Вводная лекция про моделирование в биологии

Введение
«State of the Art»

Математическая биология
или
Биоматематика
ПРЕДМЕТ?
Компьютерная биология
или
Биоинформатика
Интегративная биология
или
Системная биология
Компьютерная медицина
или
Медицинская физика

Definition: …?
Определения
What is Systems Biology?
Integrative Biology is the study of biological systems approached by incorporating many diverse perspectives and disciplines, e.g. natural, physical and sciences, that complement one another to unravel the complexity of biology.
Keita Ito, Vice Director AO Research Davos
Systems biology is an academic field that seeks to integrate high-throughput biological studies to understand how biological systems function. By studying the relationships and interactions between various parts of a biological system (e.g. metabolic pathways, organelles, cells, physiological systems, organisms etc.) it is hoped that eventually an understandable model of the whole system can be developed.
Wikipedia
Integrative biology has the same meaning as systemic biology. By the way, it is a new wording, more fashionable, for physiology...
Jean-Pierre Boissel, Lyon France
“Systems biology” is quickly emerging as the popular term describing many exciting scientific activities of postgenomic biology.
Allen W. Cowley, Jr. Editor-in-Chief, Physiological Genomics
Systems biology concerns the study of the connectivity between the components of living matter and how the connectivity between these components can lead to emergent properties i.e. the properties of a system that are not derivable by summing the properties of its component parts.
EMBL
Systems biology involves the application of experimental, theoretical, and computational techniques to the study of biological organisms at all levels, from the molecular, through the cellular, to the organ, organism, and populations. Its aim is to understand biological processes as integrated systems instead of as isolated parts.
NIH Systems Biology Workshop 2002
Системная биология включает в себя применение экспериментальных, теоретических и компьютерных методов изучения биологических организмов на всех уровнях от молекулярного, через клеточный, тканевой, до органного, организменного и популяционного. Цель – понимание биологических процессов как интегративных систем взамен изолированных частей.
NIH Systems Biology Workshop 2002

Definition: …?
Определения
What is Systems Biology?
Integrative Biology is the study of biological systems approached by incorporating many diverse perspectives and disciplines, e.g. natural, physical and sciences, that complement one another to unravel the complexity of biology.
Keita Ito, Vice Director AO Research Davos
Systems biology is an academic field that seeks to integrate high-throughput biological studies to understand how biological systems function. By studying the relationships and interactions between various parts of a biological system (e.g. metabolic pathways, organelles, cells, physiological systems, organisms etc.) it is hoped that eventually an understandable model of the whole system can be developed.
Wikipedia
Integrative biology has the same meaning as systemic biology. By the way, it is a new wording, more fashionable, for physiology...
Jean-Pierre Boissel, Lyon France
“Systems biology” is quickly emerging as the popular term describing many exciting scientific activities of postgenomic biology.
Allen W. Cowley, Jr. Editor-in-Chief, Physiological Genomics
Systems biology concerns the study of the connectivity between the components of living matter and how the connectivity between these components can lead to emergent properties i.e. the properties of a system that are not derivable by summing the properties of its component parts.
EMBL
Systems biology involves the application of experimental, theoretical, and computational techniques to the study of biological organisms at all levels, from the molecular, through the cellular, to the organ, organism, and populations. Its aim is to understand biological processes as integrated systems instead of as isolated parts.
NIH Systems Biology Workshop 2002
Perhaps surprisingly, a concise definition of Systems Biology that most of us can agree upon has yet to emerge.
Ruedi Aebersold
Institute for Systems Biology, Seattle
Возможно удивительно, но точное определение системной биологии, с которым бы согласилось большинство еще не созрело
Ruedi Aebersold
Institute for Systems Biology, Seattle

Система и Способы ее анализа…
Этимология:
Определение: (Ludwig von Bertalanffy, 1901-1972): Система – сущность, поддерживающая свое существование благодаря взаимодействию своих частей.
System
Parts
R
E
D
U
C
E
I
N
T
E
G
R
A
T
E
synthithemi, греч. ‘Собирать вместе’

Модель как Метод исследования
System Insight
Models
Relevant (уместный, подходящий,
существенный)
Representative (типичный,
характерный) Reproducible (воспроизводимый)
Reasonable (разумный)
‘…simplified description of a system, to assist calculations and predictions.’
Oxford Concise Dictionary

Многоуровневая иерархия:
молекулы, клетки, ткани,
орган, организм, популяция…
СЛОЖНОСТЬ БИОЛОГИЧЕСКИХ СИСТЕМ
Разнопорядковые
пространственно-временные
шкалы
Интеграция процессов
разнообразной
физической природы
Открытые,
неравновесные
системы

I. МАТЕМАТИЧЕСКОЕ МОДЕЛИРОВАНИЕ
Создание моделей. Иерархии моделей от субмолекулярного до надпопуляционного уровня. Качественное и количественное исследование моделей.

II. БИОИНФОРМАТИКА
Геномика. Транскриптомика. Протеомика. Метаболомика. Проблемы интерпретации экспериментальных данных. Разработка алгоритмов. Базы данных. Создание программных разработок.

III. ВЫЧИСЛИТЕЛЬНЫЕ И ИНФОРМАЦИОННЫЕ ТЕХНОЛОГИИ
Методы сбора, обработки и передачи данных для получения информации нового качества о состоянии объекта, процесса или явления. Численные методы обработки экспериментальных данных. Распознавание образов. Кластеризация. Организация параллельных вычислений. Организация распределенных вычислений. Вычислительные технологии в области молекулярного дизайна, фармакологии и биотехнологии.

Математическая генетика
Дисциплины математической биологии
Математическая экология
Математическая иммунология
Математическая физиология
Математическая эпидемиология
Популяционная динамика
Математическая молекулярно-клеточная биология

Математическая Физиология
- количественное описание физиологических процессов и систем

Talk at the STEP#1 Conference, Brussels, 2006 www.europhysiome.org

Cardiome Project
Tissue Structure
Tissue properties
Model Validation
Drug Discovery
Clinical Applications
Cellular properties
Anatomy
Heart model
Rob MacLeod, CVRTI/BE/SCII
Peter Hunter, Auckland University

Full Circle: Whole Heart to Single Cell
?

Imaging Organ Structure at Para-Cellular Resolution
Voxel size
25 μm (x/y/z)

Voxel size
25 μm (x/y/z)
Imaging Organ Structure at Para-Cellular Resolution

Imaging Structure: Cell to Organ
Pixel resolution 1 μm (x/y)

Co-Registration with Sub-Cellular Detail

Organ Data-Sets with Sub-Cellular Detail

Histo-Anatomical Models
Mesh and Model Generation