{"id":1,"date":"2013-08-13T01:48:53","date_gmt":"2013-08-13T01:48:53","guid":{"rendered":"http:\/\/www.clowersresearch.com\/main\/?p=1"},"modified":"2014-10-23T19:42:22","modified_gmt":"2014-10-23T19:42:22","slug":"scriptorium","status":"publish","type":"post","link":"http:\/\/www.clowersresearch.com\/main\/scriptorium\/","title":{"rendered":"Scriptorium"},"content":{"rendered":"<ul class=\"lcp_catlist\" id=\"lcp_instance_0\"><li><a href=\"http:\/\/www.clowersresearch.com\/main\/isims-2020-is-live-on-twitter\/\">ISIMS 2020 is Live on Twitter<\/a><div class=\"lcp_excerpt\">\n2 group members, Elvin and Cameron, have presentations at the virtual ISIMS on twitter this year. Go check out what they&#8217;ve been working on!\n\n\n\n\nhttps:\/\/twitter.com\/CameronNaylor13\/status\/1289099758762512384?s=20\n\n\n\n\n\n\nhttps:\/\/twitter.com\/ISIMSSociety\/status\/1289089957475254272?s=20\n\n\n\n\n\n\nhttps:\/\/twitter.com\/CameronNaylor13\/status\/1289103887459205120?s=20\n\n\n\n\n\n\nhttps:\/\/www.youtube.com\/watch?v=JWrDpHiWMeY&amp;feature=youtu.be\n\n\n\n<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/scriptorium-update-ion-mobility-calculator\/\">Scriptorium Update: Ion Mobility Calculator<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/scriptorium-update-ion-mobility-calculator\/\" title=\"Scriptorium Update: Ion Mobility Calculator\"><img width=\"1459\" height=\"717\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/06\/Collisions.png\" class=\"lcp_thumbnail wp-post-image\" alt=\"Scriptorium Update: Ion Mobility Calculator\" loading=\"lazy\" srcset=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/06\/Collisions.png 1459w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/06\/Collisions-300x147.png 300w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/06\/Collisions-768x377.png 768w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/06\/Collisions-1024x503.png 1024w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/06\/Collisions-250x123.png 250w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/06\/Collisions-150x74.png 150w\" sizes=\"(max-width: 1459px) 100vw, 1459px\" \/><\/a><div class=\"lcp_excerpt\">\n\n\n\nA brief, condensed tutorial of IMS calculations and simulation is provided in the following jupyter notebook.  This example code is meant to serve as an introduction to the topic and provide tractable to enable correct reporting of ion mobility measurements. \n\n\nContinued updates will pushed to the CRG github account including any changes to the ...<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/ims-spectral-simulator-arduino-edition\/\">IMS Spectral Simulator: Arduino Edition<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/ims-spectral-simulator-arduino-edition\/\" title=\"IMS Spectral Simulator: Arduino Edition\"><img width=\"619\" height=\"379\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/simspec.png\" class=\"lcp_thumbnail wp-post-image\" alt=\"IMS Spectral Simulator: Arduino Edition\" loading=\"lazy\" srcset=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/simspec.png 619w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/simspec-300x184.png 300w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/simspec-245x150.png 245w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/simspec-150x92.png 150w\" sizes=\"(max-width: 619px) 100vw, 619px\" \/><\/a><div class=\"lcp_excerpt\">\nTL\/DR &#8212; Code and wiring diagram to output a simulated spectrum WITH noise on a specified microcontroller output pin.  Requires hardware interrupts which simulate a gating pulse. \n\n\nWhen developing new approaches to signal processing or simply designing a new data acquisition system, having a reasonable reflection of the target signal is helpful during the ...<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/determining-proton-affinities-using-psi4\/\">Determining Proton Affinities using psi4<\/a><div class=\"lcp_excerpt\">\nThis is the 3rd post in a series outlining a workflow using freely available computational chemistry resources with python interfaces to evalute properties of gas-phase ions. A cursory search illustrates that there are a variety of computational packages with a direct python interface but interestingly, not all of these packages are current. PySCF appears to ...<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/geometry-optimization-in-python\/\">Geometry Optimization in Python<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/geometry-optimization-in-python\/\" title=\"Geometry Optimization in Python\"><img width=\"1280\" height=\"952\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/ibu.png\" class=\"lcp_thumbnail wp-post-image\" alt=\"Geometry Optimization in Python\" loading=\"lazy\" srcset=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/ibu.png 1280w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/ibu-300x223.png 300w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/ibu-768x571.png 768w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/ibu-1024x762.png 1024w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/ibu-202x150.png 202w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/ibu-150x112.png 150w\" sizes=\"(max-width: 1280px) 100vw, 1280px\" \/><\/a><div class=\"lcp_excerpt\">\nThis is the second post in a series aiming at generating a range of candidate structures for evaluation in the context of molecular modeling in the field of ion mobility spectrometry. In a previous post, the use of rdkit to generate structures was introduced. However, closer inspection of the code highlights a few funciton calls ...<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/conformational-searching-using-python\/\">Conformational Searching using Python<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/conformational-searching-using-python\/\" title=\"Conformational Searching using Python\"><img width=\"1280\" height=\"952\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas.png\" class=\"lcp_thumbnail wp-post-image\" alt=\"Conformational Searching using Python\" loading=\"lazy\" srcset=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas.png 1280w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas-300x223.png 300w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas-768x571.png 768w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas-1024x762.png 1024w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas-202x150.png 202w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2019\/01\/txas-150x112.png 150w\" sizes=\"(max-width: 1280px) 100vw, 1280px\" \/><\/a><div class=\"lcp_excerpt\">\nThis is the first of a series examining the use of python to generate candidate structures of molecules. These conformations may serve a variety of functions, though our particular purpose is to identify candidates for additional optimization and ultimate use in ion mobility modeling experiments. After considering a range of tools (e.g. Avogadro or ChemDraw), ...<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/updated-ims-worksheet-2018\/\">Updated IMS Worksheet &#8212; 2018<\/a><div class=\"lcp_excerpt\">For those that are interested, here is the spreadsheet used in the ASMS 2018 short course. \u00a0Thank Dr. Bill Siems if you see him.\n&nbsp;\nIon Mobility Cal v3\n<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/animation-improving-rp-by-increasing-dt-cell-length\/\">Animation: Improving Rp by Increasing DT Cell Length<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/animation-improving-rp-by-increasing-dt-cell-length\/\" title=\"Animation: Improving Rp by Increasing DT Cell Length\"><img width=\"800\" height=\"600\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2016\/12\/Gif_Length_MobilityCell.gif\" class=\"lcp_thumbnail wp-post-image\" alt=\"Animation: Improving Rp by Increasing DT Cell Length\" loading=\"lazy\" \/><\/a><div class=\"lcp_excerpt\">\nAusten has recently assembled an animation demonstrating the effect of increasing drift tube length on resolving power, calculated from peak width contributions from diffusion and gate pulse width. Click the image to view.\n<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/ims-short-course-worksheet\/\">IMS Short Course Worksheet<\/a><div class=\"lcp_excerpt\">For those that are interested, here is the spreadsheet used in the ASMS 2018 short course. \u00a0Thank Dr. Bill Siems if you see him.\n&nbsp;\nIon Mobility Cal v3\n<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/savitzky-golay-smoothing-gui\/\">Savitzky-Golay Smoothing GUI<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/savitzky-golay-smoothing-gui\/\" title=\"Savitzky-Golay Smoothing GUI\"><img width=\"659\" height=\"729\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/12\/Simple_Smoother.png\" class=\"lcp_thumbnail wp-post-image\" alt=\"Savitzky-Golay Smoothing GUI\" loading=\"lazy\" srcset=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/12\/Simple_Smoother.png 659w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/12\/Simple_Smoother-271x300.png 271w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/12\/Simple_Smoother-135x150.png 135w\" sizes=\"(max-width: 659px) 100vw, 659px\" \/><\/a><div class=\"lcp_excerpt\">\nIn an effort to create a set of simple tools that are useful for data processing and realtime analysis of data we&#8217;ve been exploring a range of tools. \u00a0Granted there are a number of canned solutions in existence (e.g. National Instruments), however, to avoid the long-term challenges of compatibility we are looking for tools that ...<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/venn-diagram-widgets\/\">Venn Diagram Widgets<\/a><div class=\"lcp_excerpt\">\nGenerally, it is recommended to avoid qualitative measures when quantitative solutions exist. \u00a0However, if the genuine need arises here are a list of useful Venn diagram widgets that may be found online:\nQuite Powerful: \u00a0http:\/\/bioinformatics.psb.ugent.be\/webtools\/Venn\/\nSimple Solution: http:\/\/www.bioinformatics.lu\/venn.php\nDownloadable: \u00a0http:\/\/pcarvalho.com\/patternlab\/vennDiagram.shtml\n<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/gantt-charts-in-matplotlib\/\">Gantt Charts in Matplotlib<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/gantt-charts-in-matplotlib\/\" title=\"Gantt Charts in Matplotlib\"><img width=\"1310\" height=\"628\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/02\/GanttPlot.png\" class=\"lcp_thumbnail wp-post-image\" alt=\"Gantt Charts in Matplotlib\" loading=\"lazy\" srcset=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/02\/GanttPlot.png 1310w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/02\/GanttPlot-300x143.png 300w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/02\/GanttPlot-1024x490.png 1024w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/02\/GanttPlot-250x119.png 250w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2014\/02\/GanttPlot-150x71.png 150w\" sizes=\"(max-width: 1310px) 100vw, 1310px\" \/><\/a><div class=\"lcp_excerpt\">Love it or hate it, the lack of a tractable options to create Gantt charts warrants frustration at times. \u00a0A recent post on Bitbucket\u00a0provides a nice implementation using matplotlib and python as a platform. \u00a0In order to expand the basic functionality a few modifications enable a set of features that highlight the relative contributions of ...<\/div><\/li><li><a href=\"http:\/\/www.clowersresearch.com\/main\/xkcd-style-plots-in-matplotlib\/\">XKCD-style Plots in Matplotlib<\/a><a href=\"http:\/\/www.clowersresearch.com\/main\/xkcd-style-plots-in-matplotlib\/\" title=\"XKCD-style Plots in Matplotlib\"><img width=\"800\" height=\"600\" src=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2013\/09\/PRS_XKCD.png\" class=\"lcp_thumbnail wp-post-image\" alt=\"XKCD-style Plots in Matplotlib\" loading=\"lazy\" srcset=\"http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2013\/09\/PRS_XKCD.png 800w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2013\/09\/PRS_XKCD-300x225.png 300w, http:\/\/www.clowersresearch.com\/main\/wp-content\/uploads\/2013\/09\/PRS_XKCD-150x112.png 150w\" sizes=\"(max-width: 800px) 100vw, 800px\" \/><\/a><div class=\"lcp_excerpt\">Now incorporated directly into the latest version of matplotlib (v1.3) here is a great alternative that brings some style to your plotting routines. I haven&#8217;t tried it out on plots with a huge number of points but I imagine it should work just fine. \u00a0Below are some simple examples. \u00a0Simple as matplotlib.pyplot.xkcd()&#8230;\nPseudo-Random Sequence with XKCD:\n\nNo ...<\/div><\/li><\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>&nbsp;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"gallery","meta":{"spay_email":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts\/1"}],"collection":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/comments?post=1"}],"version-history":[{"count":9,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts\/1\/revisions"}],"predecessor-version":[{"id":73,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/posts\/1\/revisions\/73"}],"wp:attachment":[{"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/media?parent=1"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/categories?post=1"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.clowersresearch.com\/main\/wp-json\/wp\/v2\/tags?post=1"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}