TREE2FASTA: a Flexible Perl Script for Batch Extraction of FASTA
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Treebase: an R Package for Discovery, Access and Manipulation of Online Phylogenies
Methods in Ecology and Evolution 2012, 3, 1060–1066 doi: 10.1111/j.2041-210X.2012.00247.x APPLICATION Treebase: an R package for discovery, access and manipulation of online phylogenies Carl Boettiger1* and Duncan Temple Lang2 1Center for Population Biology, University of California, Davis, CA,95616,USA; and 2Department of Statistics, University of California, Davis, CA,95616,USA Summary 1. The TreeBASE portal is an important and rapidly growing repository of phylogenetic data. The R statistical environment has also become a primary tool for applied phylogenetic analyses across a range of questions, from comparative evolution to community ecology to conservation planning. 2. We have developed treebase, an open-source software package (freely available from http://cran.r-project. org/web/packages/treebase) for the R programming environment, providing simplified, programmatic and inter- active access to phylogenetic data in the TreeBASE repository. 3. We illustrate how this package creates a bridge between the TreeBASE repository and the rapidly growing collection of R packages for phylogenetics that can reduce barriers to discovery and integration across phyloge- netic research. 4. We show how the treebase package can be used to facilitate replication of previous studies and testing of methods and hypotheses across a large sample of phylogenies, which may help make such important reproduc- ibility practices more common. Key-words: application programming interface, database, programmatic, R, software, TreeBASE, workflow include, but are not limited to, ancestral state reconstruction Introduction (Paradis 2004; Butler & King 2004), diversification analysis Applications that use phylogenetic information as part of their (Paradis 2004; Rabosky 2006; Harmon et al. -
NASP: an Accurate, Rapid Method for the Identification of Snps in WGS Datasets That Supports Flexible Input and Output Formats Jason Sahl
Himmelfarb Health Sciences Library, The George Washington University Health Sciences Research Commons Environmental and Occupational Health Faculty Environmental and Occupational Health Publications 8-2016 NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats Jason Sahl Darrin Lemmer Jason Travis James Schupp John Gillece See next page for additional authors Follow this and additional works at: http://hsrc.himmelfarb.gwu.edu/sphhs_enviro_facpubs Part of the Bioinformatics Commons, Integrative Biology Commons, Research Methods in Life Sciences Commons, and the Systems Biology Commons APA Citation Sahl, J., Lemmer, D., Travis, J., Schupp, J., Gillece, J., Aziz, M., & +several additional authors (2016). NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microbial Genomics, 2 (8). http://dx.doi.org/10.1099/mgen.0.000074 This Journal Article is brought to you for free and open access by the Environmental and Occupational Health at Health Sciences Research Commons. It has been accepted for inclusion in Environmental and Occupational Health Faculty Publications by an authorized administrator of Health Sciences Research Commons. For more information, please contact [email protected]. Authors Jason Sahl, Darrin Lemmer, Jason Travis, James Schupp, John Gillece, Maliha Aziz, and +several additional authors This journal article is available at Health Sciences Research Commons: http://hsrc.himmelfarb.gwu.edu/sphhs_enviro_facpubs/212 Methods Paper NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats Jason W. Sahl,1,2† Darrin Lemmer,1† Jason Travis,1 James M. -
Hardware Pattern Matching for Network Traffic Analysis in Gigabit
Technische Universitat¨ Munchen¨ Fakultat¨ fur¨ Informatik Diplomarbeit in Informatik Hardware Pattern Matching for Network Traffic Analysis in Gigabit Environments Gregor M. Maier Aufgabenstellerin: Prof. Anja Feldmann, Ph. D. Betreuerin: Prof. Anja Feldmann, Ph. D. Abgabedatum: 15. Mai 2007 Ich versichere, dass ich diese Diplomarbeit selbst¨andig verfasst und nur die angegebe- nen Quellen und Hilfsmittel verwendet habe. Datum Gregor M. Maier Abstract Pattern Matching is an important task in various applica- tions, including network traffic analysis and intrusion detec- tion. In modern high speed gigabit networks it becomes un- feasible to search for patterns using pure software implemen- tations, due to the amount of data that must be searched. Furthermore applications employing pattern matching often need to search for several patterns at the same time. In this thesis we explore the possibilities of using FPGAs for hardware pattern matching. We analyze the applicability of various pattern matching algorithms for hardware imple- mentation and implement a Rabin-Karp and an approximate pattern matching algorithm in Endace’s network measure- ment cards using VHDL. The implementations are evalu- ated and compared to pure software matching solutions. To demonstrate the power of hardware pattern matching, an example application for traffic accounting using hardware pattern matching is presented as a proof-of-concept. Since some systems like network intrusion detection systems an- alyze reassembled TCP streams, possibilities for hardware TCP reassembly combined with hardware pattern matching are discussed as well. Contents vii Contents List of Figures ix 1 Introduction 1 1.1 Motivation . 1 1.2 Related Work . 2 1.3 About Endace DAG Network Monitoring Cards . -
Introduction to Bioinformatics (Elective) – SBB1609
SCHOOL OF BIO AND CHEMICAL ENGINEERING DEPARTMENT OF BIOTECHNOLOGY Unit 1 – Introduction to Bioinformatics (Elective) – SBB1609 1 I HISTORY OF BIOINFORMATICS Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biologicaldata. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques. Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine. Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. "Classical" bioinformatics: "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.” The National Center for Biotechnology Information (NCBI 2001) defines bioinformatics as: "Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. -
Can Hybridization Be Detected Between African Wolf and Sympatric Canids?
Can hybridization be detected between African wolf and sympatric canids? Sunniva Helene Bahlk Master of Science Thesis 2015 Center for Ecological and Evolutionary Synthesis Department of Bioscience Faculty of Mathematics and Natural Science University of Oslo, Norway © Sunniva Helene Bahlk 2015 Can hybridization be detected between African wolf and sympatric canids? Sunniva Helene Bahlk http://www.duo.uio.no/ Print: Reprosentralen, University of Oslo II Table of contents Acknowledgments ...................................................................................................................... 1 Abstract ...................................................................................................................................... 3 Introduction ................................................................................................................................ 5 The species in the genus Canis are closely related and widely distributed ........................... 5 Next-generation sequencing and bioinformatics .................................................................. 6 The concepts of hybridization and introgression ................................................................... 8 The aim of my study ............................................................................................................... 9 Materials and Methods ............................................................................................................ 11 Origin of the samples and laboratory protocols ................................................................. -
Comprehensive Examinations in Computer Science 1872 - 1878
COMPREHENSIVE EXAMINATIONS IN COMPUTER SCIENCE 1872 - 1878 edited by Frank M. Liang STAN-CS-78-677 NOVEMBER 1078 (second Printing, August 1979) COMPUTER SCIENCE DEPARTMENT School of Humanities and Sciences STANFORD UNIVERSITY COMPUTER SC l ENCE COMPREHENSIVE EXAMINATIONS 1972 - 1978 b Y the faculty and students of the Stanford University Computer Science Department edited by Frank M. Liang Abstract Since Spring 1972, the Stanford Computer Science Department has periodically given a "comprehensive examination" as one of the qualifying exams for graduate students. Such exams generally have consisted of a six-hour written test followed by a several-day programming problem. Their intent is to make it possible to assess whether a student is sufficiently prepared in all the important aspects of computer science. This report presents the examination questions from thirteen comprehensive examinations, along with their solutions. The preparation of this report has been supported in part by NSF grant MCS 77-23738 and in part by IBM Corporation. Foreword This report probably contains as much concentrated computer science per page as any document In existence - it is the result of thousands of person-hours of creative work by the entire staff of Stanford's Computer Science Department, together with dozens of h~ghly-talented students who also helped to compose the questions. Many of these questions have never before been published. Thus I think every person interested in computer science will find it stimulating and helpful to study these pages. Of course, the material is so concentrated it is best not taken in one gulp; perhaps the wisest policy would be to keep a copy on hand in the bathroom at all times, for those occasional moments when inspirational reading is desirable. -
A Comprehensive SARS-Cov-2 Genomic Analysis Identifies Potential Targets for Drug Repurposing
PLOS ONE RESEARCH ARTICLE A comprehensive SARS-CoV-2 genomic analysis identifies potential targets for drug repurposing 1☯ 1☯ 2,3 Nithishwer Mouroug Anand , Devang Haresh Liya , Arpit Kumar PradhanID *, Nitish Tayal4, Abhinav Bansal5, Sainitin Donakonda6, Ashwin Kumar Jainarayanan7,8* 1 Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India, 2 Graduate School of Systemic Neuroscience, Ludwig Maximilian University of Munich, Munich, Germany, 3 Klinikum rechts der Isar, Technische UniversitaÈt MuÈnchen, MuÈnchen, Germany, 4 Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India, 5 Department of Chemical a1111111111 Sciences, Indian Institute of Science Education and Research, Mohali, India, 6 Institute of Molecular a1111111111 Immunology and Experimental Oncology, Klinikum rechts der Isar, Technische UniversitaÈt MuÈnchen, a1111111111 MuÈnchen, Germany, 7 The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United a1111111111 Kingdom, 8 Interdisciplinary Bioscience DTP, University of Oxford, Oxford, United Kingdom a1111111111 ☯ These authors contributed equally to this work. * [email protected] (AKP); [email protected] (AKJ) OPEN ACCESS Abstract Citation: Anand NM, Liya DH, Pradhan AK, Tayal N, The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is a novel Bansal A, Donakonda S, et al. (2021) A comprehensive SARS-CoV-2 genomic analysis human coronavirus strain (HCoV) was initially reported in December 2019 in Wuhan City, identifies potential targets for drug repurposing. China. This acute infection caused pneumonia-like symptoms and other respiratory tract ill- PLoS ONE 16(3): e0248553. https://doi.org/ ness. Its higher transmission and infection rate has successfully enabled it to have a global 10.1371/journal.pone.0248553 spread over a matter of small time. -
Trusted Research Environments (TRE) a Strategy to Build Public Trust and Meet Changing Health Data Science Needs
Trusted Research Environments (TRE) A strategy to build public trust and meet changing health data science needs Green Paper v2.0 dated 21 July 2020 – For sign off Table of Contents Executive Summary .................................................................................................................................................... 3 Status of the document .............................................................................................................................................. 5 Overview .................................................................................................................................................................... 6 Purpose ........................................................................................................................................................................... 6 Background .................................................................................................................................................................... 6 The case for TREs providing access to health data through safe settings ...................................................................... 8 Requirements for a Trusted Research Environment...................................................................................................10 Safe people ................................................................................................................................................................... 10 Safe projects ................................................................................................................................................................ -
Computational Biology and Bioinformatics
DEPARTMENT OF COMPUTATIONAL BIOLOGY AND BIOINFORMATICS UNIVERSITY OF KERALA MSc. PROGRAMME IN COMPUTATIONAL BIOLOGY SYLLABUS Under Credit and Semester System w. e. f. 2017 Admissions DEPARTMENT OF COMPUTATIONAL BIOLOGY AND BIOINFORMATICS UNIVERSITY OF KERALA MSc. PROGRAMME IN COMPUTATIONAL BIOLOGY SYLLABUS PROGRAMME OBJECTIVES Aims to equip students with basic computational and mathematical skill To impart basic life science knowledge To acquire advanced computational and modelling skills required to address problems of life sciences for computational perspectives MSc. Syllabus of the Programme Number of Semester Course Code Name of the course Credits Core Courses BIN-C-411 Introduction to Life Sciences & Bioinformatics 4 BIN-C-412 Applied Mathematics 4 BIN-C-413 Web programming and Databases 4 I BIN-C-414 Bioinformatics Lab I 3 Internal Electives BIN-E-415 (i) Python Programming (E) 2 BIN-E-415 (ii) Seminar I (E) 2 BIN-E-415 (iii) Programming in R (E) 2 BIN-E-415 (iv) Communication skill in English (Elective skill course) 2 Core Courses BIN-C-421 Creativity, Research & Knowledge Management 4 BIN-C-422 Fundamentals of Molecular Biology 4 BIN-C-423 Computational Genomics 4 BIN-C-424 Bioinformatics Lab II 3 II Internal Electives BIN-E-425 (i) Perl and BioPerl (E) 4 BIN-E-425 (ii) Case Study (E) 2 BIN-E-425 (iii) Android App Development for Bioinformatics(E) 2 BIN-E-425 (iv) Negotiated Studies(E) 2 BIN-E-425 (v) Communication skill in English (Elective skill course) 2 Core Courses BIN-C-431 Proteomics and CADD 4 BIN-C-432 Phylogenetics -
An Efficient Pipeline for Assaying Whole-Genome Plastid Variation for Population Genetics and Phylogeography
Portland State University PDXScholar Dissertations and Theses Dissertations and Theses Spring 6-2-2017 An Efficient Pipeline for Assaying Whole-Genome Plastid Variation for Population Genetics and Phylogeography Brendan F. Kohrn Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/open_access_etds Part of the Biology Commons, and the Plant Sciences Commons Let us know how access to this document benefits ou.y Recommended Citation Kohrn, Brendan F., "An Efficient Pipeline for Assaying Whole-Genome Plastid Variation for Population Genetics and Phylogeography" (2017). Dissertations and Theses. Paper 4007. https://doi.org/10.15760/etd.5891 This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. An Efficient Pipeline for Assaying Whole-Genome Plastid Variation for Population Genetics and Phylogeography by Brendan F. Kohrn A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology Thesis Committee: Mitch Cruzan, Chair Sarah Eppley Rahul Raghavan Portland State University 2017 © 2017 Brendan F. Kohrn i Abstract Tracking seed dispersal using traditional, direct measurement approaches is difficult and generally underestimates dispersal distances. Variation in chloroplast haplotypes (cpDNA) offers a way to trace past seed dispersal and to make inferences about factors contributing to present patterns of dispersal. Although cpDNA generally has low levels of intraspecific variation, this can be overcome by assaying the whole chloroplast genome. Whole-genome sequencing is more expensive, but resources can be conserved by pooling samples. -
Deep Sampling of Hawaiian Caenorhabditis Elegans Reveals
RESEARCH ARTICLE Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations Tim A Crombie1, Stefan Zdraljevic1,2, Daniel E Cook1,2, Robyn E Tanny1, Shannon C Brady1,2, Ye Wang1, Kathryn S Evans1,2, Steffen Hahnel1, Daehan Lee1, Briana C Rodriguez1, Gaotian Zhang1, Joost van der Zwagg1, Karin Kiontke3, Erik C Andersen1* 1Department of Molecular Biosciences, Northwestern University, Evanston, United States; 2Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States; 3Department of Biology, New York University, New York, United States Abstract Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral C. elegans *For correspondence: genetic diversity in the species before human influence. [email protected] Competing interests: The authors declare that no Introduction competing interests exist. Over the last 50 years, the nematode Caenorhabditis elegans has been central to many important Funding: See page 21 discoveries in the fields of developmental, cellular, and molecular biology. -
A Personalized Cloud-Based Traffic Redundancy Elimination for Smartphones Vivekgautham Soundararaj Clemson University, [email protected]
Clemson University TigerPrints All Theses Theses 5-2016 TailoredRE: A Personalized Cloud-based Traffic Redundancy Elimination for Smartphones Vivekgautham Soundararaj Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_theses Recommended Citation Soundararaj, Vivekgautham, "TailoredRE: A Personalized Cloud-based Traffic Redundancy Elimination for Smartphones" (2016). All Theses. 2387. https://tigerprints.clemson.edu/all_theses/2387 This Thesis is brought to you for free and open access by the Theses at TigerPrints. It has been accepted for inclusion in All Theses by an authorized administrator of TigerPrints. For more information, please contact [email protected]. TailoredRE: A Personalized Cloud-based Traffic Redundancy Elimination for Smartphones A Thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Master of Science Computer Engineering by Vivekgautham Soundararaj May 2016 Accepted by: Dr. Haiying Shen, Committee Chair Dr. Rong Ge Dr. Walter Ligon Abstract The exceptional rise in usages of mobile devices such as smartphones and tablets has contributed to a massive increase in wireless network traffic both Cellular (3G/4G/LTE) and WiFi. The unprecedented growth in wireless network traffic not only strain the battery of the mobile devices but also bogs down the last-hop wireless access links. Interestingly, a significant part of this data traffic exhibits high level of redundancy in them due to re- peated access of popular contents in the web. Hence, a good amount of research both in academia and in industries has studied, analyzed and designed diverse systems that attempt to eliminate redundancy in the network traffic.