{"id":1492,"date":"2016-01-05T18:18:12","date_gmt":"2016-01-06T02:18:12","guid":{"rendered":"http:\/\/antoine.wojdyla.fr\/blog\/?p=1492"},"modified":"2016-01-29T09:39:48","modified_gmt":"2016-01-29T17:39:48","slug":"science-tools-for-the-digital-age","status":"publish","type":"post","link":"http:\/\/antoine.wojdyla.fr\/blog\/2016\/01\/05\/science-tools-for-the-digital-age\/","title":{"rendered":"Wanted : science tools for the digital age"},"content":{"rendered":"<p>The internet may still be less than 10,000-days old, it still fails to deliver for scientists.<\/p>By empowering institutions to efficiently track down the number of publications, pushing even further the drive to publish many half-baked ideas and follow the hype instead of long-term research. It is true that it had never been as simple to get access to a paper and makes life easier on many aspects&#8211; collaboration often just requires sending an email, but new hurdles have appeared, and these should be removed.<a href=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/05e2e400dd1165870b3787a527e4e753-1.gif\" rel=\"attachment wp-att-1539\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-1539\" src=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/05e2e400dd1165870b3787a527e4e753-1.gif\" alt=\"05e2e400dd1165870b3787a527e4e753\" width=\"309\" height=\"243\" \/><\/a>Here is a bunch of ideas on how to use the new digital tools we have at hand to make research easier and thus more efficient, and a limited overview of what we have now.<!--more--><\/p>\n<h4>Dissemination of knowledge<\/h4>\n<blockquote><p>One of great claims of the Internet is that all the information is available, instantly and supposedly for free. The trouble, however, is that <em>knowledge<\/em> always comes with a price tag. As such, one gathers only the free, often second hand information or a collection of articles, while there are so many books available that could give a better picture of the field&#8230; when they&#8217;re bought. This is responsible for the phenomenon <a href=\"https:\/\/en.wikipedia.org\/wiki\/Thinking,_Fast_and_Slow\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/en.wikipedia.org\/wiki\/Thinking,_Fast_and_Slow', 'Daniel Kahneman calls &#8220;What you see is what there is&#8221;']);\" >Daniel Kahneman calls &#8220;What you see is what there is&#8221;<\/a>, thus giving the impression that some subjects are worth investigating, while in reality they&#8217;ve been studied over and over again and solutions to problem well-known.<\/p><\/blockquote>\n<ul>\n<li>There should be free access to all scientific articles&#8211; authors are funded by public entities<br \/>\n<em>Some journals are now open-access, such as <a href=\"http:\/\/www.plosone.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.plosone.org\/', 'PLoS']);\" >PLoS<\/a><\/em> <em><a href=\"http:\/\/www.plosone.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.plosone.org\/', 'One']);\" >One<\/a> or Optics Express, but the most prestigious (thus important) publications are still behind a paywall. Authors have copyright, and they can easily make their findings freely available or their website, but sadly this is not yet a common practice<\/em><\/li>\n<li>There should be a database for everything, with open access<br \/>\n<em>Every article should publish its data online, especially the support data that is not deemed good enough to be part of articles but still carry a lot of value (video, etc.)<\/em><\/li>\n<li>A working, live document for science&#8211; like Wikipedia, but without the restrictions<br \/>\n<em>Reinventing publishing would be fantastic.\u00a0 This would bring immense flexibility, by allowing half-baked story to emerge (<a href=\"https:\/\/www.sciencematters.io\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/www.sciencematters.io\/', 'Matters']);\" >Matters<\/a> does it) and updating past articles. The peer-review requirement would be challenging (quality), and giving proper credits would be hard to attribute (and thus grants and funding).<\/em><\/li>\n<li>A proper social network<br \/>\n<em>Now there&#8217;s <a href=\"http:\/\/researchgate.net\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/researchgate.net\/', 'ResearchGate']);\" >ResearchGate<\/a> and <a href=\"http:\/\/mysciencework.com\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/mysciencework.com\/', 'MyScienceWork']);\" >MyScienceWork<\/a>, but they&#8217;re not backed by any major entity and don&#8217;t have enough penetration to be truly effective&#8211; now they only serve to promote oneself. In addition, that could bring much more feedback and new ideas to an article, which is now limited to the revisions by co-author and reviewers, or people citing the article.<br \/>\n<\/em><\/li>\n<li>Convenient digital object identifier (for data, affixed to any figure)<br \/>\n<em>Every data mentioned somewhere should be referenced. DOIs are nice, but they are not flexible enough. A &#8220;bit.ly&#8221; equivalent would be great (for sharing on slides etc.)<\/em><\/li>\n<li>There should a proper editing language, that would abstract Word or Latex and allow to turn <em>things in a nice format reading (pdf), editing (html) or proofing.<\/em><br \/>\n<em>Word sucks for layout, while latex makes it very hard for proofing, and requires package and extra efforts for anything beyond simple graphics. And Latex2Html is deprecated<\/em><\/li>\n<li>Math-write should be standard on the web<br \/>\n<em>There&#8217;s MathML and <a href=\"http:\/\/Susan Giesecke\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/Susan Giesecke', 'MathJax']);\" >MathJax<\/a>, but they&#8217;re not available on all platform. Even Wikipedia has this ugly math feel because of the png conversion, which morevover makes copying difficult<\/em><\/li>\n<li>Plotting should not be that hard , expressing idea not so difficult<br \/>\n<em><a href=\"http:\/\/d3js.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/d3js.org\/', 'd3.js']);\" >d3.js<\/a> or <a href=\"http:\/\/worrydream.com\/Tangle\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/worrydream.com\/Tangle\/', 'tangle.js']);\" >tangle.js<\/a> do a good job at that; they could\/should be better integrated to python or Matlab.<\/em><\/li>\n<li>An equivalent to Evernote for scientists, where you can pull out data out of your simulation software, and edit it after the fact.<br \/>\n<em>It is very difficult to get data out of the software (after simulation, acquisition or processing), or you have to use proprietary software such as <a href=\"http:\/\/www.originlab.com\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.originlab.com\/', 'Origin']);\" >Origin<\/a>. Postscript and similar other vector formats allow it&#8211; but it&#8217;s very clunky). Even more ridiculous, there is no proper container for data&#8211; people are using TIFF or <a href=\"https:\/\/www.hdfgroup.org\/HDF5\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/www.hdfgroup.org\/HDF5\/', 'HDF5']);\" >HDF5<\/a>, but I&#8217;m always amazed how hard it is to share complex data (i.e. data with a real and imaginary part).<\/em><\/li>\n<li>A working, efficient bibliography manager, with highlights etc.<br \/>\n<em>There&#8217;s <a href=\"https:\/\/www.readcube.com\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/www.readcube.com\/', 'Readcube']);\" >Readcube<\/a>, <a href=\"http:\/\/mendeley.com\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/mendeley.com\/', 'Mendeley']);\" >Mendeley<\/a> and <a href=\"https:\/\/www.zotero.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/www.zotero.org\/', 'Zotero']);\" >Zotero<\/a>, but they have a hard time dealing with documents other than articles and are not very helpful to get new articles. <a href=\"http:\/\/scholar.google.com\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/scholar.google.com\/', 'Google Scholar ']);\" >Google Scholar <\/a>is a good tool, but still does not allow you to sip through all the relevant new articles.<\/em><\/li>\n<\/ul><p><strong>Theoretical aspect of science<\/strong><\/p>\n<ul>\n<li>Pull out data from a graph (and create a giant database)<br \/>\n<em>Most data available in the literature is available in the form of plots, which are very difficult to get data from. There are some attempts to digitize plots (<a href=\"http:\/\/www.datathief.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.datathief.org\/', '1']);\" >1<\/a>,<a href=\"http:\/\/arohatgi.info\/WebPlotDigitizer\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/arohatgi.info\/WebPlotDigitizer\/', '2']);\" >2<\/a>), but they&#8217;re sub-optimal. Ideally, any plot submitted to a paper should have its equivalent as a table available somewhere.<\/em><\/li>\n<li>Have an unified database for all things science<br \/>\n<em>There are database for many things (<a href=\"http:\/\/refractiveindex.info\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/refractiveindex.info\/', 'optical refractive index']);\" >optical refractive index<\/a>, <a href=\"https:\/\/plasmid.med.harvard.edu\/PLASMID\/Home.xhtml\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/plasmid.med.harvard.edu\/PLASMID\/Home.xhtml', 'plasmids']);\" >plasmids<\/a>, <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch', 'nucleotids']);\" >nucleotids<\/a>, <a href=\"http:\/\/heracles.astro.berkeley.edu\/sndb\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/heracles.astro.berkeley.edu\/sndb\/', 'supernova']);\" >supernova<\/a>), but they should all be gathered and consolidated. The data in the <a href=\"http:\/\/www.hbcpnetbase.com\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.hbcpnetbase.com\/', 'CRC handbook']);\" >CRC handbook<\/a> should be freely available. Some other efforts here at Berkeley Lab : <a href=\"https:\/\/www.materialsproject.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/www.materialsproject.org\/', 'Material Project']);\" target=\"_blank\">Material Project<\/a>, or computations like <a href=\"http:\/\/henke.lbl.gov\/optical_constants\/multi2.html\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/henke.lbl.gov\/optical_constants\/multi2.html', 'multilayer simulator']);\" target=\"_blank\">multilayer simulator<\/a>.<br \/>\n<\/em><\/li>\n<li>Redesign BLAS, LAPACK etc. so that you don&#8217;t have to use compilers that were designed at the peak of Cold Wars<br \/>\n<em>Millions of hours have been wasted trying to install g77 in vain&#8211; while virtually every other program is built on bloated frameworks&#8211; give us something that works, even if we lose 20% in efficiency.<\/em><\/li>\n<li>A software to make simulation ans share them easily, without requiring a license<br \/>\n<em><a href=\"http:\/\/junolab.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/junolab.org\/', 'Ipython']);\" >Ipython<\/a> and Julia (<a href=\"http:\/\/junolab.org\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/junolab.org\/', 'with REPL']);\" >with REPL<\/a>) do the work and they are cross platform, but they&#8217;re still clunky.<\/em><\/li>\n<li>Easy computational optimization<br \/>\n<em>Computing power is horribly wasted on parallel processors. Why can&#8217;t there be an easy\/transparent way to properly use parallel computing, without having to be a grad student with time to spare on the CUDA manual (which eventually will not work on a different platform, and the whole thing unusable to someone not acquainted with pragmas and other ugly syntactic hacks?).<\/em><\/li>\n<\/ul><p><strong>Experimental aspect of science<\/strong><\/p>\n<ul>\n<li>A software suite where you can easily get data out of an instrument without too much hassle<br \/>\n<em><a href=\"http:\/\/www.ni.com\/labview\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.ni.com\/labview\/', 'LabView']);\" >LabView<\/a>, and to some extent<a href=\"http:\/\/www.mathworks.com\/products\/simulink\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.mathworks.com\/products\/simulink\/', ' Simulink']);\" > Simulink<\/a> do the job, but they are proprietary, very difficult to maintain and work only with a limited number of devices. There are systems such as <a href=\"http:\/\/sourceforge.net\/projects\/labrad\/\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/sourceforge.net\/projects\/labrad\/', 'LabRAD']);\" >LabRAD<\/a> or <a href=\"http:\/\/www.aps.anl.gov\/epics\/about.php\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'http:\/\/www.aps.anl.gov\/epics\/about.php', 'EPICS']);\" >EPICS<\/a>, but they are in need of an overhaul and cross-platform capability.With colleagues, I wrote a full Matlab suite (instrument control and UIs) for our own use, but I&#8217;m not (yet) allowed to share it.<\/em><\/li>\n<li>Using (and reusing) tablets for display and control<br \/>\n<em>Nowadays, screens are everywhere; it would be nice to re-purpose old phones and tablets to serve science, let&#8217;s say as a monitor or a user interface. If only they could be officially &#8220;jailbroken&#8221; past a certain date&#8230;<\/em><\/li>\n<li>An augmented reality tool where you can use your phone to get the reading<br \/>\n<em>Lots of old instruments only offer analog or digital reading and no outputs (or obsolete interfaces like parallel or GPIB). Using the camera of a phone, it could be possible to log these readings&#8211; often times precision would be good enough and would greatly help tuning procedures.<\/em><\/li>\n<li>A database or off-the shelf incarnation of Arduino projects for science<br \/>\n<em>e.g. : Arduino Analog-to-digital internal converters are limited to 10bit. By using cheap components available, it is possible to have a <a href=\"https:\/\/forum.arduino.cc\/?topic=57873.0\" onclick=\"_gaq.push(['_trackEvent', 'outbound-article', 'https:\/\/forum.arduino.cc\/?topic=57873.0', '24bit device for less that $100']);\" >24bit device for less that $100<\/a> (ten thousand times more precise)<\/em><\/li>\n<\/ul><p>I&#8217;ve worked on some of these things out of necessity but&#8211; oh boy, there are so many things to do!<\/p>\n<div id=\"attachment_1517\" style=\"width: 286px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/met5gui.png\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1517\" class=\" wp-image-1517\" src=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/met5gui-1024x793.png\" alt=\"Matlab reusable instrument control and user interface\" width=\"276\" height=\"214\" srcset=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/met5gui-1024x793.png 1024w, http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/met5gui-300x232.png 300w, http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/met5gui.png 1040w\" sizes=\"auto, (max-width: 276px) 100vw, 276px\" \/><\/a><\/p>\n<p id=\"caption-attachment-1517\" class=\"wp-caption-text\">Matlab reusable instrument control and user interface<\/p>\n<\/div>\n<div id=\"attachment_1518\" style=\"width: 157px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/arduino_24bits.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1518\" class=\" wp-image-1518\" src=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/arduino_24bits.jpg\" alt=\"24-bit ADC with Arduino\" width=\"147\" height=\"214\" srcset=\"http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/arduino_24bits.jpg 495w, http:\/\/antoine.wojdyla.fr\/blog\/wp-content\/uploads\/arduino_24bits-207x300.jpg 207w\" sizes=\"auto, (max-width: 147px) 100vw, 147px\" \/><\/a><\/p>\n<p id=\"caption-attachment-1518\" class=\"wp-caption-text\">24-bit ADC with Arduino<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>The internet may still be less than 10,000-days old, it still fails to deliver for scientists.By empowering institutions to efficiently track down the number of publications, pushing even further the drive to publish many half-baked ideas and follow the hype instead of long-term research. It is true that it had never been as simple to [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11,14,16,9,5],"tags":[],"class_list":["post-1492","post","type-post","status-publish","format-standard","hentry","category-english","category-projects","category-resources","category-science","category-science-life"],"_links":{"self":[{"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/posts\/1492","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/comments?post=1492"}],"version-history":[{"count":20,"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/posts\/1492\/revisions"}],"predecessor-version":[{"id":1555,"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/posts\/1492\/revisions\/1555"}],"wp:attachment":[{"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/media?parent=1492"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/categories?post=1492"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/antoine.wojdyla.fr\/blog\/wp-json\/wp\/v2\/tags?post=1492"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}