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Cancer Immunology of Cutaneous Melanoma: a Systems Biology Approach
Cancer Immunology of Cutaneous Melanoma: A Systems Biology Approach Mindy Stephania De Los Ángeles Muñoz Miranda Doctoral Thesis presented to Bioinformatics Graduate Program at Institute of Mathematics and Statistics of University of São Paulo to obtain Doctor of Science degree Concentration Area: Bioinformatics Supervisor: Prof. Dr. Helder Takashi Imoto Nakaya During the project development the author received funding from CAPES São Paulo, September 2020 Mindy Stephania De Los Ángeles Muñoz Miranda Imunologia do Câncer de Melanoma Cutâneo: Uma abordagem de Biologia de Sistemas VERSÃO CORRIGIDA Esta versão de tese contém as correções e alterações sugeridas pela Comissão Julgadora durante a defesa da versão original do trabalho, realizada em 28/09/2020. Uma cópia da versão original está disponível no Instituto de Matemática e Estatística da Universidade de São Paulo. This thesis version contains the corrections and changes suggested by the Committee during the defense of the original version of the work presented on 09/28/2020. A copy of the original version is available at Institute of Mathematics and Statistics at the University of São Paulo. Comissão Julgadora: • Prof. Dr. Helder Takashi Imoto Nakaya (Orientador, Não Votante) - FCF-USP • Prof. Dr. André Fujita - IME-USP • Profa. Dra. Patricia Abrão Possik - INCA-Externo • Profa. Dra. Ana Carolina Tahira - I.Butantan-Externo i FICHA CATALOGRÁFICA Muñoz Miranda, Mindy StephaniaFicha de Catalográfica los Ángeles M967 Cancer immunology of cutaneous melanoma: a systems biology approach = Imuno- logia do câncer de melanoma cutâneo: uma abordagem de biologia de sistemas / Mindy Stephania de los Ángeles Muñoz Miranda, [orientador] Helder Takashi Imoto Nakaya. São Paulo : 2020. 58 p. -
Index Images Download 2006 News Crack Serial Warez Full 12 Contact
index images download 2006 news crack serial warez full 12 contact about search spacer privacy 11 logo blog new 10 cgi-bin faq rss home img default 2005 products sitemap archives 1 09 links 01 08 06 2 07 login articles support 05 keygen article 04 03 help events archive 02 register en forum software downloads 3 security 13 category 4 content 14 main 15 press media templates services icons resources info profile 16 2004 18 docs contactus files features html 20 21 5 22 page 6 misc 19 partners 24 terms 2007 23 17 i 27 top 26 9 legal 30 banners xml 29 28 7 tools projects 25 0 user feed themes linux forums jobs business 8 video email books banner reviews view graphics research feedback pdf print ads modules 2003 company blank pub games copyright common site comments people aboutus product sports logos buttons english story image uploads 31 subscribe blogs atom gallery newsletter stats careers music pages publications technology calendar stories photos papers community data history arrow submit www s web library wiki header education go internet b in advertise spam a nav mail users Images members topics disclaimer store clear feeds c awards 2002 Default general pics dir signup solutions map News public doc de weblog index2 shop contacts fr homepage travel button pixel list viewtopic documents overview tips adclick contact_us movies wp-content catalog us p staff hardware wireless global screenshots apps online version directory mobile other advertising tech welcome admin t policy faqs link 2001 training releases space member static join health -
Pragmaticperl-Interviews-A4.Pdf
Pragmatic Perl Interviews pragmaticperl.com 2013—2015 Editor and interviewer: Viacheslav Tykhanovskyi Covers: Marko Ivanyk Revision: 2018-03-02 11:22 © Pragmatic Perl Contents 1 Preface .......................................... 1 2 Alexis Sukrieh (April 2013) ............................... 2 3 Sawyer X (May 2013) .................................. 10 4 Stevan Little (September 2013) ............................. 17 5 chromatic (October 2013) ................................ 22 6 Marc Lehmann (November 2013) ............................ 29 7 Tokuhiro Matsuno (January 2014) ........................... 46 8 Randal Schwartz (February 2014) ........................... 53 9 Christian Walde (May 2014) .............................. 56 10 Florian Ragwitz (rafl) (June 2014) ........................... 62 11 Curtis “Ovid” Poe (September 2014) .......................... 70 12 Leon Timmermans (October 2014) ........................... 77 13 Olaf Alders (December 2014) .............................. 81 14 Ricardo Signes (January 2015) ............................. 87 15 Neil Bowers (February 2015) .............................. 94 16 Renée Bäcker (June 2015) ................................ 102 17 David Golden (July 2015) ................................ 109 18 Philippe Bruhat (Book) (August 2015) . 115 19 Author .......................................... 123 i Preface 1 Preface Hello there! You have downloaded a compilation of interviews done with Perl pro- grammers in Pragmatic Perl journal from 2013 to 2015. Since the journal itself is in Russian -
Bio::Graphics HOWTO Lincoln Stein Cold Spring Harbor Laboratory1 [email protected]
Bio::Graphics HOWTO Lincoln Stein Cold Spring Harbor Laboratory1 [email protected] This HOWTO describes how to render sequence data graphically in a horizontal map. It applies to a variety of situations ranging from rendering the feature table of a GenBank entry, to graphing the positions and scores of a BLAST search, to rendering a clone map. It describes the programmatic interface to the Bio::Graphics module, and discusses how to create dynamic web pages using Bio::DB::GFF and the gbrowse package. Table of Contents Introduction ...........................................................................................................................3 Preliminaries..........................................................................................................................3 Getting Started ......................................................................................................................3 Adding a Scale to the Image ...............................................................................................5 Improving the Image............................................................................................................7 Parsing Real BLAST Output...............................................................................................8 Rendering Features from a GenBank or EMBL File ....................................................12 A Better Version of the Feature Renderer ......................................................................14 Summary...............................................................................................................................18 -
Modern Perl, Fourth Edition
Prepared exclusively for none ofyourbusiness Prepared exclusively for none ofyourbusiness Early Praise for Modern Perl, Fourth Edition A dozen years ago I was sure I knew what Perl looked like: unreadable and obscure. chromatic showed me beautiful, structured expressive code then. He’s the right guy to teach Modern Perl. He was writing it before it existed. ➤ Daniel Steinberg President, DimSumThinking, Inc. A tour de force of idiomatic code, Modern Perl teaches you not just “how” but also “why.” ➤ David Farrell Editor, PerlTricks.com If I had to pick a single book to teach Perl 5, this is the one I’d choose. As I read it, I was reminded of the first time I read K&R. It will teach everything that one needs to know to write Perl 5 well. ➤ David Golden Member, Perl 5 Porters, Autopragmatic, LLC I’m about to teach a new hire Perl using the first edition of Modern Perl. I’d much rather use the updated copy! ➤ Belden Lyman Principal Software Engineer, MediaMath It’s not the Perl book you deserve. It’s the Perl book you need. ➤ Gizmo Mathboy Co-founder, Greater Lafayette Open Source Symposium (GLOSSY) Prepared exclusively for none ofyourbusiness We've left this page blank to make the page numbers the same in the electronic and paper books. We tried just leaving it out, but then people wrote us to ask about the missing pages. Anyway, Eddy the Gerbil wanted to say “hello.” Prepared exclusively for none ofyourbusiness Modern Perl, Fourth Edition chromatic The Pragmatic Bookshelf Dallas, Texas • Raleigh, North Carolina Prepared exclusively for none ofyourbusiness Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. -
Vom Weblog Lernen... Community, Peer-To-Peer Und Eigenständigkeit
Vom Weblog lernen... Community, Peer-to-Peer und Eigenst¨andigkeit als ein Modell fur¨ zukunftige¨ Wissenssammlungen∗ J¨org Kantel Der Schockwellenreiter www.schockwellenreiter.de 20. Mai 2003 Zusammenfassung Das Internet erscheint vielen als unubersichtlicher,¨ anarchischer Raum, in dem zwar alles zu finden ist, aber nicht das, wonach man sucht (Lost in Cyberspace). Die bisherigen L¨osungsans¨atze bestanden in der Regel darin, daß man versuchte, die Informationen zentral zu sammeln, zu bundeln¨ und sie geordnet“ wieder zur Verfugung¨ zu stel- ” len. Demgegenuber¨ sind in den letzten Jahre mit den Weblogs und um die Weblogs herum Strategien entstanden, wie verteilte Informationen behandelt und dennoch zug¨anglich gemacht werden k¨onnen. Dieser Ar- tikel zeigt auf, was fur¨ verteilte Informationssammlungen spricht, wie Weblogs mit uber¨ das gesamte Netz verstreuten Informationen umge- hen, um dann zu untersuchen, wie die dabei entstandenen Techniken auch auf andere Wissenssammlungen im Internet angewandt werden k¨onnen. Beispielhaft wird das an der Implementierung einer verteilten Musiknoten-Sammlung aufgezeigt. ∗Keynote speach given at BlogTalk - A European Conference On Weblogs: Web-based publishing, communication and collaboration tools for professional and private use, Vien- na, May 23 - 24, 2003 1 1 Motivation 1.1 Weblogs und pers¨onliche Wissenssammlungen 1.1.1 Was sind Weblogs Auch wenn manchmal etwas anderes behauptet wird, werden Weblogs als Medienereignis fruhestens¨ seit 1999 (in Deutschland nicht vor 2000) von der Offentlichkeit¨ wahrgenommen1. Im Gegensatz zu der schon vor 1999 existie- renden Tagebuchszene (die ihre Webseiten noch liebvoll mit handgestrick- ” tem“ HTML pflegte), sind Weblogs ohne die dazugeh¨orende Software, wie z.B. Blogger (www.blogger.com), Radio UserLand (radio.uslerland.com) oder Movable Type (www.movabletype.org) nicht zu denken. -
UCLA UCLA Electronic Theses and Dissertations
UCLA UCLA Electronic Theses and Dissertations Title Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods Permalink https://escholarship.org/uc/item/0tr9j01r Author Sun, Yidan Publication Date 2021 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Statistics by Yidan Sun 2021 © Copyright by Yidan Sun 2021 ABSTRACT OF THE DISSERTATION Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods by Yidan Sun Doctor of Philosophy in Statistics University of California, Los Angeles, 2021 Professor Jingyi Li, Chair In a bipartite network, nodes are divided into two types, and edges are only allowed to connect nodes of different types. Bipartite network clustering problems aim to identify node groups with more edges between themselves and fewer edges to the rest of the network. The approaches for community detection in the bipartite network can roughly be classified into algorithmic and model-based methods. The algorithmic methods solve the problem either by greedy searches in a heuristic way or optimizing based on some criteria over all possible partitions. The model-based methods fit a generative model to the observed data and study the model in a statistically principled way. In this dissertation, we mainly focus on bipartite clustering under two scenarios: incorporation of node covariates and detection of mixed membership communities. -
Stein Gives Bioinformatics Ten Years to Live
O'Reilly Network: Stein Gives Bioinformatics Ten Years to Live http://www.oreillynet.com/lpt/a/3205 Published on O'Reilly Network (http://www.oreillynet.com/) http://www.oreillynet.com/pub/a/network/biocon2003/stein.html See this if you're having trouble printing code examples Stein Gives Bioinformatics Ten Years to Live by Daniel H. Steinberg 02/05/2003 Lincoln Stein's keynote at the O'Reilly Bioinformatics Technology Conference was provocatively titled "Bioinformatics: Gone in 2012." Despite the title, Stein is optimistic about the future for people doing bioinformatics. But he explained that "the field of bioinformatics will be gone by 2012. The field will be doing the same thing but it won't be considered a field." His address looked at what bioinformatics is and what its future is likely to be in the context of other scientific disciplines. He also looked at career prospects for people doing bioinformatics and provided advice for those looking to enter the field. What Is Bioinformatics: Take One Stein, of the Cold Spring Harbor Laboratory, began his keynote by examining what is meant by bioinformatics. In the past such a talk would begin with a definition displayed from an authoritative dictionary. The modern approach is to appeal to an FAQ from an authoritative web site. Take a look at the FAQ at bioinformatics.org and you'll find several definitions. Stein summarized Fedj Tekaia of the Institut Pasteur--that bioinformatics is DNA and protein analysis. Stein also summarized Richard Durbin of the Sanger Institute--that bioinformatics is managing data sets. Stein's first pass at a definition of bioinformatics is that it is "Biologists using computers or the other way around." He followed by observing that whatever it is, it's growing. -
Thesis Reference
Thesis Analysis of large biological data: metabolic network modularization and prediction of N-terminal acetylation CHARPILLOZ, Christophe Abstract During last decades, biotechnology advances allowed to gather a huge amount of biological data. This data ranges from genome composition to the chemical interactions occurring in the cell. Such huge amount of information requires the application of complex algorithms to reveal how they are organized in order to understand the underlying biology. The metabolism forms a class of very complex data and the graphs that represent it are composed of thousands of nodes and edges. In this thesis we propose an approach to modularize such networks to reveal their internal organization. We have analyzed red blood cells' networks corresponding to pathological states and the obtained in-silico results were corroborated by known in-vitro analysis. In the second part of the thesis we describe a learning method that analyzes thousands of sequences from the UniProt database to predict the N-alpha-terminal acetylation. This is done by automatically discovering discriminant motifs that are combined in a binary decision tree manner. Prediction performances on N-alpha-terminal acetylation are higher than the other published classifiers. Reference CHARPILLOZ, Christophe. Analysis of large biological data: metabolic network modularization and prediction of N-terminal acetylation. Thèse de doctorat : Univ. Genève, 2015, no. Sc. 4883 URN : urn:nbn:ch:unige-860463 DOI : 10.13097/archive-ouverte/unige:86046 Available -
Computational Modeling to Design and Analyze Synthetic Metabolic Circuits
Computational modeling S467 to design and SACL 9 analyze : 201 synthetic NNT metabolic circuits Thèse de doctorat de l'Université Paris-Saclay préparée à l’Université Paris -Sud École doctorale n°577 Structure et Dynamique des Systèmes Vivants (SDSV) Spécialité de doctorat: Sciences de la Vie et de la Santé Thèse présentée et soutenue à Jouy-en-Josas, le 28/11/19, par Mathilde Koch Composition du Jury : Joerg Stelling Professeur, ETH Zurich (Department of Biosystems Science and Engineering) Président et Rapporteur Daniel Kahn Directeur de Recherche, INRA (UAR 1203, Département Mathématiques et Informatique Appliquées) Rapporteur Gregory Batt Directeur de Recherche, INRIA Examinateur Olivier Sperandio Directeur de Recherche, Institut Pasteur Examinateur Wolfram Liebermeister Chargé de Recherche, INRA (UR1404, MaIAGE, Université Paris-Saclay, Jouy-en-Josas) Examinateur Jean-Loup Faulon Directeur de Recherche, INRA (UMR 1319, Micalis, AgroParisTech, Université Paris-Saclay) Directeur de thèse Abstract The aims of this thesis are two-fold, and centered on synthetic metabolic cir- cuits, which perform sensing and computation using enzymes. The first part consisted in developing reinforcement and active learning tools to improve the design of metabolic circuits and optimize biosensing and bioproduction. In order to do this, a novel algorithm (RetroPath3.0) based on similarity- guided Monte Carlo Tree Search to improve the exploration of the search space is presented. This algorithm, combined with data-derived reaction rules and varying levels of enzyme promiscuity, allows to focus exploration toward the most promising compounds and pathways for bio-retrosynthesis. As retrosynthesis-based pathways can be implemented in whole cell or cell- free systems, an active learning method to efficiently explore the combinato- rial space of components for rational buffer optimization was also developed, to design the best buffer maximizing cell-free productivity. -
Module Kwalitee YAPC Europe 2007
Module Kwalitee YAPC Europe 2007 v2.0 (translated, edited & augmented from French Perl Workshop 2006 talk) YAPC 2007, Vienna, August 28th–30th, 1 Xavier Caron <[email protected]> Module Kwalitee “Kwalitee”? ✗ Definition attempt ✗ “Kwalitee” is an approximation of “Quality” ✗ Nobody knows what it is actually... ✗ Anyway, we believe we're able to recognize it when we see it! ✗ It's mainly a matter of confidence ✗ Built through passed tests (but it's not enough as we'll see later) ✗ Yet, absence of bugs (read “unfound”) does not imply Kwalitee! ✗ Although a correlation exists if tests functional coverage is decent ✗ “Go ahead bug, make my day!” ✗ A bug is a difference between expectation and implementation ✗ It is also a difference between test, documentation & code ✗ If documentation is missing, this is a bug indeed! YAPC 2007, Vienna, August 28th–30th, 2 Xavier Caron <[email protected]> Module Kwalitee Achtung! * Tr ** Tr u (i th u n i th c s, lu is N d th in er O g t e T h i out i s s no t on h e)**tr er u e! th . YAPC 2007, Vienna, August 28th–30th, 3 Xavier Caron <[email protected]> Module Kwalitee When & What 1 ✗ Ages before ✗ Literature ✗ CPAN ✗ Articles, conferences, /Perl Mon(k|ger)s/, etc. ✗ “Read. Learn. Evolve.” – Klortho the Magnificent ✗ Before ✗ Generate module skeleton ✗ Use an OO class builder (if applicable) ✗ Write tests (a tad of XP in your code) ✗ While (coding) ✗ Document in parallel (and why not, before?) ✗ Add more tests if required YAPC 2007, Vienna, August 28th–30th, 4 Xavier Caron <[email protected]> Module Kwalitee When & What 2 ✗ After (between coding & release) ✗ Test (test suite – acceptance and non-regression) ✗ Measure POD coverage ✗ Measure tests code coverage ✗ Measure tests functional coverage (Ha! Ha!) ✗ Generate synthetic reports ✗ For one-glance checking purposes or for traceability's sake ✗ Way after (release) ✗ Refactor early, refactor often ✗ Test suite (non-regression) should ensure nothing got broken in the process ✗ Following a bug report.. -
An Introduction to Perl for Bioinformatics
An Introduction to Perl for bioinformatics C. Tranchant-Dubreuil, F. Sabot UMR DIADE, IRD June 2015 1 / 98 Sommaire 1 Introduction Objectives What is programming ? What is perl ? Why used Perl ? Perl in bioinformatics Running a perl script 2 Perl in detail 2 / 98 • To empower you with the basic knowledge required to quickly and effectively create simple scripts to process biological data • Write your own programs once time, use many times Objectives • To demonstrate how Perl can be used in bioinformatics 3 / 98 • Write your own programs once time, use many times Objectives • To demonstrate how Perl can be used in bioinformatics • To empower you with the basic knowledge required to quickly and effectively create simple scripts to process biological data 3 / 98 Objectives • To demonstrate how Perl can be used in bioinformatics • To empower you with the basic knowledge required to quickly and effectively create simple scripts to process biological data • Write your own programs once time, use many times 3 / 98 • Programming languages : bridges between human languages (A-Z) and machine languages (0&1) • Compilers convert programming languages to machine languages What is programming • Programs : a set of instructions telling computer what to do 4 / 98 • Compilers convert programming languages to machine languages What is programming • Programs : a set of instructions telling computer what to do • Programming languages : bridges between human languages (A-Z) and machine languages (0&1) 4 / 98 What is programming • Programs : a set of instructions