IGEM:IMPERIAL/2007/Tutorials/Guide for Biologists

Another Guide for Biologists in Synthetic Biology
I'm sure all the biologists - like me - are wondering what Engineering is about... so this page is for us biologists and biochemists to familiarize ourselves with engineering concepts. Also, if there're any silly questions, feel free to add them here!

Engineering Cycle
An engineering cycle is a traditional framework used to manage engineering projects. The aim of such a framework is to spend a lot of time at the designing and planning of a project so the device is as fully characterised as possible, even before it is actually implemented. This ensures that time and resources are not wasted.

The process of engineering cycle is not rigid and can be made iterative. Therefore if a problem with the design is highlighted in the modelling, one may go back to the design and alter it.

[[Media:Engineering_cycle.ppt|Presentation slides]]

Abstraction, Signal Systems and Control
[[Media:ICGEMS_abstraction.ppt|Presentation slides]]

Logic Gates
In logic circuitry, an OR gate consists of two or more inputs, the output of which is equivalent to the OR combination of these inputs. The operation is such that the output is HIGH (logic 1) if at least one of the inputs is HIGH. So, for a two-input OR Gate, the output is HIGH if either A or B or both are HIGH. Otherwise, the output is LOW (logic 0), i.e. only if all its inputs are LOW. The Boolean expression for the OR operation is given as: $$ \begin{align} OUT = A + B \\ \end{align} $$
 * OR Gate

Here, the AND operation is performed on the gate's inputs. The output will be HIGH only when all the inputs are HIGH; for all other cases, the output will be LOW. The Boolean expression for the AND operation is given as: $$ OUT = A\cdot{B} $$
 * AND Gate

The Inverter takes one input and produces an output which is the logical inverse (complement) of the input. The Boolean expression for the AND operation is given as: $$ OUT = \overline{A} $$.
 * NOT Gate/Inverter

[[Media:Icgems_logic.ppt‎|Presentation slides]]

Questions on Engineering
--Ben Yi Tew 19:01, 10 July 2007 (EDT): Unclear about anything? Ask the engineers here!

--Johnsy 07:22, 12 July 2007 (EDT): Hi Ben (and the rest of the 2007 team)...I don't know whether to put this in the discussion page or on the main page...One thing I suggest to put on this page is also some stuff on modeling biological situations. These include Michaelis-Menten kinetics and rate laws governing transcription, translation, etc. But one thing to note is that these equations are continuous equation and can't necessarily be applied to the situations you might be working with over the summer in iGEM. In the case where you have one or a few molecules going into a cell, it might be helpful to try stochastic modeling since at that level, it is more of a discrete distribution of molecules within your volume rather than a continuous distribution. Starting to understand the modeling early is very helpful in being able to model the different biological systems that you will inevitably encounter in your project...something which I'm sure Vincent can attest to. Good luck with your project!