| Titre : | Computer simulation of an immune response against virus infection using artificial life techniques |
| Auteurs : | Belkacem Khaldi, Auteur ; Foudil Cherif, Directeur de thèse |
| Type de document : | Mémoire magistere |
| Editeur : | Biskra [Algérie] : Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, 2012 |
| ISBN/ISSN/EAN : | TINF/52 |
| Format : | 1 vol. (104p.) / ill. / 29 cm |
| Langues: | Anglais |
| Résumé : |
La simulation du système immunitaire (SI) est extrêmement complexe due aux hautes mécanismes et d’interactions qui existent derrière lui; cependant des modèles considérables ont été élaboré afin de mieux comprendre ces mécanismes et interactions. Notre travail est motivé par ce défi pour le but d'enrichir les modèles existants du SI qui ont été récemment utilisés. Le présent travail est une tentative pour simuler la première réponse immunitaire humorol monté dans les lymphatiques organes contre les antigènes de type T-indépendants et celui de type T-dépendantes.Le modèle est un système multi-agent développé sous l'outil de simulation AnyLogic dans lequel les comportements de chaque agent du système sont modélisés en utilisant le formalisme Statecharts. Les résultats issus de nos simulation AnyLogic respectent plusieurs expérimentations immunologiques (activation des cellules B, la prolifération, la différenciation et la génération d'anticorps). |
| Sommaire : |
Introduction ………………………………………………………………………………………………. 1 1. Motivation: Immune system features ………………………………………………………… 1 2. Simulating the Immune system …………………………………………………………………. 2 3. Contributions …………………………………………………………………………………………… 4 4. Organization …………………………………………………………………………………………….. 5 Chapter I: Immunology background …………………………………………………………… 6 1. The task of the immune system ………………………………………………………………….. 7 2. Functional Elements of the Immune System ………………………………………………... 7 2.1. Organs ………………………………………………………………………………………………… 7 2.1.1. Bone Marrow ……………………………………………………………………………... 8 2.1.2. Thymus ……………………………………………………………………………………... 8 2.1.3. Spleen ……………………………………………………………………………………….. 8 2.1.4. Lymph Node ………………………………………………………………………………. 9 2.2. Immune Cells and Molecules ………………………………………………………………... 9 2.2.1. B-Cells ……………………………………………………………………………………….. 9 2.2.2. Antibodies …………………………………………………………………………………. 10 2.2.3. T-Cells ……………………………………………………………………………………….. 11 2.2.4. Major Histocompatibility Complex (MHC) …………………………………… 11 2.2.5. Phagocytes and Their Relatives …………………………………………………... 12 2.3. Layers of the Immune System ………………………………………………………………. 13 2.3.1. Anatomic Barrier ……………………………………………………………………….. 13 2.3.2. Innate Immunity ………………………………………………………………………… 13 2.3.3. Adaptive Immunity …………………………………………………………………….. 14 3. Overview of Humoral Immunity Response ………………………………………………….. 15 3.1. Response to T-Dependent Antigens ……………………………………………………… 16 3.2. Response to T-Independent Antigens …………………………………………………… 17 3.3. Process of Lymphocyte recirculation ……………………………………………………. 17 3.3.1. Structure of Lymph ……………………………………………………………………. 18 4. Summary …………………………………………………………………………………………………... 19 Chapter II: Computational Models for Immune System ………………………………. 20 1. The purpose of modeling the immune system …………………………………………….. 21 1.1. For biological researchers ……………………………………………………………………. 21 1.2. For computer researchers ……………………………………………………………………. 21 2. Approaches for modeling the immune system ……………………………………………. 22 2.1. Top-down approaches …………………………………………………………………………. 22 2.2. Bottom-up approaches ………………………………………………………………………… 22 3. Related methods for modeling the immune system …………………………………….. 23 3.1. Differential Equation Based Models ……………………………………………………… 23 3.2. Cellular Automaton (CA) based Models ………………………………………………… 25 3.2.1. Related Immune system simulators based on CA …………………………. 27 ImmSim …………………………………………………………………………………….. 27 C-ImmSim, ParImm, SimTriplex and ImmunoGrid ………………………. 29 3.3. Agent-Based Models (ABM) …………………………………………………………………. 31 3.3.1. Related Immune system simulators based on ABM ……………………… 32 SIMMUNE ………………………………………………………………………………….. 32 CyCells ………………………………………………………………………………………. 33 3.4. Reactive Animation based modeling …………………………………………………….. 34 4. Comparison between different approaches ………………………………………………... 37 5. Summary ………………………………………………………………………………………………….. 39 Chapter III: Statecharts based Behavior for Agent Based Modeling ……………. 40 1. Overview of Multi-Agent Based Modeling …………………………………………………... 41 1.1. Simulation of Multi-Agent Based Models ………………………………………………. 42 1.1.1. The Behaviors Module ………………………………………………………………... 42 What is an agent? ……………………………………………………………………….. 42 Agent Architectures …………………………………………………………………… 44 Interaction ………………………………………………………………………………… 45 Modeling the agent behavior ………………………………………………………. 46 1.1.2. The Environment Module …………………………………………………………… 47 1.1.3. The Scheduling module ………………………………………………………………. 48 2. Overview of the Statecharts Formalism ……………………………………………………… 50 2.1. What are Statecharts? …………………………………………………………………………. 50 2.2. Basic concepts of Statecharts ……………………………………………………………….. 51 2.2.1. States ………………………………………………………………………………………… 51 2.2.2. Transitions ………………………………………………………………………………… 52 2.3. Advanced concepts of Statecharts ………………………………………………………… 53 2.3.1. The hierarchy of States (nested states) ……………………………………….. 53 2.3.2. Zooming-in & zooming-out ………………………………………………………… 53 2.3.3. Concurrency (orthogonal states) ………………………………………………… 54 2.3.4. Connectors ………………………………………………………………………………… 55 3. Statecharts based Agent behavior ……………………………………………………………… 57 4. Summary ………………………………………………………………………………………………….. 59 Chapter IV: The AnyLogic Simulation of the first Humorol Immune response against an antigen infection ………………………………………………………… 60 1. The AnyLogic Simulation Tool …………………………………………………………………… 61 1.1. AnyLogic Features ………………………………………………………………………………. 61 1.2. AnyLogic Modeling Framework …………………………………………………………… 63 1.3. Agent-Based modeling in AnyLogic ………………………………………………………. 64 1.3.1. Agents ……………………………………………………………………………………….. 65 1.3.2. Space ………………………………………………………………………………………… 65 1.3.3. Communication between Agents ………………………………………………… 66 1.4. AnyLogic Interfaces ……………………………………………………………………………... 66 2. Model of the Lymph Node humorol immune response ………………………………... 67 2.1. Modeling the Time ………………………………………………………………………………. 70 2.2. Modeling the LN environment ……………………………………………………………… 70 2.3. Modeling the Immune Cells agents ……………………………………………………….. 71 2.3.1. The Lymphocyte Agent ………………………………………………………………. 73 2.3.2. The Plasma Agent ………………………………………………………………………. 76 2.3.3. The Antigen Agent ……………………………………………………………………… 77 2.3.4. The Antibody Agent ……………………………………………………………………. 78 2.4. The Main Classes …………………………………………………………………………………. 80 3. Results, discussion and future work ………………………………………………………….... 82 3.1. Results ………………………………………………………………………………………………... 82 3.2. Discussion & Future works ………………………………………………………………….. 91 4. Summary ………………………………………………………………………………………………….. 94 Conclusion ………………………………………………………………………………………………….. 95 Bibliography references …………………………………………………………………………….. 98 |
| En ligne : | http://thesis.univ-biskra.dz/id/eprint/1847 |
Disponibilité (1)
| Cote | Support | Localisation | Statut |
|---|---|---|---|
| TINF/52 | Mémoire de magister | bibliothèque sciences exactes | Consultable |
