"Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow's researchers and enterpreneurs. BIG4", por Eduardo Pareja, ERA7 Information Technologies SL

Jaén 24 de Octubre 2016
www.era7bioinformatics.com
http://big4-project.eu/

Biosystematics, informatics and genomics of the big 4 insect
groups: training tomorrow's researchers and enterpreneurs
BIG4
Jornada Informativa - HORIZONTE 2020 Jornada Informativa - HORIZONTE 2020
Convocatoria ITN “Acciones Sklodowska-Curie (MSCA)”

=

NGS
Next Generation Sequencing

illumina and
PacBio

Oxford
Nanopore

Oxford
Nanopore
Ebola
Sequencing
NATURE NEWS
05 May 2015
Oxford
Nanopore
Ebola
Sequencing
NATURE NEWS
05 May 2015

Gigabyte (GB) 1.000.000.000
Terabyte (TB) 1.000.000.000.000
Petabyte (PB) 1.000.000.000.000.000
Exabyte (EB) 1.000.000.000.000.000.000
Zettabyte 1.000.000.000.000.000.000.000

Precision Medicine Initiative
1 M human genomes

Broad Institute: 1 human genome
every 8 minutes

Big Data
uses to live
in the Cloud

And the future ?

Not only Massive data but also
Massively interconnected data

Knowledge-based data in biology comes in a
graph-like form.
Just think of examples such as taxonomic or
phylogenetic trees, signalling, metabolic,
transcriptional or interaction networks, or the Gene
Ontology

Graph
Databases
have,
essentially
nodes and
edges

This is the objective of
Bio4j platform

Bio4j is a bioinformatics graph based DB including most
data available in:
- UniProt (SwissProt + Trembl)
- UniRef (50,90,100)
- Gene Ontology (GO)
- RefSeq
- NCBI taxonomy
- Enzyme DB
Era7 Bioinformatics: The bacterial Genomics
La Revolución del Microbioma Julio 2016

2.000.000.000 relationships
500.000.000 nodes
1.000.000.000 properties

Bio4j project was
selected for the
Google Summer of
Code 2014

Biographika project:
Innovative and Interactive Visualisation

Biographika project:
Completely web based developments:
• Javascript
• D3
• ……

The Microbiome Revolution era
started officially this year, May 13th

And Era7 was there

National Microbiome Initiative
“Microbiomes are the communities of
microorganisms that live on or in
people, plants, soil, oceans, and the
atmosphere. Microbiomes maintain
healthy function of these diverse
ecosystems, inEluencing human health,
climate change, food security, and other
factors”

Bacteria
are all
over the
World ……

The Sea

The
Ground

The Air

And in all
living
organisms

The Microbiome
• Human
• Environmental
• Industrial
• Places

Microbiome - PubMed

Human Microbiome
• 100 times more genes than the Human Genome
• 1.5 Kilograms
• 10 times more bacteria cells than human cells in our
body

“ The Last Organ “

“ The Second Genome “

More than 10% of the blood small
molecules come from the gut
microbiome

Human Microbiome
• Mouth
• Gut
• Skin
• Urinary Tract
• Airway
• Vagina
• Human Milk
• ………………………..

A healthy Microbiome is needed
and a “bad” Microbiome is related
with diseases

• Obesity
• Type 1 Diabetes
• Type 2 Diabetes
• Colon cancer
• Asthma
• Atherosclerosis
• Autism
• Autoimmunity
• Cardiovascular Disease
• Crohn
• Cystic Fibrosis
Some health conditions related with Gut Microbiome:
• Skin disorders
• Inflammation
• Fe deficiency
• Multiple Sclerosis
• Obesidad
• Rheumatoid Arthritis
• Parkinson
• Sarcoidosis
• Stroke
• AIDS

The Microbiome is closely related with The
Immune System and we analyse it in this
context:
• HLA typing
• TCR repertoire
• BCR repertoire

Microbiome Transplant

El Microbioma de la Boca
Podría estar involucrado en algunos Infartos Agudos
de Miocardio
Proyecto CARDIOBIOME

Mouth Microbiome could be involved in
Acute Myocardial Infarction
Era7’s CARDIOBIOME Project
400 K euros grant

Era7 is The Bacterial
Genomics Company
a
leader in Microbiome Analysis

Era7
founders
Raquel Tobes
CSO
Eduardo Pareja
CEO

Era7 has a very specialised
and multidisciplinary team
• Mathematicians
• Software engineers
• Biochemists
• Medical Doctors

Era7 is based in Cloud
Computing

Data Information Knowledge
Era7

Era7 team is very
experienced in Genomics Big
Data analysis

We started in
Granada

From 2010
in
Madrid

From 2012 in
Cambridge,
Massachusetts
USA

From 2016
A wet lab in
Granada

Co - Investment with
and a Crowdfunding open now at
Capital Cell

INTERCROSSING is an EU-funded Marie Curie
Initial Training Network,
training 13 early stage researchers (ESRs) in
genetics, informatics and statistics
2 ESRs in Era7

Biosystematics, informatics and
genomics of the big 4 insect groups:
training tomorrow's researchers and
enterpreneurs
BIG4

The
Coordinator:

Multidisciplinar
Consortium

The
Consortium:

Many partners
apart from
the Consortium

Other
Partners:

Ashish Tomar
Bioinformatics
And Biotechnology

• Storage and analysis of genomic and metagenomics data
• A layer on top of Bio4j for facilitating the use of this platform
• Genomics and metagenomics experimental design
• Cloud Computing (AWS) infrastructure
• Innovative and interactive visualisation
• Graph Databases for biological knowledge management

Innovative and interactive visualisation
• Based in D3
• Running in browsers without no plugin needed
• Using data in JSON format
• In both models, from a file and from a database query
• For metagenomics data
• For phylogenomics
• As an interface of graph databases starting from Era7’s
“DoaGraph”

Data
Visualisation

Data Visualisation

Data
Visuali.

Data
Visual.

PhD Thesis:
Tree Visualisation in
Biology

Thesis Supervisor
Professor Jose Oliver, Computational Biology
Department of Genetics
University of Granada
Supervisor:
Eduardo Pareja,
PhD, Md
Era7’s CEO

• Stat of the art of visualisation tools for data structured as a tree.
• A tree as a case of a graph and specially of a DAG (Directed Acyclic Graph). Possible solutions to visualise at
least part of the DAG as a tree
• Review of kind of Biological data that could be visualised as trees
• Identification of special problems dealing with large data sets as the whole taxonomy.
• Investigation of the potential application of tree visualisation paradigm to tabular data using cathegories
organised like trees
Technically:
• All the client side based in browser an without the need of any plugin
• Javascript, CSS , HTML5 and webGL
• Javascript libraries:
• D3
• Three.js
• create.js
• Sigma.js
• Server side graph database engine like Neo47
In summary, the objectives are:
• To compile and analyse tree visualisation tools in general.
• To identify the problems not solved in Biological data
• To develop new methods and integrating them with third party solutions to solve some of these
problems

The Coordinator found
us in a web search

For a company could be
challenging

• Research project (in a company) including PhD
• Training project
• EU funding (last 10%)
• Could be very good to employ after the project
• Management less complex now
• Be careful storing documents !!
• Dissemination
• Outreach
• Collaborations (secondments)

Thank you for your
attention !
Eduardo Pareja
epareja@era7.com

"Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow's researchers and enterpreneurs. BIG4", por Eduardo Pareja, ERA7 Information Technologies SL

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"Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow's researchers and enterpreneurs. BIG4", por Eduardo Pareja, ERA7 Information Technologies SL