Notebook

Contents 1 June 2 July 3 August 4 September 4.1 Sep. 16 2010 4.2 Sep. 17 2010 4.3 Sep. 18 2010 4.4 Sep. 19 2010 4.5 Sep. 20 2010 4.6 Sep. 21 2010 4.7 Sep. 22 2010 4.8 Sep. 25 2010 4.9 Sep. 30 2010 5 October 5.1 Oct. 1 2010 5.2 Oct. 3 2010 5.3 Oct. 4 2010 5.4 Oct. 5 2010 5.5 Oct. 6 2010 5.6 Oct. 7 2010 5.7 Oct. 8 2010 5.8 Oct. 8 2010 5.9 Oct. 9 2010 5.10 Oct. 11 2010 5.11 Oct. 12 2010 5.12 Oct. 13 2010 5.13 Oct. 14 2010 5.14 Oct. 15 2010 5.15 Oct. 16 2010 5.16 Oct. 17 2010 5.17 Oct. 19 2010 5.18 Oct. 20 2010

June

July

August

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 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.

Oct. 20 2010

Fabian
Homepage: designd the page "Home"