Bioinformatician – more than just a number cruncher (or bridging the gap between computer...

Bioinformatician - more than just a number cruncher

(bridging the gap between computer scientist and biologist)

Nathan HallLa Trobe University

Life Sciences Computation Centre, VLSCI

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

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

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

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

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

Varied projectssome 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

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

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

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

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

Case Study 1

1. 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

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

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!!

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 needs

DANGER• Most published software is rarely used by outside groups• Much software developed in reinventing the wheel

BUT• We need constant advancements in software to keep pace with advancements in

biological questions and technologies

Many scripts and tools are freely available on the web – you just have to look

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

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

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

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

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!!