BIOL 2600 EXAM QUESTIONS AND ANSWERS WITH COMPLETE
SOLUTIONS VERIFIED LATEST UPDATE
Why do we need computation
- Massive increase in data volume in the last decades - to develop more accurate
models of biological models
- Reproducibility and replicability - open access to data and its code
- Data driven hypothesis development - need good questions
Bioinformatics
is concerned with the acquisition, storage, analysis, and dissemination of biological
data, most often DNA and AA sequences (methods for handling data)
- NOT the same as computational biology
Computational biology
is the science of using biological data to developed algorithms or models in order to
understand biological systems and relationships
- Goal is biological insight by computational methods - using math to understand biology
(evolution, epidemiology)
System
a set of interacting or interdependent components forming an integrated whole
- Described by their function or by their structure
- Systems have emergent properties arising from the interaction of components
- Biological systems range in scale from ---> cells, tissues, organs
,- Biological systems are tricky to study because they have many parts and many
interactions/ processes occurring on different scales (spatial and temporal)
Biology
is the study of emergent properties of systems
- In the past, many scientists had a reductionist view
- When a complex system is observed to have properties that its parts do not have on
their own, this is described as an emergent property of the system
- We use computational biology to try to model emergent features of biological systems
One such task in biology is to predict function from structure - which usually
starts with a "parts list"
Going from parts to structure to function is HARD - but the opposite way is easier
- What would make going from a list of parts to a structure easier? --> organization and
grouping
When is a puzzle easy/ hard?
- Knowing what the pieces are part of
- Number of components (fewer is easier)
- Distinct classes of components
Knowing the rules governing interactions
- Having landmarks or a chassis
- Completness of the set
- Contamination of the set
- Stability of the set (RNA degrades)
Problem faced by biology
,biological systems are made up of 10s of 1000s of components - acting on different
scales, interacting in a multiplicity of ways, to generate a diversity of states
What is computation?
- Computation is any type of calculation that includes both arithmetical and non-
arithmetical steps and which follows a well-defined model (Ex. an algorithm)
Algorithm
is an ordered and finite set of operations that much be followed in order to solve a
problem
- Chain of instructions - ordered
- Defined objective
- Finite (it will stop when problem is solved)
Flowcharts
Useful way of representing algorithms
>Several conventions or rules for using flowcharts:
= Terminal - start and end (ovals)
= Input/ output - variables (parallelogram)
= Processing - math of algorithm (rectangle)
= Decision - equal to, greater than, less than, TRUE/FALSE
Second computational biology
- Computational biology involves the development and application of data-analytical and
theorectical methods, mathematical modelling and computational simulation techniques
to the study of biological, ecological, behavioural, and social systems
- If we aim to understand how a system works, we must collect comprehensive data
, Data (singular, datum)
- Data are units of information
- Data are a set of values of qualitative or quantitative variables about the attributes of
one or more persons or objects
- Attributes and variables
Purpose of data collection
Support the testing of a hypthesis
Attribute
characteristic of an object
Variable
is a logical set of attributes
Review of variable types
- Continuous variables
- Discrete variables
- Categorical variables
Continuous variables
- Numeric variables can have an infinite set of values within a given range
Discrete variables
- Numeric variables that have a countable number of values within a given range (Ex.
age)
Categorical variables
- Contain a finite number of categories or distinct groups. Do not have to be numeric,
through they may be represented with numbers (Ex. live and dead)
SOLUTIONS VERIFIED LATEST UPDATE
Why do we need computation
- Massive increase in data volume in the last decades - to develop more accurate
models of biological models
- Reproducibility and replicability - open access to data and its code
- Data driven hypothesis development - need good questions
Bioinformatics
is concerned with the acquisition, storage, analysis, and dissemination of biological
data, most often DNA and AA sequences (methods for handling data)
- NOT the same as computational biology
Computational biology
is the science of using biological data to developed algorithms or models in order to
understand biological systems and relationships
- Goal is biological insight by computational methods - using math to understand biology
(evolution, epidemiology)
System
a set of interacting or interdependent components forming an integrated whole
- Described by their function or by their structure
- Systems have emergent properties arising from the interaction of components
- Biological systems range in scale from ---> cells, tissues, organs
,- Biological systems are tricky to study because they have many parts and many
interactions/ processes occurring on different scales (spatial and temporal)
Biology
is the study of emergent properties of systems
- In the past, many scientists had a reductionist view
- When a complex system is observed to have properties that its parts do not have on
their own, this is described as an emergent property of the system
- We use computational biology to try to model emergent features of biological systems
One such task in biology is to predict function from structure - which usually
starts with a "parts list"
Going from parts to structure to function is HARD - but the opposite way is easier
- What would make going from a list of parts to a structure easier? --> organization and
grouping
When is a puzzle easy/ hard?
- Knowing what the pieces are part of
- Number of components (fewer is easier)
- Distinct classes of components
Knowing the rules governing interactions
- Having landmarks or a chassis
- Completness of the set
- Contamination of the set
- Stability of the set (RNA degrades)
Problem faced by biology
,biological systems are made up of 10s of 1000s of components - acting on different
scales, interacting in a multiplicity of ways, to generate a diversity of states
What is computation?
- Computation is any type of calculation that includes both arithmetical and non-
arithmetical steps and which follows a well-defined model (Ex. an algorithm)
Algorithm
is an ordered and finite set of operations that much be followed in order to solve a
problem
- Chain of instructions - ordered
- Defined objective
- Finite (it will stop when problem is solved)
Flowcharts
Useful way of representing algorithms
>Several conventions or rules for using flowcharts:
= Terminal - start and end (ovals)
= Input/ output - variables (parallelogram)
= Processing - math of algorithm (rectangle)
= Decision - equal to, greater than, less than, TRUE/FALSE
Second computational biology
- Computational biology involves the development and application of data-analytical and
theorectical methods, mathematical modelling and computational simulation techniques
to the study of biological, ecological, behavioural, and social systems
- If we aim to understand how a system works, we must collect comprehensive data
, Data (singular, datum)
- Data are units of information
- Data are a set of values of qualitative or quantitative variables about the attributes of
one or more persons or objects
- Attributes and variables
Purpose of data collection
Support the testing of a hypthesis
Attribute
characteristic of an object
Variable
is a logical set of attributes
Review of variable types
- Continuous variables
- Discrete variables
- Categorical variables
Continuous variables
- Numeric variables can have an infinite set of values within a given range
Discrete variables
- Numeric variables that have a countable number of values within a given range (Ex.
age)
Categorical variables
- Contain a finite number of categories or distinct groups. Do not have to be numeric,
through they may be represented with numbers (Ex. live and dead)
