2015 04 22_time_labs_shared

^…

22 april 2015

• ^ Biobix: Who ? Where ?• Bioinformatics• Personal Genomics• DIY Bio

^[now][transl comput]ational⎮ [epi]genomic$

22 april 2015



Ghent University at a glance

Department of Molecular Biotechnology

Lab for Bioinformatics and computational genomics

10 “genome hackers” mostly engineers (statistics)

42 scientiststechnicians, geneticists, clinicians

http://www.biolinux.org/



10 “genome hackers” mostly engineers (statistics)

42 scientiststechnicians, geneticists, clinicians

>100 people Hardware/software engineers,

mathematicians, molecular biologists


22 april 2015




22 april 2015



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 Analysisstructure prediction (HTX)

Theoretical Biology

Sequence Analysis

Computational Biology

(Molecular)Biology

Expert Annotation

Computer Science

NPDatamining

BioinformaticsDiscovery Informatics – Computational Genomics


22 april 2015




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 codeDNA



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

• ^ Biobix: Who ? Where ?• Bioinformatics• Personal Genomics• 3D printing



107 106 105 104 103 102 101 1108109

Full genome bp

GENETIC

Whole-genomesequencing

Enrichment seq(Exome)

PCREnrichment

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)







•Drink your milk (MCM6 Lactose intolerance)







•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 topush 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




22 april 2015

• ^ Biobix: Who ? Where ?• Bioinformatics• Epigenetics• Personal Genomics• DIY Bio




Howto

• http://www.rcsb.org/pdb/home/home.do

• Search “Green Fluorescent Protein”

http://www.rcsb.org/pdb/home/home.do

• Launch MaxPyMol

• Open 2YOG.PDB

Creates gfp.wrl file





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


… $

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