Modeling for Everyone!

Background

Our team had trouble starting the work on our model. We had only high-school level math, with little or no knowledge about modeling. In order to build a model, we had to learn and catch-up by ourselves in various branches of mathematics, i.e. Calculus, Algebra, Probabilities. However, knowing the math doesn't guarantee neither an easy modeling nor a great model. The starting point of building an actual model out of the math we've learnt was extremely challenging.

Motivation

We want to make a change in the field of modeling!

Modeling (and math in general) has gained a bad reputation among the public. Therefore, a lot of iGEM newcomers and even veterans fear of this field, leaving it to a few other team members. In many cases, this fear prevents from the model to be complete and beneficial.

We would like to help whoever wants to learn how to model!

So… What's new?

WE WANT TO REACH THE iGEM COMMUNITY!

A lot of modeling tutorials videos are available online, but none of them is aimed at the iGEM average modeler. In addition, not all of them provide background material or guides when necessary. As a result, we all have to search and seek for different tutorials all over the internet before the actual fun can begin. So, we thought of organizing all the tutorials, information and help you need in one place, and in an interactive way.

Introduction – What IS Modeling?

When dealing with new materials, genetic constructs in lab or a complex system, one might want to predict the results of one's actions, before the actual work begins. In addition, "trial and error" in most cases wastes time and money, so a different approach must be taken.

~Modeling gets up on the stage~

Modeling has a lot of different definitions, depending on the exact field of application, on use and on methods. In general, modeling is about describing behavior of systems mathematically. This approach differs from a "heuristic" approach by the language that is being used: A heuristic description is better for explaining the systems to the general public, for self-thinking and reflections. The modeling approach comes in handy when there's a need for numerical descriptions of the behavior of the system, for calculations, designing, making predictions or verifying results.

Methods

In order to make modeling accessible and approachable, we have been filming a series of short videos about modeling. Each video covers a single topic, subject or a specific problem. Partitioning the material in that manner makes the learning process more organized and clear, thus helps the novice modeler in the first steps.

In our videos, we strive not only for comprehension of the techniques that are presented, but also understanding what a model is, and how to build one from scratch.

Subjects covered

The flow of the videos is very easy-to-follow. We first start by introducing the need for modeling, and then introduce some of the basic mathematical tools for modeling – mainly calculus and probabilities. Each subject, method and theorem is accompanied by clear examples and references to literature and external material.

Afterwards, we obtain a few common models (i.e. population growth, chemical reaction) in order to demonstrate the power of the modeling (which isn't quite obvious to a modeling newcomer). Biological, Chemical and Physical background will be taught in the section.

Then, a few advanced modeling techniques are presented (i.e. stochastic processes, PDEs, statistical mechanics). These videos are made for the expert modelers who'd like to expand their knowledge and experience to the field of synthetic biology.

Throughout the way, tips for model designing are shown.

Highlights

After watching our videos, the viewer will be able to:

• 1. Face a modeling-problem and understand the goal of the model
• 2. Choose a proper mathematical technique or discipline
• 3. Solve the equations in a suitable manner (numerically or analytically)
• 4. Present the results clearly and concisely

Current work

Right now, we are designing, filming and editing the videos. Until the Wiki Freeze, we are planning on having about 4-5 videos uploaded to the wiki and to our YouTube channel. In the week between the Wiki Freeze the Giant Jamboree, we are planning on filming about 2-3 more videos which will go right into the YouTube channel.

Conclusion

We have been filming a series of modeling tutorial videos for everyone to watch, learn and apply. We emphasize the need of modeling; Strive for comprehension of the math and the field of modeling; Aiming for the iGEM community needs; and doing it in an interactive way.

So, come on, don't be afraid and join us on our Youtube channel for some modeling!

Example Videos

Lecture No. 1 - Introduction

Lecture No. 2 - Derivatives

Lecture No. 2 - Derivatives- Examples