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


Revision as of 09:33, 29 October 2008 by Logosandpathos (Talk | contribs)

Matthew L.E. Johnson


Personal Info

Name: Matthew L.E. Johnson

Position: Team member, UC_Berkeley_Tools

Supervisor: Doug Densmore

Lab coworkers: Nade Sritanyaratana, Anne Vandevender


June 3rd, 2008

Just received access to the wiki! Today was the first day of coding, and for me it was mostly re-familiarizing myself with Java and Swing components. We're making good progress, and if we can keep this up this amount of effort, I think we'll have something really neat to share.

June 9th, 2008

Working on implementing various features already offered in ApE, including finding the melting point of a short strand of duplex DNA.

June 16th, 2008

Even more functionality being added! Nearly finished with the enzyme library, need to finish figuring out the highlighting algorithms, but otherwise it's coming along nicely. I'll be working on integrating a lot of the basic DNA-related functions (reverse complementing, finding ORFs, calculating GC content and melting temp) later today.

Example of the Clotho Enzyme Library interface. (In case you were wondering, that is the team wiki in the background!)

June 28th, 2008

Nearly finished with the Enzyme Library - saving, loading, and searching all work. Mostly been debugging and trying to get everything currently implemented to work correctly, so that we can release a beta copy for the wet lab to play with. After this, I'd like to get started on the automatic primer and construction file generators.

The format of the enzyme library file is modeled after ApE

July 10th, 2008

We're going Alpha next week! We've got the basic features up and running, so it's mostly just ironing out the kinks for now, getting it all squared away. After this, 90% of our work should be on the novel features we're trying to implement, the new views and algorithms that will make our tool uniquely useful. And that will mean more updating here as I have more interesting things to talk about.

July 31st, 2008

Public release of Clotho Alpha! It took a lot of work, but now we can get started on some of the more interesting features we plan on implementing, some of the alternate views and schematics to assist in designing parts and systems.

October 17th, 2008

Between knee surgery and school starting up, this notebook has been looking neglected - time to spend some more time working on the wiki! Just finished writing the tutorial and taking screen shots, should be up by the end of today!

October 28th, 2008

The final night of coding before iGEM! Spent some time polishing the wiki, finishing some of the 'intelligent' Drag and Drop (DnD) support that I've been working on for weeks now, and cleaning up some of the bugs that have cropped up recently. So far, so good - we should have our code in excellent shape in time to be turned in.

Drag and Drop in Clotho, from the Parts Manager to the Sequence View

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