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Team:Berkeley Software/RichardNotebook/Journal
From 2009.igem.org
Week One
This week's been crazy busy. I've been looking for bugs in Clotho, fixing up my Cartoonist plugin, and making the [http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Plugin_Tutorial Clotho plugin tutorial]. On Monday we had an introductory meeting and safety training so we can go into the lab. Doug helped us set up Clotho and handed out some tasks for the week. On Tuesday we discussed and chose our projects for the summer and started work on identifying bugs and cleaning up documentation. I'll be working primarily on a visualization piece with Joanna.
The rest of the week I've been hammering out a [http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Plugin_Tutorial plugin tutorial for Clotho]. On Wednesday I set up a plugins project in NetBeans and wrote up a preliminary draft of the tutorial. On Thursday and Friday I cleaned up the tutorial a bit and made a sample plugin XML file. I also tried out my tutorial to look for unclear instructions and potential problem points that I would need to point out in the tutorial. Lastly, sacrificing most of my weekend, I added helpful screenshots to the wiki page and cleaned up the tutorial some more. Unfortunately, the last section of the tutorial is still incomplete; I will have to finish it on Monday.
--Legor17 07:59, 8 June 2009 (UTC)
Week Two
Monday The [http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Plugin_Tutorial tutorial] is done! Late post (from my daily notes) As for the rest of the week, I continued to look into BioJADE and ProMoT as starting points for Clotho's new visualization tool. The source code wasn't very useful or readable, so we decided to try using JavaFX. And that's where the rest of my week went- JavaFX looks great and runs fast, BUT YOU CAN'T CALL IT FROM JAVA. At least not directly, but the hacks I've found so far don't work with the latest version of the SDK, which came out just a couple weeks ago. I do have a working standalone demo that apparently calls JavaFX code as a script, but so far I can't make it work with Clotho. --Legor17 06:07, 16 June 2009 (UTC)
Week Three
Monday Half of the comp team did presentations on their projects; Joanna and I were up today for Clotho's visualization tool. We'll have something like a drag-and-drop toolbox/sandbox setup, with the workspace in the middle and a palette of parts as a side panel.
Integrating the JavaFX demo into Clotho has been a major headache. It completely breaks Clotho when we use Substance 4.1 (a pretty GUI skinning library), and while the latest Substance release doesn't crash, the JavaFX demo plugin crashes.
Thursday The past few days of working on a JavaFX solution are now moot. We did get a decent mockup of the GUI on Wednesday, so it wasn't all for naught. Today I did some more digging for a Swing solution, and I stumbled across an [http://java.dzone.com/news/how-create-visual-applications article] that shows how to use the NetBeans Visual Library API outside of a NetBeans Module. It irks me that I didn't find it until now, as that would've saved me a lot of time banging my head against a wall over JavaFX. On the bright side, we now have a working drag and drop JScrollPane as a Clotho plugin, and we may soon be able to borrow some components (namely the thumbnail panel and the drag 'n' drop to the workspace feature of [http://bluemarine.tidalwave.it/ blueMarine]. --Legor17 00:40, 19 June 2009 (UTC)
