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 'data analysis'. Sat, 03 Sep 2011 02:39:22 +0100 http://www.medworm.com/index.php?rid=4952737&cid=t_164109_86_f&fid=35599&url=http%3A%2F%2Fshrlibrary.blogspot.com%2F2011%2F06%2Fcommunity-view-collaboration.html In collaboration with the City of Saskatoon, Saskatoon Public School Division, Saskatoon Greater Catholic Schools, and other Saskatoon Regional Intersectoral Committee agencies, Public Health Services of the Saskatoon Health Region have developed a regional comprehensive community information system, the CommunityView Collaboration (CVC). The main features of the system are:- The assembly of data from multiple sources, and; - A system supported by appropriate information technologies and tools for end-user analysis including the use of a Geographic Information System (GIS). CommunityView allows for inter-sectoral and inter-jurisdictional data sharing and access among human services organisations. According to the CVC site, its primary objective of this sharing is to "ensure consistent, tim... SHR Medical Library blogs http://www.medworm.com/rss/comments.php?id=4952737 Fri, 17 Jun 2011 16:04:00 +0100 4952737 http://www.medworm.com/index.php?rid=3595710&cid=t_164109_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2010%2F05%2F24%2Fconnectomeviewer-multi-modal-multi-level-network-and-neuroimaging-visualization-and-analysis%2F Two neat tools concerned with the “connectome” (i.e. the pattern of connections in the nervous system): Semantic wiki: http://www.connectome.ch/wiki/Main_Page Desktop viewer: http://connectomeviewer.org/viewer “Multi-Modal Multi-Level Network and Neuroimaging Visualization and Analysis” (screencasts) (Source: neurodudes) neurodudes blogs http://www.medworm.com/rss/comments.php?id=3595710 Tue, 25 May 2010 02:29:22 +0100 3595710 http://www.medworm.com/index.php?rid=3487288&cid=t_164109_131_f&fid=34995&url=http%3A%2F%2Fblogs.discovermagazine.com%2Fgnxp%2F2010%2F04%2F1980-2000-the-age-of-death%2F Poking around the GSS for another reason I stumbled onto something weird. Something which I’d seen hints of, or seen referred to before, but never followed up myself. It seems that support for abortion-on-demand and the death penalty peaked concurrently in the span between 1980-2000. This is evident in two GSS variables, ABANY and CAPPUN, which ask if you support a woman’s right to an abortion for any reason and the death penalty for murder. Additionally, I decided to look at attitudes toward homosexuality using HOMOSEX as a reference as a point of contrast. Unlike abortion or the death penalty attitudes toward homosexuality have been changing in the same direction for the past 30 years. Additionally, the magnitude of the change seems to be much greater than in regards to the o... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3487288 Mon, 19 Apr 2010 18:49:26 +0100 3487288 http://www.medworm.com/index.php?rid=3322508&cid=t_164109_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2010%2F03%2F02%2Fover-time-distribution-of-shot-lengths-in-movies-has-moved-closer-to-pink-noise%2F The statistics of shot durations in 150 films from 1935 to 2005 were analyzed. From about 1970 to the present, the power spectrum of shot durations in individual films has tended to become more like pink noise (power ~= 1/f). Also, autocorrelation shows that the lengths of nearby shots has become more and more correlated. The authors, Cutting, DeLong, and Nothelfer, speculate that the pink noise bit is being driven by some process that is related to attention, since there are some other results (which they cite) showing the relevance of pink noise to attention. However, IMDB ratings were not positively correlated with the pink-noise-ness of the movie (partial correlation with release date factored out). Incidentally, this guy did his PhD thesis on cognitive science explanations for film e... neurodudes blogs http://www.medworm.com/rss/comments.php?id=3322508 Tue, 02 Mar 2010 06:12:47 +0100 3322508 http://www.medworm.com/index.php?rid=3318545&cid=t_164109_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F03%2F01%2Fcompressed-sensing-in-neuroscience%2F Wired has a nice lay-person write-up of the rapidly developing field of compressed sensing. This is a technique that allows accurate reconstructions of highly undersampled sparse datasets. This field really took off in 2004 when Emmanuel J. Candès discovered that a tomography phantom image could be reconstructed exactly even with data deemed insufficient by the Nyquist-Shannon criterion. It is probably the hottest topic in imaging theory today. Modified Shepp-Logan phantom with enhanced contrast for visual perception. According to this review, Compressed Sensing MRI, its successful application requires three conditions to be met : Transform Sparsity: The desired image must have a sparse representation in a known transform domain (i.e., it must be compressible by transform coding), I... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3318545 Mon, 01 Mar 2010 15:03:53 +0100 3318545 http://www.medworm.com/index.php?rid=3287880&cid=t_164109_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2010%2F02%2F18%2Fstatoolkit%2F http://neuroanalysis.org/ Octave/MATLAB toolkit for analysis of spike train data. Open source. Information theory-y. (Source: neurodudes) neurodudes blogs http://www.medworm.com/rss/comments.php?id=3287880 Fri, 19 Feb 2010 00:48:04 +0100 3287880 http://www.medworm.com/index.php?rid=3259100&cid=t_164109_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F02%2F09%2Fmonte-carlo-calcium-spike-detection%2F I somehow missed that Josh Vogelstein’s method on action potential detection was published last summer. In Spike Inference from Calcium Imaging Using Sequential Monte Carlo Methods, the authors use a Monte Carlo approach to determine spike times from calcium imaging with superior performance to other deconvolution methods.  It does a great job on simulated and in vitro data, I’d love to see performance on real in vivo recordings.  If you are serious about calcium imaging, you should definitely get in touch with Josh and see what magic he can do with all that math.  You should also ask him about the benefits of linen pants vs. denim, he’s got strong opinions on that subject as well… Using only strongly saturating and very noisy in vitro fluorescence measuremen... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3259100 Tue, 09 Feb 2010 18:01:42 +0100 3259100 http://www.medworm.com/index.php?rid=2857491&cid=t_164109_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F10%2F02%2Fautomated-roi-analysis-for-calcium-imaging%2F One of the most time consuming and frustrating tasks associated with fluorescence imaging in the brain is picking out your regions of interest.  Which pixels do you include in as part of the cell and which are part of the surrounding neuropil?  Often, the answer is not obvious, and even with painstaking selections you can make errors.  Eran Mukamel et. al, from Mark Schnitzer’s lab just published this Neurotechnique Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data that aims to simplify and improve the results of ROI selection.  The authors used a multistage approach to identify and quantify the calcium-dependent fluorescence changes of imaged neurons. First, they used principal component analysis to identify the components of the image that were likel... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2857491 Fri, 02 Oct 2009 23:04:54 +0100 2857491 http://www.medworm.com/index.php?rid=2820447&cid=t_164109_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2009%2F09%2F21%2Fdead-salmon-in-fmri-machine-shows-signs-of-thought-not-really%2F This poster, by Bennett, Baird, Miller, and Wolford, provides a memorable reminder that you have to do a statistical correction for multiple comparisons when you datamine a large number of things for correlation. “The task administered to the salmon involved completing an open-ended mentalizing task. The salmon was shown a series of photographs depicting human individuals in social situations with a specified emotional valence. The salmon was asked to determine what emotion the individual in the photo must have been experiencing.” Voxels in the data were searched to find voxels which show a statistically significant correlation with the experimental condition. 16 such voxels were found (without doing any correction). As the poster says, “Across the 130,000 voxels in a ty... neurodudes blogs http://www.medworm.com/rss/comments.php?id=2820447 Mon, 21 Sep 2009 19:46:50 +0100 2820447 http://www.medworm.com/index.php?rid=2705211&cid=t_164109_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=2570912&cid=t_164109_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2009%2F07%2F02%2Ftranscriptomics-of-the-fetal-human-brain%2F A cutting-edge application of the Affy total human exome GeneChip (4X coverage per exon, 40X coverage per gene): Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis. From the News and Views, I was intrigued to learn that previous transcriptome analyses of adult human brains found very little difference in gene expression between brain areas: [...] this suggests that it is the gene expression during development that largely determines higher brain functions by specifying the complexity of neural connections. Numerically, the most important genes relating to cognitive differences between species may be genes that specify how the machinery is put together. In support of this hypothesis, many of the identified differentially expressed genes ... neurodudes blogs http://www.medworm.com/rss/comments.php?id=2570912 Thu, 02 Jul 2009 04:59:16 +0100 2570912 http://www.medworm.com/index.php?rid=2441535&cid=t_164109_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F05%2Fdrug-popularity-via-google-queries-yet.html Here some drug popularity trends based on automatic Google queries. The drug names were taken from DrugBank.The top ten areCholesterolAspirinEthanolIbuprofenInsulinAcetaminophenTestosteroneCocaineOxycodoneVardenafilReferencesI used a Python script for the Google data fetching. Let me know, if you need more details.The Long Tail @WikipediaDrugBank: a knowledgebase for drugs, drug actions and drug targets. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M.Nucleic Acids Res. 2008, 36, (Database issue):D901-6.PMID: 18048412DrugBank: a comprehensive resource for in silico drug discovery and exploration.Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J.Nucleic Acids Res. 2006, 34, (Database issue):D668-72. PMID: 16381955 (So... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2441535 Fri, 29 May 2009 22:09:00 +0100 2441535 http://www.medworm.com/index.php?rid=2112204&cid=t_164109_122_f&fid=35066&url=http%3A%2F%2Fneurodudes.com%2F2009%2F01%2F17%2Fsocial-neuroscience-fmri-specious-correlations%2F Nature is reporting on potential flaw in multiple imaging (fMRI) studies of social neuroscience. Ed Vul (a graduate student in my dept) and colleagues have a paper in press that says that many of the high correlations between brain regions and social behavior are implausible, given the inherent variability/noise in fMRI. Furthermore, based on a survey of methods from individual investigators, they created a list of papers that commit, in their view, a statistical mistake (non-independence). Naturally, the authors named in the paper aren’t happy and, according to the Nature article, several rebuttals are in the works. At the very least, to my non-expert eyes, this seems like an important discussion to have about data analysis and methodology. (Source: neurodudes) neurodudes blogs http://www.medworm.com/rss/comments.php?id=2112204 Sat, 17 Jan 2009 20:02:11 +0100 2112204 http://www.medworm.com/index.php?rid=1677469&cid=t_164109_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F08%2Fdata-models-or-both.html Correlation supersedes causation, and science can advance even without coherent models, unified theories, or really any mechanistic explanation at all. [C. Anderson, Wired, 2008-07-16]First, I disagree with this statement. Second, thanks to bioinfoman3@delicious for sharing this information.Honestly, I do not get it, why are people claiming that the scientific community, e.g. drug design, is similar to the chip industry or google concepts. Here, Chris Anderson claimed that data alone will replace theoretic concepts. As said by others, in the comments to his article, is data alone not information. Amund Tveit confirms this by showing that data correlations alone might be misleading, because you can find correlations in everything, even if it makes no sense. Data means any data, so if you lo... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1677469 Sun, 03 Aug 2008 18:01:00 +0100 1677469 http://www.medworm.com/index.php?rid=1147426&cid=t_164109_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F11%2Fsix-rules-for-creating-data-driven-drug.html "The problem is that we live in the most perfect imperfect medium in the world: the Web.For now it is impossible to collect data perfectly. It is ugly, it is dirty, it is incomplete and no matter how hard you try it is not going to get perfect.Yet we can’t resist." [Occam's razor]Hahaha ... what a great statement of Avinash. Lets translate his statement about "Six Rules For Creating A Data Driven Boss!" into a drug design setting for getting "Six Rules For Creating a Data Driven Drug Design Project!".# 1: Get Over Yourself"In the past, many experimentalists shared a similar sentiment regarding of the usefulness of theoretical and computational methods to their drug discovery problems, namely: You're always explaining to me after the fact why a molecule i've already discovered is active, ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147426 Fri, 02 Nov 2007 18:14:00 +0100 1147426