The Victorian Life Sciences Computation Initiative is funded by the Victorian Government and contributing institutions, is hosted by the

University of Melbourne and includes the first IBM Research Collaboratory for Life Sciences. It exists for all Victorian life science

researchers and as at July 2012 is the biggest supercomputer facility devoted to life sciences in the world.

How we became bioinformaticians: the student experience

Harriet Dashnow, Marek Cmero and Andrew LonsdaleInCoB Sydney 2014

To everyone at the InCoB 2014 education session,

We were honoured by the opportunity to share our experiences and our passion for bioinformatics education.

We were especially touched by your acknowledgement and appreciation for the role that students can play in our own and others education.

Thank you,Harriet, Marek, Andrewand the rest of the committee

We thank you

How to make a Bioinformatician: The ideal

• Start with a well rounded, well educated individual with deep expertise in Statistics, Mathematics, Software engineering or other quantitative discipline.

• Lure them away from their lucrative career with promises of meaningful contributions to human health or knowledge. Tell them they can use their hard-won skills to make the world a better place.

• Provide them minimal (e.g. on the job) broad training in biology, particularly the terminology they will need to communicate with biologists.

• Set them loose in a Bioinformatics group and mentor them through the scientific process.

Magic?

Domain expert

Bioinformatician

How to make a Bioinformatician: The ideal

• Take a group of young recent graduates, fresh out of a degree in Computer science, Mathematics or Biology. Mix in some more experienced people who are looking for a more meaningful job or just couldn't find one.

• Train them in the fundamentals of Computer science, Statistics and Biology (as required).

• Continue to train them in their prior study, because they're not yet experts.

• Train them to read and write critically, to communicate to work in teams, generally to do science.

• Need a great Bioinformatics group and mentors

How to make a Bioinformatician: The reality

How to make a Bioinformatician: The reality

Domainstudent BioinformaticianBioinformatics

training

Coal Heat, time and pressure Diamond

MSc (Bioinformatics)University of Melbourne

Computer Science

Statistics Biology

Bioinformatics and Research Project

…Bioinformatician!

Statistics

Computer Science Biology

Bioinformatics and Research Project

Biology

Computer Science Statistics

Bioinformatics and Research Project

Andrew Lonsdale

Background• Software Engineering• Programming, tech support and server administration in

domain names/web hosting

MSc (Bioinformatics)

• Motivation (job interview version) = Looking for a way to use computing skills for a purpose beyond business and profit.

• Motivation (pub version) = Unhappy in my job, and needed a change. No idea what bioinformatics was, almost no biology background, but it looked interesting and the MSc (Bioinformatics):– was only a 2 year course– had Commonwealth Supported Places (CSP)– was eligible for student income support (Austudy payments).

• Motivation (honest) = Mean( job interview version + pub

version )

MSc (Bioinformatics)

• What I wish I'd known going in: statistics• New skills: Biology. I had almost no background, but enjoyed

(mostly) learning it. • Extending old skills: Revisiting calculus and probability from

undergraduate; chemistry from Year 12 (a long time ago!) • Background that was most useful: Linux server administration,

command line knowledge, scripting

Bioinformatician

• Bioinformatics training doesn’t end when you graduate.

• While looking for bioinformatics jobs, stayed involved with bioinformatics student groups while working in University administration.

• VLSCI funding to attend European Conference on Computational Biology (ECCB) a turning point in my career.

• Bioinformatics work - RA job in the ARC COE in Plant Cell Walls, School of Botany, University of Melbourne.

• Started a PhD in the Plant Cell Wall group.

Lessons learned• "Who you know, not what you know”. Generally true, but

especially true for bioinformatics. Led to RA job.

• Hopelessly recursive definition:“I feel like a bioinformatician when I’m around other bioinformaticians”

• Networking: involvement in student groups (e.g. COMBINE) and meeting other students at conferences. Small cohort in first year of course was motivation to find peers.

• Make friends, not contacts

Marek Cmero

Background• Computer Science & Commerce• Systems analyst & programmer

MSc (Bioinformatics)

• Motivation: was uninterested in the problems I was solving in IT, was always interested in biology, thought bioinformatics looked interesting.

• Bioinformatics students are a diverse cohort. • Diverse motivations for doing the course.

• Key skills: • Thinking like a scientist. (Computer Science is not a science)• Reading the scientific literature.• R, statistics, analysing big data, biochemistry, bioinformatics tools and

techniques.

Bioinformatician

• Masters project in a wet lab.

• Research assistant at NICTA and St. Vincent's institute.

• Currently PhD at the University of Melbourne, working on cancer evolution.

• Have been lucky enough to work on a wide range of things (even bench biology) – really got an idea of my interests.

Lessons learned

• Your lab and supervisor make a big difference.• Avoid the “lonely bioinformatician”

• Masters project got my foot in the door, but was not right project for me

• Working with other bioinformaticians at NICTA was a far more stimulating environment

• Choosing a project, consider: will I have the right guidance? Will I get to work with other bioinformaticians? Are my research goals aligned with the lab?

Harriet Dashnow

Background• Genetics, Biochemistry, Psychology• Wet lab molecular biologist

MSc (Bioinformatics)

• Motivation: "catch-up" on statistics and programming.

• The statistics coursework was full-on (but worth it).• Better foundation in calculus before the course would have

helped.

• Actually learned the most programming through the research project and was self-taught (stack overflow!).

• Vital skill: writing and communication skills.

Bioinformatician

Working at VLSCI• Bioinformatics methods development.• Clinical genomics (Melbourne Genomics Health Alliance).• Bioinformatics training– Teaching in the MSc– Running workshops for PhD students, biologists

Lessons learned

Diversity of backgrounds so lots of different gaps in knowledge.

Solutions?• Bridging subjects (equivalent to 1st-2nd year level)– Bash/python for biologists– Biology for computer scientists– Calculus

• Self learning – MOOCs?• Learning as a group, mentoring?

Conclusions

• "I feel like a bioinformatician when I am around other bioinformaticians”

• Networking: student groups, small cohorts

• Research project/placement with working bioinformaticans a critical.

• Stop the "lonely bioinformatician" syndrome before it starts.

• Diverse backgrounds• Bridging the gap by providing foundation subjects

• A group aimed at students and early-career researchers

• The official ISCB Regional Student Group for Australia

We are…

combine.org.au

Andrew Lonie(coordinator MSc Bioinformatics)

Thank you

Launch of COMBINE Sydney!

Sponsors