Integration and analysis Integration and analysis of multi-type high-of multi-type high-throughput data for throughput data for biomolecular knowledge biomolecular knowledge discoverydiscovery

Dr. Erik Bongcam-RudloffDr. Erik Bongcam-Rudloff

SGBC-SLUSGBC-SLU

Uppsala, SwedenUppsala, Sweden

Biologists modus Biologists modus operandioperandi

Observing a phenomenon that is in some way Observing a phenomenon that is in some way interesting or puzzling.interesting or puzzling.

Making a guess as to the explanation of the Making a guess as to the explanation of the phenomenon.phenomenon.

Devising a test to show how likely this Devising a test to show how likely this explanation is to be true or false.explanation is to be true or false.

Carrying out the test, and, on the basis of the Carrying out the test, and, on the basis of the results, deciding whether the explanation is a results, deciding whether the explanation is a good one or not. In the latter case, a new good one or not. In the latter case, a new explanation will (with luck) 'spring to mind' as explanation will (with luck) 'spring to mind' as a result of the first test.a result of the first test.

httphttp:://www.biology.ed.ac.uk/archive/jdeacon/statistics/tress2.html//www.biology.ed.ac.uk/archive/jdeacon/statistics/tress2.html

The Observed The Observed phenomenonphenomenon

Selection of test timesSelection of test times

But was is the real But was is the real event?event?

Sometimes you could be Sometimes you could be luckylucky

PositivePositive

““PositivePositive”” results are used results are used ““negativenegative”” rejectedrejected

Why?Why?Only positive results are publishableOnly positive results are publishable

““PositivePositive”” results are used results are used ““negativenegative”” rejectedrejected

Why?Why?Only positive results are publishableOnly positive results are publishable

Next Generation Next Generation techniquestechniques

New challengesNew challenges

1 TB data1 TB data1 TB data1 TB data

Gbases produced at Gbases produced at SangerSanger

World NGS MapWorld NGS Map

http://omicsmaps.com/http://omicsmaps.com/

But this is wonderful! But this is wonderful! Or?Or?

Sequence without knowledge connected to it is Sequence without knowledge connected to it is worth: 0worth: 0

The deluge of data produced by these hordes The deluge of data produced by these hordes of machines worldwide demand automatic of machines worldwide demand automatic workflowsworkflows

Complete new systems to shuffle data aroundComplete new systems to shuffle data around

Storage of never used amountsStorage of never used amounts

Machines with gigantic amounts of RAMMachines with gigantic amounts of RAM

COSTSCOSTS

PROBLEMSPROBLEMS

NOmenclatureNOmenclature

Publishing culturePublishing culture

Moving target developmentMoving target development

Old ways of work and resistance to changes in Old ways of work and resistance to changes in cultureculture

Publishing culture as Publishing culture as exampleexample

We get tax payers money, we pay publishers to We get tax payers money, we pay publishers to publish, the publishers sell the articles and obtain publish, the publishers sell the articles and obtain the copy rightsthe copy rights

To connect knowledge to sequences we need To connect knowledge to sequences we need automatic methods, workflows, text mining. Most automatic methods, workflows, text mining. Most of this is limited by close database systems. Only of this is limited by close database systems. Only available is PubMed. But PubMed has only short available is PubMed. But PubMed has only short abstracts. NO information about conditions, M&M abstracts. NO information about conditions, M&M etcetc

We need to change this cultureWe need to change this culture

The BLAST analogy...The BLAST analogy...

By far the most used tool by biologists By far the most used tool by biologists

Not possible if databases were not Open Not possible if databases were not Open Access and freely searchable Access and freely searchable

Imagine if Nucleotide and Protein databases Imagine if Nucleotide and Protein databases followed the life science publishing modelfollowed the life science publishing model

BLASTBLAST

BLASTBLAST

BLASTBLAST

BLASTBLAST

BLASTBLAST

Human centricHuman centric

What about all other areas of the Life What about all other areas of the Life Sciences?Sciences?

Most genes are named by sequence similarity, Most genes are named by sequence similarity, but are the functions the same?but are the functions the same?

MicrobiomeMicrobiome

http://www.secondgenome.comhttp://www.secondgenome.com

A microbiome is the A microbiome is the totality of microbes, totality of microbes,

their genetic elements their genetic elements (genomes), and (genomes), and environmental environmental

interactions in a interactions in a particular environment.particular environment.

Fat and leanFat and lean

Metabolic effects of transplanting gut microbiota Metabolic effects of transplanting gut microbiota from lean donors to subjects with metabolic from lean donors to subjects with metabolic syndrome.syndrome.A. Vrieze et al, EASD abstracts, 24 September 2012.A. Vrieze et al, EASD abstracts, 24 September 2012.

The result was: Lean donor faecal infusion The result was: Lean donor faecal infusion improves hepatic and peripheral insulin resistance improves hepatic and peripheral insulin resistance as well as fasting lipid levels in obese individuals as well as fasting lipid levels in obese individuals with the metabolic syndromewith the metabolic syndrome

Genome sizesGenome sizes

How many species?How many species?

Several orders of magnitude:Several orders of magnitude:

Some estimates:Some estimates:3-50 million species of arthropods3-50 million species of arthropods1-100 million species of nematodes1-100 million species of nematodes

Only a portion of bacterias have being Only a portion of bacterias have being identified, 99% of bacterias cannot be cultured.identified, 99% of bacterias cannot be cultured.

““Once the diversity of the microbial worldis Once the diversity of the microbial worldis catalogued, it will make astronomy to look like catalogued, it will make astronomy to look like a pitiful sciencea pitiful science””Julian Davies, Professor Emeritus. UBCJulian Davies, Professor Emeritus. UBC

New research strategiesNew research strategies

MicrobialMicrobial LivestockLivestock PlantsPlants

Typical Sources of Typical Sources of MetagenomicsMetagenomics

Soil samplesSoil samples

Sea water samplesSea water samples

Air samplesAir samples

Medical samplesMedical samples

Farm animal samplesFarm animal samples

Ancient bonesAncient bones

Human microbiomeHuman microbiome

Ion Proton: "Personal Genome Ion Proton: "Personal Genome Machine".Machine".

LIFE TECHNOLOGIES CORPORATIONLIFE TECHNOLOGIES CORPORATION

Real tests of transcriptome sequencing on the Real tests of transcriptome sequencing on the Proton. Using 500 ng of input poly-A RNA, it was Proton. Using 500 ng of input poly-A RNA, it was possible to generate 50 million reads from a possible to generate 50 million reads from a melanoma cancer sample.melanoma cancer sample.Joe Boland of the National Cancer Institute according to Genomeweb.Joe Boland of the National Cancer Institute according to Genomeweb.

Oxford NanoporeOxford Nanopore

http://http://www.nanoporetech.com/www.nanoporetech.com/

High technology High technology everywhere!everywhere!

New applicationsNew applications

Only imagination will put the limits of what its Only imagination will put the limits of what its possible to be done using Next Generation possible to be done using Next Generation Technologies!Technologies!

The big challenge:The big challenge:

Open Access, Open source, collaborative Open Access, Open source, collaborative networksnetworks

Data sharingData sharing

Common languageCommon language

Tool systems to glue all together!!Tool systems to glue all together!!

SeqAheadSeqAhead

COST Action BM1006: Next Generation COST Action BM1006: Next Generation Sequencing Data Analysis Network. 2011-2014Sequencing Data Analysis Network. 2011-2014

COST Action 25 countriesCOST Action 25 countries

http://www.seqahead.euhttp://www.seqahead.eu//

ALLBIOALLBIO

10 partners 8 countries10 partners 8 countries

FP7 projectFP7 project

Broadening the Bioinformatics Infrastructure to Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant scienceunicellular, animal, and plant science

www.allbioinformatics.euwww.allbioinformatics.eu

THANKS!!THANKS!!

Como 2012Como 2012