Bioinformatics Career Day

Slides
http://www.slideshare.net/phdcareers/

http://prezi.com/ugn43malcumr/dkfz-
careers-in-bioinformatics-day-2012/

Feedback
https://www.surveymonkey.com/s/bioi
nformaticscareerday

Scientific Career Development

Bioinformatics Career Day
Dr. Barbara Janssens

May 2012


23-May-12 Page 2 Barbara Janssens PhD Career Service

http://www.ebi.ac.uk/training/careerday
p g y
Email
 careers@dkfz.de

TWEET
 www.twitter.com
 #bxcareers

Slides
 http://www slideshare net/phdcareers/presentations
http://www.slideshare.net/phdcareers/presentations

Feedback
 https://www.surveymonkey.com/s/bioinformaticscareerday

Feel free to use our „internet cafe“ in the back
cafe

PhD Career Development
p

www.dkfz.de/phd/Careers.html
www dkfz de/phd/Careers html

www.facebook.com/phdcareers

Concept: Career as
„Scientific life beyond the lab“


Career Development
p
Target group 900 scientists at DKFZ (Masters, PhD, PostDocs)
C
Career D
Development:
l t
 Platform, tools and information
 Initiative and needs come from scientists
 What to pack in your suitcase for the next step A

Supervisor/Mentor
Advisor B

…

C

My career network
y

Playground
network

Graduate school

Teaching Editor

Careers Service Milestones


Heidelberg Career Calendar
http://tinyurl.com/5wuerfx


Career destination
Plan A vs Plan B

Adapted from Gerd Altmann www.pixelio.de


DKFZ PhD students want…


„Freedom
„Freedom“ in Academia
Temporary contracts and grants
 You have to plan funding for next year

But freedom is relative


„Safety in
„Safety“in Industry

Permanent contracts possible (often after trainee)

But also planning:
 Appraisals („Mitarbeitergespräche“)
 Projects
 Funding
 Mergers and restructuring
 Moving (Asia…)
g( )

Safety is relative


Non academic
Non-academic jobs
You can do everything!
Research in Industry (big pharma/small biotech)
Research/Project Management
Publishing, medical writing, journalism
Science communication and public relations
Patents
Teaching
Sales and Marketing
Consulting
Co su g
Clinical trials and applications
Informatics


Bioinformatics positions
Academic (publish!) System Analyst / Engineer

Core facility Technical Support

Training Database Designer /

IT Administrator

Software Applications Analyst

Biostatistics -> industry P
Programmer

Topics Marketing
g
Medical/clinical research …
Sequencing/high
throughput screening

Job hunting…

Richard Bolles, What Color Is Your Parachute?

Networking!

Start now! Look for INFORMATION

Learn to present yourself

Ask people about their work/life

Make info dates for 10 minutes

Send a personal „thank you“ so people remember you
you

Work on your skills – more important to take INITIATIVE than
increasing KNOWLEDGE or certificates


Life/work Planning L/W-P
g

It´s easier to act yourself
y
France: Daniel Porot
into a new way of thinking,
 www.porot.com
than it is to think yourself
 www careergames com
www.careergames.com
into
i t a new way of acting.
f ti
Germany: John Webb
 www.life-work-planning.de
Richard Nelson Bolles
 www.lwp-seminare.de

US: Richard N. Bolles
 www.jobhuntersbible.com

DKFZ WORKSHOPS
 Sat 07.07.2012 English (John Web)


LIKE this page! www.facebook.com/phdcareers


5/23/2012

Bioinformatik HUSAR (W180)
Core Facility Genomics Proteomics


Topics in Bioinformatics

There are two fundamental ways of modeling a Biological system (e.g., living cell)

Static
Sequences – Proteins, Nucleic acids and Peptides
Structures – Proteins, Nucleic acids, Ligands (including metabolites and drugs) and
Peptides
Interaction data among the above entities including microarray data and Networks of
proteins, metabolites

Dynamic
Systems Biology comes under this category including reaction fluxes and variable
concentrations of metabolites
Multi-Agent Based modeling approaches capturing cellular events such as signaling,
transcription and reaction dynamics

A broad sub-category under bioinformatics is structural bioinformatics.

5/23/2012 | Page 2 Karl-Heinz Glatting Bioinformatik HUSAR

Bioinformatics at DKFZ

Structure DKFZ
• Research: 70 departments and research groups in 7 research programs
• Service: 6 Core Facilities

My beginning 1994 – almost no bioinformatics , but statistics and IT core
facility
Now:
Search for „Bioinformatics“ at the DKFZ home page:
2231 Results for "bioinformatics“
e.g.
• Software
• ... for local installation. web cellHTS is accessible at: http://web-
cellhts2.dkfz.de Please cite when using web cellHTS: Pelz O, Gilsdorf M,
Boutros M. (2010). web cellHTS2: a web-application for the analysis of high-
throughput screening data. BMC Bioinformatics 11:185.


Bioinformaticians in Research and Service at DKFZ

• Research groups at DKFZ with bioinformaticians:
• Theoretical Bioinformatics (IBIOS) - Prof. Dr. Roland Eils
• Division of Systems Biology and Signal Transduction - Prof. Dr. Ursula
Klingmüller
• Signaling and Functional Genomics - Prof. Dr. Michael Boutros
• Molecular Genetics - Prof. Dr. Peter Lichter
• Molecular Genome Analysis - PD. Dr. Stefan Wiemann
• Translational Oncology - Prof. Dr. Christof von Kalle
• More coming

• Core Facility Genomics & Proteomics have bioinformaticians mainly in the
Sequencing group and the Bioinformatics (HUSAR) group


IBIOS – Prof. Dr. Eils

• iBioS - short for integrative Bioinformatics and Systems Biology - works on
the development of computer-assisted methods for the analysis of complex
data generated in the modern life sciences and develops mathematical
models for key cellular processes, for example in the context of virus
infection or cancer. Theoretical projects are carried out in close
collaboration with the experimental groups focusing on cellular death
pathways.
• Areas of major interest include:
• Modeling and simulation of cellular systems
• Data mining in molecular genetics and next generation sequencing
• Data management for high-throughput technologies and medical
samples
• Quantitative monitoring of intra-cellular processes using light-microscopy
• Biomedical computer vision


Other fields related to Bioinformatics at DKFZ

• Division of Medical and Biological Informatics - Prof. Dr. Hans-Peter
Meinzer
• imaging technologies such as computer tomography, magnetic
resonance tomography, and ultrasound.

• Division of Biophysics of Macromolecules - Prof. Dr. Jörg Langowski
• three-dimensional organization in the cell: DNA and chromatin global
structure


Hot Topics

• Analysis Next Generation Sequencing Data

• Mutation Analysis (SNPs, CNVs, …)

• Data Integration

• Systems Biology


Academia or Service

• Academic Career: In research groups it is easier to get
publications, maybe problem with first author/last author
publications
• Service: mostly no publications, but experience in certain fields
like Next Generation Sequencing, …
• Important: Networks, discussion groups, …


Bioinformatics.org


Background of People working in Bioinformatics

• Biologists, informatics, mathematicians, physicists,
medical scientists converted to Bioinformaticians

• Bioinformaticians, Biomathematicians, Computational
Biologists – now that specialised studies are possible


Example HUSAR

Example Service Bioinformatics (HUSAR)


Bioinformatics (HUSAR) Tools and Databases

• HUSAR (Sequence Analysis Environment):

• SRS (Sequence Retrieval System)

• Mascot Server (Database searches with mass spec data or peptide sequencing
data)

• Pipelines (e.g. SNP analysis, protein analysis)

• CNV programs (PennCNV, QuantiSNP)

• NGS software


Bioinformatics (HUSAR) Service includes

• Bioinformatics consulting/support

• Bioinformatics and NGS analysis courses

• Software implementation
• Tools for Microarray analysis
• NGS mapping and annotation

• Scripting (e.g. Genome analysis with Ensembl)

• Development of bioinformatics analysis pipelines, which are
complex analysis program combining different bioinformatics
applications connected by rules


End

Thank you for your attention


The European Bioinformatics Institute

EMBL-EBI
Katrina Pavelin
Scientific Outreach Officer
Services | Research | Training | Industry
katrina@ebi.ac.uk

What is EMBL-EBI?

• Bioinformatics Research & Service Institute
• Non-profit organisation
• Part of the European Molecular Biology Laboratory

EMBL-EBI

The five branches of EMBL
Heidelberg Hamburg Hinxton

• Basic research in Structural biology Bioinformatics
molecular biology
• Administration Grenoble Monterotondo
• EMBO

• 1500 staff
• >60 nationalities
Structural biology Mouse biology

EMBL-EBI

EMBL-EBI’s Mission
• To provide freely available data and bioinformatics services to all
facets of the scientific community in ways that promote scientific
progress
• To contribute to the advancement of biology through basic
investigator-driven research in bioinformatics
• To provide advanced bioinformatics training to scientists at all levels,
from PhD students to independent investigators
• To help disseminate cutting-edge technologies to industry
• To coordinate biological data provision across Europe

EMBL-EBI

What is bioinformatics?
• The science of storing,
retrieving and Growth of raw storage
analysing large at EMBL-EBI (in terabytes)
amounts of biological 12000

information 10000

8000
• An interdisciplinary

Disks (TB)
6000
science, involving
4000
biologists, computer
scientists and 2000

mathematicians 0

• At the heart of modern Year

biology

EMBL-EBI

Services
www.ebi.ac.uk/services

EMBL-EBI


Databases: molecules to systems Literature and ontologies
Genomes UKPMC, CiteXplore, GO
Ensembl
Ensembl Genomes Protein families,
EGA motifs and domains
Metagenomics InterPro
portal Functional
genomics
Macromolecular
ArrayExpress
Nucleotide sequence structure
Expression Atlas
ENA PDBe

Protein activity
IntAct, PRIDE Pathways
Reactome
Protein Sequences
UniProt

Chemical entities
ChEBI
Systems
Chemogenomics BioModels
ChEMBL BioSamples

EMBL-EBI

EBI’s search service
Access from the
EBI’s homepage

Species selector
allows for easy
comparison

Data organised
according to:
• gene Explore data,
• expression return easily to
• protein your results
• structure
• literature

EMBL-EBI

Research
www.ebi.ac.uk/groups

EMBL-EBI


Key facts about research at EMBL-EBI
• A unique
environment for
bioinformatics
research
• Nine dedicated
research groups
• Services teams also
carry out R&D
• Research and
services are mutually
supportive

EMBL-EBI

Training
www.ebi.ac.uk/training

EMBL-EBI


Pre- and postdocs at EMBL-EBI

• EMBL International PhD Programme
• Postdoctoral fellowships:
• EIPOD – EMBL-sponsored interdisciplinary fellowships
• ESPOD – EBI–Sanger combined experimental and
computational fellowships

EMBL-EBI

Thank you!

EMBL-EBI

Advanced Training @ EMBL

Dr. Helke Hillebrand
Dean of Graduate Studies
European Molecular Biology Laboratory

Training at all Levels: EICAT @ EMBL
EMBL International Center for Advanced Training
EIPOD

EMBL Postdoc ELLS (European
EMBL International Programme Learning Lab for
PhD Programme & the Life Sciences)
EMBL Collaborative
Training Programme

EMBO EMBL
Symposia

EMBL Visitors' & Scholars' Programme
2 Helke Hillebrand 08/2010 EMBL Courses &
Conferences

Predocs

EMBL International PhD Programme
EIPP

3 Helke Hillebrand 08/2010
03/2009

What can Predocs do at EMBL?

Biology
Chemistry
Physics
Mathematics
Informatics
Engineering
Molecular Medicine

www.embl.org/phdprogramme
www.embl.org/postdocs
www.embl.org.jobs

03/2009

Life of a Predoc at EMBL in a nutshell

 Highly competitive entry for >50 students per year; recruiting globally
 Expected to complete PhD studies within 3.5 – 4 years
 Tailor-made mentoring
– Individual thesis advisory committee (TAC) to meet with annually
– Complemetary skills training curriculum for individual choices

 Maintaining scientific links back home while joining EMBL
– External TAC member from home university
– Students ambassador programme

 Training all along
– Core course (1st year)
– Bioinformatics course (2nd year)
– Scientific lectures and seminar series
– Science & Society seminars and conferences
 Fostering early independence
– Predoc symposium
– Predoc retreat

03/2009

Key performance indicators of a PhD at EMBL

Graduation ceremony at EMBL in December, 2008

03/2009

Key performance indicators of a PhD at EMBL

 Application rate is at about 20:1
 Predoc to supervisor ratio is on average 2:1
 It takes about 3.5 – 4 years to finish a PhD
 Thesis submission rate of > 95% (predoc data since 1993)
 Majority of EIPP predocs obtains a doctoral degree with
distinction (>75%)
 Broad network of partner universities for joint degrees
 Excellent publication record
– 90% of predocs of a given class get (a) publication(s) from their PhD
– Predocs publish on average 2 papers on their PhD thesis topic

03/2009

What do EIPP students do after their PhD?
(Data from students who defended since 01/2004)

Scientific careers
outside research (13%)

18
9
Private sector
Academic
research (7%)
research (80%)
108


Postdocs

EMBL Interdisciplinary Postdocs EIPOD

Classical Postdoctoral Stream
Spanish Postdoctoral Programme

03/2009

The Postdoc community at EMBL
 About 220 Postdocs steady state; about 25% annual turnover
 Maximum duration of stay is 5 years; average duration is 4 years
 Entry routes – recruiting globally:
– Classical Postdoctoral Stream (intake of 25-30 p.a.)

– EMBL Interdisciplinary Postdocs (EIPOD ; intake of 20 p.a.)

– EBI-Sanger Postdoctoral Programme (ESPOD (intake of 2 p.a.)

– Spanish Postdoctoral Programme (intake of ~2 p.a.)

 Individual mentoring; 2nd mentor scheme
 Offering individual career development
 Postdocs account for about 30% of the EMBL alumni

03/2009

EMBL Interdisciplinary Postdocs (EIPOD)

Features
 Interdisciplinary research project
 Full three years of funding
 Open to all nationalities
 Hosted in two different labs at the five
EMBL sites
 Postdocs to develop own project proposals
 Marie Curie CO-FUNDing in 2009-2013
and 2012-2016
 Next call opens in June 2012
 www.embl.de/postdocs

What do Postdocs do after EMBL?
(Data from 921 postdocs whose whereabouts are known)

Scientific careers
outside research
(1%)
32
Non-scientific careers (3%)
90
Private sector
research (10%) 13

786 Academic
research (85%)


Complementary skills training

How to balance between ‚too much vs. not enough‘ ?
The right thing at the right time...
-
And what to do after PhD and Postdoc?

03/2009

Participating in non-scientific training activities
 Language training (German, English, French)
 IT courses (Microsoft Office and more)
 General training and development programme
– Personal skills
(time management, personal effectiveness, ...)
– Communication skills
(presentation skills, scientific writing, ...)
– Project management
– Grant applications & interviewing skills
– Team building & conflict management
– ...

 Career day – insight into alternative careers
03/2009

... how to avoid the Cecilia phenotype?

Complementary skills training

03/2009

Life as a scientific database curator

Sandra Orchard

EBI is an Outstation of the European Molecular Biology Laboratory.

What is a database curator

Curator – OED

- a keeper of a museum or other collection

- from LATIN curare – take care of

2/17


The job
• Creating a structure for unstructured biological data
• Generating order from chaos
• Combining literature and automated processes to provide
biomolecules with correct sequence/structure,
nomenclature, function and contextual information
• Give biological context to large experimental datasets
The qualification
• Need an attention to detail which would annoy even the
best of housemates
• Passion for reading and understanding literature

3/17


The Pros

• Read about and gain understanding of all areas of
biology

The Cons

• No specialisation
• Persuading biologists that there are benefits to this.

4/17


• The International Society for Biocuration (ISB) definition:
...integration of information relevant to biology into a
database or resource that enables integration of the
scientific literature...and large experimental data sets.
• Goals are
...accurate and comprehensive representation...
...to facilitate access to data for scientists...as a resource for
computational analysis

What does a database curator do?
Collects, annotates, and validates information (in a
database).

Extracts & organizes data from literature

Describes data using standards, protocols and
vocabularies (enabling computational queries and data
exchange).

Communicates with researchers to ensure the accuracy
of curated information and to foster good practice in data
exchange.

What does a database curator do?

Takes part in the development of shared
biomedical data standards and ontologies
and (ideally) enforces their use.

Trains users in effectively accessing and
using the data in the databases

Promotes database usage through talks,
conference attendance/posters,
publications etc…..

7/17

What do I do?

• Curate the molecular interaction database

8/17

What do I do?

Custom curation tools designed by the curation team

9/17

What do I do?

Controlled vocabulary maintenance

10/17

Qualifications for the job

• A biology B.Sc./M.Sc./PhD + lab experience

or

• A bioinformatics M.Sc

Plus – an enquiring mind, ability to write good English and
the right attitude

Training – largely database specific and will be given ‘on-
the-job’

11/17

Qualifications for the job

• Do I need to be able to do programming?

• Answer – no. It is often helpful to have some database
query ability but it is perfectly possible to do the job
without (in most databases)

12/17

Career Progression

Within the EBI
• Progress as a curator – senior curator, curation
coordinator

• Project management – grant coordinator, project leader

Post –EBI
• Curation/project leadership positions at many other
institutes
• Related areas – academic research, research project
management, lectureships, journal publishing

13/17

Will I still be allowed to publish?

Curation
The annotation of both human and mouse kinomes in
UniProtKB/Swiss-Prot - (MCP)
Data Standards
The Minimum Information required for reporting a Molecular
Interaction Experiment (MIMIx) – (NBT)
Data Formats
The HUPO PSI's molecular interaction format--a community
standard for the representation of protein interaction data.
– (NBT)

14/17

Will I still be allowed to publish?

Tool development
Rintact: enabling computational analysis of molecular
interaction data from the IntAct repository.
(Bioinformatics)
Ontologies
The use of common ontologies and controlled vocabularies
to enable data exchange and deposition for complex
proteomic experiments (Pac Symp Biocomput)
Training
Submit your interaction data the IMEx way - a step by step
guide to trouble-free deposition (Proteomics)

15/17

Curation as a profession

16/17

Curation as a profession

• Biocuration conference every 12 months – 2102 in
Cambridge, UK

• Opportunities for further training – bioinformatic tools,
programming, career development/management

• Attendance at biological/computational biology
conferences encouraged – the EBI often provides
speakers

17/17

Summary

• Curation is not for everyone – it does require a certain
mindset

• Exposes you to all areas of biology (and chemistry)

• Now a recognised profession and our numbers are
growing

• Many opportunities to be become involved in “extra-
curriculum” activities – its not all reading papers

18/17

How did I get here? My career so far...
Dr. Jennifer Cham
User Experience Analyst, EMBL-EBI (Cambridge, UK)

I studied biochemistry then bioinformatics…

Cranfield University

Cranfield University
Imperial College London

•  2000-2004 •  2004-2005 •  2005-2009

•  BSc •  MSc •  Engineering
Biochemistry Bioinformatics Doctorate
(EngD) in
•  Year in industry: •  UK university Bioinformatics
Merck KGaA, near Milton
Darmstadt, Keynes •  Sponsor: GSK
Germany
•  Project: BOKU, •  Incl. exec MBA
Vienna, Austria

June 14, 2012
2

What do I do now?

•  Nov 2009 joined the European Bioinformatics Institute
•  ‘User experience Analyst’ role in bioinformatics
4
•  Transferrable skills from my doctorate

MSc in Bioinformatics included:
•  Computer programming (Perl, Java)
•  Databases, SQL
•  Tools e.g. those at the EBI website
•  Statistics e.g. Matlab
•  5 month project
EngD in Proteomic Bioinformatics included:
•  Research project!
•  MBA for a year
•  Bioinformatics meetings and conferences
5
•  Multiple project supervisors including in pharma industry

At Cranfield University…

6

MSc project in cross-species microarray
bioinformatics
…in Vienna

Opportunities to make connections with other universities

14/06/2012
8

Working with
postdocs during
the doctorate

9

Teaching, writing
papers & reviews

14/06/2012
10

EBI role

My current role
14/06/2012
11

Consulting with service teams

14/06/2012
12

User-Centered Design e.g. card sorting

14/06/2012
13

1-to-1 usability testing
•  involves travelling
•  interacting with scientists
•  Draws in my science background

14/06/2012
14

Capturing User Requirements: workshops, focus groups, user surveys

14/06/2012
15

Thanks for listening…

16

Giulietta M. Spudich, PhD
Outreach Project Leader, Ensembl

This talk …

• Background (not bioinformatics!)
• Why I moved from research
• My job now, and how I got there
• What I like about it all

2

Background – Graduate School

• PhD from University of California, Berkeley in Molecular
and Cell Biology.
• Thesis: Interactions in the Folding Intermediate of E. coli RNase H: Comparisons
with the Native State Ensemble

• Teaching:
• Introduction to Biochemistry Lab and Lecture (TA)
• Snapshots of a Protein: Methods in Detecting Protein Structure
• Oversaw the 7 month lab project of a Master’s Student

• Teaching awards (one ‘applied’ for)

Challenges: Juggling teaching and research
Advisor wasn’t thrilled
Payoffs: Opened the door to teaching
3

Background- PostDoc

• MRC-LMB Biochemical investigation
of Myosin VI interactions with protein and lipid

• Three publications (Nature Cell Biology, Journal of Cell Biology, and
Annual Review in Cell and Dev. Biol.)

• Teaching:
• University Teaching Associate (workshops in teaching and presentation skills)
• Cambridge International Exams – Wrote and marked exams and course material in
Proteomics

Challenges: Two jobs! Takes time …
Payoffs: More teaching experience, exam writing, and
increased transferable skills like giving presentations
4

Outreach for a Genomics Resource

• Mixes science and teaching into one job
• Supports research
• Bioinformatics resource- in an active and fascinating field
• Includes many different activities.
• Presentations/ teaching
• Video tutorials
• Helpdesk (email support)
• Writing help material
• Help with web design based on user feedback
• Usability testing (recent)

Challenges: Changed fields from protein biochemistry!
Genomics and bioinformatics! Lots to learn.
5
Payoffs: Get to have one job now. Doing what I love.

Career Growth

• In Feb 2011, I applied for and moved to the Ensembl
Outreach Team Leader position.

• New job duties:
• Manage a team of 3 people
• Strategy and management meetings
• Decide directions and focus of our Outreach
• Train new members
• Maintain teaching and support

Challenges: Management is a new experience. A new
challenge! (EMBL courses help!)
Payoffs: Stimulating, I develop new skills, and what I do
has more impact on our project.
6

What worked for me?
• Working hard
• Following what I loved to do
• Finding out what others do in their jobs (career paths)
• Sticking with an interesting and active project/field
• Recognising that scientific careers extend beyond basic
research

Follow your heart! What do you find fulfilling?

7

24 May 2012

Felix Klein

Background

• physics diploma, University of Heidelberg

• diploma thesis in radiation dosimetry
at DKFZ

• measurements at HIT

2 24.05.2012 Felix Klein

Why bioinformatics?

• interdisciplinary

• programmed in R

• worked on data analysis


Progress in science is driven by technology


Chromatin loops


Investigation of chromatin 3D structure
• role of chromatin 3D structure in gene regulation

• 4C to investigate detailed interactions of
cis-regulatory modules (CRMs)

• global chromatin interactome using HiC


Investigation of chromatin 3D structure


Automated analysis of microscopy based
RNAi screens
Features
Imaging Segmentation extraction

Source image Calibrated image Segmentation mask
9.241719
g.pd

g.x g.y g.s g.p g.pdm
g.s g.p
194 67

[1,] 123.1391 3.288660 194 67 9.241719
[2,] 206.7460 9.442248 961 153 20.513190
[3,] 502.9589 7.616438 219 60 8.286918
[4,] 20.1919 22.358418 1568 157 22.219461
3.288660

[5,] 344.7959 45.501992 2259 233 35.158966
Summary Classification [6,] 188.2611 50.451863 2711 249 28.732680
g.y

[7,] 269.7996 46.404036 2131 180 26.419631
aft apt neg [8,] 106.6127 58.364243 1348 143 21.662879
[9,] 218.5582 77.299007 1913 215 25.724580
[10,] 19.1766 81.840147 1908 209 26.303760
123.1391

[11,] 6.3558 62.017647 340 68 10.314127
g.x

[12,] 58.9873 86.034128 2139 214 27.463158
[13,] 245.1087 94.387405 1048 123 18.280901
[14,] 411.2741 109.198678 2572 225 28.660816
int pos [15,]
[16,]
167.8151 107.966014 1942 160
281.7084 121.609892 2871 209
24.671533
31.577270

Phenotypic profile Objects labels Object features

8

What was important for me?
• bioinformatics group with
members of diverse
backgrounds

• PI who successfully
trained bioinformaticians

• well established group in
bioinformatics


What might be interesting for you
• turn data into biology

• interaction with people from biology groups

• communication skills !!!

• workload divides mainly into:
• programming (50 %)
• reports, meetings, email


Acknowledgements
Wolfgang Huber
Simon Anders
Joseph Barry
Bernd Fischer
Julian Gehring
Aleksandra Pekowska
Paul Theodor Pyl
Alejandro Reyes
Maria Secrier

Collaborators:
Michael Boutros
Christian Volz

Eileen Furlong
Yad Ghavi Helm


Data production rates
LHC: 1.8 GB / s at peak capacity (i.e. actively conducting a
primary aspect of the LHC’s four main experiments: ATLAS,
ALICE, CMS, and LHCb).
These experiments will take roughly a decade to complete, and
each of them is expected to produce over a 1 PB per year of
data.

One Illumina HiSeq: up to 600 Gb/run , i.e. ~600 GB/10 days =
18 TB/year (not including derived data e.g. BAM)
One Digital Embryo (2008): 3.5 TB (2048 x 2048 x 370 x 1226)
EMBL-EBI: in 9/2011, data storage capacity was 14 PB

Training and Life as a Postdoc (in case of Kota)

EMBL-EBI / DKFZ Bioinformatics Career Day

Kota Miura (miura@embl.de)

Centre for Molecular and Cellular Imaging,
EMBL Heidelberg, Germany

May 24, 2012 DKFZ, Heidelberg


Overview of CMCI (2006 - )

Image Processing & Analysis…
Teaching in many places:
EU (EMBO courses), Germany, Japan,
- Teaching Courses France, Switzerland, Austria, Italy,
Finland, Sweden, Singapore, Spain
- Organize seminars
- Consulting & Collaborations
- Developments
- Research

Consulting & Collaborations Recursive Model

Project Model 1
Experiments -> Microscopy -> Image Processing -> Image Analysis

Project Model 2
Microscopy

Experiments Image Analysis

Image Processing

Centre for Molecular and Cellular Imaging (CMCI) @EMBL

The Concept of CMCI network
Facilities
Research Units e.g. ALMF
1. Tree-like human resources structure in EMBL

2. Association of researchers crossing over different labs and units
 “CMCI as a meta-system, network”

EMBL
Cell Bio. & Biophysics Dev. Bio. Genome

Units

Groups

Kota Miura (miura@embl.de) CMCI

Background
1989 – 1993: International Christian University (Tokyo, Undergraduate)
social behavior of monkeys, macaca (field research )
cucumber stomata development (video microscopy)

1993 – 1996: Osaka University (Osaka, Master)
single cell migration, physarum 8 years of
graduate school!!

1996 – 2001: Zoological Institute, LMU (Munich, Ph.D.)
multicellular migration, dictyostelium phototaxis

2001 – 2005: Cell Biology and Biophysics, EMBL (PosDoc, Heidelberg)
phototaxis + vesicle dynamics + image analysis + simulation

2005 – : Centre for Molecular and Cellular Imaging, EMBL (Heidelberg)
Image processing & Analysis, Simulations

Zoological Institute, LMU


- What attracted you to this position?

- I like to analyze things. My job fits to this. Computer is a great tool for analysis.

- What do you enjoy most about your job?

- Satisfies curiosity in many directions. In depth discussion with people.
Resulting beautiful plots. Coding is like gardening.

- What skills are useful in your role?

- Knowledge on biology, physiology, analytical chemistry, programming. Many
more skills I need but missing still.

Bioinformatics Career Day 2012

Shinichi Sunagawa
Bork Group
www.sunagawa.de
EMBL Heidelberg
EBI / DKFZ: Bioinformatics Career Day – 24 May 2012

Current Role
Since Jan 2012 (after 1.5 years postdoc)
• Research Scientist at Bork Group: Computational Biology
- Network biology
- Comparative genomics
- Metagenomics

• Responsibilities
- coordinate / manage metagenomics projects

Qin et al. 2010, Nature; Arumugam et al. 2011, Nature Karsenti et al. 2011, PLoS Biology

- support progress of PhD students and postdocs
- own research projects

Background / atypical career path?
Diploma - Biochemistry
MSc / PhD - Aquatic Ecology / Quantitative and Systems Biology

Started programming in 2006

PhD 2010


Today and outlook
Typical activity
- using and developing programs to analyze DNA sequencing data
What attracted me to this position?
• exciting projects
• from data generation to data analysis
• diversification of skill-set
• springboard to independent researcher

What do I enjoy most about my job?
• perspective to find out something useful

Two cents for future bioinformaticians:
• in many, if not most areas of biology, computers keep gaining importance

Yann Abraham
Novartis, Basel

http://prezi.com/ugn43malcumr/dkfz‐careers‐in‐bioinformatics‐day‐2012/

24.05.2012

Dr. Matthias Scherf
Genomatix Software GmbH
Bayerstrasse 85a. 80335 Munich
http://www.genomatix.com

www.genomatix.com © 2012 Genomatix

2

My Background:

Diploma in Informatics / theoretical Medicine (minor)
(Technical University Munich)

PhD (Dr. rer. nat)
Helmholtz Zentrum Munich/TU Munich

2 years Postdoc
Helmholtz Zentrum Munich

Since 2000 Genomatix Software GmbH


3

My career-path at Genomatix

Development & Pre-sales
Genome wide promoter prediction
Mapping algorithms (RNA to DNA)
Support of sales team by scientific talks

Head of Discovery (heading a group of 5 Employees)
Genome annotation pipeline and comparative genomics
Literature & pathway analysis
microArray and NGS data analysis

CTO (Managing director)


4

My responsibilities
Strategic decisions
In-house developments
Integration of third party tools
Data background
Infrastructure

Oversee developments

Define work packages for public funded projects

Suggest data analysis solutions for consulting projects

Do presentations


5

Why Bioinformatics ?
Interest in Medicine / Biology
Understanding (disease) mechanisms at “DNA level”

What I like about my job
Working in an interdisciplinary environment
Finding creative solutions for individual challenges
Close contact to the scientific community
Teaching / Consulting

Ok… not everything is great
Lots of administration / paper work…
Only little time for programming/science left


6

Genomatix
Offers NGS data analysis solutions & consulting

Level 1 Level 2

Mapping, Clustering, Functional analysis
Results
Variant detection,
Short sequence reads Annotation
Value
(billions)

Genome annotation Gene regulation Literature & Pathway
database database database

Databases


Bioinformatics Career Day

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