Eldan Goldenberg's lab notebook http://blog.case.edu/exg39/ notes about my work and other peoples' en-us Thu, 22 Feb 2007 10:40:01 EST Thu, 22 Feb 2007 10:40:01 EST eldan.goldenberg@case.edu eldan.goldenberg@case.edu http://blogs.law.harvard.edu/tech/rss Movable Type v3.121 Why I found Collapse so depressing http://blog.case.edu/exg39/2007/02/22/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.... .... http://blog.case.edu/exg39/2007/02/22/why_i_found_collapse_so_depressing environment politics Thu, 22 Feb 2007 10:40:01 EST 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.

]]> Random number generators http://blog.case.edu/exg39/2007/02/19/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.... .... http://blog.case.edu/exg39/2007/02/19/random_number_generators tools Mon, 19 Feb 2007 14:42:59 EST 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.

]]> Learning how to use some new tools http://blog.case.edu/exg39/2007/02/16/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,... .... http://blog.case.edu/exg39/2007/02/16/learning_how_to_use_some_new_tools brainstorming tools weekly update Fri, 16 Feb 2007 17:35:35 EST 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.

]]> Matlab code working http://blog.case.edu/exg39/2007/02/15/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... http://blog.case.edu/exg39/2007/02/15/matlab_code_working status reports tools Thu, 15 Feb 2007 18:35:12 EST 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 http://blog.case.edu/exg39/2007/02/14/eberhart_e_fetz_recurrent_braincomputer_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.... .... http://blog.case.edu/exg39/2007/02/14/eberhart_e_fetz_recurrent_braincomputer_interfaces seminars Wed, 14 Feb 2007 16:38:28 EST 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.

]]> Unmentionables http://blog.case.edu/exg39/2007/02/13/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.... .... http://blog.case.edu/exg39/2007/02/13/unmentionables other people's research politics Tue, 13 Feb 2007 16:56:00 EST 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.

]]> Visualising a cell http://blog.case.edu/exg39/2007/02/12/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.... http://blog.case.edu/exg39/2007/02/12/visualising_a_cell other people's research Mon, 12 Feb 2007 18:40:39 EST 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 http://blog.case.edu/exg39/2007/02/12/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.... .... http://blog.case.edu/exg39/2007/02/12/fawwaz_ulaby_how_radar_connects_to_carbon_economics environment seminars Mon, 12 Feb 2007 17:01:29 EST 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.

]]> Incremental progress http://blog.case.edu/exg39/2007/02/09/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.... http://blog.case.edu/exg39/2007/02/09/incremental_progress weekly update Fri, 09 Feb 2007 19:23:52 EST 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 http://blog.case.edu/exg39/2007/02/08/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.... .... http://blog.case.edu/exg39/2007/02/08/raghu_ramakrishnan_the_world_online seminars Thu, 08 Feb 2007 18:21:31 EST 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.

]]>