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Team:Freiburg Software/Notebook
From 2010.igem.org
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<p class="main"> | <p class="main"> | ||
</html> | </html> | ||
| - | + | =June= | |
| - | + | =July= | |
| - | + | =August= | |
| - | + | =September= | |
| - | + | ==<font style="font-size: 12px;">Sep. 16 2010</font>== | |
| - | + | ||
''Niklas'' <br /> | ''Niklas'' <br /> | ||
Set up the BLAST Robot (Robot Registration) and started research on BLAST APIs | Set up the BLAST Robot (Robot Registration) and started research on BLAST APIs | ||
| - | + | ==<font style="font-size: 12px;">Sep. 17 2010</font>== | |
''Paresh'' <br /> | ''Paresh'' <br /> | ||
Discussed the first version of Translation Robot with team and received inputs for further improvements. | Discussed the first version of Translation Robot with team and received inputs for further improvements. | ||
| - | + | ==<font style="font-size: 12px;">Sep. 18 2010</font>== | |
''Niklas'' <br /> | ''Niklas'' <br /> | ||
Set up the Alignment Robot and implemented a first Alignment Algorithm | Set up the Alignment Robot and implemented a first Alignment Algorithm | ||
| - | + | ==<font style="font-size: 12px;">Sep. 19 2010</font>== | |
''Niklas'' <br /> | ''Niklas'' <br /> | ||
Improved Code Reusability by redesigning the Alignment Robot | Improved Code Reusability by redesigning the Alignment Robot | ||
| - | + | ==<font style="font-size: 12px;">Sep. 20 2010</font>== | |
''Paresh, Fabian, Niklas'' <br /> | ''Paresh, Fabian, Niklas'' <br /> | ||
Went to Frankfurt for Visa application, created Project abstract and agreed on a title | Went to Frankfurt for Visa application, created Project abstract and agreed on a title | ||
| - | + | ==<font style="font-size: 12px;">Sep. 21 2010</font>== | |
''Niklas, Fabian'' <br /> | ''Niklas, Fabian'' <br /> | ||
created Wiki outline, checked gold mouse pad requirements | created Wiki outline, checked gold mouse pad requirements | ||
| - | + | ==<font style="font-size: 12px;">Sep. 22 2010</font>== | |
''Niklas'' <br /> | ''Niklas'' <br /> | ||
Continued Work on Needleman/Wunsch Alignment, now custom cost functions are available | Continued Work on Needleman/Wunsch Alignment, now custom cost functions are available | ||
| - | + | ==<font style="font-size: 12px;">Sep. 25 2010</font>== | |
''Niklas'' <br /> | ''Niklas'' <br /> | ||
Added Smith/Waterman Algorithm to Alignment Robot | Added Smith/Waterman Algorithm to Alignment Robot | ||
| - | + | ==<font style="font-size: 12px;">Sep. 30 2010</font>== | |
''Niklas'' <br /> | ''Niklas'' <br /> | ||
Implemented the first Version of the PrimerDesigner (synbiowave-primerdesigner@appspot.com) | Implemented the first Version of the PrimerDesigner (synbiowave-primerdesigner@appspot.com) | ||
| - | + | =October= | |
| - | + | ==<font style="font-size: 12px;">Oct. 1 2010</font>== | |
''Paresh, Fabian''<br /> | ''Paresh, Fabian''<br /> | ||
Improved the Translation Robot. The output shows now the Frame no. in a clearer way. | Improved the Translation Robot. The output shows now the Frame no. in a clearer way. | ||
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* We discused the basic functionality of REBase-Robot (Restcritionenzym). | * We discused the basic functionality of REBase-Robot (Restcritionenzym). | ||
| - | + | ==<font style="font-size: 12px;">Oct. 3 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Continued Work on Primer Designer. | Continued Work on Primer Designer. | ||
| Line 70: | Line 69: | ||
TODO: Make sure the melting points of both primers are about the same, implement RFCs and make designed Primers available for downloading. | TODO: Make sure the melting points of both primers are about the same, implement RFCs and make designed Primers available for downloading. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 4 2010</font>== | |
''Paresh''<br /> | ''Paresh''<br /> | ||
Started working on restrictionsites robot. | Started working on restrictionsites robot. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 5 2010</font>== | |
''Niklas, Fabian''<br /> | ''Niklas, Fabian''<br /> | ||
Primer design: | Primer design: | ||
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<li>Import via BioJava</li> | <li>Import via BioJava</li> | ||
</ul> | </ul> | ||
| - | + | ==<font style="font-size: 12px;">Oct. 6 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Started writing the User Guide for the Add-on Robots | Started writing the User Guide for the Add-on Robots | ||
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Received inputs regarding the restriction sites from team. | Received inputs regarding the restriction sites from team. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 7 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Improved the synbiowave base classes SequenceUtils and Sequence and adjusted the Addon Robots to them. | Improved the synbiowave base classes SequenceUtils and Sequence and adjusted the Addon Robots to them. | ||
Also fixed a bug in the alignment robot. | Also fixed a bug in the alignment robot. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 8 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
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. | 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. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 8 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Improved the Primerdesigner Gadget: User can now enter a custom name for the primers before they get stored in Workspace.<br /> | Improved the Primerdesigner Gadget: User can now enter a custom name for the primers before they get stored in Workspace.<br /> | ||
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Made some icons for the robots. | Made some icons for the robots. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 9 2010</font>== | |
''Paresh''<br /> | ''Paresh''<br /> | ||
Improved the translation robot to show all frames one under the other using new methods in SequenceUtils class.<br /> | Improved the translation robot to show all frames one under the other using new methods in SequenceUtils class.<br /> | ||
| Line 117: | Line 116: | ||
Created a Robot that can download any part from parts registry and add it to the workspace. | Created a Robot that can download any part from parts registry and add it to the workspace. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 11 2010</font>== | |
''Paresh''<br /> | ''Paresh''<br /> | ||
Improved the translation robot to output frames faster. Wrote own translation method for converting DNA to amino acids<br /> | Improved the translation robot to output frames faster. Wrote own translation method for converting DNA to amino acids<br /> | ||
''Niklas''<br /> | ''Niklas''<br /> | ||
Did some research on the low performace and tweaked the Display functions resulting in a huge performance gain. | Did some research on the low performace and tweaked the Display functions resulting in a huge performance gain. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 12 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
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.<br /> | 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.<br /> | ||
''Fabian''<br /> | ''Fabian''<br /> | ||
Designed logos and icons. | Designed logos and icons. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 13 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
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)<br /> | 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)<br /> | ||
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Changed the translation robot to find multiple ORFs per frame.<br /> | Changed the translation robot to find multiple ORFs per frame.<br /> | ||
| - | + | ==<font style="font-size: 12px;">Oct. 14 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Made the following fileformats available in the Download section: FASTA, Genbank, EMBL<br /> | Made the following fileformats available in the Download section: FASTA, Genbank, EMBL<br /> | ||
| Line 143: | Line 142: | ||
''Paresh''<br /> | ''Paresh''<br /> | ||
Started working on likelihood robot.<br /> | Started working on likelihood robot.<br /> | ||
| - | + | ==<font style="font-size: 12px;">Oct. 15 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Imported BioBricks can now be stored into workspace via ButtonClick<br /> | Imported BioBricks can now be stored into workspace via ButtonClick<br /> | ||
Continued Work on BLAST Robot: Finally found a good solution, now using NCBI Blast URL API | Continued Work on BLAST Robot: Finally found a good solution, now using NCBI Blast URL API | ||
| - | + | ==<font style="font-size: 12px;">Oct. 16 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Created a "waiter" Gadget, that waits for the BLAST results to avoid robot timeouts.<br /> | Created a "waiter" Gadget, that waits for the BLAST results to avoid robot timeouts.<br /> | ||
''Fabian''<br /> | ''Fabian''<br /> | ||
Uploaded the homepage layout to the official wiki. | Uploaded the homepage layout to the official wiki. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 17 2010</font>== | |
''Niklas''<br /> | ''Niklas''<br /> | ||
Continued working on the BLAST robot: Wrote an XML-Parser for the ncbi blast results. They are now beeing displayed in the wave<br /> | Continued working on the BLAST robot: Wrote an XML-Parser for the ncbi blast results. They are now beeing displayed in the wave<br /> | ||
''Fabian''<br /> | ''Fabian''<br /> | ||
Bought a new laptop especially for iGEM ;) | Bought a new laptop especially for iGEM ;) | ||
| - | + | ==<font style="font-size: 12px;">Oct. 19 2010</font>== | |
''Fabian''<br /> | ''Fabian''<br /> | ||
Homepage: Made some new designs. | Homepage: Made some new designs. | ||
| - | + | ==<font style="font-size: 12px;">Oct. 20 2010</font>== | |
''Fabian''<br /> | ''Fabian''<br /> | ||
Homepage: designd the page "Home" | Homepage: designd the page "Home" | ||
Revision as of 21:30, 20 October 2010
Notebook
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"
