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2004 Interdisciplinary Workshop On Immune Systems and Computation
(How to get biologists, computer scientists, engineers and mathematicians working together)
10th and 11th May 2004
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Summary
ARTIST forum 10-11 May 2004
ARTIST (A Network for ARTifical Immune SysTems) is a network of excellence for AIS research. ARTIST is designed to help bolster AIS researchers in the UK, stimulate and extend the community of AIS practitioners within the UK and provide the necessary infrastructure and financial support for them to pursue further interactions between themselves and international collaborators in order to drive forward this area of research.
In this meeting, the theme was "How to get biologists, computer scientists, engineers and mathematicians working together."- ie to foster closer collaboration between all disciplines involved in AIS.
1) Jon Timmis (Kent) provided an overview of ARTIST, purpose and mechanics 2) Julie Mcleod (University of the West of England) provided a very clear and concise overview of the immune system from a biologist's point of view. Her slides are available here: Immunology Talk - (Disclaimer - This is an abridged view and does not cover all aspects of immunology!) , although with a caveat - they are not a definitive 'last word', being very much tailored for the ARTIST audience. However, I found them very useful so Julie has kindly allowed me to share them. I recommend looking at them if you are interested in any of the following (this is a 'table of contents' for you, a memory jogger for me).
- Innate vs adaptive (the former is more specific than previously supposed, current work on toll receptors)
- Dendritic cells vs macrophages (actually very similar, some minor phenotypic/behavioral differences)
- MHC I (all cells, used by T Killers to recognise viruses) and MHC II (only APCs, used by T Helper cells)
- IgM (big, excellent at finding antigen, speedy primary response) vs. IgG (smaller, can get through placenta, later primary response but quick, rapid and solely responsibly for secondary response)
- Affinity maturation - antigen presentation increases IgG (but not IgM) specificity, especially at low concentrations
- Gene libraries: V, D, J
- Antibody response: 'sweet spot' between damage due to microbe (too little response) and damage due to IS (too much)! 'Good' and 'Bad' antibodies can shift this response/damage curve (do we evolve to eliminate 'bad' antibodies?).
- T Helpers: Th1 (cell) vs Th2 (antibody)
- Cytokines: pleiotropy (1:many), redundancy (many:1), synergy (1+1), antagonism (1-1)
- T regulatory cells: 5-10% of T cells! cell contact vs cytokine mediated effect.
- Memory cells: 2 types of memory cell (one while antigen still around, other looks like naive cell). Too much (or too little) antigen means memory cells can get destroyed - important for vaccinations
- APCs - and danger theory. apoptosis vs. necrosis. See Danger project ****
- immunological techniques: and here we ran out of time....
3) Trip to York immunology lab very interesting, we got an overview of experimental techniques and got to see round the labs too.
4) Peter Bentley (UCL) provided some insights for effective computer scientist/biologist collaborations. He provided a simple taxonomy of collaborations which was very useful for the brainstorming session: 1. Biology driven 2. Computer science driven 3. Parallel 4. Combined (the 'ideal')
Types 1 (and especially 2) are the most common models, I thought they might also be useful stepping stones for 'getting to know' our collaborators in advance of the more ambitious type 3/4 projects.
5) Brainstorming. We talked about collaboration opportunities in 6 main areas. The interested reader should look at the ARTIST website, where there is a set of forums for taking these forward:
- Development - why is the human IS the way it is? Look at its evolution/development, with investigation into differentiation and population mechanisms/dynamics
- Engineering - can we do a principled comparison of AIS methods, capabilities, needs with a view to providing guidelines for practitioners, standard datasets, open source code packages. A planned 'retreat' on scheduling/dynamic workflow
- Data Mining - see right
- Memory - interest in immunological memory mechanisms, forgetting, and distributed memory
- Network - can we define roles of IS vs. endocrine vs. nervous system (and their interactions). What added value do we get? A 'retreat' is on the cards to get biologists and mathematicians together to discuss this in more depth (location probably Lake District)
- Danger/Innate - Both areas are proving of real interest among biologists now (eg heat shock proteins, the Swiss army knife of the IS!) so can we leverage these insights in our immune algorithms?
6) The way forward was also discussed. It was agreed that people in each
session would be encouraged to form a working group examining each of
their particular area in detail. This would entail further meetings
(which ARTIST would support with travel costs etc) in the near future.
Each group was to have a champion who would try and organise the
follow-up. It was expected that each sub-group would report back to
ARTIST within 6 months on the progress made so far. It is hoped that
grant proposals, papers etc would be a tangible outcome from these
groups.
Thank you to Steve Cayzer of HP Labs for providing this summary.
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