Using this approach, it is possible to achieve high throughput between two points on the network regardless of the delay between two points. MRelay can optionally encrypt the data and exchange some http headers before the relay process to make the traffic look like a regular http file download. This can be used to overcome the highly restrictive firewalls that are content-sensitive or can detect and block VPN traffic. ... -
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iMS2Flux is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data targeting metabolic flux analysis. To get started simply download and unzip the iMS2Flux.zip file and follow the getting started document for your OS. Current version 7.2.1 (last updated 9/30/2014) - Completes support and correction functionality for a new user specified generic data class.
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GenomicVis
Genomic data visualisation
GenomicVis is a R package that contains a collection of function for the visualisation of genomic data typically derived from high-throughput whole genome sequencing and SNP-Chip experiments. Most of the functions provided by this package are agnostic about where the data actually comes from, that is, they required input in simple data.frame instances that are not tied to a particular file format; however, we also provide many examples of creating these simply data.frames from standard file formats such as VCFs and from common software tools such as GAP and Breakdancer -
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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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Serapis
System for the evacuation and relocation of affected pop. in shelters
Serapis can be used to simulate the mass evacuation of a population from a city with constraints on transport network. Contrary to other similar software, Serapis does not simulate the full transport but focus only on throughput of congestion points. It allows to differentiate between the behaviours and possibilities of different categories of population (children, elderly people, disabled...). -
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DNA metabarcoding, which takes advantage of high throughput capacity of next-generation-sequencing (NGS) platforms, has emerged for characterizing the biodiversity of large volumes of eukaryote samples that consist of upwards of hundreds of thousands of individuals and thousands of species.
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Mutascope
Analysis software designed for PCR-amplicon sequencing data.
Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. -
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RDP FrameBot is a frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline, tutorial http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html. ...
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TCP Segment Retransmission Viewer
View, graph, record TCP segment retransmission rates
View, graph, and record TCP segment retransmissions to quickly see network congestion / problems TCP segment retransmissions are a sign of network congestion and reduced throughput. A segment is retransmitted from a client if there is no corresponding acknowledgment from the receiving host. Further analysis can be done in Wireshark at the packet level if a problem is suspected. Trends can be seen over time graphically with the graph function, which allows panning, zooming, etc. If you find this tool useful please let me know! -
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Bioimage Analysis (the Robatzek Group)
High Content and High-throughput Image Processing in Plants
High Content and High-throughput Image Processing in Plants. -
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We developed a novel mining pipeline, inGAP, which is guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms.
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VariantMaster
Extract causative variants for monogenic and sporadic genetic diseases
There is a fast growing interest in clinical genetics to the utilization of High Throughput Sequencing data for accurate diagnosis of monogenic diseases. To improve the identification of the variants from HTS, we developed VariantMaster, an original program that accurately and efficiently extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. ... -
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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. -
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This is a simple CPU burn program for the major UNIX systems: AIX, BSD, HP-UX, Linux, Solaris etc (full list in the source file #defines) and Windows. It will discover the number of available CPU cores and fork enough threads to create a load on all cores by default. The number of threads and memory block size can be changed from the command line.
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Parallel GENSENG is a parallel implementation of the GENSENG software for detecting copy number variations from high-throughput sequencing data. This software runs exactly as the original code does, except that it utilizes multiple threads where possible. OpenMP was used for multi-threading so changes to the original code were minimal. For a demo, please download the sample data linked to below and follow the README from the tarball. Example read count data: http://www.cs.unc.edu/~wangwb09/GENSENG/reviseddata4hmm_300bpSlides_chr1.txt Suggested transition matrix file http://www.cs.unc.edu/~wangwb09/GENSENG/transition_init.dat The original code can be found at these locations: v0.1: http://www.cs.unc.edu/~wangwb09/GENSENG/GENSENG_download_page.html v0.3: https://sourceforge.net/projects/genseng/
