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Bioinformatician – more than just a number cruncher (or bridging the gap between computer scientists and biologists) - Nathan Hall
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Bioinformatician – more than just a number cruncher (or bridging the gap between computer scientists and biologists) - Nathan Hall

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  • 1. Bioinformatician - more than just a number cruncher(bridging the gap between computer scientist and biologist) Nathan Hall La Trobe University Life Sciences Computation Centre, VLSCI
  • 2. What is a Bioinformatician?• Computational biologist• Systems biologist• Computer scientist• Statistician• Mathematician• Biologist• A generator of lists and tables??• ……….• Anyone who analyses (complicated) biological data
  • 3. What it takes to be a bioinformatician• http://nygenome.org/blog/what-it-takes-be- bioinformatician• Pouliot says… bioinformatics is now "more an issue of coming up with good research questions than writing code.”• Quackenbush says… bioinformatics sits at the nexus of biology, statistics, and computer science.• Quackenbush says … bioinformatics has become "an essential foundation for all molecular and genomic science," that gives him the opportunity to inquire, discover, and do things no one has ever been able to do.• Biological understanding essential
  • 4. My Background• Undergraduate Chemistry degree• PhD in quantum chemistry and enzyme mechanisms• Postdoc at LICR – Protein modelling – Self taught genomics (human genome era)• Now involved in next-gen analysis
  • 5. Bioinformatics Requirements• Next gen sequencing getting cheaper and producing more and more data• (my message to biological researchers is that if they don’t go down the next-gen route then they will be left behind)• We will only ever need more bioinformaticians• (my message to young biological researchers, learn bioinformatics skills or you’ll be left behind)• Train Biologists to become bioinformaticians – Literacy – Capability – Familiarity – Confidence – People Networks
  • 6. La Trobe Model• La Trobe Hub of the LSCC• Have 3 bioinformaticians – Genomics – Proteomics – Computer Scientist• Not a service provider but a “Bioinformatics Collaboration Group”• Strongly encourage researchers to come and talk in the experimental design phase
  • 7. Varied projects some discussions, some well underway• Cancer Genome analysis• Zebrafish (model organism) genomics• Nematode worm genome sequencing, RNA• Population analysis of worms and other non-model organisms (RAD seq)• Analysis of wolbachia (bacterial symbiot)• Plant fungal interactions, genome, RNA, proteomics• Mitochondrial genome analysis – Human and marine non-model organisms• Analysis of mouse RNA knockout data• Gemomics of electron-transferring bacteria• Yeast population analysis of KOs
  • 8. LSCC model• Previous model – LSCC provides free bioinformatics research collaborations• Now - Buy into the LSCC• Help employ more bioinformaticians• They belong to the LSCC bioinformatics community, but work on the “buy in” projects• Projects get support from LSCC expert groups, not just one bioinformatician
  • 9. Alternative Models• Bioinformatics Research Groups (MCRI,WEHI,NICTA) – Almost impossible to do in isolation – Good collaborations essential• Bioinformatics Service Providers (Not many??) – Very little bioinformatics can be done as a straight service – Research component to most projects – Bioinformatics Pipeline rarely repeated• Few bioinformatics questions are simple and straight forward• Need experts• Need research
  • 10. Who is a bioinformatician?• Should this be an inclusive or exclusive term?• I speak to many biologists doing bioinformatics who do not consider themselves bioinformaticians• Such generalist terms as computer scientist, statistician, biologist, mathematician have less relevance today as so much research is done in an interdisciplinary environment
  • 11. My personal Model• Train well and train early – Work with individual Postgraduate students and Postdocs – Train them as co-supervisor or bioinformatics mentor – Much better than not having enough time to do their analysis for them!!!• Workshops cannot train biologists to be bioinformaticians (have masters degree for this)• They can be critical for giving biologists the start they need
  • 12. Case Study 11. Run workshop on RNA-seq analysis Nov 20112. One participant (biologist) contacted me 6 months later on how to do some related analysis - Spent half a day going over some specifics - Following this they have self taught, attended whatever is available, asked lots and lots of questions - Now I would consider them a practicing bioinformatician - BUT learning NEVER stops
  • 13. Case Study 2• From the same workshop,• 8 months later a PhD student and his supervisor spoke to me about designing their experiment• 4 months later, student received VLSCI internship and spent summer with me learning how to analyse data• Like always, project never as simple as first seems• He has built up his skills, but most importantly bioinformatics has been demystified and he now has the confidence to learn (self teach) from all the info out there
  • 14. Case Study 3• Involved in a big project• Don’t have enough time to dedicate to it• PhD student starts (biologist)• Now supervise and teach Student how to be a bioinformatician• He does the work• World has another bioinformatician• Everyone Happy!!
  • 15. Alternative Bioinformatician (methods development)• Spend lots and lots of energy on a single focus• Make significant Influence on bioinformatics community with widely adopted software• Ensure this is what the community needsDANGER• Most published software is rarely used by outside groups• Much software developed in reinventing the wheelBUT• We need constant advancements in software to keep pace with advancements in biological questions and technologiesMany scripts and tools are freely available on the web – you just have to look
  • 16. Galaxy• Great tool to unify community• Excellent teaching tool• Great for instilling confidence and familiarity for biologists• (I’m not convinced that Unix is not the best teaching environment – old school)• Useful tool for research community• Clearly has great potential and has a significant role to play
  • 17. A few points….• A biological understanding of the problem is essential for complete bioinformatics solutions• Understand the technology that generates the data• Complicated problems need specialists expertise• Bioinformatics community in Australia is extremely open and communicative. Make use of this.• Discuss, discuss, discuss - talk to other people
  • 18. Bioinformaticians Challenges• Middle authorships• Often rely on central funding or other peoples moneyBUT• Able to pick interesting projects to work on• Much more varied research career• Collaborative work is much more satisfying
  • 19. The Perfect Bioinformatician• Bioinformatics is putting all the pieces together• An expert in everything!!!!• No one person can have all the skills• Multidisciplinary Approach, whereby bioinformatics is an inclusive term encompassing spectrum of contributors
  • 20. Conclusions• Need more bioinformaticians• Broad spectrum of backgrounds – Biology – Computer science – Mathematics – Statistics – Other• Must have biological input – Otherwise an informatician• Biologists – don’t be afraid to label yourself as a practicing bioinformatician. The world needs you!!