Guide to presentations and reports on systems biology modelling
===============================================================

Here is a brief summary of how to structure your material, with
time and page limits and a checklist for your preparations.

Presentations:
--------------

0. Introduction
1. Paper 1
2. Paper 2
3. Summary
4. Question and answer session
5. Filling out evaluations

Each team member should select, read, present and report on *one* paper
from those in the topic list. So a 2-person team would report on 2 papers.

Time allocation (about 20 minutes for each team)
- introduction: about 2-3 minutes
- presentation on each paper by an individual team member: about 5 minutes
- summary: about 2-3 minutes
- questions: about 2 minutes
- evaluation: about 1 minute
- N.B. time for each team member on their paper is not very long !

Materials:

PowerPoint, PDF or HTML. Anything else, contact me first.


Reports:
--------

Basically the same structure as presentations, except for questions and
evaluations.

Each team report should be around 6-10 pages, with each team member
contributing an average of around 3 pages. More is OK if you have enough
*important* material to justify the extra length, less might be insufficient
to explain the key points about the models. 

The report should be a single document prepared by the *team*.
Work on the parts individually but ensure you meet to plan first
and tie it all together as a whole at the end. 

Use diagrams and examples to communicate important information.

Checklist:
----------

The main purpose of a scientific paper is to report new results, usually
experimental, and to relate these results to previous knowledge in the field.
Papers are one of the most important ways that scientists communicate.
However, that does not mean they are ideal ways to acquire knowledge.  The
reader must be *active* in exploring what is contained in a paper: asking
questions about what they have read, what they would expect from their own
knowledge, considering how they could have done things differently, etc. In
short, papers have to be read *critically*.

Here some points referred to in lectures that should inform your
preparations for the presentation and report. 

- what is the modelling approach ?
- what biologically significant problems is the use of models
	supposed to help with ?
- is there a biological, chemical or physical basis for the model ?
- is there a statistical or probablistic basis for the model ? 
- what algorithms, data structures or other computational aspects
	are important features of the model ?
- HOW DOES THE MODEL WORK ? can you give a simple example ?
- what applications are reported for the modelling approach ? how 
	successful were they ? what limitations were reported ?
- how implementable is the model on a scale from purely theoretical
	to algorithms to (freely or commercially) available software ?
- what previous work does the modelling approach build on ? what other
	approaches is it related to and how ?
- what is your critical assessment of the modelling approach ? can you
	suggest how you would do things differently ? can you suggest
	any other areas in biology where similar methods might be applied ?

As indicated by the upper-case letters, be sure to spend an appropriate
amount of time on explaining how the modelling method works.

*Hint* this stuff is supposed to be interesting to us all. Have fun !