MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'computational'. Sat, 03 Sep 2011 02:05:03 +0100 http://www.medworm.com/index.php?rid=4848047&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2011%2F05%2F20%2Fhenry-markram-and-the-human-brain-project-reported-to-be-pursuing-1-4-billion-grant%2F This dailymail article claims that the Human Brain Project, directed by Henry Markram, is pursuing a 1 billion euro grant to simulate the human brain in 12 years. By way of Nextbigfuture, by way of Hackernews. (Source: neurodudes) neurodudes blogs http://www.medworm.com/rss/comments.php?id=4848047 Fri, 20 May 2011 22:04:03 +0100 4848047 http://www.medworm.com/index.php?rid=4098203&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2010%2F10%2F20%2Fphenotropic-computing%2F (from 2003) Jaron Lanier talks about the “phenotropic” programme, which consists of trying to design software systems that uses pattern recognition, rather than protocols, for communication between components of the system. …where might things have gone wrong? The leaders of the first generation were influenced by the metaphor of the electrical communications devices that where in use in their lifetimes, all of which centered on the sending of signals down wires. If you model information theory on signals going down a wire, you simplify your task in that you only have one point being measured or modified at a time at each end…At the same time, though, you pay by adding complexity at another level….which leads to a particular set of ideas about coding schemes... neurodudes blogs http://www.medworm.com/rss/comments.php?id=4098203 Wed, 20 Oct 2010 19:52:22 +0100 4098203 http://www.medworm.com/index.php?rid=4003254&cid=t_171908_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Freal-time-drug-safety-reports%2F2010.09.27 Researchers at Children’s Hospital in Boston and the University of North Carolina at Chapel Hill have developed an iPhone application that keeps you up-to-date with drug safety reports and allows you to submit any side effects directly to the FDA. The app, called MedWatcher can keep a list of medications for which you receive both official FDA alerts and news from other channels. Users can report side effects straight from the app and view other submitted reports. The researchers hope to lower the barrier to reporting side effects, increasing the participation in safety surveillance. Reports of serious adverse events are reviewed by members of the Children’s Computational Epidemiology Group and then submitted to the FDA. The app was developed using technology from the Outbreaks... Better Health blogs http://www.medworm.com/rss/comments.php?id=4003254 Mon, 27 Sep 2010 22:00:14 +0100 4003254 http://www.medworm.com/index.php?rid=3733121&cid=t_171908_109_f&fid=34743&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FDevelopingIntelligence%2F%7E3%2FyqEDneWICB8%2Fget_what_you_want_free_energye.php When I started this blog back in '06, new hypotheses were appearing on a possible functional architecture of the lateral prefrontal cortex - a recently-evolved brain area implicated in high-level cognitive functions like planning, analogical reasoning, and cognitive control. Since then, these hypotheses have been refined, and the results replicated numerous times. Today, it's essentially incontrovertible that the prefrontal cortex is parcellated into a functional hierarchy in which more anterior areas influence processing in more posterior areas according to the more abstract information represented anteriorly. (Though definitions of "abstract" vary somewhat). Regardless, carefully designed tasks involving multiple levels of complexity - much like a classic decision tree - show that the ... Developing Intelligence blogs http://www.medworm.com/rss/comments.php?id=3733121 Wed, 07 Jul 2010 12:05:22 +0100 3733121 http://www.medworm.com/index.php?rid=3552425&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2010%2F05%2F10%2Fwhen-will-we-be-able-to-build-brains-like-ours%2F – by Terry Sejnowski – scientificamerican.com Terry Sejnowski discusses the recent ‘catfight’ that erupted between Dharmenda Modha of IBM and Henry Markram of the EPFL over claims from Modha that his group had successfully modeled the brain of a cat. Dr. Sejnowski provides a summary of the quest to describe the nervous system using computational models and introduces a central question: What level of abstraction is appropriate? “Looking at the same neuron, physicists and engineers tend to see the simplicity whereas biologists tend to see the complexity. The problem with simplified models is that they may be throwing away the baby with the bathwater. The problem with biophysical models is that the number of details is nearly infinite and much of it is unknown. How muc... neurodudes blogs http://www.medworm.com/rss/comments.php?id=3552425 Mon, 10 May 2010 19:10:42 +0100 3552425 http://www.medworm.com/index.php?rid=3546885&cid=t_171908_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2010%2F05%2Fmolecular-design-and-molecular-modeling.html After a recent question on Blue Obelisk Exchange and ChemPedia Lab about molecular drug design (see also cross-post) and a recent book about molecular modeling basics I thought it is time highlighting more information on that topic.Drug design principles, molecular modeling, and use in medicinal chemistry:C. Bissantz, B. Kuhn, and M. Stahl, A Medicinal Chemist’s Guide to Molecular Interactions, J. Med. Chem., 2010, Article ASAP. DOI 10.1021/jm100112jBioisosterism and bioisosteric design principle articles.J. H. Jensen, Molecular modeling basics, 2010.Summary slides about molecular modeling (quantum chemistry) of Noel O'Boyle: (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=3546885 Sat, 08 May 2010 19:21:00 +0100 3546885 http://www.medworm.com/index.php?rid=3235965&cid=t_171908_122_f&fid=34736&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FChannelN-PodcastsPoweredByOdiogo%2F%7E3%2Fatafl49HkvI%2Funderstanding-the-brain-by-reverse-engineering.html Blue Brain: Year One The Blue Brain Project is an ambitious effort to model a brain, neuron by neuron, in order to understand its systems and functions in new ways and to build the facility to model brains across species. “I believe we will understand the brain before we finish building it,” says the project’s director, Henry Markram. First video release of a ten year documentary series by director Noah Hutton, following the project as it develops. Gorgeous imagery and an inspiring subject. See also: Blue Brain Neocortical Column Visualization, and the short lecture Simulated Brain by Dr. Markram. Hat tip: The Beautiful Brain. (Source: Channel N) Channel N blogs http://www.medworm.com/rss/comments.php?id=3235965 Wed, 03 Feb 2010 16:30:45 +0100 3235965 http://www.medworm.com/index.php?rid=3159840&cid=t_171908_122_f&fid=34736&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FChannelN-PodcastsPoweredByOdiogo%2F%7E3%2FuktsX7l306g%2Fbaby-robots.html [Image by Bernzilla.] Cognitive Developmental Robotics: An Approach to Understand Ourselves and to Design Robots Like Us Designing robots with the minds of infants, using human cognitive development modelling and biomimetics. Cute baby robot (CB2) video clips included. From the University of Washington’s Computer Science and Engineering Colloquia series (vodcast RSS). (Source: Channel N) Channel N blogs http://www.medworm.com/rss/comments.php?id=3159840 Mon, 11 Jan 2010 16:30:41 +0100 3159840 http://www.medworm.com/index.php?rid=3133702&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2009%2F12%2F30%2Fnew-brain-model-applied-to-%25e2%2580%259cpythagorean-harmonics%25e2%2580%259d%2F Neurodudes kindly allowed me to post links to my “alternative brain models” in 2006 ( http://neurodudes.com/2006/09/14/new-brainmind-theory/ ) and 2007 ( http://neurodudes.com/2007/02/24/more-on-quad-nets-new-brainmind-theory/ ) and I hope a third occasion is permitted as there is no comparable resource for a person like me.  I am an amateur in brain science but have a solid technical background (B.S.E.E. MIT; M.A. Physics/Materials Science, UC Berkeley). I have developed a new class of proposed devices called “timing devices.”  Timing devices are idealized models of neurons, with a variety of forms and components.  The timing devices system resembles that of components (resistances, capacitances, transistors, etc.) used in standard electronic circuits.  In both cases, there is... neurodudes blogs http://www.medworm.com/rss/comments.php?id=3133702 Wed, 30 Dec 2009 17:51:53 +0100 3133702 http://www.medworm.com/index.php?rid=2912485&cid=t_171908_136_f&fid=36070&url=http%3A%2F%2Fnetwork.nature.com%2Fpeople%2Fbasanta%2Fblog%2F2009%2F10%2F21%2Fsystems-biology-graphical-notation I haven’t updated this blog for a while, the reason being the usual for many researchers working in the US: grant writing. Part of this grant writing involved producing diagrams to illustrate various processes occurring at different scales in prostate tissue. These diagrams describe rather sophisticated intra and extra cellular interactions in the simplest possible manner. Yet these diagrams can be complicated and selecting the right symbols and colours to describe these interactions in a visually appealing but consistent manner can be far from trivial. As someone with a background in computer science I appreciate the advantage of having a standard notation to describe processes. Software engineers use tools such as UML to describe software modules and how they interact to form comp... Cancerevo: Evolution and cancer blogs http://www.medworm.com/rss/comments.php?id=2912485 Wed, 21 Oct 2009 03:40:04 +0100 2912485 http://www.medworm.com/index.php?rid=2705211&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2009%2F08%2F16%2Ffrontiers-in-neuroscience-journal%2F The journal, Frontiers in Neuroscience, edited by Idan Segev, has made it Volume 3, issue 1.  Launching last year at the Society for Neuroscience conference, its probably the newest Neuroscience-related journal. I’m a fan of it because it is an open-access journal featuring a “tiered system” and more.  From their website: The Frontiers Journal Series is not just another journal. It is a new approach to scientific publishing. As service to scientists, it is driven by researchers for researchers but it also serves the interests of the general public. Frontiers disseminates research in a tiered system that begins with original articles submitted to Specialty Journals. It evaluates research truly democratically and objectively based on the reading activity of the scienti... neurodudes blogs http://www.medworm.com/rss/comments.php?id=2705211 Sun, 16 Aug 2009 21:02:16 +0100 2705211 http://www.medworm.com/index.php?rid=2598478&cid=t_171908_149_f&fid=35784&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheChemBlog%2F%7E3%2FlPKHW7XL9Qw%2F For the last few days I have been trying to figure out how I can do a simple Monte Carlo simulation on my computer without much success. In the last few months I have become convinced that by doing my own computer modeling I could probably avoid making a lot of unnecessary molecules.  Indeed, I see no reason why the notion hasn’t struck me in the same way the concept of checking a sample after a reaction for purity why should I check the reaction before I do it to see how well it might work? Firstly, it’s become pretty obvious that computational chemistry is a giant f.ing black box.  There are lots of force fields and data sets and letters followed by ** and shit and not a goddamn easy way to deal with ANY of it.  Let’s say I want to model a transition state, what do I... The Chem Blog blogs http://www.medworm.com/rss/comments.php?id=2598478 Tue, 14 Jul 2009 04:04:56 +0100 2598478 http://www.medworm.com/index.php?rid=2232621&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2009%2F03%2F03%2Ftheory-rising%2F Although it’s a few months old, Larry Abbott has an excellent article in Neuron on the recent (last 20 years) contributions of theoretical neuroscience. (He came by MIT last week to give a talk and that’s when I found out about the article.) It’s a review that is not too long and provides a good overview with both sufficient (though not overwhelming) detail and original perspective. It’s rare to find a short piece that is so informative. (And for a more experimentally-oriented review with an eye toward the future, see Rafael Yuste’s take on the grand challenges.) Click on for some of my favorite passages from the Abbott piece. Abbott uses the following problem of input decoding Spike counts and neuronal firing rates are positive quantities. This simple fact ha... neurodudes blogs http://www.medworm.com/rss/comments.php?id=2232621 Tue, 03 Mar 2009 05:05:59 +0100 2232621 http://www.medworm.com/index.php?rid=1926551&cid=t_171908_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F438436400%2F Genome Technology highlights the very cool thing about next-gen sequencing - it puts the power in the hands of the researchers to explore genome sequence and doesn't limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke's Institute for Genome Sciences and Policy through their next-gen sequencing program. This is the way of the future where sequencing core facilities will be able to generate sequence only having to wait in the queue at the own university rather than through community sequencing project or sequencing center proposal queues. This isn't the only lichen being sequenced. Xanthoria parietina is also in the queue at JGI, but has take... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1926551 Fri, 31 Oct 2008 20:56:54 +0100 1926551 http://www.medworm.com/index.php?rid=1841018&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2008%2F09%2F30%2Fnew-yorker-article-on-number-sense%2F From March. Actually, the topic of the article is Dehaene, but it talks about some studies too. Excerpts after the break, interspersed with hyperlinks to citations that I looked up. http://www.newyorker.com/reporting/2008/03/03/080303fa_fact_holt?currentPage=all …Mr. N, had sustained a brain hemorrhage that left him with an enormous lesion in the rear half of his left hemisphere. He suffered from severe handicaps: his right arm was in a sling; he couldn’t read; and his speech was painfully slow. He had once been married, with two daughters, but was now incapable of leading an independent life and lived with his elderly parents. Dehaene had been invited to see him because his impairments included severe acalculia, a general term for any one of several deficits in number processing.... neurodudes blogs http://www.medworm.com/rss/comments.php?id=1841018 Wed, 01 Oct 2008 00:06:52 +0100 1841018 http://www.medworm.com/index.php?rid=1596354&cid=t_171908_132_f&fid=35024&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FBlindscientist%2F%7E3%2F330167276%2F Image by Aaronyx via FlickrI was at gym, proudly wearing my PLoS Computational Biology t-shirt when a person tripped in one of the corrifors me and started shouting that I was “supporting a failed model of scientific publication” and that I should start “supporting the Nature Publishing Group model of publication”. I didn’t know what to say. I just know that it was the last time I wore this t-shirt in public. Related articles by Zemanta Bulk Publishing Keeps PLoS Afloat (Source: Blind.Scientist) Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=1596354 Tue, 08 Jul 2008 21:19:45 +0100 1596354 http://www.medworm.com/index.php?rid=1517046&cid=t_171908_122_f&fid=36506&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FBrainSciencePodcastBlog%2F%7E5%2F311226376%2F39-brainscience-Arbib.mp3 Discussion Forum Subscribe via iTunes™ Subscribe in a reader or podcatcher Subscribe to Brain Science Podcast with Dr. Ginger Campbell by Email Donations and Subscriptions are appreciated (Source: the Brain Science Podcast and Blog with Dr. Ginger Campbell) the Brain Science Podcast and Blog with Dr. Ginger Campbell blogs http://www.medworm.com/rss/comments.php?id=1517046 Fri, 13 Jun 2008 21:35:30 +0100 1517046 http://www.medworm.com/index.php?rid=1426321&cid=t_171908_109_f&fid=34743&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FDevelopingIntelligence%2F%7E3%2F285491836%2Fmodeling_the_diffusion_of_info.php Complex cognition can be predicted by remarkably simple tasks. For example, the speed with which you choose one of two possible responses can reliably predict IQ. Some theories propose that this relationship is due to differences in something called "processing speed," but more recent work has shown the effect is really due to the slowness of your slowest reaction times on such simple tasks. Known as the "worst performance rule," this can be revealed through various RT distribution decomposition techniques (e.g., "binning" of reaction times or ex-gaussian analysis). A particular class of computational models provides an elegant explanation for the cognitive processes that generate this "worst performance rule." As described by Usher & McClelland, Ratcliff's diffusion model posits that inf... Developing Intelligence blogs http://www.medworm.com/rss/comments.php?id=1426321 Wed, 07 May 2008 17:47:02 +0100 1426321 http://www.medworm.com/index.php?rid=1266613&cid=t_171908_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F02%2F28%2Flarge-scale-model-of-mammalian-thalamocortical-systems%2F I’ll be the first to admit that my limited focus area in neuroscience, the levels of molecules and cells, biases me to attend to the trees, while missing the patterns in the whole forest. Many of our best recording and imaging methods, single-unit electrophysiology, fluorescence imaging and multi-unit extracellular arrays give us access to only a very tiny piece of the brain at any given moment. Yet endogenous neural activity is dependent on powerful (and subtle) interactions between geographically distant regions of the brain. Whole-brain measurement techniques, such as functional magnetic resonance imaging, magnetoencephalography, and diffusion tensor imgaging, can measure these interactions, but tend to have poor temporal-spatial resolution. Therefore, in order to understand the g... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1266613 Fri, 29 Feb 2008 00:19:12 +0100 1266613 http://www.medworm.com/index.php?rid=1100289&cid=t_171908_149_f&fid=35780&url=http%3A%2F%2Fwalkerma.wordpress.com%2F2007%2F12%2F17%2Fuseful-site%2F Free computer tools in Structural Bioinformatics and Chemoinformatics (Source: one in ten thousand) one in ten thousand blogs http://www.medworm.com/rss/comments.php?id=1100289 Mon, 17 Dec 2007 20:35:30 +0100 1100289 http://www.medworm.com/index.php?rid=1036895&cid=t_171908_109_f&fid=34743&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FDevelopingIntelligence%2F%7E3%2F187245863%2Fpredictive_nature_externalizin.php Geoff Hinton has a new TiCS paper describing recent advances in algorithms used to train multilayered neural networks. First, a little background: neural networks of a sufficient size can calculate any mathematical function (an infamous proof among neural network modelers). Unfortunately, the tricky part is figuring out how to set the connections in that network to calculate those functions. This is where learning algorithms become necessary - unless you want to tweak each connection by hand until you get a working network (not a problem if you don't care how the brain works), then you need to focus on how the network can learn. Hebbian learning is a standard algorithm that does seem to operate in biological neural networks, but it has a problem: it's not very good for training deep ne... Developing Intelligence blogs http://www.medworm.com/rss/comments.php?id=1036895 Mon, 19 Nov 2007 16:49:06 +0100 1036895 http://www.medworm.com/index.php?rid=1147431&cid=t_171908_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F10%2Ffinding-job-in-cheminformatics-and.html From: jobs at ccl.net (do not send your application there!!!)To: jobs at ccl.netDate: Mon Sep 3 07:45:15 2007Subject: 07.09.03 Senior/Principal Scientist Molecular Modeling, Tibotec, Belgium Tibotec (http://www.tibotec.com) is a pharmaceutical research and development company with headquarters in Belgium and operating subsidiaries in the United States and Ireland. The company is a subsidiary of Johnson & Johnson. Tibotec is dedicated to the discovery and development of novel drugs for HIV/AIDS and other infectious diseases with the ultimate aim of enhancing and extending peoples lives.We currently are looking for a Senior or Principal Scientist Molecular Modeling and Cheminformatics, based at our headquarters in Mechelen, Belgium.In this function you will apply computational chemistry ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147431 Thu, 11 Oct 2007 19:29:00 +0100 1147431 http://www.medworm.com/index.php?rid=925259&cid=t_171908_109_f&fid=34743&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FDevelopingIntelligence%2F%7E3%2F164738084%2Funcertainty_reduction_linguist.php Ambiguity is a constant problem for any embodied cognitive agent with limited resources. Decisions need to be made, and their consequences understood, despite the probabilistic veil of uncertainty enveloping everything from sensory input to action execution. Clearly, there must be mechanisms for dealing with or resolving such ambiguity. A nice sample domain for understanding ambiguity resolution is language, where problems of uncertainty have been long appreciated. The meaning of words in general (not to mention referents like "that" or "he") can be highly ambiguous (see "the gavagai problem"). A similar problem abounds in grammar, famously in the case of garden path sentences ("the horse raced past the barn fell"), where grammatical ambiguities are often completely overlooked until a dif... Developing Intelligence blogs http://www.medworm.com/rss/comments.php?id=925259 Wed, 03 Oct 2007 16:07:09 +0100 925259 http://www.medworm.com/index.php?rid=914090&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2007%2F09%2F29%2Fpostdoctoral-position-in-nonlinear-dynamics-of-memory-and-active-perception%2F POSTDOCTORAL RESEARCH in NONLINEAR DYNAMICS of MEMORY and ACTIVE PERCEPTION Biologically Inspired Neural & Dynamical Systems (BINDS) Laboratory University of Massachusetts Amherst The postdoc work will be concentrating on: How memories are modified, what other systems take part of it, how can the system benefit from changing memories? These questions are asked from the functional and computational view, and will be tackled using theories of dynamical systems, knowledge of neurobiology and memory system, mathematical analysis and control. The modeling created will then be transferred into crisp principles and from there to machine learning, detection, and navigation. The successful candidate will have a Ph.D. in Computer Science, Cognitive Science, Psychology, Engineering or a rel... neurodudes blogs http://www.medworm.com/rss/comments.php?id=914090 Sun, 30 Sep 2007 00:22:29 +0100 914090 http://www.medworm.com/index.php?rid=807322&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2007%2F08%2F18%2Fsteve-grand-on-strong-ai%2F Interview with Steve Grand on building human level artificial intelligence at Machines Like Us. Really interesting. Via Chris Chatham at (the excellent) Developing Intelligence. In particular, MLU asks why his current project to create an android was done as a physical robot rather than as a simulation. The answer, that you can cheat too much in a simulation, is familiar to those from the Brooksian school of embodied intelligence. He says that simulations still aren’t good enough to provide the kinds of physical constraints, like gravity and friction, etc, that you get when building real robots . However, with the availability of free 3D simulation environments that handle physics, like Breve, we are getting a lot closer. Building a robot within a simulation like this, particula... neurodudes blogs http://www.medworm.com/rss/comments.php?id=807322 Sun, 19 Aug 2007 01:58:53 +0100 807322 http://www.medworm.com/index.php?rid=765052&cid=t_171908_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2007%2F07%2Fwhat-good-is-map.html Imagine being stranded on a raft......An object is floating in the water. You paddle hard to get it. Once you do, you realize its a map. Hooray, you can finally find some land. Or can you? There are some significant questions to ask yourself prior to having any utility gained from that map.Can you read the map? I used to be in the Navy. We learned how to read nautical maps. But my father, a retired colonel in the Army, would have no clue where to begin. Imagine someone who had no training......Where are you on that map? If you have no orientation, how could you hope to navigate. Where does the sun rise? Simple question. However, when asked almost 15% of Americans do not know the answer. What is on the land you will be paddling to? If you paddle hard to get there only to find out that there... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=765052 Sun, 29 Jul 2007 15:59:00 +0100 765052 http://www.medworm.com/index.php?rid=733593&cid=t_171908_109_f&fid=34743&url=http%3A%2F%2Fscienceblogs.com%2Fdevelopingintelligence%2F2007%2F07%2Fdirected_inhibitory_structure.php Well, maybe it's "exotic" only to neuroscientists. Inhibitory structure in neocortex has usually been seen as fairly homogenous and simple, where the wide variety of inhibitory interneuron types was viewed as misleading: at bottom, they all perform a simple regulatory function of keeping only a few representations active at once. Thus, in contrast to subcortical regions, inhibitory networks in cortex were thought to involve mostly "vanilla" axon-to-dendrite connections in a semi-regular latticework of connections. However, in the current issue of Nature Neuroscience, Conners & Cruikshank review recent evidence that neocortex might have some more complex inhibitory microcircuitry than previously thought. The authors review evidence indicating that excitatory neurons might synapse directly ... Developing Intelligence blogs http://www.medworm.com/rss/comments.php?id=733593 Fri, 13 Jul 2007 17:11:41 +0100 733593 http://www.medworm.com/index.php?rid=682608&cid=t_171908_109_f&fid=34743&url=http%3A%2F%2Fscienceblogs.com%2Fdevelopingintelligence%2F2007%2F06%2Fcracking_the_neural_code_is_th.php How does your brain represent the feelings and thoughts that are a part of conscious experience? Even the simplest aspects of this question are still a matter of heated debate, reflecting science's continuing uncertainty about "the neural code." The fact is that we still don't have a clear picture of the ways in which neurons transmit information. Here's a quick guide to current theories, beginning with well-established theories and moving into ideas that are considered more theoretical. The canonical model: firing rate Clearly, neurons encode some information in the rate of their firing. Although individual neurons are relatively unreliable and noisy devices, average firing rates across hundreds or thousands of neurons provides a more reliable spatio-temporal code for conveying informat... Developing Intelligence blogs http://www.medworm.com/rss/comments.php?id=682608 Mon, 18 Jun 2007 18:57:28 +0100 682608 http://www.medworm.com/index.php?rid=587896&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2007%2F05%2F03%2Fcompetition-single-neuron-prediction%2F Gerstner’s group in Lausanne, Switzerland has announced a competition to predict the electrical behavior of individual neurons in two respects: 1) predict the timing of every spike that a neuron emits with a precision of 2ms. 2) predict the subthreshold membrane potential with a precision of 2mV for arbitrary input. Details on the competition, including the dataset (released 16 March 2007), are here. Note that the first prize winner receives: - 4 nights of hotel in Lausanne at the Lake Geneva, June 23-27. - Free participation in the Quantitative Neuron Modeling workshop June 25/26 - 35-minute-slot for talk as an Invited Speaker in the workshop. get coding. (Source: neurodudes) neurodudes blogs http://www.medworm.com/rss/comments.php?id=587896 Thu, 03 May 2007 06:59:52 +0100 587896 http://www.medworm.com/index.php?rid=534121&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2007%2F04%2F09%2Fenabling-neural-engineering-ought-to-be-the-goal-of-neuroscience%2F The field of neuroscience naturally focuses its inquiry into neurons. This approach to understanding the brain by studying its parts has been thought to have a greater potential than that of psychology to understand how the brain works, a comment made by no less than Daniel L. Schacter, chair of Harvard’s Department of Psychology, in his book, The Seven Sins of Memory. However promising the field has been thus far, even the most accomplished neuroscientists will admit that we still do not understand how the brain really works. I would submit that the current reductionist nature of neuroscience has shed much light on the dynamics of how neurons work, but has to a far lesser degree shed light on how neurons process information. The difference between these two lines of inquiry is impo... neurodudes blogs http://www.medworm.com/rss/comments.php?id=534121 Tue, 10 Apr 2007 05:52:39 +0100 534121 http://www.medworm.com/index.php?rid=486211&cid=t_171908_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2007%2F03%2F16%2Fadvice_to_a_young_computational_biologist Just when I though Bosco was posting too much poetry, he comes out with this truly excellent post on advice for young computational biologists. Bosco has managed to distill his 10 years of experience into eleven succinct points that are relevant to not only those just starting out in computational biology, but experienced hackers as well. This post is a must read, I highly recommend his advice in point four on using configuration files. It is a simple way of adding value to scripts, by extracting out the parameters into a config file and then writing another script to iterate over different values. Python has a default module for this, with many other third party options. And of course point eight, using command line plotting software, my current favorite is Ploticus. read more (Source: no... nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=486211 Fri, 16 Mar 2007 05:45:16 +0100 486211 http://www.medworm.com/index.php?rid=486197&cid=t_171908_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2007%2F02%2F20%2Fso-how-do-real-neuronal-networks-compute%2F What is the right level of biological realism to model neuronal systems in order to understand their computational properties? Some recent papers may help shed some light on the subject. Models of the computational properties of local networks of neurons are starting to come into their own. This year has already seen at least two articles published in experimentalist journals based on the same core of theoretical work. To bring you up to speed, I need to remind you what is going on in the world of experimental neuroscience. Experimentalists are now able to record the single-cell activities of a whole population of neurons simultaneously. From Briggman, Abarbanel, Kristan (2006): By using multi-electrode arrays or optical imaging, investigators can now record from many individual neurons... neurodudes blogs http://www.medworm.com/rss/comments.php?id=486197 Tue, 20 Feb 2007 20:24:48 +0100 486197