Entries for February 2007
Why I found Collapse
so depressing
On Monday, Mano Singham wrote about The odd response to global warming warnings, and this reminded me that I never finished my response to Jared Diamond's Collapse
. I finished reading the book some time ago, and unfortunately continued to be more convinced by the doom-and-gloom side of the argument...than the hopeful side
.
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so depressing"
Random number generators
Starting to use some tools I haven't used before for original work, I'm wondering about details that didn't matter when I was only using Matlab for course exercises. Specifically, I'm trying to figure out whether to trust its random number generator, considering that issues with the C++ random number generator have caused me trouble before, and in the near future I'm likely to find myself using monte carlo methods to estimate the properties of systems.
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Learning how to use some new tools
Most of what I have accomplished in the past two weeks amounts to learning how to use the BN/PBN toolbox, and re-learning how to use Matlab. In a sense it's a bit frustrating—all this time not actually progressing in research—but it's also clearly necessary to do this sometimes.
The experiment replication I had almost finished with yesterday is now up and running, and replicates the published results very neatly. It turns out that my error wasn't in the code itself, but a simple typo in the input matrix.... I've also discovered that there is an existing function in the toolbox to do essentially the same thing as my code, which makes me feel a tad foolish, but really the point of the exercise was to learn the tools, so it wasn't entirely wasted effort. I was going to try and do the same thing in C++, but I feel like now that I'm over the hump of working out how to use it, the BN/PBN toolbox saves so much wheel-reinvention that it's just foolish not to use it, so unless I can find a C/C++ library to do the same sort of thing I'll stick to what I know.
This means I'm ready to start doing some 'real' work next week, and I'll sketch out one idea for this work behind the cut.
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Matlab code working
It took me longer than I had intended, partly because I was re-learning to use Matlab and partly because I've written something more general than I had originally set out to, but my attempt at replicating a GRN model from literature is up and running. I've written some code that makes it easy for me to convert a list of "Node A activates Node B and Node C inhibits it" type interactions into a fully-specified GRN, and I'm using that to try and replicate Li et al's yeast cell cycle network.
So far, the network I have isn't behaving the same as the one reported in their paper, but I haven't done anywhere near enough debugging yet. I'll be spending tomorrow doing just that, because the chances are the lack of correspondence between my results and theirs stems from a logic error in my code.
Oh, and it's been really nice interacting with Matlab again. I had forgotten quite how much I liked it as a development environment.
Eberhart E. Fetz - Recurrent brain-computer interfaces
The third of last Thursday's talks was at the UW bioengineering department. Eberhart E. Fetz of the Washington National Primate Research Center presented current work on implantable brain-computer interfaces.
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Unmentionables
I read a rather depressing article this morning: Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word. The paper presented a [not exhaustive, but reasonably convincing] survey of articles about the phenomenon of antibiotic resistant pathogens, in which the authors found a striking difference between the use of language in the 'evolutionary' literature versus papers in the 'biomedical' literature.
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Visualising a cell
Just a short post to draw attention to something I was too impressed with to leave it on the linkblog only:
A group at Harvard has put together an amazing animation of the inner life of the cell. There are also narrated versions here (all the Inner Life links; the 'speed' refers to the connection speed they're targeted for), and a mostly-complete text description of what's going on here.
Picked up from Livejournal user plantae, via tylik.
Fawwaz Ulaby - How Radar Connects to Carbon Economics
Last Thursday I went to a Electrical Engineering colloquium at the UW. The speaker was Fawwaz Ulaby of the University of Michigan, and he presented a project based on using radar satellites to audit carbon sinks.
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Incremental progress
I didn't get quite as much done this week as I was hoping, because I underestimated the speed difference between working in an environment I'm used to (C++ with header files I've been using for 3 years) and one I'm not (Matlab with a toolbox I first looked at last week). I'm not unhappy with my progress, all told, but I was being a little overoptimistic when I set my goals for this week. Both the literature survey and the GRN model are under way, and I do at least feel like I know what I'm doing with both now. It's just going to take me another day or two till I have anything to show for that.
Raghu Ramakrishnan - The World Online
Today felt like being back in taught courses, with three seminars at UW in one day. Once again this is very convenient, but I'll be spreading the write-ups out so as not to take up too long a block of time with them.
The CSE department had Raghu Ramakrishnan of Yahoo! Research talking about the social, participatory web, which as far is can tell is Yahoo!'s prime focus these days. He gave several examples of relatively well-known participatory sites, some of which Yahoo! owns (Flickr, Yahoo! Answers, Yahoo! Groups), and some of which it probably wishes it did (Freecycle and YouTube), to illustrate the general area he's working in, and then spoke about some of the challenges and benefits of sites that are heavily based on user-supplied content.
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Re-learning Matlab
As well as defining a project for me to do, I have to pick a platform to use for the actual experiments. I'm naturally drawn towards write stuff mostly from scratch in C++, using a few header files people have supplied
, because that's how I'm most used to working, but it may not be the right approach here. When I was working with CTRNNs it was natural, because Randy had supplied me with headers that implemented a CTRNN very efficiently, and provided a very flexible basic structure for the evolutionary algorithm. Now that I'm likely to be working with a discrete type of network model, the closest such resource I know of is Ilya's BN/PBN Matlab toolbox, so I'm giving Matlab a try as a platform.
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Farren Isaacs - Design, Synthesis and Control of Genetic and Genomic Systems
Thursday's other talk was in the Bioengineering department at the UW. I feel rather stupid for having taken this long to discover this department and its seminar series, since they have quite a few interesting talks each semester. Anyway, the presenter was a faculty candidate from the Center for Computational Genomics at Harvard, giving an overview talk about his work on engineering biological systems; for me this was probably an appropriate first talk to go to in the series.
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Reading and more reading
I'm going to revive the weekly updates because I find that having to report on my progress, even if only to myself, helps me keep focussed. Over the next couple of weeks I should be putting together something like a roadmap, and then I can start to compare progress to the plan, but until then it's still useful to make myself sit down and say this is how much I got done in 5 days
. I'll probably make a habit of writing these on Friday afternoons, because it ought to [in a good week at least] be a nice way to close the working week.
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Martin Tompa - What can we do with lots of genome sequences?
I went to two seminars at the UW today—very considerate of them to start clumping the talks I'm most interested in together—and I'll write about one today and one later.
Martin Tompa of the UW Genome Sciences and Computer Science & Engineering departments, gave a talk about computational genomics, focussing mainly on how comparing data across many species is useful.
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