Ed's Big Plans

I had previously installed 4GB of memory (over two banks) in Tin– receiving a an addressable 3.3GB, while Pewter uses 2GB (over two banks). I’ve decided now to put 3GB of memory (2GB + 1GB) in each Tin and Pewter now as it makes the most use of the memory– empirical testing shows no difference whether or not the larger chip is in the first bank. Dual channel is now disabled, but there is no appreciable difference– all system functions and software still behave the same. According to Softpedia, I really only had access to 3.0GB anyway, even though 4.0GB were installed– I also notice that it’s actually an Intel Core 2 Duo addressing issue rather than an Apple motherboard issue. The honesty from Apple about the hardware limitation is appreciated.

Only 3GB was ever available on either machine.

The conflicting report about maximum RAM (3.0GB or 3.3GB) from multiple sources really had me wondering, so I used activity monitor to figure out what was actually in use by the system– it turned out it actually was only 3.0GB.

At least this way, both machines have maxed out their memory and I won’t have to worry about memory upgrades again.

On a side note– the 2•1.0GB chips (that came from Apple in Tin) actually run really hot when the CPU is full throttle in both Pewter OR Tin, regularly reaching in excess of 90ºC, while the 2•2.0GB chips run at a more reasonable 70ºC at full throttle. With the machines now handling one hot and one cold chip each, they now both operate at 85ºC at full throttle. This was tested with a simple Python script that infinitely loops and performs a bunch of arbitrary memory and arithmetic operations. I might post some details about what chips are in each machine and the precise operating temperature if I have time. I’m also quite happy that I rarely use all the memory on my system — thus am also unlikely to have any page outs

Zinc grows an eyeball.

So, before Cara and I left home yesterday, I decided on a whim to quickly attach an ancient webcam to Zinc to use as an ad hoc surveillance device — well ok, it’s mostly for fun. This webcam was actually purchased and used with Bronze (my very first laptop), so the refresh rate, white balance and optical zoom are all from circa 2004.

Here, Zinc’s eyeball has been mounted with macam and works like a charm. The frame rate is inexcusably horrendous– but over a VNC connection, I seriously don’t care.

Eventually, Zinc will use macam’s quicktime application component to automatically shoot a photo once every x minutes, and send an e-mail to me if there is significant optical difference between the two images. In a stagnant room– this is not very challenging technically.

Giving Zinc an eyeball has granted us more peace of mind whenever we decide to travel– thus improving again the value of the mac mini… wait till you see what I’ve got planned next…

Brief: Here’s a work in progress entry in my own wiki for the DNAClass.

The Operator Group (UWiGem/Modeling/Operators) had a meeting about a week ago– the meeting ended up being between three people: Matthew, Andre and me at the iGem office. We’ve basically figured out everything we needed to in terms of raw interfaces between our module and the remaining two modules (Filtering Group and Giant Scaffold Group). The DNAClass was updated with the needs Andre presented– one of which is the ability to iterate over a DNAObject while returning yielding both the token index and token in a duplet: (index, token).

The implementation of the enumerate() built-in in Python (PEP 279) doesn’t allow for abstract function overriding. It always counts a collection as it iterates over it starting from zero. Ideally, the count should reflect the index of the circular DNA strand which means that it should be able to count forward or backward (iterate as reverse compliment), and count from any arbitrary position in the loop.

Note that the reverse compliment copy constructor (DNAObject.rc()) does not cause indexes to be reversed… It actually produces a reverse compliment strand and doesn’t do anything special with the indices (i.e. The new strand increments positively as it iterates forwardly). This behaviour is being debated now– On the one hand, it’s correct because a reverse compliment strand is a new strand; however, it is not a strand de novo– it came from a positive sequence.

I’m now waiting for Andre to let me know about the functions and data frameworks needed for the Operators module; my feeling is that the functions will be the straight forward integrase enzyme actions and that the data framework will simply be a python list.

Brief: Just needed a simple EOL (end of line) converter — Chris is working on a windows system while Stefan and I work in Mac OS — here’s the source.

Wow! Go Chris!

With Chris’ dataset collection finished, it’s time to convert every single into a nice suite of descriptor sets. Chris has went and learned the CDK in and out — what started as a complicated and frustrated struggle against Java in Windows and the technicalities of class paths etc., has turned into a fruitful and promising endeavour. While he was working with that, I stumbled onto Bioclipse which utilizes CDK internally for some of its molecule data conversions. Interestingly, the QSAR feature is not yet complete– or is experimental. It looks to be promising in future, but I received an e-mail from Chris telling me all was figured with CDK before I could figure Bioclipse’s QSAR feature out.

The Windows NN port that I’ve been working on is almost done, I’d say I’ll want two more days– today to finish the port and test on a windows box– and tomorrow to figure out how to chain everything together with a windows port of GNU make and some windows variante of GCC.

We’ve decided that the format to express the molecules will be as follows…

• Each descriptor set has its own file
• Each file corresponds to a target species and a target organ
• Each row in each file corresponds to a molecule
• Each row has the columns <Comma Delimited QSAR Descriptor Elements>; Range (LD50); Species; Organ

If we keep on track, we’ll have the first experiments running on SharcNet by early next week.

So a more or less solid date has been set for the Masters’ defense– it’ll more likely happen on July 15th.

The final pre-defense revisions for my thesis have already been sent in, and I’ve just signed the request for examination form today.

The primary focus of any slide show I put together for the presentation must be about all of the new work put into the NGN with less emphasis on the background. I’ve also been advised to mention the math while not going into its detail.

I should get going on those slides.

Brief: Andre has recruited me for the Operators team since the DNAClass is complete.

Brief: Not a lot to report, papers are being edited and written– I’ve just finished the QSAR briefing, NGN design and experimental design sections of the IEEE paper… Thesis corrections are due Monday…

Brief: Met with Stefan today. The conference paper we’re working on has a page limit of eight pages, not six– but I’ve just been told this must include everything including the references and of course figures. With respect to the thesis, the request for examination paperwork has just been completed, and the abstract for the thesis document has been submitted. A few corrections are to be completed on the thesis document. Present work focuses on said corrections, the conference paper and software completion for Chris’ project. There is presently no benefit to working on anything more in parallel.