iGEM 2010 — Team Freiburg_Software

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# Team:Freiburg Software/Notebook

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[Notebook](https://2010.igem.org/Team%3AFreiburg_Software/Notebook)

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[User Guide](https://2010.igem.org/Team%3AFreiburg_Software/User/Guide)

[The Robots](https://2010.igem.org/Team%3AFreiburg_Software/User/Robots)

[Developer](https://2010.igem.org/Team%3AFreiburg_Software/Developer)

[Guide](https://2010.igem.org/Team%3AFreiburg_Software/Developer/Guide)

[Technologies](https://2010.igem.org/Team%3AFreiburg_Software/Developer/Technologies)

[Architecture](https://2010.igem.org/Team%3AFreiburg_Software/Developer/Architecture)

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# Notebook

# April

## Apr. 6 2010

*Paul, Jörg*

As Google has introduced its new APIv2 and is going to break backwards compatibility to version 1 soon, we are working hard to port SynBioWave to the new API.
We have rewritten most of the code of the SynBioWave-Robot, and we were able to implement several major improvements using new possibilities of the APIv2.

## Apr. 13 2010

*Paul, Jörg*

Menu-events now trigger callback-functions, which further simplifies robot-programming and results in much cleaner code. As the state of a gadget can now be updated without reloading the gadget completely every time, we are using this feature to provide a smoother menu. We use the new “Active API” to improve upload integration.

## Apr. 20 2010

*Paul, Jörg*

we are currently writing a detailed guide for SynBioWave-Robot programming and will post it on the project site.

# May

## May. 10 2010

*Paul, Jörg*

Developer guide is available, so programming additional robots using the SynBioWave Robot would be easier.

# June

## Jun. 06 2010

*Paul, Jörg*

The new Attachmend-API greatly simplifies the up- and download of sequences. Sequences attached to a wave (at least those in common formats) using wave’s generic file attachment functionality are automatically imported.

## Jun. 10 2010

*Paul, Jörg, kristian*

We have new members in Team now. Fabian Haas, Paresh Paradkar and Niklas Meinzer joined Freiburg\_Software Team. We gave an introduction to them about iGEM and SynBioWave.

# July

## Jul. 05 2010

*Paresh, Niklas*

Started developing primary versions of the robots.

## Jul. 16 2010

*Fabian*

Paresh Paradkar and Niklas Meinzer have now got their accounts for WIKI.

# August

## Aug. 03 2010

*Paresh, Fabian*

We discussed about the US visa form and concerned formalities.

# September

## Sep. 16 2010

*Niklas*

Set up the BLAST Robot (Robot Registration) and started research on BLAST APIs

## Sep. 17 2010

*Paresh*

Discussed the first version of Translation Robot with team and received inputs for further improvements.

## Sep. 18 2010

*Niklas*

Set up the Alignment Robot and implemented a first Alignment Algorithm

## Sep. 19 2010

*Niklas*

Improved Code Reusability by redesigning the Alignment Robot

## Sep. 20 2010

*Paresh, Fabian, Niklas*

Went to Frankfurt for Visa application, created Project abstract and agreed on a title

## Sep. 21 2010

*Niklas, Fabian*

created Wiki outline, checked gold mouse pad requirements

## Sep. 22 2010

*Niklas*

Continued Work on Needleman/Wunsch Alignment, now custom cost functions are available

## Sep. 25 2010

*Niklas*

Added Smith/Waterman Algorithm to Alignment Robot

## Sep. 30 2010

*Niklas*

Implemented the first Version of the PrimerDesigner (synbiowave-primerdesigner@appspot.com)

# October

## Oct. 1 2010

*Paresh, Fabian*

Improved the Translation Robot. The output shows now the Frame no. in a clearer way.
\* Also, Paresh made the output more comfortable for users by adding length, start and end positions of ORFs.
\* We discused the basic functionality of REBase-Robot (Restcritionenzym).

## Oct. 3 2010

*Niklas*

Continued Work on Primer Designer.
Now calculation the melting points according to [Oligocalc](http://www.basic.northwestern.edu/biotools/oligocalc.html) as recommended by Volker. I furthermore resolved the issues I had with the Display Gadget and the Sequences are displayed in right order.
TODO: Make sure the melting points of both primers are about the same, implement RFCs and make designed Primers available for downloading.

## Oct. 4 2010

*Paresh*

Started working on restrictionsites robot.

## Oct. 5 2010

*Niklas, Fabian*

Primer design:

* describe the Sequence with their names
* a input matrix for the position where the primer should start
* implement binary search for primer position

Alignment:

* show Start - End - position

Database:

* Import via BioJava

## Oct. 6 2010

*Niklas*

Started writing the User Guide for the Add-on Robots

*Paresh*

Changed translation robot to color the ORF in the output.
Received inputs regarding the restriction sites from team.

## Oct. 7 2010

*Niklas*

Improved the synbiowave base classes SequenceUtils and Sequence and adjusted the Addon Robots to them.
Also fixed a bug in the alignment robot.

## Oct. 8 2010

*Niklas*

Experimented with Gadgets to make our Robots more interactive. Created a simple Button Gadget and included it in Primerdesigner: Now the user can store the Primers in the workspace by clicking a button.

## Oct. 8 2010

*Niklas*

Improved the Primerdesigner Gadget: User can now enter a custom name for the primers before they get stored in Workspace.

*Fabian*

Made some icons for the robots.

## Oct. 9 2010

*Paresh*

Improved the translation robot to show all frames one under the other using new methods in SequenceUtils class.

*Niklas*

Created a Robot that can download any part from parts registry and add it to the workspace.

## Oct. 11 2010

*Paresh*

Improved the translation robot to output frames faster. Wrote own translation method for converting DNA to amino acids

*Niklas*

Did some research on the low performace and tweaked the Display functions resulting in a huge performance gain.

## Oct. 12 2010

*Niklas*

Updated the Main Robot and included all library files edited in the past weeks into the synbiowave library; released synbiowave-V2-001.jar as the new developer library. Also the Main Robot now uses the new XML parser to import parts from part registry.

*Fabian*

Designed logos and icons.

## Oct. 13 2010

*Niklas*

Fixed a bug in Abstract Robot: The robot now checks if the gadget is the MainMenu before he tries to evaluate it, which enables us to use other interactive Gadgets. (New abstract robot can be found in synbiowave-V2-002.jar on svn)

Reviewed the Primerdesigner: No RFC Prefixes are available, but start and stop point. Also the Primers are now no longer wrong way.

*Fabian*

Wrote pages for the wiki and made some Homepage designs.

*Paresh*

Changed the translation robot to find multiple ORFs per frame.

## Oct. 14 2010

*Niklas*

Made the following fileformats available in the Download section: FASTA, Genbank, EMBL

*Fabian*

Wrote pages for the wiki.

*Paresh*

Started working on likelihood robot.

## Oct. 15 2010

*Niklas*

Imported BioBricks can now be stored into workspace via ButtonClick.Continued Work on BLAST Robot: Finally found a good solution, now using NCBI Blast URL API.

## Oct. 16 2010

*Niklas*

Created a "waiter" Gadget, that waits for the BLAST results to avoid robot timeouts.

*Fabian*

Uploaded the homepage layout to the official wiki.

## Oct. 17 2010

*Niklas*

Continued working on the BLAST robot: Wrote an XML-Parser for the ncbi blast results. They are now beeing displayed in the wave

*Fabian*

Bought a new laptop especially for iGEM ;)

## Oct. 19 2010

*Fabian*

Homepage: Made some new designs.

*Niklas*

Started writing content for the wiki.

## Oct. 20 2010

*Fabian*

Homepage: designd the page "Home".

## Oct. 22 2010

*Fabian*

Made the Team Page. Wrote some standard classes.

## Oct. 23 2010

*Fabian*

Made the Team portrait and some images.

## Oct. 24 2010

*Fabian*

Uploaded data to the wiki. Wrote text for the Team page.

## Oct. 25 2010

*Fabian*

Tried to implement a javascript into the wiki for a slideshow... The slideshow looks...hmmm. Uploaded the pictutes to Picasa.

## Oct. 26 2010

*Fabian*

Uploaded data and text to the wiki.

*Niklas*

Wrote the Human Practise part of the wiki.

*Paresh*

Updated Notebook and meeting pages of the wiki to HTML style to maintain consistency and made some spelling corrections in some parts of the wiki.

## Oct. 27&28 2010

*Whole Team*

The last days before the wiki freeze the whole team worked hard and stayed up till early morning to get the wiki finished.

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