Towards Rigorous Agent-Based Modelling Linking, Extending, and Using Existing Software Platforms
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
The Algebra of Open and Interconnected Systems
The Algebra of Open and Interconnected Systems Brendan Fong Hertford College University of Oxford arXiv:1609.05382v1 [math.CT] 17 Sep 2016 A thesis submitted for the degree of Doctor of Philosophy in Computer Science Trinity 2016 For all those who have prepared food so I could eat and created homes so I could live over the past four years. You too have laboured to produce this; I hope I have done your labours justice. Abstract Herein we develop category-theoretic tools for understanding network- style diagrammatic languages. The archetypal network-style diagram- matic language is that of electric circuits; other examples include signal flow graphs, Markov processes, automata, Petri nets, chemical reaction networks, and so on. The key feature is that the language is comprised of a number of components with multiple (input/output) terminals, each possibly labelled with some type, that may then be connected together along these terminals to form a larger network. The components form hyperedges between labelled vertices, and so a diagram in this language forms a hypergraph. We formalise the compositional structure by intro- ducing the notion of a hypergraph category. Network-style diagrammatic languages and their semantics thus form hypergraph categories, and se- mantic interpretation gives a hypergraph functor. The first part of this thesis develops the theory of hypergraph categories. In particular, we introduce the tools of decorated cospans and corela- tions. Decorated cospans allow straightforward construction of hyper- graph categories from diagrammatic languages: the inputs, outputs, and their composition are modelled by the cospans, while the `decorations' specify the components themselves. -
MODELLER 10.1 Manual
MODELLER A Program for Protein Structure Modeling Release 10.1, r12156 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/03/12 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
MODELLER 10.0 Manual
MODELLER A Program for Protein Structure Modeling Release 10.0, r12005 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/01/25 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 11 June 2019 doi:10.20944/preprints201906.0091.v1 Peer-reviewed version available at Biomolecules 2019, 9; doi:10.3390/biom9040123 Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood Abheepsa Mishra1, 2,* and Satyahari Dey1 1Plant Biotechnology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India; [email protected] (A.M.); [email protected] (S.D.) 2Department of Internal Medicine, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA *Correspondence: [email protected]; Tel.:+1(518) 881-9196 Abstract Natural products from plants such as, chemopreventive agents attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide based therapeutics have been developed to combat several health disorders including cancers, metabolic disorders, heart-related, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, until date the activities of cyclic peptides towards molecular targets such as protein kinases, proteases, and apoptosis related proteins have never been explored. In this study we explore the in silico kinase and protease inhibitor potentials of cyclosaplin as well as study the interactions of cyclosaplin with other cancer-related proteins. -
Agent-Based Architectures and Algorithms for Energy Management in Smart Gribs : Application to Smart Power Generation and Residential Demand Response Robin Roche
Agent-Based Architectures and Algorithms for Energy Management in Smart Gribs : Application to Smart Power Generation and Residential Demand Response Robin Roche To cite this version: Robin Roche. Agent-Based Architectures and Algorithms for Energy Management in Smart Gribs : Application to Smart Power Generation and Residential Demand Response. Other. Université de Technologie de Belfort-Montbeliard, 2012. English. NNT : 2012BELF0191. tel-00864268 HAL Id: tel-00864268 https://tel.archives-ouvertes.fr/tel-00864268 Submitted on 20 Sep 2013 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université de Technologie de Belfort–Montbéliard Institut de Recherche sur les Transports, l’Énergie et la Société Laboratoire Systèmes et Transports École Doctorale Sciences pour l’Ingénieur et Microtechniques Algorithmes et Architectures Multi-Agents pour la Gestion de l’Énergie dans les Réseaux Électriques Intelligents Application aux Centrales à Turbines à Gaz et à l’Effacement Diffus Résidentiel Thèse no191 présentée et soutenue publiquement en vue de l’obtention du titre de Docteur en Génie Électrique par Robin Roche le 7 décembre 2012 Membres du jury : M. Mohamed Benbouzid IUT de Brest, LBMS Président M. Nouredine Hadjsaid INP Grenoble, G2Elab Rapporteur M. -
Hy Documentation Release 0.12.1+64.G5eb9283
hy Documentation Release 0.12.1+64.g5eb9283 Paul Tagliamonte Apr 14, 2017 Contents 1 Documentation Index 3 1.1 Quickstart................................................4 1.2 Tutorial..................................................5 1.2.1 Basic intro to Lisp for Pythonistas...............................5 1.2.2 Hy is a Lisp-flavored Python..................................7 1.2.3 Macros............................................. 12 1.2.4 Hy <-> Python interop..................................... 13 1.2.5 Protips!............................................. 14 1.3 Hy Style Guide.............................................. 14 1.3.1 Prelude............................................. 15 1.3.2 Layout & Indentation...................................... 15 1.3.3 Coding Style.......................................... 16 1.3.4 Conclusion........................................... 17 1.3.5 Thanks............................................. 17 1.4 Documentation Index.......................................... 18 1.4.1 Command Line Interface.................................... 18 1.4.2 Hy <-> Python interop..................................... 19 1.4.3 Hy (the language)........................................ 21 1.4.4 Hy Core............................................. 47 1.4.5 Reader Macros......................................... 65 1.4.6 Internal Hy Documentation................................... 66 1.5 Extra Modules Index........................................... 72 1.5.1 Anaphoric Macros....................................... 72 1.5.2 -
R-Based Strategies for DH in English Linguistics: a Case Study
R-based strategies for DH in English Linguistics: a case study Nicolas Ballier Paula Lissón Université Paris Diderot Université Paris Diderot UFR Études Anglophones UFR Études Anglophones CLILLAC-ARP (EA 3967) CLILLAC-ARP (EA 3967) nicolas.ballier@univ- [email protected] paris-diderot.fr paris-diderot.fr language for research in linguistics, both in a Abstract quantitative and qualitative approach. Developing a culture based on the program- This paper is a position statement advocating ming language R (R Core Team 2016) for NLP the implementation of the programming lan- among MA and PhD students doing English Lin- guage R in a curriculum of English Linguis- guistics is no easy task. Broadly speaking, most tics. This is an illustration of a possible strat- of the students have little background in mathe- egy for the requirements of Natural Language matics, statistics, or programming, and usually Processing (NLP) for Digital Humanities (DH) studies in an established curriculum. R feel reluctant to study any of these disciplines. plays the role of a Trojan Horse for NLP and While most PhD students in English linguistics statistics, while promoting the acquisition of are former students with a Baccalauréat in Sci- a programming language. We report an over- ences, some MA students pride themselves on view of existing practices implemented in an having radically opted out of Maths. However, MA and PhD programme at the University of we believe that students should be made aware of Paris Diderot in the recent years. We empha- the growing use of statistical and NLP methods size completed aspects of the curriculum and in linguistics and to be able to interpret and im- detail existing teaching strategies rather than plement these techniques. -
IT Project Quality Management
10 IT Project Quality Management CHAPTER OVERVIEW The focus of this chapter will be on several concepts and philosophies of quality man- agement. By learning about the people who founded the quality movement over the last fifty years, we can better understand how to apply these philosophies and teach- ings to develop a project quality management plan. After studying this chapter, you should understand and be able to: • Describe the Project Management Body of Knowledge (PMBOK) area called project quality management (PQM) and how it supports quality planning, qual ity assurance, quality control, and continuous improvement of the project's products and supporting processes. • Identify several quality gurus, or founders of the quality movement, and their role in shaping quality philosophies worldwide. • Describe some of the more common quality initiatives and management sys tems that include ISO certification, Six Sigma, and the Capability Maturity Model (CMM) for software engineering. • Distinguish between validation and verification activities and how these activi ties support IT project quality management. • Describe the software engineering discipline called configuration management and how it is used to manage the changes associated with all of the project's deliverables and work products. • Apply the quality concepts, methods, and tools introduced in this chapter to develop a project quality plan. GLOBAL TECHNOLOGY SOLUTIONS It was mid-afternoon when Tim Williams walked into the GTS conference room. Two of the Husky Air team members, Sitaraman and Yan, were already seated at the 217 218 CHAPTER 10 / IT PROJECT QUALITY MANAGEMENT conference table. Tim took his usual seat, and asked "So how did the demonstration of the user interface go this morning?" Sitaraman glanced at Yan and then focused his attention on Tim's question. -
Computer Algebra and Mathematics with the HP40G Version 1.0
Computer Algebra and Mathematics with the HP40G Version 1.0 Renée de Graeve Lecturer at Grenoble I Exact Calculation and Mathematics with the HP40G Acknowledgments It was not believed possible to write an efficient program for computer algebra all on one’s own. But one bright person by the name of Bernard Parisse didn’t know that—and did it! This is his program for computer algebra (called ERABLE), built for the second time into an HP calculator. The development of this calculator has led Bernard Parisse to modify his program somewhat so that the computer algebra functions could be edited and cause the appropriate results to be displayed in the Equation Editor. Explore all the capabilities of this calculator, as set out in the following pages. I would like to thank: • Bernard Parisse for his invaluable counsel, his remarks on the text, his reviews, and for his ability to provide functions on demand both efficiently and graciously. • Jean Tavenas for the concern shown towards the completion of this guide. • Jean Yves Avenard for taking on board our requests, and for writing the PROMPT command in the very spirit of promptness—and with no advance warning. (refer to 6.4.2.). © 2000 Hewlett-Packard, http://www.hp.com/calculators The reproduction, distribution and/or the modification of this document is authorised according to the terms of the GNU Free Documentation License, Version 1.1 or later, published by the Free Software Foundation. A copy of this license exists under the section entitled “GNU Free Documentation License” (Chapter 8, p. 141). -
Easybuild Documentation Release 20210706.0 Ghent University
EasyBuild Documentation Release 20210907.0 Ghent University Tue, 07 Sep 2021 08:55:25 Contents 1 What is EasyBuild? 3 2 Concepts and terminology 5 2.1 EasyBuild framework..........................................5 2.2 Easyblocks................................................6 2.3 Toolchains................................................7 2.3.1 system toolchain.......................................7 2.3.2 dummy toolchain (DEPRECATED) ..............................7 2.3.3 Common toolchains.......................................7 2.4 Easyconfig files..............................................7 2.5 Extensions................................................8 3 Typical workflow example: building and installing WRF9 3.1 Searching for available easyconfigs files.................................9 3.2 Getting an overview of planned installations.............................. 10 3.3 Installing a software stack........................................ 11 4 Getting started 13 4.1 Installing EasyBuild........................................... 13 4.1.1 Requirements.......................................... 14 4.1.2 Using pip to Install EasyBuild................................. 14 4.1.3 Installing EasyBuild with EasyBuild.............................. 17 4.1.4 Dependencies.......................................... 19 4.1.5 Sources............................................. 21 4.1.6 In case of installation issues. .................................. 22 4.2 Configuring EasyBuild.......................................... 22 4.2.1 Supported configuration -
An Industrial Strength Theorem Prover for a Logic Based on Common Lisp
An Industrial Strength Theorem Prover for a Logic Based on Common Lisp y z Matt Kaufmannand J Strother Moore Personal use of this material is permitted. particular style of formal veri®cation that has shown consid- However, permission to reprint/republish this erable promise in recent years is the use of general-purpose material for advertising or promotional pur- automated reasoning systems to model systems and prove poses or for creating new collective works for properties of them. Every such reasoning system requires resale or redistribution to servers or lists, or considerable assistance from the user, which makes it im- to reuse any copyrighted component of this portant that the system provide convenient ways for the user work in other works must be obtained from the to interact with it. IEEE.1 One state-of-the-art general-purpose automated reason- ing system is ACL2: ªA Computational Logic for Applica- AbstractÐACL2 is a re-implemented extended version tive Common Lisp.º A number of automated reasoning of Boyer and Moore's Nqthm and Kaufmann's Pc-Nqthm, systems now exist, as we discuss below (Subsection 1.1). In intended for large scale veri®cation projects. This paper this paper we describe ACL2's offerings to the user for con- deals primarily with how we scaled up Nqthm's logic to an venientªindustrial-strengthºuse. WebegininSection2with ªindustrial strengthº programming language Ð namely, a a history of theACL2 project. Next, Section 3 describes the large applicative subset of Common Lisp Ð while preserv- logic supportedby ACL2, which has been designed for con- ing the use of total functions within the logic. -
Use of Bio-Inspired Techniques to Solve Complex Engineering Problems: Industrial Automation Case Study
Use of Bio-inspired Techniques to Solve Complex Engineering Problems: Industrial Automation Case Study José Fernando Lopes Barbosa Relatório de Projecto para obtenção do grau de Mestre em Engenharia Industrial ramo de especialização em Engenharia Electrotécnica Supervision: Prof. Dr. Paulo Leitão September, 2010 Dedication To Inês and Mariana ii Acknowledgements First of all I want to express my most grateful thanks to Professor Paulo Leitão for his knowledge, patient, support and constant motivation during the development of this work without which the conclusion was not possible. Next, I want to thank all my friends for their support, incentive and motivation. I also want to thank my parents for all the support and love throughout the years. A special thank to my beautiful grandmother that with her love and affection made me feel to be her special grandson. Finally, but not the least, I want to thank my wife Inês for her support and comprehension and to my daughter Mariana just to make me constantly smile. iii Abstract Nowadays local markets have disappeared and the world lives in a global economy. Due to this reality, every company virtually competes with all others companies in the world. In addition to this, markets constantly search products with higher quality at lower costs, with high customization. Also, products tend to have a shorter period of life, making the demanding more intense. With this scenario, companies, to remain competitive, must constantly adapt themselves to the market changes, i.e., companies must exhibit a great degree of self-organization and self-adaptation. Biology with the millions of years of evolution may offer inspiration to develop new algorithms, methods and techniques to solve real complex problems.