Designing a gene or "Gene design"

On this tutorial you can see an easy way to design oligos for gene synthesis, or in other words Gene design.

The description is based on the Instructional Videos from the iGEM website!

Gene design in less than 10 minutes!

Good luck!!!




Some usefull tools:

1. Gene design web page
2. Tools at DNA20
3. Tools at DNA Works
4. A Revese-Complement Tool
5. Gene designer a comprehensive tool to artificial gene design from DNA20 described here.


If you would like to read about the application of design principles in Drug Discovery you should read this book:
 

IDEA Generation and Brain storming

One of the first step in generating a project is to generate ideas. One of the best known technique for idea generation is  Brainstorming.

Below you can see excerpts from the very well writen and detailed description of the Wikipedia:

Basic rules:

There are four basic rules in brainstorming. These are intended to reduce social inhibitions among group members, stimulate idea generation, and increase overall creativity of the group.

1. Focus on quantity.


2. Withhold criticism. In brainstorming, criticism of ideas generated should be put 'on hold'. By suspending judgment, participants will feel free to generate unusual ideas.


3. Welcome unusual ideas. They can be generated by looking from new perspectives and suspending assumptions. These new ways of thinking may provide better solutions.


4. Combine and improve ideas: Good ideas may be combined to form a single better good idea, as suggested by the slogan "1+1=3". It is believed to stimulate the building of ideas by a process of association.

 

Method

 

Set the problem

Before a brainstorming session, it is critical to define the problem.

Create a background memo

The background memo is the invitation and informational letter for the participants, containing the session name, problem, time, date, and place. The problem is described in the form of a question, and some example ideas are given. The memo is sent to the participants well in advance, so that they can think about the problem beforehand.

Select participants

1. The facilitator

2. Participants:

• a. core members


• b. guests from outside the project, with affinity to the problem.

3. One idea collector who records the suggested ideas.

 

Create a list of lead questions

The facilitator should stimulate creativity by suggesting a lead question to answer, such as Can we combine these ideas? or How about looking from another perspective?. It is best to prepare a list of such leads before the session begins.

Another alternative method that could be used even on-line is the one described as:

"Group passing technique

Each person in a circular group writes down one idea, and then passes the piece of paper to the next person in a clockwise direction, who adds some thoughts. This continues until everybody gets his or her original piece of paper back. By this time, it is likely that the group will have extensively elaborated on each idea.

The group may also create an "Idea Book" and post a distribution list or routing slip to the front of the book. On the first page is a description of the problem. The first person to receive the book lists his or her ideas and then routes the book to the next person on the distribution list. The second person can log new ideas or add to the ideas of the previous person. This continues until the distribution list is exhausted. A follow-up "read out" meeting is then held to discuss the ideas logged in the book. This technique takes longer, but it allows individuals time to think deeply about the problem."

I think an iGEM group could create these tools for the group on the google group page which the members can access at the group site.

Another very good web site in the topic is JBP.

Have fun!

What is a COMMITMENT?

Dear Collegues,

 

Please find below some words of Yehuda Berg about what a Commitment means.

 

"...a commitment is ongoing. It needs to be made and remade every day.

If you decide to run a marathon, you aren’t just choosing to show up on the day of the event.

You’re choosing a path, and that means conditioning every day. If you skip a week of training, you might not make it to the marathon.

Being committed to a spiritual path means sometimes we’ll be alone. We might feel like a black sheep. Other times, people might want us to fail. Or at least when we succeed, their insecurities will be awakened and they won’t be happy about our success.

And one thing’s for sure: we will be tested. Not on our decision, but on our commitment."

Starting a project, any project, needs a commitment.

A succesfull  iGEM teem needs a written commitment as described in the paper of  Wayne Materi.  We commit ourselfs to work hard, teach/learn lots and have fun.

Worth thinking about Yehuda's thoughts in general.

 

Best,

 Balint.

Prezi - a new tool for making better prezentations

One of the most interesting development in the field of prezentation tools is Prezi.



Beside using it for presentations, you can use it for Mind Mapping too, like here:



And here you can see some tricks for masters:



You can use it for free, and if you are using it for educational purposes, there is an edu version for it, with lot of cool features.

So, why not using a better tool for the same job?