How we became bioinformaticians - Harriet Dashnow, Marek Cmero and Andrew Lonsdale


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Three perspectives on the process of converting the raw materials of intelligence, inquisitiveness and enthusiasm into "diamond-hard" bioinformaticians, using heat, time and pressure.

Students and early career researchers in bioinformatics are encouraged to connect to COMBINE (, the official ISCB Regional Student Group for Australia, and vibrant participant in the Australian Bioinformatics Network.

Presented at InCoB 2014 special session on Bioinformatics Education and Training:

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How we became bioinformaticians - Harriet Dashnow, Marek Cmero and Andrew Lonsdale

  1. 1. 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 Lonsdale InCoB Sydney 2014
  2. 2. 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, Andrew and the rest of the committee We thank you
  3. 3. 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.
  4. 4. Magic? Domain expert Bioinformatician How to make a Bioinformatician: The ideal
  5. 5. • 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
  6. 6. How to make a Bioinformatician: The reality Domain student Bioinformatician Bioinformatics training Coal Heat, time and pressure Diamond
  7. 7. 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
  8. 8. Andrew Lonsdale Background • Software Engineering • Programming, tech support and server administration in domain names/web hosting
  9. 9. 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 )
  10. 10. 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
  11. 11. 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.
  12. 12. 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
  13. 13. Marek Cmero Background • Computer Science & Commerce • Systems analyst & programmer
  14. 14. 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.
  15. 15. 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.
  16. 16. 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?
  17. 17. Harriet Dashnow Background • Genetics, Biochemistry, Psychology • Wet lab molecular biologist
  18. 18. 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.
  19. 19. 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
  20. 20. 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?
  21. 21. 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
  22. 22. • A group aimed at students and early-career researchers • The official ISCB Regional Student Group for Australia We are…
  23. 23. Andrew Lonie (coordinator MSc Bioinformatics) Thank you
  24. 24. COMBINE SOCIAL IN SYDNEY COMBINE is a bioinformatics and computational biology group aimed at students and early-career researchers and the official International Society for Computational Biology (ISCB) Regional Student Group (RSG) for Australia. COMBINE is committed to bringing together students and early-career researchers in bioinformatics and computational biology from around Australia. To coincide with the the 13th International Conference on Bioinformatics (InCoB2014) being held in Sydney this week, we will be hosting a networking event aimed at both conference attendees and local students on Thursday July 31st. This event will launch COMBINE’s activities in the Sydney area, and provide an opportunity to meet both Australian and international research students, as well as COMBINE organisers, in a relaxed setting.   Thursday July 31st, 7pm onwards  Trinity Bar  (Upstairs in Eden room)  505 Crown Street,  Surry Hills NSW 2010      Attending InCoB?  Launch of COMBINE Sydney! Sponsors
  25. 25. By bioinforma cians, for bioinforma cians. October 11th & 12th 2014 The Royal Children’s Hospital, Melbourne For more informa on, please go to: h p://bioinforma ABiC 2014 is generously supported by: Registra ons & abstract submissions now open! Invited speakers: Dr. Ana Conesa Cegarra Genomics of Gene Expression Lab Principe Felipe Research Centre Valencia, Spain Prof. Terry Speed Bioinformatics Division Walter & Eliza Hall Institute Parkville, VIC Asst. Prof. Titus Brown Depts of Microbiology & Computer Science Michigan State University Dr. Sylvain Forêt Bioinformatics, Genomics and Epigenomics Lab Australian National University, Canberra, ACT ² Abstract submissions close Aug 13 (for talks) and Oct 1 (for posters) ² Student travel bursaries available (must register by Aug 13)