Using Web Frameworks for Scientific Applications
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Open Source Web GUI Toolkits
Open Source Web GUI Toolkits "A broad and probably far too shallow presentation on stuff that will probably change 180 degrees by the time you hear about it from me" Nathan Schlehlein [email protected] 1 Why Web Developers Drink... Can't get away with knowing one thing A Fairly Typical Web App... ➔ MySQL – Data storage ➔ PHP – Business logic ➔ Javascript - Interactivity ➔ HTML – Presentation stuff ➔ CSS – Presentation formatting stuff ➔ Images – They are... Purdy... ➔ httpd.conf, php.ini, etc. Problems are liable to pop up at any stage... 2 The Worst Thing. Ever. Browser Incompatibilities! Follow the rules, still lose Which is right? ➔ Who cares! You gotta make it work anyways! Solutions More work or less features? ➔ Use browser-specific stuff - Switch via Javascript ➔ Use a subset of HTML that most everyone agrees on 3 Web Application? Web sites are... OK, but... Boring... Bounce users from page to page Stuff gets messed up easily ➔ Bookmarks? Scary... ➔ Back button 4 Why A Web Toolkit? Pros: Let something else worry about difficult things ➔ Layout issues ➔ Session management ➔ Browser cross-compatibility ➔ Annoying RPC stuff 5 >INSERT BUZZWORD HERE< Neat web stuff has been happening lately... AJAX “Web 2.0” Google maps Desktop app characteristics on the web... 6 Problem With >BUZZWORDS< Nice, but... Lots of flux ➔ Technology ➔ Expectations of technology Communications can get tricky Yet another thing to program... ➔ (Correctly) 7 Why A Web Toolkit? Pros: Let something else worry about difficult things ➔ Communications management ➔ Tested Javascript code ➔ Toolkit deals with changes, not the programmer 8 My Criteria Bonuses For... A familiar programming language ➔ Javascript? Unit test capability ➔ Test early, test often, sleep at night Ability to incrementally introduce toolkit Compatibility with existing application Documentation Compelling Examples 9 Web Toolkits – Common Features ■ Widgets ■ Layouts ■ Manipulation of page elements DOM access, etc. -
Lightweight Django USING REST, WEBSOCKETS & BACKBONE
Lightweight Django USING REST, WEBSOCKETS & BACKBONE Julia Elman & Mark Lavin Lightweight Django LightweightDjango How can you take advantage of the Django framework to integrate complex “A great resource for client-side interactions and real-time features into your web applications? going beyond traditional Through a series of rapid application development projects, this hands-on book shows experienced Django developers how to include REST APIs, apps and learning how WebSockets, and client-side MVC frameworks such as Backbone.js into Django can power the new or existing projects. backend of single-page Learn how to make the most of Django’s decoupled design by choosing web applications.” the components you need to build the lightweight applications you want. —Aymeric Augustin Once you finish this book, you’ll know how to build single-page applications Django core developer, CTO, oscaro.com that respond to interactions in real time. If you’re familiar with Python and JavaScript, you’re good to go. “Such a good idea—I think this will lower the barrier ■ Learn a lightweight approach for starting a new Django project of entry for developers ■ Break reusable applications into smaller services that even more… the more communicate with one another I read, the more excited ■ Create a static, rapid prototyping site as a scaffold for websites and applications I am!” —Barbara Shaurette ■ Build a REST API with django-rest-framework Python Developer, Cox Media Group ■ Learn how to use Django with the Backbone.js MVC framework ■ Create a single-page web application on top of your REST API Lightweight ■ Integrate real-time features with WebSockets and the Tornado networking library ■ Use the book’s code-driven examples in your own projects Julia Elman, a frontend developer and tech education advocate, started learning Django in 2008 while working at World Online. -
Magnetic Silica Particles Functionalized with Guanidine Derivatives For
www.nature.com/scientificreports OPEN Magnetic silica particles functionalized with guanidine derivatives for microwave‑assisted transesterifcation of waste oil Petre Chipurici1,6, Alexandru Vlaicu1,2,6, Ioan Călinescu1, Mircea Vînătoru1, Cristina Busuioc1, Adrian Dinescu3, Adi Ghebaur1,4, Edina Rusen1, Georgeta Voicu1, Maria Ignat5 & Aurel Diacon1* This study aimed to develop a facile synthesis procedure for heterogeneous catalysts based on organic guanidine derivatives superbases chemically grafted on silica‑coated Fe3O4 magnetic nanoparticles. Thus, the three organosilanes that were obtained by reacting the selected carbodiimides (N,N′‑ dicyclohexylcarbodiimide (DCC), N,N′‑diisopropylcarbodiimide (DIC), respectively 1‑ethyl‑3‑(3‑ dimethylaminopropyl) carbodiimide (EDC) with 3‑aminopropyltriethoxysilane (APTES) were used in a one‑pot synthesis stage for the generation of a catalytic active protective shell through the simultaneous hydrolysis/condensation reaction with tetraethyl orthosilicate (TEOS). The catalysts were characterized by FTIR, TGA, SEM, BET and XRD analysis confrming the successful covalent attachment of the organic derivatives in the silica shell. The second aim was to highlight the capacity of microwaves (MW) to intensify the transesterifcation process and to evaluate the activity, stability, and reusability characteristics of the catalysts. Thus, in MW‑assisted transesterifcation reactions, all catalysts displayed FAME yields of over 80% even after 5 reactions/activation cycles. Additionally, the infuence of FFA content on the catalytic activity was investigated. As a result, in the case of Fe3O4@ SiO2‑EDG, a higher tolerance towards the FFA content can be noticed with a FAME yield of over 90% (for a 5% (weight) vs oil catalyst content) and 5% weight FFA content. Biodiesel can represent a suitable renewable alternative for the direct replacement of standard diesel fuels derived from petroleum sources1,2. -
Flask Documentation Release 0.7Dev July 14, 2014
Flask Documentation Release 0.7dev July 14, 2014 Contents I User’s Guide1 1 Foreword3 1.1 What does “micro” mean?...........................3 1.2 A Framework and an Example........................4 1.3 Web Development is Dangerous.......................4 1.4 The Status of Python 3.............................4 2 Installation7 2.1 virtualenv....................................7 2.2 System Wide Installation...........................8 2.3 Living on the Edge...............................9 2.4 easy_install on Windows............................9 3 Quickstart 11 3.1 A Minimal Application............................ 11 3.2 Debug Mode.................................. 12 3.3 Routing..................................... 13 3.4 Static Files.................................... 17 3.5 Rendering Templates.............................. 17 3.6 Accessing Request Data............................ 19 3.7 Redirects and Errors.............................. 22 3.8 Sessions..................................... 22 3.9 Message Flashing................................ 23 3.10 Logging..................................... 24 3.11 Hooking in WSGI Middlewares....................... 24 4 Tutorial 25 4.1 Introducing Flaskr............................... 25 4.2 Step 0: Creating The Folders......................... 26 4.3 Step 1: Database Schema........................... 27 4.4 Step 2: Application Setup Code........................ 27 i 4.5 Step 3: Creating The Database........................ 29 4.6 Step 4: Request Database Connections.................... 30 4.7 Step -
Wepgw003 High-Level Applications for the Sirius Accelerator Control System
10th Int. Particle Accelerator Conf. IPAC2019, Melbourne, Australia JACoW Publishing ISBN: 978-3-95450-208-0 doi:10.18429/JACoW-IPAC2019-WEPGW003 HIGH-LEVEL APPLICATIONS FOR THE SIRIUS ACCELERATOR CONTROL SYSTEM X. R. Resende ∗, F. H. de Sá, G. do Prado, L. Liu, A. C. Oliveira, Brazilian Synchrotron Light Laboratory (LNLS), Campinas, Brazil Abstract the sequence we detail the architecture of the HLA and its Sirius is the new 3 GeV low-emittance Brazilian Syn- current development status. Finally we describe how the chrotron Light source under installation and commissioning integration of the CS has been evolving during machine at LNLS. The machine control system is based on EPICS commissioning and end the paper with conclusion remarks and when the installation is complete it should have a few on what the next steps are in HLA development and testing. hundred thousand process variables in use. For flexible inte- gration and intuitive control of such sizable system a con- CONTROL SYSTEM OVERVIEW siderable number of high-level applications, input/output The Sirius accelerator control system (SCS) is based on controllers and graphical user interfaces have been devel- EPICS [3], version R3.15. All SCS software components oped, mostly in Python, using a variety of libraries, such are open-source solutions developed collaboratively using as PyEpics, PCASPy and PyDM. Common support service git version control and are publicly available in the Sirius applications (Archiver Appliance, Olog, Apache server, a organization page [4] at Github. mongoDB-based configuration server, etc) are used. Matlab The naming system used in Sirius for devices and CS prop- Middle Layer is also an available option to control EPICS erties is based on ESS naming system [5]. -
A Framework for Online Investment Algorithms
A framework for online investment algorithms A.B. Paskaramoorthy T.L. van Zyl T.J. Gebbie Computer Science and Applied Maths Wits Institute of Data Science Department of Statistical Science University of Witwatersrand University of Witwatersrand University of Cape Town Johannesburg, South Africa Johannesburg, South Africa Cape Town, South Africa [email protected] [email protected] [email protected] Abstract—The artificial segmentation of an investment man- the intermediation of human operators. As a result, workflows, agement process into a workflow with silos of offline human at least in finance, lack sufficient adaption since the update operators can restrict silos from collectively and adaptively rates are usually orders of magnitude slower that the informa- pursuing a unified optimal investment goal. To meet the investor objectives, an online algorithm can provide an explicit incremen- tion flow in actual markets. tal approach that makes sequential updates as data arrives at the process level. This is in stark contrast to offline (or batch) Additionally, the compartmentalisation of the components processes that are focused on making component level decisions making up the asset management workflow poses a vari- prior to process level integration. Here we present and report ety of behavioural challenges for system validation and risk results for an integrated, and online framework for algorithmic management. Human operators can be, both unintentionally portfolio management. This article provides a workflow that can in-turn be embedded into a process-level learning framework. and intentionally, incentivised to pursue outcomes that are The workflow can be enhanced to refine signal generation and adverse to the overall achievement of investment goals. -
Scalability in Web Apis
Worcester Polytechnic Institute Scalability in Web APIs Ryan Baker Mike Perrone Advised by: George T. Heineman 1 Worcester Polytechnic Institute 1 Introduction 2 Background 2.1 Problem Statement 2.2 Game Services and Tools 2.2.1 Graphics Engine 2.2.2 Map Editor 2.2.3 Friend Network 2.2.4 Achievements 2.2.5 Leaderboards 2.3 Our Service Definition 2.3.1 Leaderboards 2.4 Service Requirements 2.4.1 Administrative Ease 2.4.2 Security 2.4.3 Scalability 2.5 Internal Service Decisions 2.5.1 Application Framework 2.5.2 Cloud Computing 3 Methodology 3.1 Decisions of Design and Architecture 3.1.1 Leaderboards 3.1.2 API Documentation 3.1.3 Developer Console 3.1.4 Admin Console 3.1.5 Java Client Package 3.1.6 Logging 3.2 Decisions of Implementation 3.2.1 Enterprise vs Public 3.2.2 Front End Implementation 3.2.3 Cloud Computing Provider (AWS) 3.2.4 Web Application Framework Implementation (Flask) 3.2.5 Continuous Integration Service 3.2.6 API 3.2.7 Logging 3.2.8 Database Schema 4 Success Metrics 4.1 Resiliency 4.1.1 Simulated Traffic 4.1.2 Load Testing and Scalability 4.2 Design 4.2.1 Client Perspective 2 4.2.3 Admin Perspective 5 Conclusions & Future Work 5.1 Client Conclusions 5.2 Administrator Conclusions 5.3 The Future 6 References 7 Appendix A Why we chose Leaderboards B Facebook’s Game Development API C Playtomic’s API D Front End Tooling Decision E API Documentation Tool F Elastic Beanstalk 3 1 Introduction Game developers, especially those that make social games, undertake a large amount of work to create them. -
Evaluation and Optimization of ICOS Atmosphere Station Data As Part of the Labeling Process
Atmos. Meas. Tech., 14, 89–116, 2021 https://doi.org/10.5194/amt-14-89-2021 © Author(s) 2021. This work is distributed under the Creative Commons Attribution 4.0 License. Evaluation and optimization of ICOS atmosphere station data as part of the labeling process Camille Yver-Kwok1, Carole Philippon1, Peter Bergamaschi2, Tobias Biermann3, Francescopiero Calzolari4, Huilin Chen5, Sebastien Conil6, Paolo Cristofanelli4, Marc Delmotte1, Juha Hatakka7, Michal Heliasz3, Ove Hermansen8, Katerinaˇ Komínková9, Dagmar Kubistin10, Nicolas Kumps11, Olivier Laurent1, Tuomas Laurila7, Irene Lehner3, Janne Levula12, Matthias Lindauer10, Morgan Lopez1, Ivan Mammarella12, Giovanni Manca2, Per Marklund13, Jean-Marc Metzger14, Meelis Mölder15, Stephen M. Platt9, Michel Ramonet1, Leonard Rivier1, Bert Scheeren5, Mahesh Kumar Sha11, Paul Smith13, Martin Steinbacher16, Gabriela Vítková9, and Simon Wyss16 1Laboratoire des Sciences du Climat et de l’Environnement (LSCE-IPSL), CEA-CNRS-UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France 2European Commission Joint Research Centre (JRC), Via E. Fermi 2749, 21027 Ispra, Italy 3Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 223 62, Lund, Sweden 4National Research Council of Italy, Institute of Atmospheric Sciences and Climate, Via Gobett 101, 40129 Bologna, Italy 5Centre for Isotope Research (CIO), Energy and Sustainability Research Institute Groningen (ESRIG), University of Groningen, Groningen, the Netherlands 6DRD/OPE, Andra, 55290 Bure, France 7Finnish Meteorological Institute, -
Software Engineer – Wt and Jwt
Software Engineer – Wt and JWt Emweb is a software engineering company specialized in the development of innovative software. We are located in Herent (Leuven, Belgium) and serve customers all over the world. Emweb's major products are Wt, an open source library for the development of web applications, and Genome Detective, a software platform for microbial High Throughput Sequencing analysis. Our solutions excel in quality and efficiency, and are therefore applied in complex applications and environments. As we continuously grow, we are currently looking for new colleagues with the following profile to join our team in Herent. Your responsibility is to develop our own products, as well as to work on challenging customer projects and integrations. We are active in multiple applications domains: Web applications Bio-informatics, computational biology and molecular epidemiology Embedded software development Data Analysis, Modeling, Statistical Analysis, Digital Signal Processing Your responsibilities are: The design, development and maintenance of Wt and JWt You will regularly participate in development of our own software products, as well as projects for our customers Maintaining the quality, performance and scalability of the software Provide support and training to customers with respect to the use of Wt and JWt in their own applications (architectural questions, security analysis, bug reports, new features, …) With the following skills, you are the perfect match to complete our team: Master degree in informatics or computer -
Monitoring Wilderness Stream Ecosystems
United States Department of Monitoring Agriculture Forest Service Wilderness Stream Rocky Mountain Ecosystems Research Station General Technical Jeffrey C. Davis Report RMRS-GTR-70 G. Wayne Minshall Christopher T. Robinson January 2001 Peter Landres Abstract Davis, Jeffrey C.; Minshall, G. Wayne; Robinson, Christopher T.; Landres, Peter. 2001. Monitoring wilderness stream ecosystems. Gen. Tech. Rep. RMRS-GTR-70. Ogden, UT: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 137 p. A protocol and methods for monitoring the major physical, chemical, and biological components of stream ecosystems are presented. The monitor- ing protocol is organized into four stages. At stage 1 information is obtained on a basic set of parameters that describe stream ecosystems. Each following stage builds upon stage 1 by increasing the number of parameters and the detail and frequency of the measurements. Stage 4 supplements analyses of stream biotic structure with measurements of stream function: carbon and nutrient processes. Standard methods are presented that were selected or modified through extensive field applica- tion for use in remote settings. Keywords: bioassessment, methods, sampling, macroinvertebrates, production The Authors emphasize aquatic benthic inverte- brates, community dynamics, and Jeffrey C. Davis is an aquatic ecolo- stream ecosystem structure and func- gist currently working in Coastal Man- tion. For the past 19 years he has agement for the State of Alaska. He been conducting research on the received his B.S. from the University long-term effects of wildfires on of Alaska, Anchorage, and his M.S. stream ecosystems. He has authored from Idaho State University. His re- over 100 peer-reviewed journal ar- search has focused on nutrient dy- ticles and 85 technical reports. -
Impact Accounting for Product Use: a Framework and Industry-Specific Models
Impact Accounting for Product Use: A Framework and Industry-specific Models George Serafeim Katie Trinh Working Paper 21-141 Impact Accounting for Product Use: A Framework and Industry-specific Models George Serafeim Harvard Business School Katie Trinh Harvard Business School Working Paper 21-141 Copyright © 2021 by George Serafeim and Katie Trinh. Working papers are in draft form. This working paper is distributed for purposes of comment and discussion only. It may not be reproduced without permission of the copyright holder. Copies of working papers are available from the author. Funding for this research was provided in part by Harvard Business School. Impact Accounting for Product Use: A Framework and Industry-specific Models George Serafeim and Katie Trinh∗ Harvard Business School Impact-Weighted Accounts Project Research Report Abstract This handbook provides the first systematic attempt to generate a framework and industry-specific models for the measurement of impacts on customers and the environment from use of products and services, in monetary terms, that can then be reflected in financial statements with the purpose of creating impact-weighted financial accounts. Chapter 1 introduces product impact measurement. Chapter 2 outlines efforts to measure product impact. Chapter 3 describes our product impact measurement framework with an emphasis on the choice of design principles, process for building the framework, identification of relevant dimensions, range of measurement bases and the use of relative versus absolute benchmarks. Chapters 4 to 12 outline models for impact measurement in nine industries of the economy. Chapter 13 describes an analysis of an initial dataset of companies across the nine industries that we applied our models and constructed product impact measurements. -
Design and Evaluation of Interactive Proofreading Tools for Connectomics
Design and Evaluation of Interactive Proofreading Tools for Connectomics Daniel Haehn, Seymour Knowles-Barley, Mike Roberts, Johanna Beyer, Narayanan Kasthuri, Jeff W. Lichtman, and Hanspeter Pfister Fig. 1: Proofreading with Dojo. We present a web-based application for interactive proofreading of automatic segmentations of connectome data acquired via electron microscopy. Split, merge and adjust functionality enables multiple users to correct the labeling of neurons in a collaborative fashion. Color-coded structures can be explored in 2D and 3D. Abstract—Proofreading refers to the manual correction of automatic segmentations of image data. In connectomics, electron mi- croscopy data is acquired at nanometer-scale resolution and results in very large image volumes of brain tissue that require fully automatic segmentation algorithms to identify cell boundaries. However, these algorithms require hundreds of corrections per cubic micron of tissue. Even though this task is time consuming, it is fairly easy for humans to perform corrections through splitting, merging, and adjusting segments during proofreading. In this paper we present the design and implementation of Mojo, a fully-featured single- user desktop application for proofreading, and Dojo, a multi-user web-based application for collaborative proofreading. We evaluate the accuracy and speed of Mojo, Dojo, and Raveler, a proofreading tool from Janelia Farm, through a quantitative user study. We designed a between-subjects experiment and asked non-experts to proofread neurons in a publicly available connectomics dataset. Our results show a significant improvement of corrections using web-based Dojo, when given the same amount of time. In addition, all participants using Dojo reported better usability. We discuss our findings and provide an analysis of requirements for designing visual proofreading software.