2015 04 22_time_labs_shared

22 april 2015
• ^ Biobix: Who ? Where ?
• Bioinformatics
• Personal Genomics
• DIY Bio
^[now][transl comput]ational⎮ [epi]genomic$

Ghent University at a glance
Department of
Molecular Biotechnology
Lab for Bioinformatics and
computational genomics
10 “genome hackers”
mostly engineers (statistics)
42 scientists
technicians, geneticists, clinicians

Lab for Bioinformatics and computational genomics
Lab for Bioinformatics and
computational genomics
10 “genome hackers”
mostly engineers (statistics)
42 scientists
technicians, geneticists, clinicians
>100 people
Hardware/software engineers,
mathematicians, molecular biologists

22 april 2015
• Bioinformatics
• DIY Bio

Bioinformatics ?
•Application of information
technology to the storage,
management and analysis of
biological information
•Facilitated by the use of computers

Math Algorithm
Development
Informatics
Interface Design
Bioinformatics, a scientific discipline …
AI, Image Analysis
structure prediction (HTX)
Theoretical Biology
Sequence Analysis
Computational Biology
(Molecular)
Biology
Expert Annotation
Computer Science
NP
Datamining
Bioinformatics
Discovery Informatics – Computational Genomics

Cell Theory
• All organisms are
composed of one or
more cells.
• Cells are the smallest
living units of all living
organisms.
• Cells arise only by
division of a previously
existing cell.

Cell Theory

Genetic code
DNA

The human genome comprises the information contained in one
set of human chromosomes which themselves contain about 3
billion base pairs (bp) of DNA in 46 chromosomes (22
autosome pairs + 2 sex chromosomes). The total length of DNA
present in one adult human is calculated by the multiplication of
(length of 1 bp)(number of bp per cell)(number of cells in the body)
DNA: Structure and Function

(0.34 × 10-9
m)(6 × 109
)(1013
)
2.0 × 1013
meters

(0.34 × 10-9
m)(6 × 109
)(1013
)
2.0 × 1013
meters
That is the equivalent of nearly 70 trips from the earth to
the sun and back.

22 april 2015
• Bioinformatics
• 3D printing

107
106
105
104
103
102
101
1108
109
Full genome bp
G
E
N
E
T
I
C
Whole-genome
sequencing
Enrichment seq
(Exome)
PCR
Enrichment
Targeted Panels
Instrument and Assay providers
CLIA Lab service providers

The genome fits as an e-mail attachment

Overview
• Who ? Where ?
• > Genetics
• Technology: Next Gen
Sequencing
• Personal …. Medicine/Genomics
• Manifesto
• The App

Molecular Profiling
The study of specific patterns (fingerprints) of proteins,
DNA, and/or mRNA and how these patterns correlate
with an individual's physical characteristics or
symptoms of disease.

Overview
• Who ? Where ?
• > Genetics
• Technology: Next Gen
Sequencing
• … Personal Genomics
• Manifesto
• The App

Generic Health advice
•Exercise (Hypertrophic Cardiomyopathy)
•Drink your milk (MCM6 Lactose intolarance)
•Eat your green beans (glucose-6-phosphate
dehydrogenase Deficiency)
•& your grains (HLA-DQ2 – Celiac disease)
•& your iron (HFE - Hemochromatosis)
•Get more rest (HLA-DR2 - Narcolepsy)

Generic Health advice (UNLESS)
•Drink your milk (MCM6 Lactose intolarance)

Generic Health advice (UNLESS)
•Drink your milk (MCM6 Lactose intolerance)

my genome is too important (for me)
to leave it (only) to doctors

NXTGNT biohackerspace …

PGMv2: Personal Genomics Manifesto

Everyone should have the power and legitimacy to
be able to discover, develop and find new things
about their own genome data.
Intelligent exploration, experimentation and trial to
push the boundaries of knowledge are a basic
human right.

Personal genome data access should be
affordable to all irrespective of nationality, gender,
social background or any other circumstance.
Not having access to a personal genetic test is in
itself a new kind of discrimination.

Whether one wants to share genome data or keep it
private should be a matter of personal choice.
Whatever attitude a person has towards personal
genome privacy, it should be utterly respected.
Corporate interest can never compromise any human
right. Laws must fully protect individual human rights of
equality for every person, irrespective of predicted risks
from genetic data.

Stating that genetic tests merely provide non-
clinical information misses the point of what
personal genomics is all about.
Most genomic information is uninterpretable and
may well be meaningless. But those are not
reasons to deny it to people.
Genetic test results are not unrelated to
someone’s health, one’s ability to respond to
certain drugs and one’s ethnic ancestry.

Education in risks and opportunities for personal
genetic testing should be the primary aim of
policy makers.
Restricting access to interested people makes
no sense and it is virtually impossible to ensure.
Access to personal genomics data and tools for
its interpretation should become accessible to
everyone.

Epigenome(s)

22 april 2015
• Bioinformatics
• Epigenetics
• DIY Bio

Howto
• http://www.rcsb.org/pdb/home/home.do
• Search “Green Fluorescent Protein”

The goal: printing a fully functional artificial leaf, one
actually capable of photosynthesis.

Is there DIY Bio Tissue ?
Set-out a few dates to browse/follow/journal club Biocoder
Select a (few) projects (iGem)
Start Biohacking

… $

2015 04 22_time_labs_shared

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2015 04 22_time_labs_shared