This document provides information about a Bioinformatics Career Day event held at the German Cancer Research Center (DKFZ). It discusses the agenda for the event, which included presentations on bioinformatics topics and careers, networking opportunities, and a discussion on academic vs industry careers in bioinformatics. Resources provided include links to slides, feedback surveys, and social media accounts for further information.
Career Paths in the Life Sciences. Janssens, Summer 2012phdcareers
Slides of presentation at Career Day in Lübeck
http://www.gradschool.uni-luebeck.de/index.php?id=13&no_cache=1&tx_ttnews%5Btt_news%5D=199&cHash=579a927bdfcf2c7d26862c28f74c0a76
Science to Data Science: PhDs and postdocs moving to startups and industry (2...AI Guild
How to get interviews and the employment contract. A roadmap workshop on transitioning to the industry in a #datacareer, e.g. Data Scientist, Data Analyst, ML engineer, NLP practitioner, etc.
Benefit from the insights of Europe's leading 1000+ practitioner community, including Ph.D. role models from STEM disciplines and the social sciences that now enjoy a #datacareer.
Career Paths in the Life Sciences. Janssens, Summer 2012phdcareers
Slides of presentation at Career Day in Lübeck
http://www.gradschool.uni-luebeck.de/index.php?id=13&no_cache=1&tx_ttnews%5Btt_news%5D=199&cHash=579a927bdfcf2c7d26862c28f74c0a76
Science to Data Science: PhDs and postdocs moving to startups and industry (2...AI Guild
How to get interviews and the employment contract. A roadmap workshop on transitioning to the industry in a #datacareer, e.g. Data Scientist, Data Analyst, ML engineer, NLP practitioner, etc.
Benefit from the insights of Europe's leading 1000+ practitioner community, including Ph.D. role models from STEM disciplines and the social sciences that now enjoy a #datacareer.
Watching the workers: researching information behaviours in, and for, workplacesHazel Hall
Keynote presentation on researching information behaviours in workplaces delivered at Association for Information Science and Technology (ASIST) Annual Symposium on Information Needs Seeking and Use 2016.
Full citation:
Hall, H. (2016). Watching the workers: researching information behaviours in, and for, workplace environments. Opening keynote presented at Information behavior in workplaces: Association for Information Science and Technology (ASIST) Annual Symposium on Information Needs Seeking and Use 2016, Copenhagen, Denmark, 15 October 2016.
Transcript of Webinar: Data management plans (DMPs) - audioARDC
Video and slides available via: http://www.ands.org.au/news-and-events/presentations/2017
Have you implemented a Data Mangement Plan (DMP) tool at your institution or are you currently involved in discussions to implement one? Woudl you like to connect with others who are involved in implementing DMPs? Then this webinar is for you!
This webinar brings together those involved in planning or implementing DMP to exchange information and explore ideas around DMP.
Getting Up to Speed with R: Certificate Program in R for Statistical Analysis...Revolution Analytics
The Institute for Statistics Education at Statistics.com offers a graduate-level certificate program in R for those who want to use the R statistical programming environment for statistical analysis, visualization and modeling. The Institute offers continuing education credits as well as a Program completion certificate. Courses are offered year-round (there is no semester system) on a flexible schedule. The content of the Program is the equivalent of 18 credits, in the US academic system. Faculty include R core development team members, package developers, authors of books on R: Paul Murrell, Hadley Wickham, Thomas Lumley, Sudha Purohit, Luis Torgo, John Verzani, others.
Join this webinar to learn about the structure of the certificate and available courses through the Institute, which are offered in 3 categories:
Basic programming skills in R
Statistical methods implemented in R
R applied to specific domains
This presentation was provided by David Parsons of Digital Science, during the fifth session of the Spring 2023 NISO Training Series "Quality Assurance of Data Sets." The class focused on Discoverability, and was held May 25, 2023.
Profiles of 186 women data analytics experts. Includes fields such as statistical analysis, data mining, text mining, data analysis, data science, ethnographics, business intelligence, and more.
Data For Policy Influence: How to Manage, Distribute, and Present Your DataForum One
To make smart policy decisions on important issues – whether global, national or local – leaders and influencers need information, analysis, and insight.
If your organization is in the business of supplying that information, then you already know that Data is an essential ingredient for success. You also know that in this digital age your briefs and reports – the traditional distribution tools for your insights – are competing for attention in an extremely competitive and noisy online marketplace of ideas. Attention is scarce, and gaining attention with 20-page PDFs online is not very easy.
So how can you put your data to better use digitally to extend your influence?
In this presentation, Laura Castillo-Page of the American Association of Medical Colleges (AAMC) and Kurt Voelker of Forum One dig into real-world examples from the AAMC and others about the first steps that organizations like yours can take to better present their data.
IN THIS PRESENTATION YOU WILL LEARN how NGO’s can evolve their use of data to be more digitally native by:
• Presenting data as engaging interactive visualizations
• Distributing data in more accessible formats
• Managing data more effectively on the backend
PRESENTED BY:
Laura Castillo-Page, Ph.D.
Senior Director, Diversity and Programs and Organizational Capacity Building Portfolio
Association of American Medical Colleges (aamc.org)
Kurt Voelker
Chief Technology Officer
Forum One (forumone.com)
*These slides are from a Forum One Webinar. Check out our YouTube channel (http://youtube.com/forumonevideo) for the audio/video of this virtual event.*
Watching the workers: researching information behaviours in, and for, workplacesHazel Hall
Keynote presentation on researching information behaviours in workplaces delivered at Association for Information Science and Technology (ASIST) Annual Symposium on Information Needs Seeking and Use 2016.
Full citation:
Hall, H. (2016). Watching the workers: researching information behaviours in, and for, workplace environments. Opening keynote presented at Information behavior in workplaces: Association for Information Science and Technology (ASIST) Annual Symposium on Information Needs Seeking and Use 2016, Copenhagen, Denmark, 15 October 2016.
Transcript of Webinar: Data management plans (DMPs) - audioARDC
Video and slides available via: http://www.ands.org.au/news-and-events/presentations/2017
Have you implemented a Data Mangement Plan (DMP) tool at your institution or are you currently involved in discussions to implement one? Woudl you like to connect with others who are involved in implementing DMPs? Then this webinar is for you!
This webinar brings together those involved in planning or implementing DMP to exchange information and explore ideas around DMP.
Getting Up to Speed with R: Certificate Program in R for Statistical Analysis...Revolution Analytics
The Institute for Statistics Education at Statistics.com offers a graduate-level certificate program in R for those who want to use the R statistical programming environment for statistical analysis, visualization and modeling. The Institute offers continuing education credits as well as a Program completion certificate. Courses are offered year-round (there is no semester system) on a flexible schedule. The content of the Program is the equivalent of 18 credits, in the US academic system. Faculty include R core development team members, package developers, authors of books on R: Paul Murrell, Hadley Wickham, Thomas Lumley, Sudha Purohit, Luis Torgo, John Verzani, others.
Join this webinar to learn about the structure of the certificate and available courses through the Institute, which are offered in 3 categories:
Basic programming skills in R
Statistical methods implemented in R
R applied to specific domains
This presentation was provided by David Parsons of Digital Science, during the fifth session of the Spring 2023 NISO Training Series "Quality Assurance of Data Sets." The class focused on Discoverability, and was held May 25, 2023.
Profiles of 186 women data analytics experts. Includes fields such as statistical analysis, data mining, text mining, data analysis, data science, ethnographics, business intelligence, and more.
Data For Policy Influence: How to Manage, Distribute, and Present Your DataForum One
To make smart policy decisions on important issues – whether global, national or local – leaders and influencers need information, analysis, and insight.
If your organization is in the business of supplying that information, then you already know that Data is an essential ingredient for success. You also know that in this digital age your briefs and reports – the traditional distribution tools for your insights – are competing for attention in an extremely competitive and noisy online marketplace of ideas. Attention is scarce, and gaining attention with 20-page PDFs online is not very easy.
So how can you put your data to better use digitally to extend your influence?
In this presentation, Laura Castillo-Page of the American Association of Medical Colleges (AAMC) and Kurt Voelker of Forum One dig into real-world examples from the AAMC and others about the first steps that organizations like yours can take to better present their data.
IN THIS PRESENTATION YOU WILL LEARN how NGO’s can evolve their use of data to be more digitally native by:
• Presenting data as engaging interactive visualizations
• Distributing data in more accessible formats
• Managing data more effectively on the backend
PRESENTED BY:
Laura Castillo-Page, Ph.D.
Senior Director, Diversity and Programs and Organizational Capacity Building Portfolio
Association of American Medical Colleges (aamc.org)
Kurt Voelker
Chief Technology Officer
Forum One (forumone.com)
*These slides are from a Forum One Webinar. Check out our YouTube channel (http://youtube.com/forumonevideo) for the audio/video of this virtual event.*
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
How to Build a Module in Odoo 17 Using the Scaffold MethodCeline George
Odoo provides an option for creating a module by using a single line command. By using this command the user can make a whole structure of a module. It is very easy for a beginner to make a module. There is no need to make each file manually. This slide will show how to create a module using the scaffold method.
Safalta Digital marketing institute in Noida, provide complete applications that encompass a huge range of virtual advertising and marketing additives, which includes search engine optimization, virtual communication advertising, pay-per-click on marketing, content material advertising, internet analytics, and greater. These university courses are designed for students who possess a comprehensive understanding of virtual marketing strategies and attributes.Safalta Digital Marketing Institute in Noida is a first choice for young individuals or students who are looking to start their careers in the field of digital advertising. The institute gives specialized courses designed and certification.
for beginners, providing thorough training in areas such as SEO, digital communication marketing, and PPC training in Noida. After finishing the program, students receive the certifications recognised by top different universitie, setting a strong foundation for a successful career in digital marketing.
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
4. 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
23-May-12 Page 3 Barbara Janssens PhD Career Service
5. 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“
23-May-12 Page 4 Barbara Janssens PhD Career Service
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
…
C
23-May-12 Page 5 Barbara Janssens PhD Career Service
7. My career network
y
Playground
network
Graduate school
Teaching Editor
23-May-12 Page 6 Barbara Janssens PhD Career Service
10. Career destination
Plan A vs Plan B
Adapted from Gerd Altmann www.pixelio.de
23-May-12 Page 9 Barbara Janssens PhD Career Service
11. DKFZ PhD students want…
23-May-12 Page 10 Barbara Janssens PhD Career Service
12. „Freedom
„Freedom“ in Academia
Temporary contracts and grants
You have to plan funding for next year
But freedom is relative
23-May-12 Page 11 Barbara Janssens PhD Career Service
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 relative
23-May-12 Page 12 Barbara Janssens PhD Career Service
14. 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
23-May-12 Page 13 Barbara Janssens PhD Career Service
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 screening
23-May-12 Page 14 Barbara Janssens PhD Career Service
16.
17. Job hunting…
Richard Bolles, What Color Is Your Parachute?
23-May-12 Page 16 Barbara Janssens PhD Career Service
18. 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
23-May-12 Page 17 Barbara Janssens PhD Career Service
19. 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)
23-May-12 Page 18 Barbara Janssens PhD Career Service
20. LIKE this page! www.facebook.com/phdcareers
23-May-12 Page 19 Barbara Janssens PhD Career Service
21. 5/23/2012
Bioinformatik HUSAR (W180)
Core Facility Genomics Proteomics
Bioinformatics Career Day
22. 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
23. 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.
5/23/2012 | Page 3 Karl-Heinz Glatting Bioinformatik HUSAR
24. 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
5/23/2012 | Page 4 Karl-Heinz Glatting Bioinformatik HUSAR
25. 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
5/23/2012 | Page 5 Karl-Heinz Glatting Bioinformatik HUSAR
26. 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
5/23/2012 | Page 6 Karl-Heinz Glatting Bioinformatik HUSAR
27. Hot Topics
• Analysis Next Generation Sequencing Data
• Mutation Analysis (SNPs, CNVs, …)
• Data Integration
• Systems Biology
5/23/2012 | Page 7 Karl-Heinz Glatting Bioinformatik HUSAR
28. 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
31. 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
5/23/2012 | Page 11 Karl-Heinz Glatting Bioinformatik HUSAR
33. 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
5/23/2012 | Page 13 Karl-Heinz Glatting Bioinformatik HUSAR
34. 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
5/23/2012 | Page 14 Karl-Heinz Glatting Bioinformatik HUSAR
35. End
Thank you for your attention
5/23/2012 | Page 15 Karl-Heinz Glatting Bioinformatik HUSAR
36. The European Bioinformatics Institute
EMBL-EBI
Katrina Pavelin
Scientific Outreach Officer
Services | Research | Training | Industry
katrina@ebi.ac.uk
37. What is EMBL-EBI?
• Bioinformatics Research & Service Institute
• Non-profit organisation
• Part of the European Molecular Biology Laboratory
EMBL-EBI
38. 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
39. 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
40. 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
42. 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
43. 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
45. 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
51. Advanced Training @ EMBL
Dr. Helke Hillebrand
Dean of Graduate Studies
European Molecular Biology Laboratory
52. 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
54. 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
4 Helke Hillebrand 08/2010
03/2009
55. 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
5 Helke Hillebrand 08/2010
03/2009
56. Key performance indicators of a PhD at EMBL
Graduation ceremony at EMBL in December, 2008
6 Helke Hillebrand 08/2010
03/2009
57. 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
7 Helke Hillebrand 08/2010
03/2009
58. 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
8 Helke Hillebrand 08/2010
60. 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
10 Helke Hillebrand 08/2010
03/2009
61. 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
11 Helke Hillebrand 08/2010
62. 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
63. 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
64. 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
14 Helke Hillebrand 08/2010
03/2009
65. ... how to avoid the Cecilia phenotype?
Complementary skills training
15 Helke Hillebrand 08/2010
03/2009
67. Life as a scientific database curator
Sandra Orchard
EBI is an Outstation of the European Molecular Biology Laboratory.
68. What is a database curator
Curator – OED
- a keeper of a museum or other collection
- from LATIN curare – take care of
2/17
69. 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 literature
3/17
70. 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
71. 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 representation...
...to facilitate access to data for scientists...as a resource for
computational analysis
72. 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.
73. 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
74. What do I do?
• Curate the molecular interaction database
8/17
75. What do I do?
Custom curation tools designed by the curation team
9/17
76. What do I do?
Controlled vocabulary maintenance
10/17
77. 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
78. 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
79. 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
80. 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
81. 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
83. 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
84. 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
85. How did I get here? My career so far...
Dr. Jennifer Cham
User Experience Analyst, EMBL-EBI (Cambridge, UK)
86. 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
88. What do I do now?
• Nov 2009 joined the European Bioinformatics Institute
• ‘User experience Analyst’ role in bioinformatics
4
• Transferrable skills from my doctorate
89. 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
102. 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
103. 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
104. 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
105. 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.
106. 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
107. 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
109. Background
• physics diploma, University of Heidelberg
• diploma thesis in radiation dosimetry
at DKFZ
• measurements at HIT
2 24.05.2012 Felix Klein
110. Why bioinformatics?
• interdisciplinary
• programmed in R
• worked on data analysis
3 24.05.2012 Felix Klein
113. 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
6 24.05.2012 Felix Klein
116. What was important for me?
• bioinformatics group with
members of diverse
backgrounds
• PI who successfully
trained bioinformaticians
• well established group in
bioinformatics
9 24.05.2012 Felix Klein
117. 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
10 24.05.2012 Felix Klein
118. 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
11 24.05.2012 Felix Klein
119. 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
120. 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
Kota Miura (miura@embl.de)
121. 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
122. Consulting & Collaborations Recursive Model
Project Model 1
Experiments -> Microscopy -> Image Processing -> Image Analysis
Project Model 2
Microscopy
Experiments Image Analysis
Image Processing
123. 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
124. 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
Kota Miura (miura@embl.de)
126. - 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.
127. Bioinformatics Career Day 2012
Shinichi Sunagawa
Bork Group
www.sunagawa.de
EMBL Heidelberg
EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
128. 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
EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
129. Background / atypical career path?
Diploma - Biochemistry
MSc / PhD - Aquatic Ecology / Quantitative and Systems Biology
Started programming in 2006
PhD 2010
EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
130. 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
EBI / DKFZ: Bioinformatics Career Day – 24 May 2012
131. Yann Abraham
Novartis, Basel
http://prezi.com/ugn43malcumr/dkfz‐careers‐in‐bioinformatics‐day‐2012/