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Contrasting the Performance of Compression Algorithms on Genomic Data
Contrasting the Performance of Compression Algorithms on Genomic Data Cornel Constantinescu, IBM Research Almaden Outline of the Talk: • Introduction / Motivation • Data used in experiments • General purpose compressors comparison • Simple Improvements • Special purpose compression • Transparent compression – working on compressed data (prototype) • Parallelism / Multithreading • Conclusion Introduction / Motivation • Despite the large number of research papers and compression algorithms proposed for compressing genomic data generated by sequencing machines, by far the most commonly used compression algorithm in the industry for FASTQ data is gzip. • The main drawbacks of the proposed alternative special-purpose compression algorithms are: • slow speed of either compression or decompression or both, and also their • brittleness by making various limiting assumptions about the input FASTQ format (for example, the structure of the headers or fixed lengths of the records [1]) in order to further improve their specialized compression. 1. Ibrahim Numanagic, James K Bonfield, Faraz Hach, Jan Voges, Jorn Ostermann, Claudio Alberti, Marco Mattavelli, and S Cenk Sahinalp. Comparison of high-throughput sequencing data compression tools. Nature Methods, 13(12):1005–1008, October 2016. Fast and Efficient Compression of Next Generation Sequencing Data 2 2 General Purpose Compression of Genomic Data As stated earlier, gzip/zlib compression is the method of choice by the industry for FASTQ genomic data. FASTQ genomic data is a text-based format (ASCII readable text) for storing a biological sequence and the corresponding quality scores. Each sequence letter and quality score is encoded with a single ASCII character. FASTQ data is structured in four fields per record (a “read”). The first field is the SEQUENCE ID or the header of the read. -
Download Media Player Codec Pack Version 4.1 Media Player Codec Pack
download media player codec pack version 4.1 Media Player Codec Pack. Description: In Microsoft Windows 10 it is not possible to set all file associations using an installer. Microsoft chose to block changes of file associations with the introduction of their Zune players. Third party codecs are also blocked in some instances, preventing some files from playing in the Zune players. A simple workaround for this problem is to switch playback of video and music files to Windows Media Player manually. In start menu click on the "Settings". In the "Windows Settings" window click on "System". On the "System" pane click on "Default apps". On the "Choose default applications" pane click on "Films & TV" under "Video Player". On the "Choose an application" pop up menu click on "Windows Media Player" to set Windows Media Player as the default player for video files. Footnote: The same method can be used to apply file associations for music, by simply clicking on "Groove Music" under "Media Player" instead of changing Video Player in step 4. Media Player Codec Pack Plus. Codec's Explained: A codec is a piece of software on either a device or computer capable of encoding and/or decoding video and/or audio data from files, streams and broadcasts. The word Codec is a portmanteau of ' co mpressor- dec ompressor' Compression types that you will be able to play include: x264 | x265 | h.265 | HEVC | 10bit x265 | 10bit x264 | AVCHD | AVC DivX | XviD | MP4 | MPEG4 | MPEG2 and many more. File types you will be able to play include: .bdmv | .evo | .hevc | .mkv | .avi | .flv | .webm | .mp4 | .m4v | .m4a | .ts | .ogm .ac3 | .dts | .alac | .flac | .ape | .aac | .ogg | .ofr | .mpc | .3gp and many more. -
Divx Codec Package
Divx codec package Videos. How To Use DivX Mux GUI · How to Stream DivX Plus HD (MKV) files to your Xbox · more. Guides. There are no guides available. Search FAQs. Téléchargement gratuit. Inclut DivX Codec et tout ce dont vous avez besoin pour lire les fichiers DivX, AVI ou MKV dans n'importe quel lecteur multimédia. Kostenloser Download. Umfasst DivX Codec und alles, was Du zur Wiedergabe von DivX-, AVI- oder MKV-Dateien in einem beliebigen Media-Player brauchst. H codecs compress digital video files so that they only use half the space of MPEG-2, to deliver the same quality video. An H encoder delivers. Download grátis. Inclui DivX Codec e tudo o mais de que você precisa para reproduzir arquivos DivX, AVI ou MKV em qualquer player de mídia. Free video software downloads to play & stream DivX (AVI) & DivX Plus HD (MKV) video. Find devices to play DivX video and Hollywood movies in DivX format. You can do it all in one go and be ready for any video format that comes your way. Codec Pack All-in-1 includes: DivX ; XviD Codec Media Player Codec Pack for Microsoft Windows, 10, , 8, 7, Vista, XP, , x | h | HEVC | 10bit x | x | h | AVCHD | AVC | DivX | XviD. They feature improved HEVC and AVC decoders for better stability and the DivX codec pack has been removed for consistency around the. Codec Pack All in 1, free and safe download. Codec Pack All in 1 latest version: A free Video program for Windows. Codec Pack All in 1 is a good, free Windows. -
Installation Manual
CX-20 Installation manual ENABLING BRIGHT OUTCOMES Barco NV Beneluxpark 21, 8500 Kortrijk, Belgium www.barco.com/en/support www.barco.com Registered office: Barco NV President Kennedypark 35, 8500 Kortrijk, Belgium www.barco.com/en/support www.barco.com Copyright © All rights reserved. No part of this document may be copied, reproduced or translated. It shall not otherwise be recorded, transmitted or stored in a retrieval system without the prior written consent of Barco. Trademarks Brand and product names mentioned in this manual may be trademarks, registered trademarks or copyrights of their respective holders. All brand and product names mentioned in this manual serve as comments or examples and are not to be understood as advertising for the products or their manufacturers. Trademarks USB Type-CTM and USB-CTM are trademarks of USB Implementers Forum. HDMI Trademark Notice The terms HDMI, HDMI High Definition Multimedia Interface, and the HDMI Logo are trademarks or registered trademarks of HDMI Licensing Administrator, Inc. Product Security Incident Response As a global technology leader, Barco is committed to deliver secure solutions and services to our customers, while protecting Barco’s intellectual property. When product security concerns are received, the product security incident response process will be triggered immediately. To address specific security concerns or to report security issues with Barco products, please inform us via contact details mentioned on https://www.barco.com/psirt. To protect our customers, Barco does not publically disclose or confirm security vulnerabilities until Barco has conducted an analysis of the product and issued fixes and/or mitigations. Patent protection Please refer to www.barco.com/about-barco/legal/patents Guarantee and Compensation Barco provides a guarantee relating to perfect manufacturing as part of the legally stipulated terms of guarantee. -
Implementing Compression on Distributed Time Series Database
Implementing compression on distributed time series database Michael Burman School of Science Thesis submitted for examination for the degree of Master of Science in Technology. Espoo 05.11.2017 Supervisor Prof. Kari Smolander Advisor Mgr. Jiri Kremser Aalto University, P.O. BOX 11000, 00076 AALTO www.aalto.fi Abstract of the master’s thesis Author Michael Burman Title Implementing compression on distributed time series database Degree programme Major Computer Science Code of major SCI3042 Supervisor Prof. Kari Smolander Advisor Mgr. Jiri Kremser Date 05.11.2017 Number of pages 70+4 Language English Abstract Rise of microservices and distributed applications in containerized deployments are putting increasing amount of burden to the monitoring systems. They push the storage requirements to provide suitable performance for large queries. In this paper we present the changes we made to our distributed time series database, Hawkular-Metrics, and how it stores data more effectively in the Cassandra. We show that using our methods provides significant space savings ranging from 50 to 95% reduction in storage usage, while reducing the query times by over 90% compared to the nominal approach when using Cassandra. We also provide our unique algorithm modified from Gorilla compression algorithm that we use in our solution, which provides almost three times the throughput in compression with equal compression ratio. Keywords timeseries compression performance storage Aalto-yliopisto, PL 11000, 00076 AALTO www.aalto.fi Diplomityön tiivistelmä Tekijä Michael Burman Työn nimi Pakkausmenetelmät hajautetussa aikasarjatietokannassa Koulutusohjelma Pääaine Computer Science Pääaineen koodi SCI3042 Työn valvoja ja ohjaaja Prof. Kari Smolander Päivämäärä 05.11.2017 Sivumäärä 70+4 Kieli Englanti Tiivistelmä Hajautettujen järjestelmien yleistyminen on aiheuttanut valvontajärjestelmissä tiedon määrän kasvua, sillä aikasarjojen määrä on kasvanut ja niihin talletetaan useammin tietoa. -
Pack, Encrypt, Authenticate Document Revision: 2021 05 02
PEA Pack, Encrypt, Authenticate Document revision: 2021 05 02 Author: Giorgio Tani Translation: Giorgio Tani This document refers to: PEA file format specification version 1 revision 3 (1.3); PEA file format specification version 2.0; PEA 1.01 executable implementation; Present documentation is released under GNU GFDL License. PEA executable implementation is released under GNU LGPL License; please note that all units provided by the Author are released under LGPL, while Wolfgang Ehrhardt’s crypto library units used in PEA are released under zlib/libpng License. PEA file format and PCOMPRESS specifications are hereby released under PUBLIC DOMAIN: the Author neither has, nor is aware of, any patents or pending patents relevant to this technology and do not intend to apply for any patents covering it. As far as the Author knows, PEA file format in all of it’s parts is free and unencumbered for all uses. Pea is on PeaZip project official site: https://peazip.github.io , https://peazip.org , and https://peazip.sourceforge.io For more information about the licenses: GNU GFDL License, see http://www.gnu.org/licenses/fdl.txt GNU LGPL License, see http://www.gnu.org/licenses/lgpl.txt 1 Content: Section 1: PEA file format ..3 Description ..3 PEA 1.3 file format details ..5 Differences between 1.3 and older revisions ..5 PEA 2.0 file format details ..7 PEA file format’s and implementation’s limitations ..8 PCOMPRESS compression scheme ..9 Algorithms used in PEA format ..9 PEA security model .10 Cryptanalysis of PEA format .12 Data recovery from -
Improved Neural Network Based General-Purpose Lossless Compression Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
JOURNAL OF LATEX CLASS FILES, VOL. 14, NO. 8, AUGUST 2015 1 DZip: improved neural network based general-purpose lossless compression Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa Abstract—We consider lossless compression based on statistical [4], [5] and generative modeling [6]). Neural network based data modeling followed by prediction-based encoding, where an models can typically learn highly complex patterns in the data accurate statistical model for the input data leads to substantial much better than traditional finite context and Markov models, improvements in compression. We propose DZip, a general- purpose compressor for sequential data that exploits the well- leading to significantly lower prediction error (measured as known modeling capabilities of neural networks (NNs) for pre- log-loss or perplexity [4]). This has led to the development of diction, followed by arithmetic coding. DZip uses a novel hybrid several compressors using neural networks as predictors [7]– architecture based on adaptive and semi-adaptive training. Unlike [9], including the recently proposed LSTM-Compress [10], most NN based compressors, DZip does not require additional NNCP [11] and DecMac [12]. Most of the previous works, training data and is not restricted to specific data types. The proposed compressor outperforms general-purpose compressors however, have been tailored for compression of certain data such as Gzip (29% size reduction on average) and 7zip (12% size types (e.g., text [12] [13] or images [14], [15]), where the reduction on average) on a variety of real datasets, achieves near- prediction model is trained in a supervised framework on optimal compression on synthetic datasets, and performs close to separate training data or the model architecture is tuned for specialized compressors for large sequence lengths, without any the specific data type. -
Lossless Compression of Internal Files in Parallel Reservoir Simulation
Lossless Compression of Internal Files in Parallel Reservoir Simulation Suha Kayum Marcin Rogowski Florian Mannuss 9/26/2019 Outline • I/O Challenges in Reservoir Simulation • Evaluation of Compression Algorithms on Reservoir Simulation Data • Real-world application - Constraints - Algorithm - Results • Conclusions 2 Challenge Reservoir simulation 1 3 Reservoir Simulation • Largest field in the world are represented as 50 million – 1 billion grid block models • Each runs takes hours on 500-5000 cores • Calibrating the model requires 100s of runs and sophisticated methods • “History matched” model is only a beginning 4 Files in Reservoir Simulation • Internal Files • Input / Output Files - Interact with pre- & post-processing tools Date Restart/Checkpoint Files 5 Reservoir Simulation in Saudi Aramco • 100’000+ simulations annually • The largest simulation of 10 billion cells • Currently multiple machines in TOP500 • Petabytes of storage required 600x • Resources are Finite • File Compression is one solution 50x 6 Compression algorithm evaluation 2 7 Compression ratio Tested a number of algorithms on a GRID restart file for two models 4 - Model A – 77.3 million active grid blocks 3.5 - Model K – 8.7 million active grid blocks 3 - 15.6 GB and 7.2 GB respectively 2.5 2 Compression ratio is between 1.5 1 compression ratio compression - From 2.27 for snappy (Model A) 0.5 0 - Up to 3.5 for bzip2 -9 (Model K) Model A Model K lz4 snappy gzip -1 gzip -9 bzip2 -1 bzip2 -9 8 Compression speed • LZ4 and Snappy significantly outperformed other algorithms -
User Commands GZIP ( 1 ) Gzip, Gunzip, Gzcat – Compress Or Expand Files Gzip [ –Acdfhllnnrtvv19 ] [–S Suffix] [ Name ... ]
User Commands GZIP ( 1 ) NAME gzip, gunzip, gzcat – compress or expand files SYNOPSIS gzip [–acdfhlLnNrtvV19 ] [– S suffix] [ name ... ] gunzip [–acfhlLnNrtvV ] [– S suffix] [ name ... ] gzcat [–fhLV ] [ name ... ] DESCRIPTION Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77). Whenever possible, each file is replaced by one with the extension .gz, while keeping the same ownership modes, access and modification times. (The default extension is – gz for VMS, z for MSDOS, OS/2 FAT, Windows NT FAT and Atari.) If no files are specified, or if a file name is "-", the standard input is compressed to the standard output. Gzip will only attempt to compress regular files. In particular, it will ignore symbolic links. If the compressed file name is too long for its file system, gzip truncates it. Gzip attempts to truncate only the parts of the file name longer than 3 characters. (A part is delimited by dots.) If the name con- sists of small parts only, the longest parts are truncated. For example, if file names are limited to 14 characters, gzip.msdos.exe is compressed to gzi.msd.exe.gz. Names are not truncated on systems which do not have a limit on file name length. By default, gzip keeps the original file name and timestamp in the compressed file. These are used when decompressing the file with the – N option. This is useful when the compressed file name was truncated or when the time stamp was not preserved after a file transfer. Compressed files can be restored to their original form using gzip -d or gunzip or gzcat. -
Software to Extract Cab Files
Software to extract cab files click here to download You can use WinZip to extract CAB files by following the steps listed below. file extension associated with WinZip program, just double-click on the file. PeaZip offers read-only support (open and extract cab files) for Microsoft Cabinet file format, providing a free alternative utility to open (list content) and www.doorway.ru packages, or disassemble single files from the container, under Windows and Linux operating systems. Moreover, the OS can create, extract, or rebuild cab files. This means you do not require any additional third-party software for this task. All CAB. For a number of years, Microsoft has www.doorway.ru files to compress software that was distributed on disks. Originally, these files were used to minimize the number . The InstallShield installer program makes files with the CAB However, you can also open or extract CAB files with a file decompression tool. Open, browse, extract, or view Microsoft CAB files with Altap Salamander File Manager. High quality software with emphasis on error states. Affordable cost: . Microsoft uses cab files to package software programs. You can view the contents of a cab file by unzipping it and extracting its contents to a. Hi, I need some help www.doorway.ru files. I have to extract a patch for one game, so i used universal extractor for to extract www.doorway.ru Now I have to. cab Extension - List of programs that can www.doorway.ru files. www.doorway.ru, Inventoria Stock Manager, NCH Software, Extract with Express Zip, Low. -
The Ark Handbook
The Ark Handbook Matt Johnston Henrique Pinto Ragnar Thomsen The Ark Handbook 2 Contents 1 Introduction 5 2 Using Ark 6 2.1 Opening Archives . .6 2.1.1 Archive Operations . .6 2.1.2 Archive Comments . .6 2.2 Working with Files . .7 2.2.1 Editing Files . .7 2.3 Extracting Files . .7 2.3.1 The Extract dialog . .8 2.4 Creating Archives and Adding Files . .8 2.4.1 Compression . .9 2.4.2 Password Protection . .9 2.4.3 Multi-volume Archive . 10 3 Using Ark in the Filemanager 11 4 Advanced Batch Mode 12 5 Credits and License 13 Abstract Ark is an archive manager by KDE. The Ark Handbook Chapter 1 Introduction Ark is a program for viewing, extracting, creating and modifying archives. Ark can handle vari- ous archive formats such as tar, gzip, bzip2, zip, rar, 7zip, xz, rpm, cab, deb, xar and AppImage (support for certain archive formats depends on the appropriate command-line programs being installed). In order to successfully use Ark, you need KDE Frameworks 5. The library libarchive version 3.1 or above is needed to handle most archive types, including tar, compressed tar, rpm, deb and cab archives. To handle other file formats, you need the appropriate command line programs, such as zipinfo, zip, unzip, rar, unrar, 7z, lsar, unar and lrzip. 5 The Ark Handbook Chapter 2 Using Ark 2.1 Opening Archives To open an archive in Ark, choose Open... (Ctrl+O) from the Archive menu. You can also open archive files by dragging and dropping from Dolphin. -
File Management Tools
File Management Tools ● gzip and gunzip ● tar ● find ● df and du ● od ● nm and strip ● sftp and scp Gzip and Gunzip ● The gzip utility compresses a specified list of files. After compressing each specified file, it renames it to have a “.gz” extension. ● General form. gzip [filename]* ● The gunzip utility uncompresses a specified list of files that had been previously compressed with gzip. ● General form. gunzip [filename]* Tar (38.2) ● Tar is a utility for creating and extracting archives. It was originally setup for archives on tape, but it now is mostly used for archives on disk. It is very useful for sending a set of files to someone over the network. Tar is also useful for making backups. ● General form. tar options filenames Commonly Used Tar Options c # insert files into a tar file f # use the name of the tar file that is specified v # output the name of each file as it is inserted into or # extracted from a tar file x # extract the files from a tar file Creating an Archive with Tar ● Below is the typical tar command used to create an archive from a set of files. Note that each specified filename can also be a directory. Tar will insert all files in that directory and any subdirectories. tar cvf tarfilename filenames ● Examples: tar cvf proj.tar proj # insert proj directory # files into proj.tar tar cvf code.tar *.c *.h # insert *.c and *.h files # into code.tar Extracting Files from a Tar Archive ● Below is the typical tar command used to extract the files from a tar archive.