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Team:Freiburg Software/Notebook
From 2010.igem.org
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<h1>Notebook</h1> | <h1>Notebook</h1> | ||
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<h1>April</h1> | <h1>April</h1> | ||
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<h2><font style="font-size: 12px;">Apr. 6 2010</font></h2> | <h2><font style="font-size: 12px;">Apr. 6 2010</font></h2> | ||
<i><p class="main">Paul, Jörg</p></i> | <i><p class="main">Paul, Jörg</p></i> | ||
<p class="main">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. | <p class="main">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.</p> | 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.</p> | ||
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<h2><font style="font-size: 12px;">Apr. 13 2010</font></h2> | <h2><font style="font-size: 12px;">Apr. 13 2010</font></h2> | ||
<i><p class="main">Paul, Jörg</p></i> | <i><p class="main">Paul, Jörg</p></i> | ||
<p class="main">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.</p> | <p class="main">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.</p> | ||
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<h2><font style="font-size: 12px;">Apr. 20 2010</font></h2> | <h2><font style="font-size: 12px;">Apr. 20 2010</font></h2> | ||
<i><p class="main">Paul, Jörg</p></i> | <i><p class="main">Paul, Jörg</p></i> | ||
<p class="main">we are currently writing a detailed guide for SynBioWave-Robot programming and will post it on the project site.</p> | <p class="main">we are currently writing a detailed guide for SynBioWave-Robot programming and will post it on the project site.</p> | ||
<h1>May</h1> | <h1>May</h1> | ||
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<h2><font style="font-size: 12px;">May. 10 2010</font></h2> | <h2><font style="font-size: 12px;">May. 10 2010</font></h2> | ||
<i><p class="main">Paul, Jörg</p></i> | <i><p class="main">Paul, Jörg</p></i> | ||
<p class="main">Developer guide is available, so programming additional robots using the SynBioWave Robot would be easier.</p> | <p class="main">Developer guide is available, so programming additional robots using the SynBioWave Robot would be easier.</p> | ||
<h1>June</h1> | <h1>June</h1> | ||
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<h2><font style="font-size: 12px;">Jun. 06 2010</font></h2> | <h2><font style="font-size: 12px;">Jun. 06 2010</font></h2> | ||
<i><p class="main">Paul, Jörg</p></i> | <i><p class="main">Paul, Jörg</p></i> | ||
<p class="main">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. </p> | <p class="main">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. </p> | ||
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<h2><font style="font-size: 12px;">Jun. 10 2010</font></h2> | <h2><font style="font-size: 12px;">Jun. 10 2010</font></h2> | ||
<i><p class="main">Paul, Jörg, kristian</p></i> | <i><p class="main">Paul, Jörg, kristian</p></i> | ||
<p class="main">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.</p> | <p class="main">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.</p> | ||
<h1>July</h1> | <h1>July</h1> | ||
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<h2><font style="font-size: 12px;">Jul. 05 2010</font></h2> | <h2><font style="font-size: 12px;">Jul. 05 2010</font></h2> | ||
<i><p class="main">Paresh, Niklas</p></i> | <i><p class="main">Paresh, Niklas</p></i> | ||
<p class="main">Started developing primary versions of the robots.</p> | <p class="main">Started developing primary versions of the robots.</p> | ||
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<h2><font style="font-size: 12px;">Jul. 16 2010</font></h2> | <h2><font style="font-size: 12px;">Jul. 16 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Paresh Paradkar and Niklas Meinzer have now got their accounts for WIKI.</p> | <p class="main">Paresh Paradkar and Niklas Meinzer have now got their accounts for WIKI.</p> | ||
<h1>August</h1> | <h1>August</h1> | ||
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<h2><font style="font-size: 12px;">Aug. 03 2010</font></h2> | <h2><font style="font-size: 12px;">Aug. 03 2010</font></h2> | ||
<i><p class="main">Paresh, Fabian</p></i> | <i><p class="main">Paresh, Fabian</p></i> | ||
<p class="main">We discussed about the US visa form and concerned formalities.</p> | <p class="main">We discussed about the US visa form and concerned formalities.</p> | ||
<h1>September</h1> | <h1>September</h1> | ||
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<h2><font style="font-size: 12px;">Sep. 16 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 16 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Set up the BLAST Robot (Robot Registration) and started research on BLAST APIs</p> | <p class="main">Set up the BLAST Robot (Robot Registration) and started research on BLAST APIs</p> | ||
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<h2><font style="font-size: 12px;">Sep. 17 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 17 2010</font></h2> | ||
<i><p class="main">Paresh</p></i> | <i><p class="main">Paresh</p></i> | ||
<p class="main">Discussed the first version of Translation Robot with team and received inputs for further improvements.</p> | <p class="main">Discussed the first version of Translation Robot with team and received inputs for further improvements.</p> | ||
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<h2><font style="font-size: 12px;">Sep. 18 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 18 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Set up the Alignment Robot and implemented a first Alignment Algorithm</p> | <p class="main">Set up the Alignment Robot and implemented a first Alignment Algorithm</p> | ||
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<h2><font style="font-size: 12px;">Sep. 19 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 19 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Improved Code Reusability by redesigning the Alignment Robot</p> | <p class="main">Improved Code Reusability by redesigning the Alignment Robot</p> | ||
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<h2><font style="font-size: 12px;">Sep. 20 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 20 2010</font></h2> | ||
<i><p class="main">Paresh, Fabian, Niklas</p></i> | <i><p class="main">Paresh, Fabian, Niklas</p></i> | ||
<p class="main">Went to Frankfurt for Visa application, created Project abstract and agreed on a title</p> | <p class="main">Went to Frankfurt for Visa application, created Project abstract and agreed on a title</p> | ||
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<h2><font style="font-size: 12px;">Sep. 21 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 21 2010</font></h2> | ||
<i><p class="main">Niklas, Fabian</p></i> | <i><p class="main">Niklas, Fabian</p></i> | ||
<p class="main">created Wiki outline, checked gold mouse pad requirements</p> | <p class="main">created Wiki outline, checked gold mouse pad requirements</p> | ||
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<h2><font style="font-size: 12px;">Sep. 22 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 22 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Continued Work on Needleman/Wunsch Alignment, now custom cost functions are available</p> | <p class="main">Continued Work on Needleman/Wunsch Alignment, now custom cost functions are available</p> | ||
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<h2><font style="font-size: 12px;">Sep. 25 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 25 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Added Smith/Waterman Algorithm to Alignment Robot</p> | <p class="main">Added Smith/Waterman Algorithm to Alignment Robot</p> | ||
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<h2><font style="font-size: 12px;">Sep. 30 2010</font></h2> | <h2><font style="font-size: 12px;">Sep. 30 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Implemented the first Version of the PrimerDesigner (synbiowave-primerdesigner@appspot.com)</p> | <p class="main">Implemented the first Version of the PrimerDesigner (synbiowave-primerdesigner@appspot.com)</p> | ||
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<h1>October</h1> | <h1>October</h1> | ||
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* We discused the basic functionality of REBase-Robot (Restcritionenzym). | * We discused the basic functionality of REBase-Robot (Restcritionenzym). | ||
</p> | </p> | ||
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<h2><font style="font-size: 12px;">Oct. 3 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 3 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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Now calculation the melting points according to <a href="http://www.basic.northwestern.edu/biotools/oligocalc.html">Oligocalc</a> as recommended by Volker. I furthermore resolved the issues I had with the Display Gadget and the Sequences are displayed in right order.<br /> | Now calculation the melting points according to <a href="http://www.basic.northwestern.edu/biotools/oligocalc.html">Oligocalc</a> as recommended by Volker. I furthermore resolved the issues I had with the Display Gadget and the Sequences are displayed in right order.<br /> | ||
TODO: Make sure the melting points of both primers are about the same, implement RFCs and make designed Primers available for downloading.</p> | TODO: Make sure the melting points of both primers are about the same, implement RFCs and make designed Primers available for downloading.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 4 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 4 2010</font></h2> | ||
<i><p class="main">Paresh</p></i> | <i><p class="main">Paresh</p></i> | ||
<p class="main">Started working on restrictionsites robot.</p> | <p class="main">Started working on restrictionsites robot.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 5 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 5 2010</font></h2> | ||
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<p class="main">Primer design: </p> | <p class="main">Primer design: </p> | ||
<ul> | <ul> | ||
| - | <li | + | <li>describe the Sequence with their names</li> |
| - | <li | + | <li>a input matrix for the position where the primer should start</li> |
| - | <li | + | <li>implement binary search for primer position</li> |
</ul> | </ul> | ||
<p class="main">Alignment:</p> | <p class="main">Alignment:</p> | ||
<ul> | <ul> | ||
| - | <li | + | <li>show Start - End - position</li> |
</ul> | </ul> | ||
<p class="main">Database:</p> | <p class="main">Database:</p> | ||
<ul> | <ul> | ||
| - | <li | + | <li>Import via BioJava</li> |
</ul> | </ul> | ||
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<h2><font style="font-size: 12px;">Oct. 6 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 6 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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<p class="main">Changed translation robot to color the ORF in the output. | <p class="main">Changed translation robot to color the ORF in the output. | ||
Received inputs regarding the restriction sites from team.</p> | Received inputs regarding the restriction sites from team.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 7 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 7 2010</font></h2> | ||
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<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">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.</p> | <p class="main">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.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 8 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 8 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Made some icons for the robots.</p> | <p class="main">Made some icons for the robots.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 9 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 9 2010</font></h2> | ||
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<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Created a Robot that can download any part from parts registry and add it to the workspace.</p> | <p class="main">Created a Robot that can download any part from parts registry and add it to the workspace.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 11 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 11 2010</font></h2> | ||
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<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Did some research on the low performace and tweaked the Display functions resulting in a huge performance gain.</p> | <p class="main">Did some research on the low performace and tweaked the Display functions resulting in a huge performance gain.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 12 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 12 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Designed logos and icons.</p> | <p class="main">Designed logos and icons.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 13 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 13 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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<i><p class="main">Paresh</p></i> | <i><p class="main">Paresh</p></i> | ||
<p class="main">Changed the translation robot to find multiple ORFs per frame.</p> | <p class="main">Changed the translation robot to find multiple ORFs per frame.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 14 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 14 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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<i><p class="main">Paresh</p></i> | <i><p class="main">Paresh</p></i> | ||
<p class="main">Started working on likelihood robot.</p> | <p class="main">Started working on likelihood robot.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 15 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 15 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">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.</p> | <p class="main">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.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 16 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 16 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Uploaded the homepage layout to the official wiki.</p> | <p class="main">Uploaded the homepage layout to the official wiki.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 17 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 17 2010</font></h2> | ||
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
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<h2><font style="font-size: 12px;">Oct. 19 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 19 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
| - | <p class="main">Homepage: Made some new designs./p> | + | <p class="main">Homepage: Made some new designs.</p> |
<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Started writing content for the wiki.</p> | <p class="main">Started writing content for the wiki.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 20 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 20 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Homepage: designd the page "Home".</p> | <p class="main">Homepage: designd the page "Home".</p> | ||
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<h2><font style="font-size: 12px;">Oct. 22 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 22 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Made the Team Page. Wrote some standard classes.</p> | <p class="main">Made the Team Page. Wrote some standard classes.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 23 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 23 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Made the Team portrait and some images.</p> | <p class="main">Made the Team portrait and some images.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 24 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 24 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Uploaded data to the wiki. Wrote text for the Team page.</p> | <p class="main">Uploaded data to the wiki. Wrote text for the Team page.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 25 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 25 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
<p class="main">Tried to implement a javascript into the wiki for a slideshow... The slideshow looks...hmmm. Uploaded the pictutes to Picasa.</p> | <p class="main">Tried to implement a javascript into the wiki for a slideshow... The slideshow looks...hmmm. Uploaded the pictutes to Picasa.</p> | ||
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<h2><font style="font-size: 12px;">Oct. 26 2010</font></h2> | <h2><font style="font-size: 12px;">Oct. 26 2010</font></h2> | ||
<i><p class="main">Fabian</p></i> | <i><p class="main">Fabian</p></i> | ||
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<i><p class="main">Niklas</p></i> | <i><p class="main">Niklas</p></i> | ||
<p class="main">Wrote the Human Practise part of the wiki.</p> | <p class="main">Wrote the Human Practise part of the wiki.</p> | ||
| + | <i><p class="main">Paresh</p></i> | ||
| + | <p class="main">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.</p> | ||
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| + | <h2><font style="font-size: 12px;">Oct. 27&28 2010</font></h2> | ||
| + | <i><p class="main">Whole Team</p></i> | ||
| + | <p class="main">The last days before the wiki freeze the whole team worked hard and stayed up till early morning to get the wiki finished. </p> | ||
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</div> | </div> | ||
</html> | </html> | ||
Latest revision as of 03:14, 28 October 2010
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 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.
