Lecture 1

Question 1

what is systems biology?

Answer 1

a biology based interdisciplinary field of study that focuses on complex interactions within biological systems, using a more holistic approach to biological and biomedical research.

Question 2

What does systems biology require and involve?

Answer 2

requires integration of experimental and computational approaches. involves application of experimental, theoretical, and computational techniques.

Question 3

what is the definition of reductionism?

Answer 3

theory that every complex phenomenon, especially in biology or psychology, can be explained by analyzing the simplest, most basic physical mechanisms that are in operation during the phenomenon.

Question 4

what is the definition of holism?

Answer 4

theory that parts of a whole are in intimate interconnection, such that they cannot exist or be understood independently of the whole.

Question 5

what are the three categories of holistic approaches?

Answer 5

1. top down
2. bottom up
3. middle out

Question 6

what types of holistic approaches are used by systems biology? what about traditional lab techniques?

Answer 6

systems bio uses top down which is broad and integrative. often described as nonhypothesis driven. Traditional lab techniques used bottom up, hypothesis driven.

Question 7

for top down approaches, system level studies are often built on what?

Answer 7

built on molecular and genetic findings and “omics” studies such as genomics, proteomics, and metabolomics.

Question 8

what are the main challenges in systems biology?

Answer 8

the complexity of the systems, the vast quantities of data and the scattered pieces of knowledge. all these must be integrated. thus systematic computational tools are important.

Question 9

what is the concept of top down approaches?

Answer 9

captures the state of a system by measuring large number of components simultaneously. the aim is to understand human physiology quantitatively as a dynamic system and all relevant levels between genes and the organism.

Question 10

what are the tools to extract information from large data sets?

Answer 10

bioinformatics, probability and statistics, mathematics, and computational analysis

Question 11

what is the bottom up approach?

Answer 11

piecing together of systems to give rise to more complex systems, thus making the original systems sub-systems of the emergent system

Question 12

what is the strategy behind bottom up approaches?

Answer 12

• model system components in detail based on experimental data
• combine these in an integrative model that captures system behavior
• emergent properties of the system arise by describing the components properly

Question 13

what is the definition of middle out approaches?

Answer 13

combining bottom up (model) and top down (data) and allowing for the available in vivo information utilization to determine unknown or uncertain parameters of the model

Question 14

what is hypothesis driven research?

Answer 14

starts with scientific hypothesis, experiments are performed to test hypothesis, hypothesis is refined and tested again

Question 15

what is discovery driven research?

Answer 15

aka data driven discovery mines datasets to detect patterns in data which then can be used to form hypothesis and predictions

Question 16

what are the core aspects for standards for data management?

Answer 16

• minimum information
• file formats
• ontologies

Question 17

what is minimum information?

Answer 17

a checklist of required supporting information for data sets from different experiments

Question 18

what is data driven network inference?

Answer 18

uses computational methods to derive relationships between molecular entities (proteins, genes, transcription factors, metabolites) from high throughout data and time course experimental data that has been collected under various perturbations

Question 19

what are the approaches for data driven network inference

Answer 19

regression, correlation methods, machine learning ,statistics, etc

Question 20

what is the deep curation approach?

Answer 20

creates a detailed molecular interaction map by the large scale integration of knowledge, such as information from publications, databases and high throughput data.

Question 21

what does deep curation approach develop?

Answer 21

develops a molecular network through integration of knowledge from various sources including literature, databases, and experiments

Question 22

what is the difference between Deep curation and data driven approaches?

Answer 22

Unlike the data-driven approach, in which hypotheses about interactions are generated
automatically, the deep curation approach constructs the model manually or semi-manually,
thus making it easier for researchers to add their own hypotheses into it

Question 23

what are some traits of simulation by modeling?

Answer 23

• aka in silico
• captures system dynamics using ODE’s. PDE’s, SDE’s, difference equations, agent based modeling etc.
• well constrained and validated

Question 24

what is multi scale modeling?

Answer 24

• integrates information across multiple spatial and temporal scales
• leverages multiple experimental and computational methods

Question 25

what are some needs for the future?

Answer 25

• integrated modeling platforms
• combines experimental information from different sources
• combines different types of computations