Model Parameter estimation for Predictive Medicine

I am delighted to have been invited as a tutor to the Wellcome-Trust funded course on Model Parameter Estimation for Predictive Medicine organized by Sara Jabbari and Joanne Dunster. The course is being held from 4th-7th July at the University of Birmingham and is jointly run with the University of Nottingham.

The course promises to be extremely interesting, covering classical approaches to fitting dynamical models to data along with its main focus on Bayesian approaches, especially MCMC. Particularly pleased to be teaching alongside my colleagues Simon Preston and Theodore Kypraios.

Fitting models to data is a crucially important skill that has been somewhat neglected in mainstream mathematical biology and medicine so it is really great that Sara and Joanne have organized this and that Wellcome Trust has funded it. Do sign up!

Visit to Oxley Primary School, Shepshed: Outreach / Impact Activity Part 1.

As part of our research grant from BBSRC on Bioluminescence, we have developed a two-week activity on microbiology and modelling aimed at Year 5 primary school students (aged ~10). The development has been in conjunction with my colleagues Phil Hill and Jon Hobman, the West Midlands Association of Science Educators Field Officer Gaynor Sharp, and the Gifted and Talented Coordinator at Oxley Primary School, Shepshed, Lorraine Levine. We carried out the first visit today together with PhD student and STEM ambassador James Williamson and the second visit will be next week (watch for another post!) We had considerable help in the lesson from class teacher Darryl Morris and Lorraine. The two most important objectives of these visits are:

1. To provide children with exciting opportunities to engage with real science in a way that is fun, interesting and relevant to them.
2. To support primary schools in delivering the “working scientifically” elements of the National Curriculum.

The aim of this week’s visit was to discuss microbes and have the children design and carry out their own microbiology experiment. We started with general discussion about what microbes were, showing images of microbes, and discussing also the positive uses of microbes (making bread, chocolate and so forth). We then got more exciting when discussing just how small these microbes are. The giant microbes got passed around (they went down very well!) and this was followed by live images from a microscope with its own digital camera projecting to the interactive white board via USB/laptop. Rhizopus, Saccharomyces, E. coli all went down very well! We then discussed glow-in-the-dark microbes, with suitable reference to the angler fish in Finding Nemo.

Next the experiment: we had brought in pre-poured nutrient agar plates so we can culture some bugs and bring them back (sealed) next week. I had also brought in some plates that I had put my fingers in the week before and now had interesting fungal and bacterial colonies – all nicely sealed. These got passed around to suitable levels of disgust and excitement! With 36 children in the class, we have carried out a 6-way comparison:

1. Hands (touching the plate with fingers)
2. Hands rubbed through hair
3. Hands washed with just water
4. Hands washed with soap and water
5. Hands washed with alcohol gel
6. Feet (really!)

The children suggested putting their fingers into their noses / ears and put on the plates but we had to veto that for safety grounds (good chance of growing a large dose of something pathogenic). The children of course liked the idea of us bringing back potentially deadly pathogens to their classroom – but obviously not a good idea! The children loved putting on the lab coats we provided and got stuck in very excitedly.

In parallel, we had brought along two flasks of bioluminescent bacteria, a pop-up dark sensory tent, some disposable pipettes and bijoux, and some detox spray. James manned the tent and each child had the chance to go into the tent and see the glow in the dark sample – and confirm that they could be killed by the antibacterial spray (they stopped glowing). Another resounding success. While this was going on, I had many children come to see and use the microscope, and we looked at various prepared slides of bacteria, fungi and even decidedly non-microbial animal hairs. They were quite impressed that they could also see the image on my laptop and on the class screen.

The plates will now be incubated at room temperature for a week, and next week we will seal them and bring them back. The plan is to do some data analysis (this is where the maths will come in) and for the children (in groups) to create posters as a form of scientific reporting. This is the link to the blog post for the second week.

As a final note I would like to thank again Class Teacher Darryl Morris and Head Teacher Jeanette Hadley for their support and facilitation of these visits.

 

 

Teaching maths to biologists – report from HE Academy event

Yesterday I attended an event at the University of Reading run by the Bioscience centre of the Higher Education Academy. At that event, I heard talks from or had informal discussions with academics teaching mathematics to biology undergraduates / postgraduates at a number of institutions, including Abertay, Anglia Ruskin, Bath, Cambridge, Cardiff, Liverpool and Reading. Very interesting key points to emerge that will help inform my maths teaching next year, especially to the first year undergraduates.

1. All institutions are facing the same issues, regardless of ‘status’. Specifically:
   1. General recognition of the quite separate issues of teaching basic maths skills to all u/g biologists and the teaching of higher level skills to biologists to become involved in Systems Biology research.
   2. The skills required by all undergraduate biologists around units, concentrations, powers, logarithms, exponentials, basic algebra (manipulating equations) and basic numeracy (is the answer plausible).
   3. The range of background / abilities of students coming into university study. This is linked to a wide range of school experience, from students with no more maths teaching after a ‘C’ in GCSE maths through to students with an ‘A’ in A-level maths, and everything in between.
2. The importance of gathering the right data and evidence. This includes:
   1. Information on background of students, including numbers of students with GCSE, AS and A2 maths, and grades of those students.
   2. Feedback on different elements of the teaching, specifically how helpful the students are finding lectures, practicals, worksheets, on-line materials and so forth.
   3. Formative assessment during the course of the term to identify students who are struggling with particular elements and direct (often limited) tutorial resource to those students.
3. The importance of blended approaches, specifically:
   1. The findings from Liverpool that the students found workshops and tutorials far more valuable than the lectures: they had six 3 hour workshops AND sign-in tutorials
   2. The findings from Abertay that a system of regular on-line tests with extra tutorials if not meeting goals and electronic nagging massively improved results
   3. The use in Bath of on-line tests with 100% pass marks but many attempts allowed to improve learning of key concepts.
4. Helpful ideas about approaches, three C’s from Anglia Ruskin:
   1. Context: very important to include biological context – embedding the mathematics in biological problems. Reading used the analogy of teaching people to make hammers and screwdrivers without telling them about nails and screws.
   2. Confidence: very important to build students’ confidence, even if this means giving very high marks (doesn’t matter as in most universities 1st year marks only count for progression).
   3. Continuity: need to link both with school-level work and with material in other 1st, 2ns and 3rd year modules: this is a challenge for all module leaders/lecturers.
5. A large number of on-line resources, which I have not yet looked at, including:
   1. Bionrich
   2. Essential maths for medics and vets
   3. mathtutor
   4. NuMBers
   5. SUMS
   6. biomathtutor
   7. mathstore
   8. And, quite differently, StarLogo TNG

All-in-all, a highly successful and interesting day, very timely given by first-year teaching, and I look forward to embedding some of these ideas, practices and resources in next year’s running of the module.