“What is systems biology” – the students talk

This year was the 5th instalment of our Wellcome-Trust / EMBL-EBI course “in silico systems biology“.

This course finds its origin a few years ago in a workshop of the EBI industry programme on “Pathways and models”. The workshop, that lasted 2 days, was praised by the attendees. However, the time limitation caused a bit of frustration and made us skip entire aspects we would have liked to cover. I therefore decided to try making it into a full-blown course with the help of Vicky Schneider then responsible of training at the EBI.

The first course, supported by EMBO, lasted 4 days. It was well received. However, we tried to cover too much, from functional genomics and network reconstruction to quantitative modelling of biological processes. Fortunately, the existence of another EBI course “Networks and pathways“, allowed us to focus on modelling. We progressively improved the programme through 1 FEBS course and 3 Wellcome-Trust advanced courses. Without boasting, the current course, co-organised with Julio Saez-Rodriguez and Laura Emery, reached almost perfection. The programme always evolves, but the changes slowed down with time, and we are now more in an optimisation/refinement phase. One of the big advantages is that we kept a core of trainers, who help improving the consistency and quality of the content. We are now happy to see our first generations of students having become active figures in systems biology. Some group leaders who attended the course in the past now send their own students every year. A forthcoming post will discuss a few things I learnt from organising those courses.

Beside the regular training, we always have a few group activities. This year, they were split in small groups at the beginning, and had to answer a few questions. One of them was …

What is systems biology?

Everyone has their own idea about that one, including myself (for more on the history, nature and challenges of systems biology). Here I provide you with the unfiltered and unclustered responses of 25 students (repetitions originate from different groups coming with the same answers):

  • Mechanisms on different levels
  • Wholistic view (tautology intended)
  • Dynamics of biological systems
  • Fun
  • Mathematical modeling
  • Insight to the systems
  • Predictions
  • Looking at the system as a whole and not per component
  • Should also be: formal, unambiguous
  • Holistic approach
  • Using modelling to answer biological questions
  • understanding dynamics of a system in terms of predictability
  • Mechanistic insight
  • A tool to complement experimental data
  • Experiments-modeling cycle leading to discovery
  • formalisms
  • Technology+bio data+ in silico
  • integrating levels of biological processes
  • reaching the experimentally unapproachable

Interesting isn’t it? At first it looks pretty much all over the place. Let-me re-order the answers and group them:

  1. Entire systems
    • Wholistic view (tautology intended)
    • Looking at the system as a whole and not per component
    • Holistic approach
  2. Mechanisms
    • Insight to the systems
    • Mechanistic insight
    • Mechanisms on different levels
    • integrating levels of biological processes
  3. Dynamics
    • Dynamics of biological systems
    • understanding dynamics of a system in terms of predictability
  4. Modeling
    • Mathematical modeling
    • Should also be: formal, unambiguous
    • formalisms
    • Using modelling to answer biological questions
  5. Complement the observation
    • A tool to complement experimental data
    • reaching the experimentally unapproachable
    • Experiments-modeling cycle leading to discovery
    • Predictions
    • Technology+bio data+ in silico
  6. And of course
    • Fun

We basically fall back on the two global positions in the field: a philosophical statement about life sciences (1,2,3), and a set of techniques (4,5). That reminds me a lot the discussions we had about molecular biology at university a few decades ago …

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