Team:Freiburg Software/User/Guide

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Another way to import sequence data into SynBioWave is by directly copy-pasting it into a Blip, selecting it and clicking the "Convert to Sequence" button in the "Sequence" menu. The main robot will then convert the selected text to a sequence, try to recognize its type (DNA, RNA or protein) and store it in the workspace.  <br />
Another way to import sequence data into SynBioWave is by directly copy-pasting it into a Blip, selecting it and clicking the "Convert to Sequence" button in the "Sequence" menu. The main robot will then convert the selected text to a sequence, try to recognize its type (DNA, RNA or protein) and store it in the workspace.  <br />
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The second function - "Circular view" - takes the selected sequence form the workspace and displays it assuming its a circular one.<br />
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The second function - "Circular view" - launches our new Sequence View Gadget. Read more about it <a href="http://2010.igem.org/Team:Freiburg_Software/Special/CircularView">here</a><br />
Finally "Combine" is pretty much straightforward: It takes two sequences from the workspace and combines them to one sequence.
Finally "Combine" is pretty much straightforward: It takes two sequences from the workspace and combines them to one sequence.
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Latest revision as of 02:45, 28 October 2010

Video Tutorial

We have created a series of Tutorialvideos for SynBioWave 2.0. Following you will find the Video for the main robot. Find the Videos for the add-on robots on the respective sites.

Getting Started

Before we tell you what SynBioWave is, we would like to tell you what it is not:
SynBioWave is not a software that you have to download, install and then run on you local PC. SynBioWave is not a stand-alone web application that runs on a server somewhere.
But: SynBioWave is an extension to the Wave environment.

Wave? What is that?

The Google Wave Logo

The concept of the online collaboration environment wave may be familiar to some of you. If that is the case you may simply skip this paragraph.
Wave was first introduced by Google in 2009. For further information please see the used technologies section.
SynBioWave was developed and currently runs using Google Wave. That's why you will need an account there if you want to test it. If you already have a google account (for Google Mail or Calender) you can simply use this one.
Now log in to Google Wave! It should look something like this:

This is what Google wave looks like once you are logged in. On the left side you see folder navigation and contact list. In the middle is the currently selected folder and on the right side you will see the actual wavelet once you've selected or created one.

Communication on wave is done within the so called wavelets. You can think of the wavelets like email correspondences, instant messenger conversations or forum threads. In fact they are a mixture of all of those.
While people communicate in the wave via text messages, they can edit or delete old messages, import media files like pictures, videos and sounds and use special wave extensions: Gadgets and Robots. SynBioWave makes use of the latter two.
To open a new wavelet simply click the "blank wave" button in the right area.

How do I turn my wave into SynBioWave?

As mentioned before, SynBioWave is a System that uses Robots and Gadgets to extend the capabilities of the wave. However you only have to deal with the robots and they will then add Gadgets if they need any.
Each robot has a specific adress that looks like an email adress. For example the SynBioWave main robot has the adress synbiowave@appspot.com
You can add people and robots to a wavelet by clicking the plus symbol on top of the wavelet. Please add the SynBioWave main robot now!

Note: If you don't want to type the address every time, you can also add robots to you contact list on the lower left.

Once you have added the main robot to the wavelet it will deploy the SynBioWave Menu Gadget in the first Blip (Each wavelet is divided into so called Blips). The SynBioWave Menu Gadget is the main control area of SynBioWave. Every robot adds his submenu there and you can use its functions from there. The second thing the main robot will add is another Wavelet called the Workspace. It will also add all participants of the original Wavelet to the workspace. You can see the workspace in your current folder in the middle window. The Workspace is used to hold and organize all the sequence data that you are currently working on. We will tell you how to use it later. For now we want to take a look at the Menu and its four submenus:

The SynBioWave main menu can always be found in the very first blip of a wavelet.

File

The File menu handles all exchange of data between your local hard drive and the wave. To import a file from your computer click the "Upload" button in the file menu and select the file you want to submit. SynBioWave can currently import the following file formats: FASTA, Genbank and EMBL.
If you want to export one or more Sequences you must first make sure that they are selected in the workspace (you will learn how to do that in the workspace section below). Then click the "Download" button in the file menu, select the desired output format and click "Send". The Robot will then load the sequences from the workspace, encode them in the specified format and make the output file available in a new Blip at the end of the Wavelet. Now simply click on the Attachment symbol to download the file.

Sequence

Another way to import sequence data into SynBioWave is by directly copy-pasting it into a Blip, selecting it and clicking the "Convert to Sequence" button in the "Sequence" menu. The main robot will then convert the selected text to a sequence, try to recognize its type (DNA, RNA or protein) and store it in the workspace.
The second function - "Circular view" - launches our new Sequence View Gadget. Read more about it here
Finally "Combine" is pretty much straightforward: It takes two sequences from the workspace and combines them to one sequence.

Database

The "Database" menu lets you import Sequences from external services. Right now there is only the parts registry. You can download a BioBrick by simply entering its identifier (e.g. BBa_B0100) and clicking "Send". SynBioWave will then download the file from the parts registry and display it in a new Blip. If you want to work with this part, click the "Store in workspace" Button underneath the display and the sequence will be saved in the workspace.

Workspace

As mentioned before the workspace is a separate Wavelet where all the sequences are stored. The SynBioWave main robot creates a new Blip there for every sequence that you save to the workspace. Please do not modify the Blips on your own! Otherwise SynBioWave might not be working properly.

Every sequence that is stored in the workspace is represented by one Blip like this one

The only thing you are allowed to do here is clicking the check boxes labeled "Active". Whenever you are about to do something with sequences the robots will load all the active sequences from the workspace and will only work if you have selected the right number. For example the Primer Designer will only accept one sequence and display an error if you try to run it with multiple sequences and the Alignment Robot will only accept two sequences.

Now you know the basics about how to work with SynBioWave. Right now you can't really work with the parts yet. That's what the add-on robots are there for. To learn all about them please go to the second part of this user guide.