{"id":2133,"date":"2016-02-25T18:38:03","date_gmt":"2016-02-26T02:38:03","guid":{"rendered":"http:\/\/softwaredaily.wpengine.com\/?p=2133"},"modified":"2021-11-04T02:10:40","modified_gmt":"2021-11-04T09:10:40","slug":"computational-neuroscience-with-jeremy-freeman","status":"publish","type":"post","link":"https:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/","title":{"rendered":"Computational Neuroscience with Jeremy Freeman"},"content":{"rendered":"<p><img data-attachment-id=\"2134\" data-permalink=\"https:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/jeremy-freeman\/\" data-orig-file=\"https:\/\/i0.wp.com\/softwareengineeringdaily.com\/wp-content\/uploads\/2016\/02\/jeremy-freeman.jpg?fit=175%2C175&amp;ssl=1\" data-orig-size=\"175,175\" data-comments-opened=\"0\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"jeremy-freeman\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/softwareengineeringdaily.com\/wp-content\/uploads\/2016\/02\/jeremy-freeman.jpg?fit=175%2C175&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/softwareengineeringdaily.com\/wp-content\/uploads\/2016\/02\/jeremy-freeman.jpg?fit=175%2C175&amp;ssl=1\" decoding=\"async\" loading=\"lazy\" class=\"alignright size-full wp-image-2134\" style=\"border-radius: 50%; border: 1px solid #000000;\" src=\"https:\/\/i0.wp.com\/softwaredaily.wpengine.com\/wp-content\/uploads\/2016\/02\/jeremy-freeman.jpg?resize=175%2C175\" alt=\"jeremy-freeman\" width=\"175\" height=\"175\" srcset=\"https:\/\/i0.wp.com\/softwareengineeringdaily.com\/wp-content\/uploads\/2016\/02\/jeremy-freeman.jpg?w=175&amp;ssl=1 175w, https:\/\/i0.wp.com\/softwareengineeringdaily.com\/wp-content\/uploads\/2016\/02\/jeremy-freeman.jpg?resize=150%2C150&amp;ssl=1 150w, https:\/\/i0.wp.com\/softwareengineeringdaily.com\/wp-content\/uploads\/2016\/02\/jeremy-freeman.jpg?resize=80%2C80&amp;ssl=1 80w\" sizes=\"(max-width: 175px) 100vw, 175px\" data-recalc-dims=\"1\" \/><\/p>\n<h3>\u201cYou want to take a scientist who knows a little bit of matlab programming and try to teach them mapreduce, and write a mapreduce program in java to do image processing? It\u2019s a disaster!\u201d<\/h3>\n<p>Apache Spark is replacing MATLAB in the domain of computational neuroscience. The constraints of running MATLAB on a single machine can\u2019t support the demands of neuroscience, which has huge collections of images and time-series data sets.<\/p>\n<p>Jeremy Freeman is a computational neuroscientist who is adopting Apache Spark to be able to analyze these giant data sets that do not fit on a single machine. But Apache Spark was not designed with neuroscience in mind. For this reason, Jeremy has helped to build several libraries on top of Spark. Thunder is a library for standard, distributed representation of data. Lightning is an API for reproducible web visualizations. These abstractions sit on top of Spark, and add a layer of usability. As it turns out, solving these problems for neuroscience have produced tools that are useful in a variety of other domains. In our discussion with Jeremy Freeman, we talk about Apache Spark, neuroscience, and the technological and cultural problems faced by traditional academic research.<\/p>\n<h3>Questions<\/h3>\n<ul>\n<li>What is exciting at the intersection of neuroscience and computation right now, in January 2016?<\/li>\n<li>What are the technical developments that have enabled recent advancements in neuroscience?<\/li>\n<li>What types of data do you deal with in neuroscience research, and how do you deal with the analysis?<\/li>\n<li>Why is Spark an appealing tool for computational neuroscience and dealing with images and time-series data?<\/li>\n<li>Can you walk through an experiment and give an example of how data is analyzed?<\/li>\n<li>Does research stagnate because people are stubborn and refuse to learn new technologies, or is it due to a lack of training?<\/li>\n<li>How is our changing understanding of the brain introducing us to new ideas about computation?<\/li>\n<li>What are your personal goals with your research?<\/li>\n<\/ul>\n<h3>Links<\/h3>\n<ul>\n<li><a href=\"http:\/\/thunder-project.org\/\">Thunder<\/a><\/li>\n<li><a href=\"https:\/\/www.janelia.org\/lab\/freeman-lab\">Freeman lab<\/a><\/li>\n<li><a href=\"http:\/\/lightning-viz.org\/lightning-python\/\">Lightning: interactive data visualization<\/a><\/li>\n<li><a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0959438815000756\">Open source tools for large-scale neuroscience<\/a><\/li>\n<li><a href=\"http:\/\/www.jeremyfreeman.net\/\">Jeremy&#8217;s personal page<\/a><\/li>\n<\/ul>\n<h3><\/h3>\n","protected":false},"excerpt":{"rendered":"<p>\u201cYou want to take a scientist who knows a little bit of matlab programming and try to teach them mapreduce, and write a mapreduce program in java to do image processing? It\u2019s a disaster!\u201d Apache Spark is replacing MATLAB in the domain of computational neuroscience. The constraints of running MATLAB on a single machine can\u2019t<\/p>\n","protected":false},"author":2,"featured_media":2135,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false,"_exactmetrics_sitenote_active":false,"_exactmetrics_sitenote_note":"","_exactmetrics_sitenote_category":0,"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_newsletter_tier_id":0,"footnotes":"","jetpack_publicize_message":"","jetpack_is_tweetstorm":false,"jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false}}},"categories":[1363,1081,14],"tags":[231,228,347,238,234,66],"jetpack_publicize_connections":[],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Computational Neuroscience with Jeremy Freeman - Software Engineering Daily<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"http:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Computational Neuroscience with Jeremy Freeman - Software Engineering Daily\" \/>\n<meta property=\"og:description\" content=\"\u201cYou want to take a scientist who knows a little bit of matlab programming and try to teach them mapreduce, and write a mapreduce program in java to do image processing? 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The constraints of running MATLAB on a single machine can\u2019t\" \/>\n<meta property=\"og:url\" content=\"http:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/\" \/>\n<meta property=\"og:site_name\" content=\"Software Engineering Daily\" \/>\n<meta property=\"article:published_time\" content=\"2016-02-26T02:38:03+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-11-04T09:10:40+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/i0.wp.com\/softwareengineeringdaily.com\/wp-content\/uploads\/2016\/02\/computational-neuroscience.jpg?fit=720%2C288\" \/>\n\t<meta property=\"og:image:width\" content=\"720\" \/>\n\t<meta property=\"og:image:height\" content=\"288\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Pranay\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@software_daily\" \/>\n<meta name=\"twitter:site\" content=\"@software_daily\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Pranay\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"http:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/#article\",\"isPartOf\":{\"@id\":\"http:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/\"},\"author\":{\"name\":\"Pranay\",\"@id\":\"https:\/\/softwareengineeringdaily.com\/#\/schema\/person\/609dd9667c84e7f6b8406a7a1bd2fb5c\"},\"headline\":\"Computational Neuroscience with Jeremy Freeman\",\"datePublished\":\"2016-02-26T02:38:03+00:00\",\"dateModified\":\"2021-11-04T09:10:40+00:00\",\"mainEntityOfPage\":{\"@id\":\"http:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/\"},\"wordCount\":344,\"publisher\":{\"@id\":\"https:\/\/softwareengineeringdaily.com\/#organization\"},\"keywords\":[\"Academia\",\"Computational Biology\",\"MATLAB\",\"Neuroscience\",\"Research\",\"Spark\"],\"articleSection\":[\"All Content\",\"Data\",\"Podcast\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"http:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/\",\"url\":\"http:\/\/softwareengineeringdaily.com\/2016\/02\/25\/computational-neuroscience-with-jeremy-freeman\/\",\"name\":\"Computational Neuroscience with Jeremy Freeman - 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