1st Edition

Immune System Modelling and Simulation

ISBN 9781466597488
Published April 7, 2015 by CRC Press
286 Pages 52 Color & 24 B/W Illustrations

USD $125.00

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Book Description

The book describes a computational model of the immune system reaction, C-ImmSim, built along the lines of the computer model known as the Celada-Seiden model (CS-model). The computational counterpart of the CS-model is called IMMSIM which stands for IMMune system SIMulator. IMMSIM was written in 1992 by the physicist Phil E. Seiden and the immunologist Franco Celada. This model was built around the idea of developing a computerized system to perform experiments similar in vivo experiments; a tool developed to help biologists testing theories and hypothesis about how the immune system works.

C-ImmSim is best viewed as a collection of models in a single program. It incorporates the principal core facts of today’s immunological knowledge, such as the diversity of specific elements, MHC restriction, clonal selection, thymic education of T cells, antigen processing and presentation (both the cytosolic and endocytic pathways are implemented), cell-cell cooperation, homeostasis of cells created by the bone marrow, hyper mutation of antibodies, maturation of the cellular and humoral response, and memory. Besides, an antigen can represent a bacterium, a virus, or an allergen or a tumor cell. C-ImmSim has been recently customized to simulate the HIV-1 infection. Moreover, it can simulate the immunotherapy for cancer. These features are all present in the code and people can choose to turn them on and off at compiling time.

The book presents the basic model as well as the various customizations to implement the description of different diseases and the way they have been used in practice to produce new knowledge either from hypothesis or from lab-experiment data. In this respect, the book can be used as a practical guide to implement a computational model with which to study a specific disease and to try to address realistic clinical questions.

Table of Contents

Immunology for aliens

Leo Szilard paradox: Grand Central Terminal

Non-specific defense

Levels of evolution

How is a trait selected if it was not needed?

Luck or foresight?

Blood brothers

The members of the winning team are rewarded

Somatic recombination produces diversity among equals

The workshop of the adaptive response


A battalion of one

Self-inflicted damage threatens survival

Don’t think, but reason and understand

Full cover comes at a cost

A bet, not a fantasy, about earliest happenings

The cooperation of very different cells multiplies jobs that can be done

Thymus deeds

Hypothesis is a bet: Tips for the Aliens

To grow and to change

Philosophy storm


In the beginning

The linear transmission of activation

Recipe for complete Freund have them

An antibody is an antibody (or two?)

Scientific Myths: God's mess with human cognition

A monument to interdisciplinarity

Scientific Myths 2: Apollo roams about the hills of Tennessee

Plain reasoning breaks the Spell

Of wolfs, dogs and shepherds

How to block anti-self

Controlling self- damage needs structures: the lymphoid organs

Time of strengthening


A cognitive system? A floating brain?

Cellular Automaton makes sense

Memory is in the numbers

The power rests with whoever issues regulatory signals

The seed is prepared during the primary response

The challenge

Competition in the minefield of cross reactions

The compensated immune system wants to understand

The two immune systems

The cellular branch confronts a virus infection

How to model the cellular and the humoral together

Body and soul, actions and philosophy

What steps can and should be simulated

Attrition and cross-reaction

Memory is strong, sometimes too strong

IMMSIM reveals MaN (Memory anti Naïve) as a cause of aging

A course leading to aging of the immune system

A new challenge for modelers: conformation

Protein Conformation and the immune system

Antibody mediated activation of a mutant enzyme

More fields for models, and where to find them

A note to encourage cross referencing

An unconventional glossary for aliens

Aliens for immunology

The unusual mix of immunology and computer science

Classical modeling techniques versus the "new kind of science"

From spin-like to agent-based models

The ancestors

The others

C-ImmSim unveiled

Model compartments

The cells

The molecules

The repertoire

The molecular affinity

Reshaping the affinity landscape

Haematopoiesis and cell homeostasis

The selection of cells in the thymus

The Hayflick limit

Cell aging and death

A (dynamic) immune memory

The hyper-mutation of antibodies

Immune activation


Interactions among entities

Antigen digestion and presentation

Cell motion and diffusion of molecules

Main procedures

Notes on the expressed repertoire

Scaling the system size

Few words on the definition of molecular quanta

The choice of the MHC molecules

The parameters

What to monitor?

Benchmarks aka qualitative model validation

Primary and secondary response


Bacterial Infection

Viral infection

Modelling idiotypes and the idiotype network

Specific applications

A multi-scale approach to model hypersensitivity

HIV infection and AIDS

Immunodominance in cancer immunotherapies

Embedding immunoinformatics predictions

One last word


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Filippo Castiglione, Franco Celada