DOCSLIB.ORG

MAGPIE: Simplifying Access and Execution of Computational Models in the Life Sciences

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
MAGPIE: Simplifying Access and Execution of Computational Models in the Life Sciences RESEARCH ARTICLE MAGPIE: Simplifying access and execution of computational models in the life sciences Christoph Baldow1☯, Sebastian Salentin2☯, Michael Schroeder2, Ingo Roeder1,3, Ingmar Glauche1* 1 Institute for Medical Informatics and Biometry, Medizinische FakultaÈt Carl Gustav Carus, Technische UniversitaÈt Dresden, Dresden, Germany, 2 Biotechnology Center (BIOTEC), Technische UniversitaÈt Dresden, Dresden, Germany, 3 National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany a1111111111 ☯ These authors contributed equally to this work. a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Over the past decades, quantitative methods linking theory and observation became increasingly important in many areas of life science. Subsequently, a large number of mathe- OPEN ACCESS matical and computational models has been developed. The BioModels database alone lists more than 140,000 Systems Biology Markup Language (SBML) models. However, while the Citation: Baldow C, Salentin S, Schroeder M, Roeder I, Glauche I (2017) MAGPIE: Simplifying exchange within specific model classes has been supported by standardisation and data- access and execution of computational models in base efforts, the generic application and especially the re-use of models is still limited by the life sciences. PLoS Comput Biol 13(12): practical issues such as easy and straight forward model execution. MAGPIE, a Modeling e1005898. https://doi.org/10.1371/journal. pcbi.1005898 and Analysis Generic Platform with Integrated Evaluation, closes this gap by providing a software platform for both, publishing and executing computational models without restric- Editor: TimotheÂe Poisot, Universite de Montreal, CANADA tions on the programming language, thereby combining a maximum on flexibility for pro- grammers with easy handling for non-technical users. MAGPIE goes beyond classical Received: July 20, 2017 SBML platforms by including all models, independent of the underlying programming lan- Accepted: November 27, 2017 guage, ranging from simple script models to complex data integration and computations. We Published: December 15, 2017 demonstrate the versatility of MAGPIE using four prototypic example cases. We also outline Copyright: © 2017 Baldow et al. This is an open the potential of MAGPIE to improve transparency and reproducibility of computational mod- access article distributed under the terms of the els in life sciences. A demo server is available at magpie.imb.medizin.tu-dresden.de. Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This is a PLOS Computational Biology Software paper. Data Availability Statement: The source code of the latest server application can be downloaded from the GitHub repository at https://github.com/ christbald/magpie. Furthermore, the source code at Introduction the time of publication can be found at https:// zenodo.org/record/1044034. The corresponding R Although the development and use of computational models is gaining more and more impor- package, providing a remote access to MAGPIE, is tance in the era of biological and big data, there is a distinct gap between the development of available at https://github.com/christbald/magpie_ computational models by theoreticians and their application by end users in experimental api_r. research or clinical practice [1±3]. In many cases, technical issues limit the application of Funding: This work was partly supported by the computational approaches: models commonly lack an easily accessible user interface or German Federal Ministry of Education and require advanced programming skills on the side of the end user. Furthermore, the limited PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1005898 December 15, 2017 1 / 11 MAGPIE: Simplifying access and execution of computational models Research (www.bmbf.de/en/), Grant number access to models, or missing versioning of underlying algorithms, data, and parameters lead to 031A315 ªMessAgeº to IG and Grant number model developments, which in many cases can not be easily reproduced [4, 5]. In a recent sur- 031A424 ªHaematoOptº to IR. The funders had no vey conducted by Nature, more than half of the participating researchers believed that there is role in study design, data collection and analysis, decision to publish, or preparation of the a significant crisis in model and data reproducibility [6]. Our platform MAGPIE addresses this manuscript. issue by providing a single platform where researchers from different domains can publish, exchange and execute models on-line (Fig 1) as well as publish and exchange data. Competing interests: The authors have declared that no competing interests exist. In the past, there have been several approaches to provide a unified platform for computa- tional models in the biological domain: Standardised description languages for models, fore- most SBML (Systems Biology Markup Language) [7, 8], but also CellML [9], NeuroML [10] or MultiCellDS [11] and associated model databases such as BioModels [12] provide platforms to store and exchange standardised models. The Cardiac Electrophysiology Web Lab [13] is a fur- ther example of a database for standardised models, which allows to compare model behaviour under different conditions. Such tailor-made approaches for the description of specific pro- cesses are valuable for specific domains, but impose restrictions on other applications and their interoperatibility. Going one step further, workflow tools such as Taverna or GALAXY [14, 15] are application-oriented and help the user to integrate multiple analysis steps. Here, it is possible to combine SBML models, custom scripts, and web services. While this approach is powerful, the platforms themselves bring a high overhead when it comes to simple applications and may be unintuitive for inexperienced users. On the other side of the software spectrum, social networks for scientists, e.g. ResearchGate or Mendeley, aim to make individual research more visible by allowing the exchange of publications and expertise. However, they do not cur- rently offer to share and publish data-driven analyses or modelling approaches. The main objective of MAGPIE is to provide a user-friendly system to publish, version, access and execute models in an environment that is accessible for different end users. Con- trary to the idea of developing a new modelling standard, different types of computational Fig 1. Collaborative research with MAGPIE. Physicians and biologists (left) can use models provided by computational experts (right) to analyse their data in MAGPIE (center). The central element of the platform comprises a computing framework and a model database. https://doi.org/10.1371/journal.pcbi.1005898.g001 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1005898 December 15, 2017 2 / 11 MAGPIE: Simplifying access and execution of computational models models can be uploaded with minimal preparation. While MAGPIE also supports SBML, it puts no restrictions on programming languages or frameworks. The focus for model execution is not on complex workflows, but on one-click execution of single models. This makes it easy for end users to apply algorithms that have been previously deposited by computational experts. A hashtag-based system allows to share results and projects with other users. The central layers of MAGPIE are a repository of models and analysis tools, a project-ori- ented access to the models that allows changing parameter configurations and data input, pro- gram execution, visualization of results, as well as a twitter-like hashtag system to simplify the sharing of results increasing the visibility of individual researchers. Automated version control, remote access, and virtualization are available by default. Design and implementation MAGPIE server MAGPIE was implemented in Ruby on Rails 5. The public demo server is based on an nginx [16] environment in combination with foreman [17], Phusion Passenger [18], and Sidekiq [19] for simplified application management. Furthermore, it allows flexible scaling of MAGPIE for local installations and distributed cluster environments. The demo server uses PostgreSQL [20] as a database backend system. Security and virtualization MAGPIE ensures security features such as separateness, reproducibility and computation security, thereby allowing to be applied in systems medicine and potentially in clinical practice. It is implemented in a privacy-oriented fashion, such that everything a user wants to share has to be published explicitly. Additionally, MAGPIE relies on Docker [21] virtualization for exe- cuting jobs using docker-api for Rails. This brings the advantage of separateness and at the same time it can be ensured that a model can not harm the host system (e.g. the web server itself). The Docker containers also provide lightweight virtual model execution environments. Administrators of MAGPIE can install components and programming languages in these con- tainers to be used by the models or completely exchange the execution environment. Addi- tionally, they can use a role-based access control system. Version control The storage of models and corresponding data is organized by the repository system git to enable full reproducibility of calculated results. Whenever a new model is uploaded or an exist- ing model is updated, a new git repository is created or the existing model
Load more

Recommended publications
  • Interfacing Apache HTTP Server 2.4 with External Applications
    Interfacing Apache HTTP Server 2.4 with External Applications Jeff Trawick Interfacing Apache HTTP Server 2.4 with External Applications Jeff Trawick November 6, 2012 Who am I? Interfacing Apache HTTP Server 2.4 with External Applications Met Unix (in the form of Xenix) in 1985 Jeff Trawick Joined IBM in 1990 to work on network software for mainframes Moved to a different organization in 2000 to work on Apache httpd Later spent about 4 years at Sun/Oracle Got tired of being tired of being an employee of too-huge corporation so formed my own too-small company Currently working part-time, coding on other projects, and taking classes Overview Interfacing Apache HTTP Server 2.4 with External Applications Jeff Trawick Huge problem space, so simplify Perspective: \General purpose" web servers, not minimal application containers which implement HTTP \Applications:" Code that runs dynamically on the server during request processing to process input and generate output Possible web server interactions Interfacing Apache HTTP Server 2.4 with External Applications Jeff Trawick Native code plugin modules (uhh, assuming server is native code) Non-native code + language interpreter inside server (Lua, Perl, etc.) Arbitrary processes on the other side of a standard wire protocol like HTTP (proxy), CGI, FastCGI, etc. (Java and \all of the above") or private protocol Some hybrid such as mod fcgid mod fcgid as example hybrid Interfacing Apache HTTP Server 2.4 with External Applications Jeff Trawick Supports applications which implement a standard wire protocol, no restriction on implementation mechanism Has extensive support for managing the application[+interpreter] processes so that the management of the application processes is well-integrated with the web server Contrast with mod proxy fcgi (pure FastCGI, no process management) or mod php (no processes/threads other than those of web server).
    [Show full text]
  • Integrating Openshift Enterprise with Identity Management (Idm) in Red Hat Enterprise Linux
    Integrating OpenShift Enterprise with Identity Management (IdM) in Red Hat Enterprise Linux OpenShift Enterprise 2.2 IdM in Red Hat Enterprise Linux 7 Windows Server 2012 - Active Directory Integration Mark Heslin Principal Systems Engineer Version 1.1 January 2015 1801 Varsity Drive™ Raleigh NC 27606-2072 USA Phone: +1 919 754 3700 Phone: 888 733 4281 Fax: +1 919 754 3701 PO Box 13588 Research Triangle Park NC 27709 USA Linux is a registered trademark of Linus Torvalds. Red Hat, Red Hat Enterprise Linux and the Red Hat "Shadowman" logo are registered trademarks of Red Hat, Inc. in the United States and other countries. Microsoft and Windows are U.S. registered trademarks of Microsoft Corporation. UNIX is a registered trademark of The Open Group. Intel, the Intel logo and Xeon are registered trademarks of Intel Corporation or its subsidiaries in the United States and other countries. All other trademarks referenced herein are the property of their respective owners. © 2014 by Red Hat, Inc. This material may be distributed only subject to the terms and conditions set forth in the Open Publication License, V1.0 or later (the latest version is presently available at http://www.opencontent.org/openpub/). The information contained herein is subject to change without notice. Red Hat, Inc. shall not be liable for technical or editorial errors or omissions contained herein. Distribution of modified versions of this document is prohibited without the explicit permission of Red Hat Inc. Distribution of this work or derivative of this work in any standard (paper) book form for commercial purposes is prohibited unless prior permission is obtained from Red Hat Inc.
    [Show full text]
  • Insight: Semantic Provenance and Analysis Platform for Multi-Center Neurology Healthcare Research
    INSIGHT: SEMANTIC PROVENANCE AND ANALYSIS PLATFORM FOR MULTI-CENTER NEUROLOGY HEALTHCARE RESEARCH by PRIYA RAMESH Submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Department of Electrical Engineering and Computer Science CASE WESTERN RESERVE UNIVERSITY January, 2016 ii CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis of PRIYA RAMESH candidate for the Master of Science degree*. (signed) Dr. Satya S. Sahoo, Ph.D. (Chair of the committee) Dr. Kenneth A. Loparo, Ph.D. Dr. Martha Sajatovic, MD. (date) November 5th, 2015 *We also certify that written approval has been obtained for any proprietary material contained therein. iii Copyright © Priya Ramesh January, 2016 All rights reserved. iv TABLE OF CONTENTS TABLE OF CONTENTS iv LIST OF FIGURES vi LIST OF TABLES vii ACKNOWLEDGEMENT viii CHAPTER 1. INTRODUCTION 10 CHAPTER 2. BACKGROUND 13 2.1 Managing Epilepsy Well Network 13 2.1.1 Introduction 13 2.1.2 MEW database workgroup 16 2.1.3 MEW Network survey results 17 2.1.4 A common terminology for epilepsy self-management 19 2.1.5 Standardization of data elements 20 2.1.6 Data curation workflow for MEW Network datasets 21 2.1.7 MEW Network database design and functionality 26 2.2 Research Studies 27 CHAPTER 3. METHODS 30 3.1. Semantic Integration Module using MEW Common Data Elements (CDEs) 33 3.2. Data Exploration and Query Module 34 3.3. Ontology-based Inference Module 36 CHAPTER 4. INSIGHT SOFTWARE DEVELOPMENT 38 4.1 Objective 38 4.2 Agile Methodology 39 4.3 User Interface Development 41 CHAPTER 5.
    [Show full text]
  • Vasili Korol
    Vasili Korol Senior Software Developer Odense, Denmark Age: 35 mob.: +45 20 68 50 23 Married, have son (born 2010) e-mail: [email protected] ​ Personal Statement ⚬ Strong IT skills (16+ years of versatile experience) ⚬ Background in physics research ⚬ Work effectively both as team member and leader ⚬ Enthusiastic and committed ⚬ Spoken languages: Russian (native), English (fluent), Danish (Prøve i Dansk 3 / level B2) ​ ​ ​ ​ Education 2006–2008: Master’s degree (with distinction) in applied physics. ​ 2002–2006: Bachelor’s degree (with distinction) in applied physics. Under- to postgraduate student at St. Petersburg State Polytechnical University, Faculty of Physics and Technology, Dept. of Cosmic Physics. The thesis “Search for possible space-time variations of the fine-structure constant and isotopic shifts” (a supervisor Prof. ​ M.G. Kozlov). ​ 1992-2002: School education in St. Petersburg, Russia and Belfast, UK (in 1993). Professional Career 2015 – Feb 2021: Software developer in the QuantBio research group at the University of ​ ​ ​ ​ Southern Denmark (SDU), Institute of Physics, Chemistry and Pharmacy (HPC section). I am the principal developer of VIKING, a service providing a web interface for configuring ​ ​ ​ and running scientific computational tasks on supercomputers. I designed the software architecture, developed the system core and coordinated the work of several developers. 2014 – 2015: Lead programmer (Perl) at Internet Projects LLC, russian informational portals subscribe.ru and sendsay.ru (St. Petersburg, Russia). ​ ​ ​ Worked with a team of developers on projects targeted at developing an API for news aggregation and content processing services. This involved integration with various online platforms (Facebook, Twitter, Vkontakte, LiveJournal, Google Analytics), web scraping and designing instruments for user publications at the portals and beyond.
    [Show full text]
  • Configuration Management at the Los Alamos National Laboratory
    Mac Configuration Management at the Los Alamos National Laboratory By Allan Marcus April, 2010 Overview.....................................................................................................................................1 The Challenge ...........................................................................................................................2 Product Selection.....................................................................................................................3 Getting Started..........................................................................................................................7 Basic Implementation............................................................................................................8 Configuration Management .............................................................................................. 14 Advanced Implementation................................................................................................ 16 How LANL uses Puppet ....................................................................................................... 20 Lessons Learned ................................................................................................................... 24 About the Author .................................................................................................................. 29 Appendix 1: puppet.sh........................................................................................................ 30 Appendix
    [Show full text]
  • Version Control Graphical Interface for Open Ondemand
    VERSION CONTROL GRAPHICAL INTERFACE FOR OPEN ONDEMAND by HUAN CHEN Submitted in partial fulfillment of the requirements for the degree of Master of Science Department of Electrical Engineering and Computer Science CASE WESTERN RESERVE UNIVERSITY AUGUST 2018 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of Huan Chen candidate for the degree of Master of Science Committee Chair Chris Fietkiewicz Committee Member Christian Zorman Committee Member Roger Bielefeld Date of Defense June 27, 2018 TABLE OF CONTENTS Abstract CHAPTER 1: INTRODUCTION ............................................................................ 1 CHAPTER 2: METHODS ...................................................................................... 4 2.1 Installation for Environments and Open OnDemand .............................................. 4 2.1.1 Install SLURM ................................................................................................. 4 2.1.1.1 Create User .................................................................................... 4 2.1.1.2 Install and Configure Munge ........................................................... 5 2.1.1.3 Install and Configure SLURM ......................................................... 6 2.1.1.4 Enable Accounting ......................................................................... 7 2.1.2 Install Open OnDemand .................................................................................. 9 2.2 Git Version Control for Open OnDemand
    [Show full text]
  • Websocket Notifier
    Università degli Studi di Padova Dipartimento di Matematica Corso di Laurea in Informatica WebSocket Notifier: una RubyGem basata su WebSocket Tesi di laurea triennale Relatore Prof. Tullio Vardanega Laureando Federico Gobbo Anno Accademico 2015–2016 Federico Gobbo: WebSocket Notifier: una RubyGem basata su WebSocket, Tesi di laurea triennale, c Oct 2016. Sommario Il presente documento rappresenta la relazione finale dell’esperienza di stage condotta nell’azienda Si14 Spa. Esso è organizzato in quattro capitoli: 1. Descrizione dell’azienda: le origini, la natura, il mercato, i processi aziendali; 2. Le motivazioni alla base dell’esperienza di stage: i punti di vista dei portatori di interesse, ovvero l’azienda, l’università e il sottoscritto; 3. Presentazione del progetto di stage: processi e prodotti; 4. Valutazione retrospettiva sull’esperienza di stage. Convenzioni tipografiche Nel testo vengono utilizzate delle convenzioni tipografiche col seguente significato: • Corsivo: termine in lingua inglese; • Grassetto: termine rilevante; • Verbatim: nomi di file, codice; • Glossariojgj: termine presente nel glossario; • Riferimento1: termine associato a un riferimento bibliografico. iii “Make the best of the situation” — Eric Clapton Ringraziamenti Vorrei ringraziare il Prof. Tullio Vardanega, relatore della mia tesi, per l’aiuto, i buoni consigli e la disponibilità che ha dimostrato nei miei confronti. Ringrazio la mia famiglia, la mia ragazza e i miei amici per avermi permesso, col loro sostegno, di raggiungere questo traguardo. Padova, Oct 2016 Federico Gobbo v Indice 1 L’azienda: Si141 1.1 Storia . .1 1.2 Contesto aziendale . .1 1.2.1 I vantaggi dell’ecosistema M31 . .2 1.2.2 Tecnologia e innovazione . .2 1.2.3 Spin-off aziendali .
    [Show full text]
  • Le Web Social Table Des Matières
    Le Web Social Table des matières 1 Web social 1 1.1 Historique ............................................... 1 1.2 L'évolution du web social ....................................... 1 1.2.1 Blogs et wiki ......................................... 1 1.2.2 L'art social .......................................... 2 1.2.3 Le crowdsourcing ...................................... 2 1.2.4 Le développement d'applications mobiles .......................... 2 1.2.5 Des projets de logiciels communautaires ........................... 2 1.3 Du web social à la vie réelle ..................................... 2 1.4 Bibliographie ............................................. 3 1.5 Notes et références .......................................... 3 1.6 Voir aussi ............................................... 3 2 Réseautage social 4 2.1 Histoire ................................................ 4 2.2 Applications .............................................. 4 2.3 Modèle économique ......................................... 5 2.3.1 Commerce des données ................................... 5 2.3.2 Vente d'espaces publicitaires ................................. 5 2.3.3 Cession des actifs ....................................... 5 2.4 Domaines d'application ........................................ 5 2.4.1 Réseaux internes versus réseaux externes ........................... 6 2.4.2 Services en ligne de réseautage professionnels ........................ 6 2.4.3 Réseaux sociaux d'amis de la vie réelle ............................ 6 2.4.4 Services en ligne d'ancien
    [Show full text]
  • Rails Connector for CMS Fiona Infopark CMS Fiona Rails Connector for CMS Fiona
    Infopark CMS Fiona Rails Connector for CMS Fiona Infopark CMS Fiona Rails Connector for CMS Fiona While every precaution has been taken in the preparation of all our technical documents, we make no expressed or implied warranty of any kind and assume no responsibility for errors or omissions. No liability is assumed for incidental or consequential damages in connection with or arising out of the use of the information or programs contained herein. All trademarks and copyrights referred to in this document are the property of their respective owners. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form, or by any means, electronic, mechanical, photocopying, recording, or otherwise, without our prior consent. Contents 1 Concepts . 7 1.1 Moving to Rails? . 7 1.1.1 Editorial and Live System . 7 1.1.2 Editorial Content and Layout are Handled Equally . 7 1.1.3 The Classical Live System is heterogeneous . 8 1.1.4 Ruby on Rails is an Integrated Framework . 8 1.1.5 Moving to Ruby on Rails . 8 1.1.6 Frequently Asked Questions About Moving to Rails . 9 1.2 What Is Ruby on Rails? . 10 1.3 Functions of Infopark Rails Connector . 11 1.4 Usage Scenarios for the Rails Connector . 11 1.5 The Playland Demo Application . 12 1.6 The Layout of a Rails Application . 18 1.7 Deployment . 18 1.8 CMS Layouts as Extensible Page Types . 19 1.9 Dedicated Controllers for Specific CMS File Formats . 20 1.10 Using the Rails Application as a Preview Server .
    [Show full text]
  • Read My Resume
    Eli Thorkelson [email protected] github.com/decasia TL;DR I’m a full-stack web software engineer with a doctorate in cultural anthropology. I’m currently doing back-end development for the Nebo Agency in Atlanta, where I’ve had a special focus on improving testing and web stack performance in our client projects. I previously designed and built more than a dozen Ruby on Rails applications for the University of Chicago’s Humanities Division. I’ve maintained Linux servers, web software stacks, and relational and NoSQL databases; I’m especially interested in software design patterns and user interfaces. I recently returned to software after a few years in academic teaching and research. TECHNICAL SKILLS Languages: Ruby, PHP, Python, SQL; HTML, CSS, Javascript; college coursework in Java and C++. Web development frameworks: Ruby on Rails (~7 years), Drupal 6/7/8, Node.js, WordPress. Databases: PostgreSQL, MySQL, SQLite, Mongo, Redis. Web front end: Ember.js, jQuery, d3.js, Freeboard, Mobiledoc, jPlayer, PanoJS, Bootstrap; SASS, CoffeeScript/ES6. Web server software: Apache, Nginx, Phusion Passenger, Apache Solr, Nagios, Ansible, Shibboleth SP. Development software: Cucumber, RSpec, qUnit; Git (GitHub/GitLab/BitBucket); Asana. Web services: AWS, DigitalOcean, EngineYard, Algolia, New Relic, Mailchimp, Mailgun. EMPLOYMENT Feb 2020– Back End Web and Applications Engineer, Nebo Agency, Atlanta Built websites and web applications (mainly Ruby and PHP), maintained web servers and database systems. Interfaced with clients and internal project teams, provided estimates for engineering tasks. Improved server response times by 10x on a high-profile client project (down to <200ms from over 2000ms). Built an OSX native application for internal task management (in Swift).
    [Show full text]
  • TPR01: Higher Ed on Rails Sven Aas, Web Team Lead, Mount Holyoke College, [email protected]
    TPR01: Higher Ed on Rails Sven Aas, Web Team Lead, Mount Holyoke College, [email protected] Links to presentation materials and additional information will be available at my website: http://www.mtholyoke.edu/~saas/ This is an incomplete and highly subjective set of lists, but I hope it will be a useful resource: Resources for Ruby and Rails Training Materials Official sites Online Training Materials Ruby (use 1.8.x for production, for now): Why's (Poignant) Guide to Ruby: http://www.ruby-lang.org/ http://poignantguide.net/ruby/ Rails: PeepCode Screencasts: http://www.rubyonrails.org/ http://peepcode.com/ Official News Books on Ruby Ruby News: Programming Ruby, 3rd Edition http://www.ruby-lang.org/en/news/ 2008, by D. Thomas, C. Fowler, and A. Hunt Riding Rails: http://weblog.rubyonrails.org/ The Ruby Way, 2nd Edition 2006, by H. Fulton Other Good Blogs Ruby Inside: The Ruby Programming Language http://www.rubyinside.com/ 2008, by D. Flanagan and Y. Matsumoto Giant Robots …: http://giantrobots.thoughtbot.com/ Books on Rails Rail Spikes: Agile Web Development with Rails, 3rd Edition http://railspikes.com/ 2008, by S. Ruby, D. Thomas, D. Hansson Rails Envy: http://www.railsenvy.com/ The Rails Way Railscasts: 2007, by O. Fernandez http://railscasts.com/ Rails Recipes 2006, by C. Fowler Advanced Rails Recipes 2008, by M. Clark Copyright 2008, Sven Aas Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License TPR01: Higher Ed on Rails Sven Aas, Web Team Lead, Mount Holyoke College, [email protected] Rails Tool Chain
    [Show full text]
  • Deploying and Monitoring Ruby on Rails a Practical Guide
    Mit hotfixes von Carsten Bormann 2011-03-05 + 2013-02-28 Deploying and Monitoring Ruby on Rails A practical guide Mathias Meyer and Jonathan Weiss, 25.05.2009 Danke! Peritor GmbH Mashed up with... 2011-03-05 Deployment/Scaling/ Caching/Debugging jan krutisch mindmatters gmbh&co. kg [email protected] http://mindmatters.de Deployment Real artists ship! Komponenten client (Browser) rails database client Heute: (Browser) ➔ railsthin mongrel (∨database unicorn) mongrel ist schnell apache ist schneller client webserver rails Dateisystem public/ database rails ist nicht threadsafe client rails webserver rails database Dateisystem rails public/ webserver rails webserver rails oldschool: CGI / SCGI / FastCGI newschool: http mongrel versus... mod_proxy_balancer (in Apache/nginx/lighttpd) oder ein richtiger proxy oder ein richtiger balancer Varnish HAProxy, Squid, etc. true school: passenger Apache-Modul client rails webserver rails database rails Dateisystem public/ mod_passenger automagisch. it just works. http://modrails.com Infrastructure Infrastructure 5 Simple Rails Setup One Rails instance handles all requests Rails is single-threaded: There is only one concurrent request 6 Rails Setup 7 Rails Setup 8 Typical Rails Setup •! A load-balancer distributes the incoming requests •! Some load-balancers will deliver static requests themselves •! Several Rails instances handle all requests •! Number of concurrent requests equals number of Rails instances 9 Rails Setup Options 10 Deployment Questions Apache? Pound? mod_proxy_balancer? FastCGI? Mongrel? Proxy? Load-balancer? Nginx? mod_rails? Ebb? HA-Proxy? Reverse Proxy? Swiftiply? Phusion Passenger? Thin? Pen? Rails Application Server? Lighttpd? 11 What we are going to cover today Rails Application Server Proxy/Web Server •! FastCGI •! Apache2 •! Mongrel •! Nginx •! mod_rails / Phussion Passenger •! Lighttpd •! JRuby + Glassfish & Co.
    [Show full text]