Team:UC Berkeley Tools/Notebook/Nade's Notebook

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Latest revision as of 00:59, 19 February 2009

Nade hard at work. Sort of.

This is the notebook of Nade Sritanyaratana. I got involved in iGEM through word of my instructor. I am a 4th year undergraduate at UC Berkeley in Bioengineering with a concentration in imaging, and I hope to attend a PhD graduate program in the upcoming year. My prior research experience consists of working with bioengineering professor Steven Conolly in the summer and fall of 2007. Beyond imaging, my academic interests include biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.

Now that iGEM is over, my new role as a part of Dr. Douglas Densmore's lab is to solidify the tool, iron out any bugs, and make the Clotho Parts Manager user-customizable. My team roles during iGEM can be found here.

EDIT: As of after iGEM and the start of Spring 2009, the purpose of this notebook has now changed.

Personal Info

Name: Nade Sritanyaratana

Position: Team member, UC_Berkeley_Tools

Supervisor: Doug Densmore

Lab coworkers: Matthew Johnson, Anne Van Devender

Contact: Nadesri@berkeley.edu

Log

iGEM Stuff

Click here to access my old bio, archived iGEM logs, and my old wiki how-to.

January 8, 2009: This notebook's new purpose

For some time now, I have misplaced my iGEM (paper) notebook. I realize getting another notebook may only end up with me losing it once again. So I hereby declare that all my thoughts will go here, on my WIKI notebook.

The first thing I need to do is figure out this xml deal to give the parts manager more flexibility.

The second thing I must do it reconstruct what Anderson and Josh wanted me to do with the Parts Manager. I forgot their entire scheme with ctrl+click, shift+click, etc. I'll hold a meeting with them to do this.

That's all that comes to mind right now. Hopefully I finish the xml deal by the 15th. I'll keep posted.

January 14, 2009: Meeting with Doug. Archival. XML developments.

Short talk. Met with Doug today, back from Columbia. Has vision about plan for Spring semester with circular flow. Will talk about it on Friday with rest of team. Cleaned up my notebook; old entries are now on different page, changed up bio to better fit new semester. Now know how to write XML, validate XML documents, make a DTD, write XML documents via Java. Have to learn how to read XML via Java, which includes learning about different XML parsers. Do I sound like Rorschach? Hurmm.

I've decided. I'm going to use the SAX2 API, and the Xerces parser.

January 26, 2009: Parts Manager Plan - Prep for meeting 1 of new semester

The parts manager is an interface connection that is in charge of parts connected to a MySQL-PoBoL database. It gathers these parts and arranges them into a table by order of hierarchy. By default, this hierarchy is defined as: 1. Biobrick, 2. DNA, 3. Sample.

The flow for the Parts manager is as follows:

1. grab parts from database, including collections data

2. Dialog box pops up, asking if parts manager should be populated or empty (sidenote, there will be a "Remember this option" checkbox, so this box need not open every time)

3. Parts manager opens

3A. At this time, the user can optionally repopulate the parts manager table via a plug in. The plug in will tell the parts manager HOW to populate the table, i.e. how the hierarchy and columns should be organized. The user can define this order via an XML document.

3B. User can open up collections window to open up their own collection.

4. User will create a part. There is fortunately already some support I've built for this, but I need to debug it some.

4A. At this time, the user can create compound parts and define rules for compound part creation via a plug in.

5. Save back to DB

6. Close PM

The following work must be done to complete this workflow:

1. Dialog box for populated or empty PM, uses preferences for that checkbox

2. Parts repopulation Plug in. This requires a few substeps:

2a. Develop XML schema/DTD that defines the rules needed for a PM repop

2b. Write XML document for defaulted pop

2c. Cater the parser to correctly read Parts Manager XML documents. Will use SAX2 for API, and Xerces for parser.

2d. Create plug in that holds all this stuff. Will definitely need some help here.

3. Collection window. I already had a quickly hacked version of this for iGEM but I never got to complete it all the way. I'll just build on that.

4. Debugging of part creation

5. Saving back to Database

6. Compound parts plug-in. I have no idea how to start here, so I'm hoping to meet with Josh and Chris when I get to this.

February 2, 2009: Code update

Thursday: Met with Roger, worked with plug-ins. Need to talk to Brian about XML DTDs.

Sunday: Plug-in extension point for parts manager created. Enum for PM plug-in type created.

Monday: Parts Manager can now open empty PM (vs prepopulated). ClothoHelpConnection can now support html. Search fixed. However search still does not work with html help documents. Has something to do with how JTextPane.getDocument() doesn't carry over line breaks(br tag) from html.

February 7, 2009: ToDo: Reorganizing Parts Manager

To create a plug-in customized displayable element for the Parts Manager, I need to do the following in the short term:

Isolate RenderData and TreeModel/RowModel private classes in the frame class to public classes RENAMED DefaultRenderData and DefaultTreeModel/DefaultRowModel classes, with interfaces RenderData and TreeModel/RowModel so that plug-ins can use them.
Make gui selectable item for choosing analyzers. This'd better be quick.
Meet with Brian and design schema for Parts Manager.

February 9, 2009: ToDo: Requests from Clotho meeting

From Matt:

Empty PM doesn't add parts right CHECK
ClothoHelp: Highlighting (low priority).

From Doug:

Find function should search for circular in sequenceview
I should not be working on the plug-ins myself. Work with Roger. CHECK
Make a "hello world" plug in
ClothoHelp: Next/Previous should NOT browse through articles.

From Josh:

Vector/Part sorted incorrectly in PM
Triggering PM should open one dialog box asking for Empty or CHOOSE COLLECTION DROPDOWN (not fully prepopulated.)

Misc Notes:

We are "voting" on separate Parts Managers. Matt thinks it should be one PM. Possibly tabs? Aesthetics.
Delete TestPlugin from src code. Ask Doug to take it out of repository. (whoops)

February 18, 2009: Meeting with Roger

Met with Roger today. We decided on the following ToDo list with a 4 week window (til March 20th).

Both:

XML format
Parsing/defining schema
Define configuration

Me:

Collections
Fixing PM Frame
Start grabbing fields by ROW

Roger:

Parser frame start
GUI XML document chooser - collab
Connection <--> XML document communication
Conditionals

@@ Line 4: / Line 4: @@
-This is the notebook of Nade Sritanyaratana. I got involved in iGEM through word of my instructor. I am a 4th year undergraduate at UC Berkeley in Bioengineering with a concentration in imaging, and I hope to apply for a PhD graduate program in the upcoming year. My prior research experience consists of working with bioengineering professor Steven Conolly in the summer and fall of 2007. Beyond imaging, my academic interests include biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.
+This is the notebook of Nade Sritanyaratana. I got involved in iGEM through word of my instructor. I am a 4th year undergraduate at UC Berkeley in Bioengineering with a concentration in imaging, and I hope to attend a PhD graduate program in the upcoming year. My prior research experience consists of working with bioengineering professor Steven Conolly in the summer and fall of 2007. Beyond imaging, my academic interests include biomechanics; signals and systems; circuit analysis; systems biology; and linear optimization.
-My primary role as a Tools Team member is to produce connections to plug into Clotho's core infrastructure; that is, to make functional tools that communicate with Clotho's "command center". Clotho is a project that my post-doc, Doug Densmore, had initiated as one of his side projects. It implements his notion of Platform-Based Design, which involves the optimal interaction between the Application-space and Architecture-space of a program (see [http://biocad-server.eecs.berkeley.edu/wiki/index.php/Platform_Based_Design Platform Based Design] in more detail). This notebook will be used to document any noteworthy updates on my progress in the UCB Tools Team.
+Now that iGEM is over, my new role as a part of Dr. Douglas Densmore's lab is to solidify the tool, iron out any bugs, and make the Clotho Parts Manager user-customizable. My team roles during iGEM can be found [[Team:UC_Berkeley_Tools/Notebook/Nade's_Notebook/iGEM_Logs|here.]]
-EDIT: As of after iGEM and the start of the new semester, the purpose of this notebook has now changed.
+'''EDIT:''' As of after iGEM and the start of Spring 2009, the purpose of this notebook has now [[#January_8.2C_2009:_This_notebook.27s_new_purpose|changed.]]
 ==Personal Info==
@@ Line 23: / Line 23: @@
 ==Log==
-===June 8, 2008: Getting Acquainted===
+===iGEM Stuff===
-This is my '''first''' post in my notebook. Project Clotho has been really fun so far. I finally finished (the first draft) of the help window. Hopefully for the next assignment I don't take over four days again to finish!
+Click [[Team:UC_Berkeley_Tools/Notebook/Nade's_Notebook/iGEM_Logs|here]] to access my old bio, archived iGEM logs, and my old wiki how-to.
-[[Image:ClothoHelpWindow.png|center|frame|First draft of the Clotho help window.]]
+===January 8, 2009: This notebook's new purpose===
-My bio should be finished and ready to send to Doug. Once it's up I'll post the link.
+For some time now, I have misplaced my iGEM (paper) notebook. I realize getting another notebook may only end up with me losing it once again. So '''I hereby declare''' that all my thoughts will go here, on my WIKI notebook.
+The first thing I need to do is figure out this xml deal to give the parts manager more flexibility.
-===June 11, 2008===
+The second thing I must do it reconstruct what Anderson and Josh wanted me to do with the Parts Manager. I forgot their entire scheme with ctrl+click, shift+click, etc. I'll hold a meeting with them to do this.
-Doug has now assigned me to work on the Features Library, Features Connection, and gave me permission to mess with the Sequence View Tools frame. Expect pictures soon.
+That's all that comes to mind right now. Hopefully I finish the xml deal by the 15th. I'll keep posted.
+===January 14, 2009: Meeting with Doug. Archival. XML developments.===
-===June 16, 2008: Screenshots===
+Short talk. Met with Doug today, back from Columbia. Has vision about plan for Spring semester with circular flow. Will talk about it on Friday with rest of team. Cleaned up my notebook; old entries are now on different page, changed up bio to better fit new semester. Now know how to write XML, validate XML documents, make a DTD, write XML documents via Java. Have to learn how to read XML via Java, which includes learning about different XML parsers. Do I sound like Rorschach? Hurmm.
-Here's the first draft of the Sequence View Tools. Primitive for now, but constructed so to be easy to add buttons and connectors and such later on.
+I've decided. I'm going to use the SAX2 API, and the Xerces parser.
-[[Image:ClothoSequenceViewTools.png|center|frame|First draft of the Clotho Sequence View Tools window.]]
+===January 26, 2009: Parts Manager Plan - Prep for meeting 1 of new semester===
-Also ready to display is my envisioning of the Features library window. It will look very similar to the NetBeans 6.1 interface for managing Java libraries, simply because I like the customizability and sleekness of their window.
+The parts manager is an interface connection that is in charge of parts connected to a MySQL-PoBoL database. It gathers these parts and arranges them into a table by order of hierarchy. By default, this hierarchy is defined as: 1. Biobrick, 2. DNA, 3. Sample.
-[[Image:ClothoFeaturesLibrary.png|center|frame|First draft of the Clotho Features Library.]]
-Still working on the Features Connection. Currently I'm placing priority to finish the Features Library and a new helper, ClothoFileChooser, which will, as named, act as a file chooser akin to Windows explorer. Priority was given because both were requested from Doug and Matt.
+The flow for the Parts manager is as follows:
-===June 19, 2008===
+. grab parts from database, including collections data
-Doug's been out this week as he gets married on Friday. This translates to many good news and a tinge of the bad.
+. Dialog box pops up, asking if parts manager should be populated or empty (sidenote, there will be a "Remember this option" checkbox, so this box need not open every time)
-Good news: Doug's gets married. We get off of going to lab for a full week.
+. Parts manager opens
-Bad news: I've honestly been goofing off the past two days.
+A. At this time, the user can optionally repopulate the parts manager table via a plug in. The plug in will tell the parts manager HOW to populate the table, i.e. how the hierarchy and columns should be organized. The user can define this order via an XML document.
+B. User can open up collections window to open up their own collection.
-The filechoosers are all done, for now. I doubt a picture would really tell you much, 'cuz you've all probably seen a filechooser before. I'm working on fleshing out that features library now, as well as the features connection. Hopefully they'll be near done by Monday.
+. User will create a part. There is fortunately already some support I've built for this, but I need to debug it some.
+A. At this time, the user can create compound parts and define rules for compound part creation via a plug in.
-===July 1, 2008===
+. Save back to DB
-Been a while since my last update. I've been reworking through a bunch of ClothoHelper extensions and creating a few more, like highlighting, underlining, shrinking highlights, filechoosers, highlight data storage, etc.
+. Close PM
-I've mostly been working on file i/o with my ClothoLibraryConnection, which I'd posted before. I have also created a few new frames for "new library" and "add feature". Once they're fully functional (and I have more time) I'll gladly post the visuals :). Oh! And I made some leaf/node graphics for my help window in the JListPane. Will also show, soon =).
-Recently also just got a camera (Canon Rebel EOS XTi!). I've been hugging it constantly for the last three days. Expect some good changes to the wiki soon :).
+The following work must be done to complete this workflow:
-===July 7, 2008: Meet Homer===
+. Dialog box for populated or empty PM, uses preferences for that checkbox
-So perhaps those good changes to the wiki will have to wait. We're currently in some sort of coding bum rush because testing begins the 14th. So long story short: this week is going to be quite the week for me :). For now though, behold the very first real-life picture uploaded to this wiki of inarguably our best teammate -
+. Parts repopulation Plug in. This requires a few substeps:
-[[Image:HomerBioPic.jpg|center|100px|frame|Homer Simpson chillin at the DOP.]]
+a. Develop XML schema/DTD that defines the rules needed for a PM repop
-I bring you Homer Simpson.
+b. Write XML document for defaulted pop
-===July 17, 2008: Testing Sessions (with pictures!)===
+c. Cater the parser to correctly read Parts Manager XML documents. Will use SAX2 for API, and Xerces for parser.
-Alright. So testing is over. And now we are preparing for our Alpha release, perhaps also fated to be a crazy rush for me. Here are the pics from our testing sessions! Obviously, I'm not present in any of them. Who else would be behind the viewfinder? :)
+d. Create plug in that holds all this stuff. Will definitely need some help here.
-[[Test Session 1]]
+. Collection window. I already had a quickly hacked version of this for iGEM but I never got to complete it all the way. I'll just build on that.
-[[Image:ClothoTestingSession1_Prep.png|center|frame|Doug and Anne waiting for the session to begin. We're all pretty excited it seems. :)]]
+. Debugging of part creation
-[[Image:ClothoTestingSession1_Prep2.png|center|frame|Matt, Doug, and Anne starting up Clotho on Matt's system. I believe this was about when we realized business was about to begin. Hence the game faces. Anne looks as flattering as ever, I'm sure.]]
+. Saving back to Database
-[[Image:ClothoTestingSession1_MattAndDirk.png|center|frame|Matt helping out Dirk, one of the members from the iGEM 2008 Cal Wetlab Team. Go [[Team:UC_Berkeley|check them out]] if you haven't already!]]
+. Compound parts plug-in. I have no idea how to start here, so I'm hoping to meet with Josh and Chris when I get to this.
-[[Image:ClothoTestingSession1_DougAndCici.png|center|frame|Doug helping out Cici, another member from the [[Team:UC_Berkeley|iGEM 2008 Cal Wetlab]] Team.]]
-[[Image:ClothoTestingSession1_FinalRemarks.png|center|frame|Here we are, with advisors Doug Densmore and Chris Anderson, getting everyone's final remarks about Clotho and collaborating on our next steps.]]
+===February 2, 2009: Code update===
+* Thursday: Met with Roger, worked with plug-ins. Need to talk to Brian about XML DTDs.
-[[Test Session 2]]
+* Sunday: Plug-in extension point for parts manager created. Enum for PM plug-in type created.
-The lack of images in test session 2 were probably due to me being useful most of the time. I wasn't able to get my camera out until near the end of this session. Hope this doesn't bum out anyone!
+* Monday: Parts Manager can now open empty PM (vs prepopulated). ClothoHelpConnection can now support html. Search fixed. However search still does not work with html help documents. Has something to do with how JTextPane.getDocument() doesn't carry over line breaks(br tag) from html.
-[[Image:ClothoTestingSession2_FinalRemarks.png|center|frame|Doug recording some of the bugs as testers from [[Team:UC_Berkeley|wetlab]] threw them out.]]
+===February 7, 2009: ToDo: Reorganizing Parts Manager===
+To create a plug-in customized displayable element for the Parts Manager, I need to do the following in the short term:
-===July 21, 2008: Code Rush #2===
+* Isolate RenderData and TreeModel/RowModel private classes in the frame class to public classes RENAMED DefaultRenderData and DefaultTreeModel/DefaultRowModel classes, with interfaces RenderData and TreeModel/RowModel so that plug-ins can use them.
+* Make gui selectable item for choosing analyzers. This'd better be quick.
+* Meet with Brian and design schema for Parts Manager.
-We're nearing our alpha release, which (finally set in stone) is Friday. Or Saturday. Admittedly, we set this on wobbly stone. But it'll be out, I promise :). Contain yourselves.
+===February 9, 2009: ToDo: Requests from Clotho meeting===
+From Matt:
-<i>Today</i> we met with some [http://www.jbei.org/ JBEI] members and one of the developers of BioStudio. Jonathan Goler, [http://www.jbei.org/ JBEI], worked on [http://web.mit.edu/jagoler/www/biojade/ BioJADE] and talked a bit about his current status with [http://web.mit.edu/jagoler/www/biojade/ BioJADE's] development (he also initiated the MIT Parts registry! Wow! =O). Sarah Richardson, one of the developers of [http://slam.bs.jhmi.edu/gd/ BioStudio], is a genetics grad student from John Hopkins working here at Berkeley during the summer at Arkin lab. Tim, [http://www.jbei.org/ JBEI], has a fair amount experience with the Biobricks/Pobol community and hopes to set further standards for the synthetic biology community. Tim is part of the [http://www.jbei.org/ JBEI] registry project. One more person had come to the meeting, but admittedly I completely forgot how to correctly pronounce his name let alone spell it, but I do know he's from [http://www.jbei.org/ JBEI] (Doug, any help here?). Sorry!
+* Empty PM doesn't add parts right CHECK
+* ClothoHelp: Highlighting (low priority).
-Either way, I really hope to work with Sarah and Jonathan regarding new views for Clotho. Both have very good already-implemented ideas and it would be great to incorporate them into Clotho.
+From Doug:
-<i>Tuesday</i> is Anne's day with the [http://www.lpfi.org/education/smash.html SMASH] kids. I might head over to Cory to get a few pictures with them.
+* Find function should search for circular in sequenceview
+* I should not be working on the plug-ins myself. Work with Roger. CHECK
-<i>Wednesday</i> should be a normal coding day, with the exception of Zachary's for lunch with Anne and Doug. I also hope to put my foot down on Wednesday with major changes with my code.
+* Make a "hello world" plug in
+* ClothoHelp: Next/Previous should NOT browse through articles.
-<i>Thursday</i> is [http://www.lpfi.org/education/smash.html SMASH] presentation and icon making day.
-<i>Friday</i> is cleaning up visuals (resizing windows, confirming working buttons, etc.) and (hopefully) releasing.
-<i>Saturday</i> is slack day.
-I'll try to get a week's worth of pictures this week. We'll see how much time coding will take from me.
-===July 26, 2008: ALPHA VERSION RELEASED===
-We're done with the Alpha release. From my understanding the road should be smoother from here on out. Unfortunately, no pictures for this week. Like I said above: We'll see how much time coding will take from me :). But, without further ado,
-[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development <b>HERE IS THE LINK FOR THE ALPHA VERSION OF CLOTHO</b>]
-If you do not see the link to the download on the above page, it is most likely because you came here way too early and Doug has not yet uploaded the release to his wiki. Plans are that it'll be uploaded by the end of Saturday. I'll keep everyone updated.
-===July 28, 2008: Release Confirmed ===
-The Alpha release is official. Download it while it's still hot!
-I'm going to be working on the website most of this week. As well prepping for the GRE. Graduate school business is coming up quickly!
-===October 21, 2008: Things are really starting to shake up===
-Been a few months since last update. GRE's went great! I got my 800 in math, a 530 in verbal =(, and a 5.5 on essay. Now letters of recommendation left, and those are coming along pretty well. We've gone through a bunch of changes to the site and Clotho, but lately I've also been bombarded with schoolwork and societies and such. Jamboree's coming up so fast! We're working hard to ensure all of you see a great product. Watch out, MIT!
-===January 8, 2009: This notebook's new purpose===
-For some time now, I have misplaced my iGEM (paper) notebook. I realize getting another notebook may only end up with me losing it once again. So '''I hereby declare''' that all my thoughts will go here, on my WIKI notebook.
-The first thing I need to do is figure out this xml deal to give the parts manager more flexibility.
-The second thing I must do it reconstruct what Anderson and Josh wanted me to do with the Parts Manager. I forgot their entire scheme with ctrl+click, shift+click, etc. I'll hold a meeting with them to do this.
-That's all that comes to mind right now. Hopefully I finish the xml deal by the 15th. I'll keep posted.
-==My Wiki How-to==
+From Josh:
-===Uploading and displaying images===
+* Vector/Part sorted incorrectly in PM
-Here's where I first learned how to upload images: [[Team:Hawaii/Wiki_Help]]
+* Triggering PM should open one dialog box asking for Empty or CHOOSE COLLECTION DROPDOWN (not fully prepopulated.)
-Props to Hawaii team!
+Misc Notes:
-More information was found at [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page#Links_and_URLs Wikipedia: How to edit a page]
+* We are "voting" on separate Parts Managers. Matt thinks it should be one PM. Possibly tabs? Aesthetics.
+* Delete TestPlugin from src code. Ask Doug to take it out of repository. (whoops)
-If you're having trouble first uploading an image, click your edit link, (LITERALLY) type in <nowiki> [[Image: imagename.jpg]] </nowiki> where you want the image, save the page, and you'll find the upload link back on the edited page! You can add modifiers to the image, as found on the Hawaii team and wiki links above.
+===February 18, 2009: Meeting with Roger===
+Met with Roger today. We decided on the following ToDo list with a 4 week window (til March 20th).
+Both:
-===How to link to other pages===
+* XML format
-I found how to post links at "How to edit a page" (see my "Uploading and displaying images" above). There's also a built-in button on top of the text view when editing a page for posting links.
+* Parsing/defining schema
+* Define configuration
-====Internal links====
+Me:
-{| border = "1"
-|-
-! width="100" align="left" | Instructions:
-| width="300" | For urls within igem 2008, you can type in: || width="300" | <nowiki>[[The pathname that follows after "title="]]</nowiki>
-|-
-! align="left" | Example:
-| For the Hawaii Wiki Help page, I typed: || <nowiki>[[Team:Hawaii/Wiki_Help]]</nowiki>
-|}
-====External links====
+* Collections
+* Fixing PM Frame
+* Start grabbing fields by ROW
-{| border="1" cellpadding="2"
+Roger:
-|-
-|width="100pt"|<b>Instructions:</b>
-|width="300pt"|For outside links, you can type:
-|width="150pt"|<nowiki>[url [space] name]</nowiki>
-|-
-|<b>Example: </b>|| i.e., for the "Wiki: How to edit a page", I typed: || <nowiki>[http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page#Links_and_URLs Wikipedia: How to edit a page]</nowiki>.
-|}
-That name modifier works as well for the local page format.
+* Parser frame start
+* GUI XML document chooser - collab
+* Connection <--> XML document communication
+* Conditionals