Bioinformatics Career Day


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Bioinformatics Career Day

  1. 1. Slides careers-in-bioinformatics-day-2012/ Feedback nformaticscareerday
  2. 2. Scientific Career Development Bioinformatics Career DayDr. Barbara JanssensMay 2012
  3. 3. Bioinformatics Career Day23-May-12 Page 2 Barbara Janssens PhD Career Service
  4. 4. p g y Email  TWEET   #bxcareers Slides  http://www slideshare net/phdcareers/presentations Feedback  Feel free to use our „internet cafe“ in the back cafe23-May-12 Page 3 Barbara Janssens PhD Career Service
  5. 5. PhD Career Development p www dkfz de/phd/Careers html Concept: Career as „Scientific life beyond the lab“23-May-12 Page 4 Barbara Janssens PhD Career Service
  6. 6. 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 … C23-May-12 Page 5 Barbara Janssens PhD Career Service
  7. 7. My career network y Playground networkGraduate school Teaching Editor23-May-12 Page 6 Barbara Janssens PhD Career Service
  8. 8. Careers Service Milestones23-May-12 Page 7 Barbara Janssens PhD Career Service
  9. 9. Heidelberg Career Calendar Page 8 Barbara Janssens PhD Career Service
  10. 10. Career destination Plan A vs Plan B Adapted from Gerd Altmann www.pixelio.de23-May-12 Page 9 Barbara Janssens PhD Career Service
  11. 11. DKFZ PhD students want…23-May-12 Page 10 Barbara Janssens PhD Career Service
  12. 12. „Freedom„Freedom“ in Academia Temporary contracts and grants  You have to plan funding for next year But freedom is relative23-May-12 Page 11 Barbara Janssens PhD Career Service
  13. 13. „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 relative23-May-12 Page 12 Barbara Janssens PhD Career Service
  14. 14. Non academicNon-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 Informatics23-May-12 Page 13 Barbara Janssens PhD Career Service
  15. 15. 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 screening23-May-12 Page 14 Barbara Janssens PhD Career Service
  16. 16. Job hunting… Richard Bolles, What Color Is Your Parachute?23-May-12 Page 16 Barbara Janssens PhD Career Service
  17. 17. 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 certificates23-May-12 Page 17 Barbara Janssens PhD Career Service
  18. 18. Life/work Planning L/W-P g It´s easier to act yourself y France: Daniel Porot into a new way of thinking,  than it is to think yourself  www careergames com into i t a new way of acting. f ti Germany: John Webb  Richard Nelson Bolles  US: Richard N. Bolles  DKFZ WORKSHOPS  Sat 07.07.2012 English (John Web)23-May-12 Page 18 Barbara Janssens PhD Career Service
  19. 19. LIKE this page! Page 19 Barbara Janssens PhD Career Service
  20. 20. 5/23/2012 Bioinformatik HUSAR (W180) Core Facility Genomics Proteomics Bioinformatics Career Day
  21. 21. 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
  22. 22. Bioinformatics at DKFZStructure DKFZ• Research: 70 departments and research groups in 7 research programs• Service: 6 Core FacilitiesMy beginning 1994 – almost no bioinformatics , but statistics and IT core facilityNow: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- 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 11:185.5/23/2012 | Page 3 Karl-Heinz Glatting Bioinformatik HUSAR
  23. 23. 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) group5/23/2012 | Page 4 Karl-Heinz Glatting Bioinformatik HUSAR
  24. 24. 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 vision5/23/2012 | Page 5 Karl-Heinz Glatting Bioinformatik HUSAR
  25. 25. 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 structure5/23/2012 | Page 6 Karl-Heinz Glatting Bioinformatik HUSAR
  26. 26. Hot Topics• Analysis Next Generation Sequencing Data• Mutation Analysis (SNPs, CNVs, …)• Data Integration• Systems Biology5/23/2012 | Page 7 Karl-Heinz Glatting Bioinformatik HUSAR
  27. 27. 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, …5/23/2012 | Page 8 Karl-Heinz Glatting Bioinformatik HUSAR
  28. 28. LinkedIn5/23/2012 | Page 9 Karl-Heinz Glatting Bioinformatik HUSAR
  29. 29. Bioinformatics.org5/23/2012 | Page 10 Karl-Heinz Glatting Bioinformatik HUSAR
  30. 30. Background of People working in Bioinformatics• Biologists, informatics, mathematicians, physicists, medical scientists converted to Bioinformaticians• Bioinformaticians, Biomathematicians, Computational Biologists – now that specialised studies are possible5/23/2012 | Page 11 Karl-Heinz Glatting Bioinformatik HUSAR
  31. 31. Example HUSARExample Service Bioinformatics (HUSAR)5/23/2012 | Page 12 Karl-Heinz Glatting Bioinformatik HUSAR
  32. 32. 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 software5/23/2012 | Page 13 Karl-Heinz Glatting Bioinformatik HUSAR
  33. 33. 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 rules5/23/2012 | Page 14 Karl-Heinz Glatting Bioinformatik HUSAR
  34. 34. EndThank you for your attention5/23/2012 | Page 15 Karl-Heinz Glatting Bioinformatik HUSAR
  35. 35. The European Bioinformatics Institute EMBL-EBIKatrina PavelinScientific Outreach Officer Services | Research | Training |
  36. 36. What is EMBL-EBI?• Bioinformatics Research & Service Institute• Non-profit organisation• Part of the European Molecular Biology Laboratory EMBL-EBI
  37. 37. The five branches of EMBLHeidelberg Hamburg Hinxton• Basic research in Structural biology Bioinformatics molecular biology• Administration Grenoble Monterotondo• EMBO• 1500 staff• >60 nationalities Structural biology Mouse biology EMBL-EBI
  38. 38. 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
  39. 39. 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
  40. 40. EMBL-EBI Services | Research | Training | Industry
  41. 41. Databases: molecules to systems Literature and ontologies Genomes UKPMC, CiteXplore, GO EnsemblEnsembl 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
  42. 42. EBI’s search service Access from the EBI’s homepage Species selector allows for easy comparisonData organisedaccording to:• gene Explore data,• expression return easily to• protein your results• structure• literature EMBL-EBI
  43. 43. EMBL-EBI Services | Research | Training | Industry
  44. 44. 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
  45. 45. EMBL-EBI Services | Research | Training | Industry
  46. 46. 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
  47. 47. EMBL-EBI
  48. 48. 14 EMBL-EBI
  49. 49. Thank you! EMBL-EBI
  50. 50. Advanced Training @ EMBLDr. Helke HillebrandDean of Graduate StudiesEuropean Molecular Biology Laboratory
  51. 51. 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 Programme2 Helke Hillebrand 08/2010 EMBL Courses & Conferences
  52. 52. Predocs EMBL International PhD Programme EIPP3 Helke Hillebrand 08/2010 03/2009
  53. 53. What can Predocs do at EMBL? Biology Chemistry Physics Mathematics Informatics Engineering Molecular Medicine Helke Hillebrand 08/2010 03/2009
  54. 54. 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 retreat5 Helke Hillebrand 08/2010 03/2009
  55. 55. Key performance indicators of a PhD at EMBL Graduation ceremony at EMBL in December, 20086 Helke Hillebrand 08/2010 03/2009
  56. 56. 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 topic7 Helke Hillebrand 08/2010 03/2009
  57. 57. 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%) 1088 Helke Hillebrand 08/2010
  58. 58. Postdocs EMBL Interdisciplinary Postdocs EIPOD Classical Postdoctoral Stream Spanish Postdoctoral Programme9 Helke Hillebrand 08/2010 03/2009
  59. 59. 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 alumni10 Helke Hillebrand 08/2010 03/2009
  60. 60. 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  Helke Hillebrand 08/2010
  61. 61. 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%)12 Helke Hillebrand 08/2010
  62. 62. 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?13 Helke Hillebrand 08/2010 03/2009
  63. 63. 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 careers14 Helke Hillebrand 08/2010 03/2009
  64. 64. ... how to avoid the Cecilia phenotype? Complementary skills training15 Helke Hillebrand 08/2010 03/2009
  65. 65. Thank you!
  66. 66. Life as a scientific database curator Sandra Orchard EBI is an Outstation of the European Molecular Biology Laboratory.
  67. 67. What is a database curator Curator – OED - a keeper of a museum or other collection - from LATIN curare – take care of2/17
  68. 68. What is a database curator 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 literature3/17
  69. 69. What is a database curator 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
  70. 70. What is a database curator• 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 facilitate access to data for a resource for computational analysis
  71. 71. What does a database curator do?Collects, annotates, and validates information (in adatabase).Extracts & organizes data from literatureDescribes data using standards, protocols andvocabularies (enabling computational queries and dataexchange).Communicates with researchers to ensure the accuracyof curated information and to foster good practice in dataexchange.
  72. 72. 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
  73. 73. What do I do? • Curate the molecular interaction database8/17
  74. 74. What do I do? Custom curation tools designed by the curation team9/17
  75. 75. What do I do? Controlled vocabulary maintenance10/17
  76. 76. 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
  77. 77. 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
  78. 78. 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 publishing13/17
  79. 79. 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 PSIs molecular interaction format--a community standard for the representation of protein interaction data. – (NBT)14/17
  80. 80. 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
  81. 81. Curation as a profession16/17
  82. 82. 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 speakers17/17
  83. 83. 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 papers18/17
  84. 84. How did I get here? My career so far...Dr. Jennifer ChamUser Experience Analyst, EMBL-EBI (Cambridge, UK)
  85. 85. 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, 20122
  86. 86. 14/06/20123
  87. 87. What do I do now? •  Nov 2009 joined the European Bioinformatics Institute •  ‘User experience Analyst’ role in bioinformatics4 •  Transferrable skills from my doctorate
  88. 88. 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 conferences5 •  Multiple project supervisors including in pharma industry
  89. 89. At Cranfield University…6
  90. 90. MSc project in cross-species microarraybioinformatics …in Vienna
  91. 91. Opportunities to make connections with other universities 14/06/20128
  92. 92. Working with postdocs during the doctorate9
  93. 93. Teaching, writing papers & reviews 14/06/201210
  94. 94. EBI role My current role 14/06/201211
  95. 95. Consulting with service teams 14/06/201212
  96. 96. User-Centered Design e.g. card sorting 14/06/201213
  97. 97. 1-to-1 usability testing •  involves travelling •  interacting with scientists •  Draws in my science background 14/06/201214
  98. 98. Capturing User Requirements: workshops, focus groups, user surveys 14/06/201215
  99. 99. Thanks for listening… 16
  100. 100. Bioinformatics Career DayGiulietta M. Spudich, PhDOutreach Project Leader, Ensembl
  101. 101. This talk … • Background (not bioinformatics!) • Why I moved from research • My job now, and how I got there • What I like about it all2
  102. 102. 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 thrilledPayoffs: Opened the door to teaching3
  103. 103. 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 presentations4
  104. 104. 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.
  105. 105. 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
  106. 106. 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
  107. 107. Bioinformatics Career Day24 May 2012Felix Klein
  108. 108. Background • physics diploma, University of Heidelberg • diploma thesis in radiation dosimetry at DKFZ • measurements at HIT2 24.05.2012 Felix Klein
  109. 109. Why bioinformatics? • interdisciplinary • programmed in R • worked on data analysis3 24.05.2012 Felix Klein
  110. 110. Progress in science is driven by technology4 24.05.2012 Felix Klein
  111. 111. Chromatin loops5 24.05.2012 Felix Klein
  112. 112. 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 HiC6 24.05.2012 Felix Klein
  113. 113. Investigation of chromatin 3D structure7 24.05.2012 Felix Klein
  114. 114. 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 31.577270Phenotypic profile Objects labels Object features 8
  115. 115. What was important for me? • bioinformatics group with members of diverse backgrounds • PI who successfully trained bioinformaticians • well established group in bioinformatics9 24.05.2012 Felix Klein
  116. 116. 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, email10 24.05.2012 Felix Klein
  117. 117. AcknowledgementsWolfgang HuberSimon AndersJoseph BarryBernd FischerJulian GehringAleksandra PekowskaPaul Theodor PylAlejandro ReyesMaria SecrierCollaborators:Michael BoutrosChristian VolzEileen FurlongYad Ghavi Helm11 24.05.2012 Felix Klein
  118. 118. Data production ratesLHC: 1.8 GB / s at peak capacity (i.e. actively conducting aprimary aspect of the LHC’s four main experiments: ATLAS,ALICE, CMS, and LHCb).These experiments will take roughly a decade to complete, andeach of them is expected to produce over a 1 PB per year ofdata.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
  119. 119. Training and Life as a Postdoc (in case of Kota) EMBL-EBI / DKFZ Bioinformatics Career Day Kota Miura ( Centre for Molecular and Cellular Imaging, EMBL Heidelberg, Germany May 24, 2012 DKFZ, HeidelbergKota Miura (
  120. 120. 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
  121. 121. Consulting & Collaborations Recursive Model Project Model 1 Experiments -> Microscopy -> Image Processing -> Image Analysis Project Model 2 Microscopy Experiments Image Analysis Image Processing
  122. 122. 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 GroupsKota Miura ( CMCI
  123. 123. 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, SimulationsKota Miura (
  124. 124. Zoological Institute, LMUKota Miura (
  125. 125. - 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. Manymore skills I need but missing still.
  126. 126. Bioinformatics Career Day 2012 Shinichi Sunagawa Bork Group EMBL Heidelberg EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
  127. 127. Current RoleSince 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 EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
  128. 128. Background / atypical career path?Diploma - BiochemistryMSc / PhD - Aquatic Ecology / Quantitative and Systems Biology Started programming in 2006 PhD 2010 EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
  129. 129. Today and outlookTypical 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 researcherWhat do I enjoy most about my job? • perspective to find out something usefulTwo cents for future bioinformaticians: • in many, if not most areas of biology, computers keep gaining importance EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
  130. 130. Yann Abraham Novartis, Basel‐careers‐in‐bioinformatics‐day‐2012/
  131. 131. Bioinformatics Career Day 24.05.2012Dr. Matthias ScherfGenomatix Software GmbHBayerstrasse 85a. 80335 Munich © 2012 Genomatix
  132. 132. 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 © 2012 Genomatix
  133. 133. 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) © 2012 Genomatix
  134. 134. 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 © 2012 Genomatix
  135. 135. 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 © 2012 Genomatix
  136. 136. 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 © 2012 Genomatix