Bioinformatics questions and
answers
What are the strengths of a bioinformatics
approach over the classic molecular biology
approach? - answer Biology is inherently
interconnected (molecular biology approach
focuses on single protein/treatment and its effects)
Bigger data sets allow you to find larger or more
subtle patterns of behaviour within larger systems
(e.g. the set of genes that respond to a treatment,
not just the effect of a single gene)
More representative of a wider biological context
What can you do in the field of bioinformatics? -
answer compare across species at the genome
level
find details about evolutionary biology
use predictive models to elucidate gene/protein
function
find implications of the wider response to a
common perturbation
What are the elements of good bioinformatics
research? - answer Strongly hypothesis driven
(large data sets bring unique challenges; the level
of noise can be non-trivial).
,Intelligent study design leads to the best
outcomes.
Need to make sure we are asking the right
questions.
When did the modern era of bioinformatics begin? -
answer With development of Sanger sequencing in
1977.
By 1981, >500 genes had been mapped
In 1982 the first sequence data was available on
EMBL
What was the human genome project? - answer
Aimed to sequence the entire human genome.
Ran from 1990-2003
cost $2.7 billion
resulted in a reduction in the estimated number of
gene (from 100,000 down to 30-40,000) although
that estimate is even lower now (22,000) - however
this does not consider alternative splicing
What was the first example of Next Generation
Sequencing? - answer 454 released by life sciences
in 2004
,What is the relationship between Moore's Law and
sequencing costs? - answer Moore's law describes
the observation that the number of transistors per
square inch on integrated circuits has doubled
every year since their invention, resulting in a
doubling of computing power every year. This
trend is now slowing off.
Sequencing costs have been decreasing every year
since their introduction at a rate greater than
Moore's law. As costs plummet the amount of data
generation increases exponentially.
What is the issue with this sudden increase in
sequencing data? - answer Aren't enough people
with skills to analyse the data.
Data processing capacity is limited.
Data storage capacity is limited.
More data does not equal genuine biological
knowledge.
What is the problem with increasing volumes of
data? - answer Data is cheaper to generate than it
is to store.
What is an EB? - answer Exobyte
, Scale for data? - answer Kings make great tyrants,
peasants excellent zeolots
Byte = 8 bits
Kilobytes = 1000 bytes
Megabyte = 10^6 bytes
Gigabyte = 10^9 bytes
Terabyte = 10^12 bytes
Petabyte = 10^15 bytes
Exabyte = 10^18 bytes
Zettabyte = 10^21
What is the relationship between a GB, TB, PB, EB,
& ZB. - answer 1 ZB = 1000 EB or 10^12 GB
1 EB = 1000PB = 10^6 TB = 10^9 GB
Applications of Genomics? - answer Whole genome
sequencing (assembling a genome from fragments)
ChIP seq (Using DNA binding protein to pull down
specific sequences and identify the sequence motif
the protein binds to).
Variant calling - GWAS
What are the two types of alignment? - answer
Global alignment and Local alignment
answers
What are the strengths of a bioinformatics
approach over the classic molecular biology
approach? - answer Biology is inherently
interconnected (molecular biology approach
focuses on single protein/treatment and its effects)
Bigger data sets allow you to find larger or more
subtle patterns of behaviour within larger systems
(e.g. the set of genes that respond to a treatment,
not just the effect of a single gene)
More representative of a wider biological context
What can you do in the field of bioinformatics? -
answer compare across species at the genome
level
find details about evolutionary biology
use predictive models to elucidate gene/protein
function
find implications of the wider response to a
common perturbation
What are the elements of good bioinformatics
research? - answer Strongly hypothesis driven
(large data sets bring unique challenges; the level
of noise can be non-trivial).
,Intelligent study design leads to the best
outcomes.
Need to make sure we are asking the right
questions.
When did the modern era of bioinformatics begin? -
answer With development of Sanger sequencing in
1977.
By 1981, >500 genes had been mapped
In 1982 the first sequence data was available on
EMBL
What was the human genome project? - answer
Aimed to sequence the entire human genome.
Ran from 1990-2003
cost $2.7 billion
resulted in a reduction in the estimated number of
gene (from 100,000 down to 30-40,000) although
that estimate is even lower now (22,000) - however
this does not consider alternative splicing
What was the first example of Next Generation
Sequencing? - answer 454 released by life sciences
in 2004
,What is the relationship between Moore's Law and
sequencing costs? - answer Moore's law describes
the observation that the number of transistors per
square inch on integrated circuits has doubled
every year since their invention, resulting in a
doubling of computing power every year. This
trend is now slowing off.
Sequencing costs have been decreasing every year
since their introduction at a rate greater than
Moore's law. As costs plummet the amount of data
generation increases exponentially.
What is the issue with this sudden increase in
sequencing data? - answer Aren't enough people
with skills to analyse the data.
Data processing capacity is limited.
Data storage capacity is limited.
More data does not equal genuine biological
knowledge.
What is the problem with increasing volumes of
data? - answer Data is cheaper to generate than it
is to store.
What is an EB? - answer Exobyte
, Scale for data? - answer Kings make great tyrants,
peasants excellent zeolots
Byte = 8 bits
Kilobytes = 1000 bytes
Megabyte = 10^6 bytes
Gigabyte = 10^9 bytes
Terabyte = 10^12 bytes
Petabyte = 10^15 bytes
Exabyte = 10^18 bytes
Zettabyte = 10^21
What is the relationship between a GB, TB, PB, EB,
& ZB. - answer 1 ZB = 1000 EB or 10^12 GB
1 EB = 1000PB = 10^6 TB = 10^9 GB
Applications of Genomics? - answer Whole genome
sequencing (assembling a genome from fragments)
ChIP seq (Using DNA binding protein to pull down
specific sequences and identify the sequence motif
the protein binds to).
Variant calling - GWAS
What are the two types of alignment? - answer
Global alignment and Local alignment
