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Distributed Cloud-Based Approaches to the Genomic Data Analysis
08 Fall Czech Technical University Faculty of Electrical Engineering Distributed cloud-based approaches to the genomic data analysis (Master’s thesis) Bc. Filip Mihalovič Supervisor: doc. Ing. Jiří Kléma, PhD. Study programme: Open Informatics Specialization: Software Engineering May 2016 ii Acknowledgements I wish to express my sincere thanks to my supervisor doc. Ing. Jiří Kléma, PhD. for sharing his expertise and for his continuous guidance. I am grateful to my family and friends for their encouragement and support during my studies. Access to computing and storage facilities owned by parties and projects contributing to the National Grid Infrastructure MetaCentrum, provided under the programme "Projects of Large Research, Development, and Innovations Infrastructures" (CESNET LM2015042), is greatly appreciated. iii iv vi Declaration I declare that I worked out the presented thesis independently and I quoted all used sources of information in accord with Methodical instructions about ethical principles for writing academic thesis. In Prague on 24th May 2016 …………………………………….. Author vii Abstract The advance of genome analysis bound to next-generation sequencing has allowed scientists to conduct research to deeper understand the biological structure of organisms. A problem of computationally demanding genome assembly based on a high volume of sequence reads is introduced. Several sequential solutions for de novo genome assembly are reviewed. Two fundamental types of genome assembly approaches exist, the sequence reconstruction via de Bruijn graph and the overlap graph method. We focus on parallelization of the genome assembly task using the overlap graph approach and the utilization of Apache Spark big data engine. We demonstrate that subtasks of genome assembly can be parallelized and computed in a distributed manner. -
Download and Unpack It: Tar -Zxvf Leptospirashermanidata.Tar.Gz
Hsieh et al. BMC Bioinformatics (2020) 21:528 https://doi.org/10.1186/s12859‑020‑03788‑9 SOFTWARE Open Access Clover: a clustering‑oriented de novo assembler for Illumina sequences Ming‑Feng Hsieh1, Chin Lung Lu1 and Chuan Yi Tang1,2* *Correspondence: [email protected] Abstract 1 Department of Computer Background: Next‑generation sequencing technologies revolutionized genomics Science, National Tsing Hua University, Hsinchu 30013, by producing high‑throughput reads at low cost, and this progress has prompted the Taiwan recent development of de novo assemblers. Multiple assembly methods based on de Full list of author information Bruijn graph have been shown to be efcient for Illumina reads. However, the sequenc‑ is available at the end of the article ing errors generated by the sequencer complicate analysis of de novo assembly and infuence the quality of downstream genomic researches. Results: In this paper, we develop a de Bruijn assembler, called Clover (clustering‑ oriented de novo assembler), that utilizes a novel k‑mer clustering approach from the overlap‑layout‑consensus concept to deal with the sequencing errors generated by the Illumina platform. We further evaluate Clover’s performance against several de Bruijn graph assemblers (ABySS, SOAPdenovo, SPAdes and Velvet), overlap‑layout‑con‑ sensus assemblers (Bambus2, CABOG and MSR‑CA) and string graph assembler (SGA) on three datasets (Staphylococcus aureus, Rhodobacter sphaeroides and human chromo‑ some 14). The results show that Clover achieves a superior assembly quality in terms of corrected N50 and E‑size while remaining a signifcantly competitive in run time except SOAPdenovo. In addition, Clover was involved in the sequencing projects of bacterial genomes Acinetobacter baumannii TYTH‑1 and Morganella morganii KT. -
Mac OS Hacking Professionelle Werkzeuge Und Methoden Zur Forensischen Analyse Des Apple-Betriebssystems
Alle Übungen im Buch zum Download Marc Brandt Mac OS Hacking Professionelle Werkzeuge und Methoden zur forensischen Analyse des Apple-Betriebssystems • Sicherungs- und Analysetechniken für digitale Spuren • Integrierte Mac-OS-Sicherheitssysteme angreifen und überwinden • Forensische Analysestrategien zu Spotlight, Time Machine und iCloud 60551-9 Titelei.qxp_Layout 1 13.07.17 10:18 Seite 1 Marc Brandt Mac OS Hacking 60551-9 Titelei.qxp_Layout 1 13.07.17 10:18 Seite 3 Marc Brandt Mac OS Hacking Professionelle Werkzeuge und Methoden zur forensischen Analyse des Apple-Betriebssystems • Sicherungs- und Analysetechniken für digitale Spuren • Integrierte Mac-OS-Sicherheitssysteme angreifen und überwinden • Forensische Analysestrategien zu Spotlight, Time Machine und iCloud 60551-9 Titelei.qxp_Layout 1 13.07.17 10:18 Seite 4 Bibliografische Information der Deutschen Bibliothek Die Deutsche Bibliothek verzeichnet diese Publikation in der Deutschen Nationalbibliografie; detaillierte Daten sind im Internet über http://dnb.ddb.de abrufbar. Alle Angaben in diesem Buch wurden vom Autor mit größter Sorgfalt erarbeitet bzw. zusammengestellt und unter Einschaltung wirksamer Kontrollmaßnahmen reproduziert. Trotzdem sind Fehler nicht ganz auszuschließen. Der Verlag und der Autor sehen sich deshalb gezwungen, darauf hinzuweisen, dass sie weder eine Garantie noch die juristische Verantwortung oder irgendeine Haftung für Folgen, die auf fehlerhafte Angaben zurückgehen, überneh- men können. Für die Mitteilung etwaiger Fehler sind Verlag und Autor jederzeit dankbar. Internetadressen oder Ver- sionsnummern stellen den bei Redaktionsschluss verfügbaren Informationsstand dar. Verlag und Autor übernehmen keinerlei Verantwortung oder Haftung für Veränderungen, die sich aus nicht von ihnen zu vertretenden Umständen ergeben. Evtl. beigefügte oder zum Download angebotene Dateien und Informationen dienen ausschließlich der nicht gewerblichen Nutzung. -
Wednesday, April 17, 2013 4000-1200 B.C
APPLE Wednesday, April 17, 2013 4000-1200 B.C. Inhabitants of 3000 B.C. The abacus is invented the first known in Babylonia. civilization in Sumer keep records of 250-230 B.C. The Sieve of commercial Eratosthenes is used to determine transactions on prime numbers. clay tablets. About 79 A.D. The “Antikythera Archives IBM Device,” when set correctly About 1300 The more familiar wire- according to latitude and day of and-bead abacus replaces the Chinese The University Museum, University of Pennsylvania of University Museum, University The the week, gives alternating calculating rods. 29- and 30-day lunar months. 4000 B.C. — 1300 Wednesday, April 17, 2013 1612-1614 John Napier uses the printed decimal point, devises logarithms, and 1622 William Oughtred 1666 In uses numbered sticks, or Napiers Bones, invents the circular England, for calculating. slide rule on the basis Samuel of Napier’s logarithms. Morland produces a mechanical calculator 1623 William (Wilhelm) that can add Schickard designs a and subtract. “calculating clock” with a gear-driven carry mechanism to aid in Museum Computer The multiplication of multi- 1642-1643 Blaise Pascal creates a gear-driven digit numbers. adding machine called the “Pascalene,” the The Computer Museum Computer The first mechanical adding machine. 1600s Wednesday, April 17, 2013 First Computer Bug - 1945 • Relay switches part of computers • Grace Hopper found a moth stuck in a relay responsible for a malfunction • Called it “debugging” a computer Wednesday, April 17, 2013 1832 Babbage and 1834-35 Babbage shifts his focus to Joseph Clement designing the Analytical Engine. produce a portion of the Difference Engine. -
Apple Programmers
PROGRAMMER’S AID #1 INSTALLATION AND OPERATING MANUAL TM Apple Utility Programs Published by APPLE COMPUTER INC. 10260 Bandley Drive Cupertino. California 95014 (408) 996—1010 All rights reserved. @1978 by APPLE COMPUTER INC. Reorder APPLE Product #A2L0011 (030—0026) TABLE OF CONTENTS INTRODUCTION XI Features of Programmer s Aid #1 XII How to install the Programmer’s Aid ROM CHAPTER 1 RENUMBER 2 Renumbering an entire BASIC program 2 Renumbering a portion of a BASIC program 4 Comments CHAPTER 2 APPEND 6 Appending one BASIC program to another 6 Comments II CHAPTER 3 TAPE VERIFY (BASIC) 8 VerifyIng a Basic program saved on tape 8 Comments III CHAPTER 4 TAPE VERIFY (Machine Code or Data) 10 Verifying a portion of memory saved on tape 10 Comments IV CHAPTER 5 RELOCATE 12 Part A: Theory of operation 12 Relocating machine—language code 13 Program model 14 Blocks and Segments 15 Code and Data Segments 16 How to use the Code—Relocation feature 18 Part B: Examples of Code relocation 18 Example 1. Straightforward relocation 19 Example 2. Index into Block 20 Example 3. Immediate address reference 20 Example 4. Unusable Block ranges 21 Example 5. Changing the page zero variable allocation 22 Example 6. Split Blocks with cross—referencing 23 Example 7. Code deletion 24 Example 8. Relocating the APPLE II Monitor ($F800-$FFFF) to run in RAM ($800—$FFF) 25 Part C: Further details 25 Technical Information 26 Algorithm used by the Code—Relocation feature 27 Comments V CHAPTER 6 RAM TEST 30 Testing APPLE’s memory 31 Address ranges for standard memory configurations 32. -
Pnas.Org/Lookup/Suppl/Doi:10
Assembler for de novo assembly of large genomes PNAS PLUS Te-Chin Chua,b, Chen-Hua Lua, Tsunglin Liuc, Greg C. Leeb, Wen-Hsiung Lid,e,1, and Arthur Chun-Chieh Shiha,f,1 aInstitute of Information Science, dBiodiversity Research Center, and fResearch Center for Information Technology Innovation, Academia Sinica, Taipei 115, Taiwan; bDepartment of Computer Science and Information Engineering, National Taiwan Normal University, Taipei 106, Taiwan; cInstitute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan; and eDepartment of Ecology and Evolution, The University of Chicago, Chicago, IL 60637 Contributed by Wen-Hsiung Li, July 25, 2013 (sent for review March 15, 2013) Assembling a large genome using next generation sequencing Assembly By Short Sequences (ABySS) (6), ALLPATHS-LG reads requires large computer memory and a long execution time. (7), EULER-USR (8), SOAPdenovo (9, 10), and Velvet (11). To reduce these requirements, we propose an extension-based The de Bruijn graph approach requires more memory than assembler, called JR-Assembler, where J and R stand for “jumping” both the OLC and the extension approach because it needs to extension and read “remapping.” First, it uses the read count to save the entire graph in memory for assembly. To handle a large select good quality reads as seeds. Second, it extends each seed by genome such as a 3 Gb genome, ALLPATHS-LG and SOAP- a whole-read extension process, which expedites the extension denovo (7, 9, 10) have been carefully engineered, but most other process and can jump over short repeats. Third, it uses a dynamic de Bruijn graph assemblers cannot handle large genomes when back trimming process to avoid extension termination due to se- the memory is limited. -
A Nybble on the Apple, April 1977, BYTE Magazine
A Nybble .on the Apple capabilities, I suggested that we sit down and implement a "Color Eater" algorithm with Apple-II's integer BASIC interpreter with color graphics extensions. I had first seen the Color Eater program demonstrated in an advanced graphics research laboratory late in 1975 (the idea of the program is not original with me, and I will provide the source upon request). The Color Eater always lives in the matrix in the color TV display at some point. The Color Eater is a very simple animal. It looks at its nearest neighbors in the color matrix, searching in a clockwise direction for its current "digestible" color. If it finds this color, it moves its location to the matrix position oJ that color, digests it into a new color, and reiterates its search. Occasionally, the Color Eater becomes a very frustrated little animal. It eats itself into a corner and no longer is able to find any digestible colors . When this catastrophe happens, it throws a fit and turns itself into another variety of Color Eater which can eat itself out of the frustration point. The result is a constantly changing random color pattern on the screen, illustrated in one state in this photo made with the Apple-II computer's output to a standard color television. That evening last November, Steve Jobs, Steve Wozniak and I sat down and Notes by Carl Helmers proceeded to use the Apple-II BASIC (which is a 5 K interpreter with 16 bit integer arithmetic) to program the Color Eater Next month, we'll have an article by Steve game. -
(TIL) Apple II Articles
––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Apple II Computer Family Technical Information ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Apple Technical Information Library (TIL) Apple II Articles ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Date March 1997 ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Source Compuserve Apple II Computer Family Technical Information Apple Technical Information Library (TIL) Apple II Articles : March 1997 : 1 of 681 ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– ================================================================================ DOCUMENT March 1997 A2TIL.Catalog ================================================================================ Apple ][ Articles from the Apple Technical Information Library March 1997 -- David T. Craig ([email protected]) Columns: 1 - File name 2 - Pages (assumes 60 lines per page) 3 - Lines 4 - Longest line length 5 - Article title A2TIL001.TXT 6 358 84 Apple Tech Info Library Overview: How to Search for Articles A2TIL002.TXT 2 102 75 16K RAM / Language Cards: Alternate Suppliers A2TIL003.TXT 2 105 79 80-Column Text Card: Applesoft Control Codes (11/96) A2TIL004.TXT 1 31 78 80-Column Text Cards: Apple II & II Plus Compatibility (11/96) A2TIL005.TXT 1 27 76 Access II and Apple IIc Plus: No 40-Column Mode A2TIL006.TXT 1 15 77 Access II: Does Not Support VT100 Line Graphics A2TIL007.TXT 1 52 76 Access II: Specifications (Discontinued) A2TIL008.TXT 1 48 78 Apple 3.5 Drive: Description -
Apple II Versus Apple III Hardware Architecture Comments ______
_______________ Apple /// Computer Historical Information _______________ _____________________________________________________________________________ Apple II versus Apple III Hardware Architecture Comments _____________________________________________________________________________ December 2002 eMail correspondence between Steven Weyhrich Rick Auricchio (Apple) David Craig Compiled by David T Craig on 05 September 2004 __________________________________________________________________________________________ Apple II versus Apple III Hardware Architecture Comments -- December 2002 eMail correspondence between Steven Weyhrich, Rick Auricchio (Apple), David Craig Compiled by David T Craig on 05 September 2004 -- Page 1 of 23 _______________ Apple /// Computer Historical Information _______________ From: Steven Weyhrich Sent: Saturday, December 14, 2002 2:05 PM To: David Craig Subject: CD's I am sorry I didn't e-mail you sooner to let you know that I did receive the package of CD's that you kindly sent to me. What a treasure trove of information you have collected and organized! I have not yet had an opportunity to look at them in detail, but what I have seen looks pretty neat. You seem to be more of a trivia pack rat than even _I_ am! I did notice one item: The Byte magazine "letter from Wozniak" does appear to be a joke by the guy writing the column, rather than a true letter from Wozniak. This may not be news to you, but I thought I'd put my two cents worth. :-) You asked something about whether or not a disassembly of PRODOS had been done anywhere. I had thought that the writers of Beneath Apple ProDOS had published a disassembly listing, but it was only a listing of pertinent parts of the code (what a certain part of the code does, not the disassembly listing of the opcodes). -
Efficient Algorithms for Prokaryotic Whole Genome Assembly And
Old Dominion University ODU Digital Commons Computer Science Theses & Dissertations Computer Science Fall 2015 Efficient Algorithms for okarPr yotic Whole Genome Assembly and Finishing Abhishek Biswas Old Dominion University, [email protected] Follow this and additional works at: https://digitalcommons.odu.edu/computerscience_etds Part of the Bioinformatics Commons, and the Computer Sciences Commons Recommended Citation Biswas, Abhishek. "Efficient Algorithms for okarPr yotic Whole Genome Assembly and Finishing" (2015). Doctor of Philosophy (PhD), Dissertation, Computer Science, Old Dominion University, DOI: 10.25777/ znmw-nt79 https://digitalcommons.odu.edu/computerscience_etds/3 This Dissertation is brought to you for free and open access by the Computer Science at ODU Digital Commons. It has been accepted for inclusion in Computer Science Theses & Dissertations by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. EFFICIENT ALGORITHMS FOR PROKARYOTIC WHOLE GENOME ASSEMBLY AND FINISHING by Abhishek Biswas B. E. August 2007, Visvesvaraya Technological University, India A Thesis Submitted to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY COMPUTER SCIENCE OLD DOMINION UNIVERSITY December 2015 Approved by: ________________________ Desh Ranjan (Director) ________________________ David Gauthier (Member) __________________________ Mohammad Zubair (Co-Director) _______________________ Jing He (Member) ABSTRACT EFFICIENT ALGORITHMS FOR PROKARYOTIC WHOLE GENOME ASSEMBLY AND FINISHING Abhishek Biswas Old Dominion University, 2015 Director: Dr. Desh Ranjan Co-Director: Dr. Mohammad Zubair De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. -
Calling Conventions for Different C++ Compilers and Operating Systems
5. Calling conventions for different C++ compilers and operating systems By Agner Fog. Copenhagen University College of Engineering. Copyright © 2004 - 2012. Last updated 2012-02-29. Contents 1 Introduction ....................................................................................................................... 3 2 The need for standardization............................................................................................. 5 3 Data representation...........................................................................................................6 4 Data alignment .................................................................................................................. 8 5 Stack alignment................................................................................................................. 9 6 Register usage ................................................................................................................10 6.1 Can floating point registers be used in 64-bit Windows? ........................................... 13 6.2 YMM vector registers................................................................................................ 14 6.3 Register usage in kernel code................................................................................... 14 7 Function calling conventions ........................................................................................... 16 7.1 Passing and returning objects.................................................................................. -
Steve Wozniak Column by Jim Rue
The Merry Prankster of Computing: Steve Wozniak Column By Jim Rue teve “Woz” Wozniak is Club members asked the Steves to build the boards, and so they did— one of the early wizards in Jobs’ parents’ garage. The buyer was responsible for providing Sof computing. When niceties like a case. Two hundred of the Apple I circuit boards were the ‘desktop computer’ was sold. When the Apple II came out, though, buyers of the Apple I were not yet conceived, when even offered a swap. Only a few Apple Is survived. The only known Apple the earlier ‘personal computer’ I that still works went for $14,000 at auction held in 2000. had yet to acquire the name, The proceeds from sales of the Apple Is became seed money for the Woz was already tinkering new company. Apple Computer, Inc. was formed on April 1, 1976. with microprocessors. The Shortly afterward, new partners provided for the hiring of thousands of son of a Lockheed aerospace employees and the manufacture of thousands of Apple IIs (also engineer, Woz was an elec- designed by Wozniak), and Jobs and Wozniak dove down the rabbit tronics prodigy. He got his hole into commercial and technical stardom. ham radio license before he It is notable that Apple Computer began doing business on April 1. was twelve and designed cir- It is in keeping with the thought processes of Steve Wozniak that this cuits for a childhood hobby. would be the date. The same was true for the cost of the Apple I. They At an early age he built a sold them for $666.66 each.