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HTTP/1.1 200 OKCache-Control: privateContent-Type: text/html; charsetutf-8Server: Microsoft-IIS/10.0Content-Style-Type: text/cssContent-Script-Type: text/javascriptX-Powered-By: ASP.NETDate: Thu, 12 Sep 2024 13:48:45 GMTContent-Length: 61039 !DOCTYPE html>html langen>head>meta http-equivcontent-type contenttext/html; charsetutf-8 /> link relcontents titleArchive href/archive /> link relstart titleTaoffis blog href/ /> link typeapplication/rsd+xml reledituri titleRSD hrefhttp://taoffi.isosoft.org/rsd.axd /> link typeapplication/rdf+xml relmeta titleSIOC hrefhttp://taoffi.isosoft.org/sioc.axd /> link typeapplication/apml+xml relmeta titleAPML hrefhttp://taoffi.isosoft.org/apml.axd /> link typeapplication/rdf+xml relmeta titleFOAF hrefhttp://taoffi.isosoft.org/foaf.axd /> link typeapplication/rss+xml relalternate titleTaoffis blog (RSS) hrefhttp://taoffi.isosoft.org/syndication.axd /> link typeapplication/atom+xml relalternate titleTaoffis blog (ATOM) hrefhttp://taoffi.isosoft.org/syndication.axd?formatatom /> link typeapplication/opensearchdescription+xml relsearch titleTaoffis blog hrefhttp://taoffi.isosoft.org/opensearch.axd /> link href/Content/Auto/Global.css relstylesheet typetext/css />meta nameviewport contentwidthdevice-width, initial-scale1.0, maximum-scale1.0, user-scalableno />link hrefhttps://fonts.googleapis.com/css?familyRoboto:300,400,500,700 relstylesheet typetext/css />link hrefCustom/Themes/Standard/css/styles.css relstylesheet />link relshortcut icon hrefContent/images/blog/blogengine.ico typeimage/x-icon />link hrefscripts/syntaxhighlighter/styles/shCore.css relstylesheet typetext/css />link hrefscripts/syntaxhighlighter/styles/shThemeDefault.css relstylesheet typetext/css /> script typetext/javascript src/en-us.res.axd>/script> script typetext/javascript src/Scripts/Auto/01-jquery-1.9.1.min.js>/script> script typetext/javascript src/Scripts/Auto/02-jquery.cookie.js>/script> script typetext/javascript src/Scripts/Auto/04-jquery-jtemplates.js>/script> script typetext/javascript src/Scripts/Auto/05-json2.min.js>/script> script typetext/javascript src/Scripts/Auto/blog.js>/script> script typetext/javascript src/scripts/syntaxhighlighter/scripts/XRegExp.js>/script> script typetext/javascript src/scripts/syntaxhighlighter/scripts/shCore.js>/script> script typetext/javascript src/scripts/syntaxhighlighter/scripts/shAutoloader.js>/script> script typetext/javascript src/scripts/syntaxhighlighter/shActivator.js>/script> meta namedescription contentTaoffi's blog - prisonniers du temps - prisonniers du temps /> meta namekeywords content.NET,Anti-patterns,ASP.NET,C#,C++,covid-19,DeepZoom,DNA,Egypt,France,History,HTML,Internet,JavaScript,json,Meta-models,Music,Nucleotidic modeling,OpenXML,Opinions,pInvoke,Search engines,SharePoint,Silverlight,society,SQL,SQL Server,TFS,Tools,VB.NET,wcf,Windows,Windows Server,Windows7,WPF,Xamarin Forms,Xaml,xslt /> meta nameauthor contentTaoffi Nassar />title> Taoffis blog | prisonniers du temps/title>/head>body classltr> form methodpost action/ idaspnetForm>div classaspNetHidden>input typehidden name__VIEWSTATE id__VIEWSTATE value9NI3L92jE7KZjvxxRXVPqNgLi6VuWG5Fay4lKzrRk0WtQgT5Dj3wUnGbA2lTSKCMJKDE6mIVAfBjhDsjnxHE0iQohJ4 />/div> div classwrapper> header classheader text-uppercase> div classcontainer> div classheader-title float-left> h1>a hrefhttp://taoffi.isosoft.org/>Taoffis blog/a>/h1> p>prisonniers du temps/p> /div> nav classheader-nav float-right> ul> li>a hrefhttp://taoffi.isosoft.org/>Home/a>/li> li>a hrefhttp://taoffi.isosoft.org/archive>Archive/a>/li> li>a hrefhttp://taoffi.isosoft.org/contact>Contact/a>/li> /ul> /nav> /div> /header> div classcontainer> div classcontent-wrapper float-left> div idctl00_cphBody_divError>/div> div idctl00_cphBody_PostList1_posts classposts>article classpost post-home idpost0> header classpost-header> h2 classpost-title> a href/post/2022/09/07/Shira-Ovide-the-past-Apple-era!>Shira Ovide: the past-Apple era!/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>07 September 2022/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/Opinions>Opinions/a>/span> a relnofollow classpull-right href/post/2022/09/07/Shira-Ovide-the-past-Apple-era!#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>img stylemargin-right: 10px; margin-bottom: 20px; width: 164px; src/image.axd?pictureshiraovide2209.jpg altshira ovideportrait alignleft />/p>p stylemargin-left: 10px;>If you have never read Shira Ovides papers (on nytimes)… well, you should do at least once a month! That should be inspiring!/p>p stylemargin-left: 10px;>Shira Ovide is predicting a post-Apple era, in spite of the companys brilliant financial health (valued $3 Trillion). a titleShira Ovides On Tech hrefhttps://messaging-custom-newsletters.nytimes.com/template/oakv2?productCodeOT&te1&nlon-tech-with-shira-ovide&emcedit_ot_20220906&urinyt://newsletter/6c823d2d-c59b-5a15-ad32-c9305f6b0dc6 target_blank>In a recent paper/a>, she explains how Apple, with smartphones sales stagnation, is now leaning toward selling ads (more… but differently)! ... Hello money, good-bye privacy protection and other hypocrisiesspan stylefont-family: Wingdings;>J/span>/p>p stylemargin-bottom: 40px;> /p> /section> /article>article classpost post-home idpost1> header classpost-header> h2 classpost-title> a href/post/2021/10/27/was-there-any-algerian-nation-before>Was there any algerian nation before?!/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>27 October 2021/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/Anti-patterns>Anti-patterns/a>, a href/category/Opinions>Opinions/a>, a href/category/society>society/a>, a href/category/France>France/a>/span> a relnofollow classpull-right href/post/2021/10/27/was-there-any-algerian-nation-before#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>img styleborder: 1px solid black; src/image.axd?picture/2021/aalz-micron-nation-francaise-en.jpg alt width493 height408 />/p> /section> /article>article classpost post-home idpost2> header classpost-header> h2 classpost-title> a href/post/2021/10/27/zammour-clown-whistle>zammour (clown whistle)/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>27 October 2021/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/Anti-patterns>Anti-patterns/a>, a href/category/France>France/a>, a href/category/Opinions>Opinions/a>, a href/category/society>society/a>/span> a relnofollow classpull-right href/post/2021/10/27/zammour-clown-whistle#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>In arabic: zammour (زمّور)... and probably in hebrew too, means a clown whistle... or, in modern times: klaxon !br /> Searching the word on Internet produces some interesting images... a hrefhttps://www.bing.com/images/search?q%d8%b2%d9%85%d9%91%d9%88%d8%b1&qpvt%d8%b2%d9%85%d9%91%d9%88%d8%b1&formIQFRML&first1&tscImageHoverTitle target_blank> as you might see here 😊/a>/p>p>img styleborder: 1px solid black; src/image.axd?picture/2021/zammour.jpg altzammour (زمّور) width582 height226 />/p> /section> /article>article classpost post-home idpost3> header classpost-header> h2 classpost-title> a href/post/2021/08/26/Search-within-image!>Search within image!/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>26 August 2021/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/Anti-patterns>Anti-patterns/a>, a href/category/Search-engines>Search engines/a>, a href/category/society>society/a>/span> a relnofollow classpull-right href/post/2021/08/26/Search-within-image!#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>Search engines can sometimes help search things within a given picture./p>p>Here, results for a search within Frances PM (Jean Castex) photo!/p>p>img src/image.axd?picture/2021/castex-search-20211016231311572.jpg alt />/p>p> /p> /section> /article>article classpost post-home idpost4> header classpost-header> h2 classpost-title> a href/post/2021/08/24/Shadowcopy-viewer>Shadowcopy viewer/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>24 August 2021/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>/span> a relnofollow classpull-right href/post/2021/08/24/Shadowcopy-viewer#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>Just discovered this interesting tool… a hrefhttps://www.nirsoft.net/utils/shadow_copy_view.html>ShadowCopyView/a> (freeware)/p>div>table styleborder-collapse: collapse; background: #e2efd9; border0>colgroup>col stylewidth: 623px; />/colgroup>tbody valigntop>tr>td stylepadding-left: 7px; padding-right: 7px; border: solid 0.5pt;>p>span stylecolor: navy; font-family: Arial; font-size: 10pt;>strong>Description /strong>/span>/p>p>span stylecolor: black; font-family: Segoe UI; font-size: 10pt;>ShadowCopyView is simple tool for Windows 10/8/7/Vista that lists the snapshots of your hard drive created by the Volume Shadow Copy service of Windows. Every snapshot contains an older versions of your files and folders from the date that the snapshot was created, you can browse the older version of your files and folders, and optionally copy them into a folder on your disk./span>/p>/td>/tr>/tbody>/table>/div>p> /p>p>span stylecolor: #595959; font-size: 9pt;>From <a hrefhttps://www.nirsoft.net/utils/shadow_copy_view.html>span stylecolor: blue; text-decoration: underline;>https://www.nirsoft.net/utils/shadow_copy_view.html/span>/a>> /span>/p> /section> /article>article classpost post-home idpost5> header classpost-header> h2 classpost-title> a href/post/2021/08/20/afghanistan-After-the-fall>afghanistan - After the fall/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>20 August 2021/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/History>History/a>, a href/category/Opinions>Opinions/a>, a href/category/society>society/a>/span> a relnofollow classpull-right href/post/2021/08/20/afghanistan-After-the-fall#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> table border0 cellspacing0 cellpadding2>tbody>tr>td valigntop>p>a href/image.axd?pictureclip_image001.png>img styledisplay: inline; background-image: none; titleclip_image001 src/image.axd?pictureclip_image001_thumb.png altclip_image001 width224 height244 border0 />/a>/p>/td>/tr>/tbody>/table>table border1 cellspacing0 cellpadding2>tbody>tr>td stylepadding: 4px; back-ground-color: beige; valigntop>span stylefont-family: Arial; font-size: 12pt;>The shambolic withdrawal does not reduce the obligation of America and its allies to ordinary Afghans, but increases it. They should use what leverage they still have to urge moderation on the Taliban, especially in their treatment of women. The displaced will need humanitarian aid. Western countries should also admit more Afghan refugees, the ranks of whom are likely to swell, and provide generous assistance to Afghanistan’s neighbours to look after those who remain in the region. The haste of European leaders to declare that they cannot take in many persecuted Afghans even as violent zealots seize control is almost as lamentable as America’s botched exit. It is too late to save Afghanistan, but there is still time to help its people. ■/span>/td>/tr>/tbody>/table>p>span stylecolor: #595959; font-size: 9pt;>From <a hrefhttps://www.economist.com/leaders/2021/08/21/the-fiasco-in-afghanistan-is-a-grave-blow-to-americas-standing>https://www.economist.com/leaders/2021/08/21/the-fiasco-in-afghanistan-is-a-grave-blow-to-americas-standing/a>>/span>/p> /section> /article>article classpost post-home idpost6> header classpost-header> h2 classpost-title> a href/post/2020/03/20/covid-5ync-coronavirus-curiosities!>covid-5ync – coronavirus curiosities!/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>20 March 2020/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/covid-19>covid-19/a>, a href/category/DNA>DNA/a>, a href/category/society>society/a>/span> a relnofollow classpull-right href/post/2020/03/20/covid-5ync-coronavirus-curiosities!#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>Just noticed this while working and debugging covid5ync app. Dont know if that may have sense from a biotechnology view... still, it worth to be mentioned:/p>ul>li>A fragment (15 nucleotides) of the RNA sequence looks to be a palindrome -:) of itself… Position 22901 -22916 br />strong>Note: /strong>the top part of the figures below reads sequences nucleotides in the direction 5->3, the lower should be read in the reverse direction 3->5 (which is the complementary of the upper part (i.e. a complementary to t and g to c))…/li>/ul>p>img src/image.axd?picture032020_1014_covid5yncco1.png alt />/p>ul>li>A similar palindrome fragment (15 nucleotides): 6089 - 6104/li>/ul>p>img src/image.axd?picture032020_1014_covid5yncco2.png alt />/p>ul>li>Similar with a small shift: (5744 – 5764)/li>/ul>p>img src/image.axd?picture032020_1014_covid5yncco3.png alt />/p> /section> /article>article classpost post-home idpost7> header classpost-header> h2 classpost-title> a href/post/2020/03/15/covid-5ync-the-fight-against-the-crowned-virus!>covid-5ync – the fight against the crowned virus!/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>15 March 2020/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/NET>.NET/a>, a href/category/C>C#/a>, a href/category/covid-19>covid-19/a>, a href/category/DNA>DNA/a>/span> a relnofollow classpull-right href/post/2020/03/15/covid-5ync-the-fight-against-the-crowned-virus!#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>I continue posting about covid-5ync app (a helper app contribution in the fight against the latest coronavirus epidemic)/p>p>A major step now done: serializing applications information into xml files!/p>p>Hopefully this will allow transmitting research session work among members of our target community: biotechnology engineers./p>p>I also downloaded a hrefhttps://www.ncbi.nlm.nih.gov/nuccore/MT163719 target_blank>(@NCBI site/a>) a recent version of the virus RNA sequence (referred to as: span stylecolor: black; font-family: Consolas; font-size: 9pt;>MT163719 29903bp RNA linear VRL 10-MAR-2020/span>). A daily work is done by the application to retrieve significant regions on the sequence. The a hrefhttp://covid-5.5ync.net/covid19-work-in-progress.covid-5ync target_blank>updated version of the (xml) file/a> is then uploaded to the a hrefhttp://covid-5.5ync.net/ target_blank>projects web site/a> which will allow gaining time in some tedious analysis tasks./p>h3>Serialization / deserialization/h3>p>Reminder: Technically speaking, the sequences data structures can be summarized as:/p>ul>li>div>Sequence: (that is a collection of nodes, each referring to an item of collection of bases)/div>ul>li>Identification and info of the sequence (Id, Name, Summary…)/li>li>A collection of named-regions (identified by start / end index + name and summary)/li>li>A collection of sub-sequences of repeats occurrences/li>li>A collection of sub-sequences of hairpins (or pair-repeats) occurrences/li>/ul>/li>/ul>p> /p>p>img src/image.axd?picture031520_1805_covid5yncth1.png alt />/p>p>To serialize these information… (in regards of the urgency matters) I decided to simply use a DataContractSerializer (which, as I said in other posts, is not really the best solution for extensibility)./p>p>The encountered difficulty was on several aspects:/p>ul>li>Some information is redundant, notably for sub-sequences (collections of repeats and hairpins)/li>li>The sequence object being itself a collection of nodes, the serializer did not really allow an easy way to handle its sub-objects. Here we fall into a known problem of cycling!/li>/ul>p> /p>p>The solution used was:/p>ul>li>Transform sub-sequences to region lists (start/end indexes + name + occurrences) and deserialize back to sub-sequences/li>li>Create a serialization-specialized object (using DataContract / DataMember attributes) and process the serialization through that object to avoid the cycling errors./li>/ul>p>img src/image.axd?picture031520_1805_covid5yncth2.png alt />/p>p> /p>p>The second difficulty was errors encountered on deserialization while locating and assigning various regions start/end indexes to the sequences nodes./p>p>Actually, the deserialization submits the sequences node as a string to be parsed asynchrony. And as you may have guessed, the collection of sequences nodes was being altered while locating the regions nodes!/p>p>The solution:/p>ul>li>The Parse method raises Parse Complete event/li>li>Subscribe to that event and proceed to these operations./li>/ul>p> /p>p>That is the short story… will keep you posted about more details later this week!/p>p>KEEP SAFE: wash your hands + do not touch your face + keep hope: span stylefont-size: 14pt;>Humanity will prevail! /span>/p> /section> /article>article classpost post-home idpost8> header classpost-header> h2 classpost-title> a href/post/2020/03/08/covid-5ync-dna-search-using-Linq>covid-5ync – dna search using Linq/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>08 March 2020/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/NET>.NET/a>, a href/category/covid-19>covid-19/a>, a href/category/DNA>DNA/a>, a href/category/WPF>WPF/a>/span> a relnofollow classpull-right href/post/2020/03/08/covid-5ync-dna-search-using-Linq#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>This post, follows in the series about technical details of covid-5ync (an a hrefhttp://covid-5.5ync.net/>open source application/a> contribution in the fight against the new covid-19 virus)./p>p>This time, our talk is about searching nucleotides within a dna sequence./p>p>Search is an important task for analyzing a sequence. Actually, to understand the structure of a genome, one task is to locate and classify identical regions and complementary regions (complementary regions where nucleotides are paired: aspan stylefont-family: Wingdings;>ó/span>t, gspan stylefont-family: Wingdings;>ó/span>c). From the IT point of view, such a task is obviously related to search… and should particularly be optimized./p>h3>Using Linq/h3>p>To locate a sequence of nucleotides (i.e. a string) within a (global) sequence, we may simply iterate into the global sequence nodes (each of which is a char) until we find the searched string. To find all occurrences, we can repeat the process starting at the next location and so on./p>p>Despite the artisanal aspect of the process, that works well for searching a predefined string./p>p>Another task that looks related to search, is to find repeats (Repeats are identical regions on a sequence)./p>p>It is somehow different from searching a strong>predefined/strong> string. The application actually has to iterate through the sequence, and at each position take a number of nucleotides to compose a string to be searched all over the sequence… (and keep coordinates of the found occurrences)./p>h3>Proposed solution/h3>p>In covid-5ync, a dna sequence is a span stylecolor: #339933;>span stylefont-family: Consolas; font-size: 10pt;>List<dna node>/span> /span>where each node contains an span stylefont-family: Consolas; font-size: 10pt;>Index/span> (int). Using Linq, we can define a method that returns the string of a given length at a given location (node Index) of the sequence:/p>div>table styleborder-collapse: collapse; border0>colgroup>col stylewidth: 626px; />/colgroup>tbody valigntop>tr>td stylepadding-left: 7px; padding-right: 7px; border: solid 0.5pt;>pre classbrush:csharp;auto-links:false;toolbar:false contenteditablefalse>public string StringAtIndex(int index, int len){ string str ; var nodes this.SkipWhile(i > i.Index < index).Take(len); foreach(var n in nodes) str + n.Code.ToString(); return str;}/pre>/td>/tr>/tbody>/table>/div>p> /p>p>With this method in place, we can efficiently locate all starting nodes of occurrences of a string on the sequence:/p>div>table styleborder-collapse: collapse; border0>colgroup>col stylewidth: 626px; />/colgroup>tbody valigntop>tr>td stylepadding-left: 7px; padding-right: 7px; border: solid 0.5pt;>pre classbrush:csharp;auto-links:false;toolbar:false contenteditablefalse>IEnumerable<iDnaNode> AllStartoccurrencesOfString(string str){ int len str.Length; return this.Where(i > StringAtIndex(i.Index, len) str);}/pre>/td>/tr>/tbody>/table>/div>p> /p>h3>Sample usage: locate and select occurrences of a string/h3>div>table styleborder-collapse: collapse; border0>colgroup>col stylewidth: 626px; />/colgroup>tbody valigntop>tr>td stylepadding-left: 7px; padding-right: 7px; border: solid 0.5pt;>pre classbrush:csharp;auto-links:false;toolbar:false contenteditablefalse>// get all starting nodes of the stringVar allStarts AllStartoccurrencesOfString(str).ToList();// visit the found starting nodes and select (str.Length) consecutive nodes…foreach( var item in allStarts){ var subSeq this.SkipWhile(n > n.Index < item.Index).Take(str.Length); subSeq.SelectAllNodes();}/pre>/td>/tr>/tbody>/table>/div>p> /p>p>img src/image.axd?picture030820_0102_covid5yncdn1.png alt width479 height351 />/p> /section> /article>article classpost post-home idpost9> header classpost-header> h2 classpost-title> a href/post/2020/03/03/covid5ync-dna-analysis-helper-application-progress!>covid-5ync – dna analysis helper application: progress!/a> /h2> div classpost-info clearfix> span classpost-date>i classicon-calendar>/i>03 March 2020/span> span classpost-author>i class icon-user>/i>a hrefhttp://taoffi.isosoft.org/author/Taoffi-Nassar>Taoffi-Nassar/a>/span> span classpost-category>i class icon-folder>/i>a href/category/NET>.NET/a>, a href/category/C>C#/a>, a href/category/covid-19>covid-19/a>, a href/category/DNA>DNA/a>, a href/category/WPF>WPF/a>, a href/category/Xaml>Xaml/a>/span> a relnofollow classpull-right href/post/2020/03/03/covid5ync-dna-analysis-helper-application-progress!#comment> i classicon-comment>/i>(0) /a> /div> /header> section classpost-body text> p>A quick post to talk about the progress in this project with a few technical details./p>p>First, a screen capture of what it looks like today (just a little better than before!):/p>p>img src/image.axd?picture030320_1103_covid5yncdn1.png alt />/p>p> /p>p>The first version of the a hrefhttp://covid5.5ync.net/covid5App/publish.htm target_blank>application is already online/a>: click-once installation. And Yes, we dont have money to have a certificate for the deployment… install only if you trust!... any suggestions about sponsors are also greatly welcome!/p>p> /p>p>A few features implemented:/p>ul>li>Search for string and search for the complementary of string./li>li>Paging/li>li>Zoom-in / out on the sequence/li>/ul>p>Next steps:/p>ul>li>Search enhancement: visually locate occurrences/li>li>Search for unique fragments according to user-provided settings/li>li>Open file / save selection/li>/ul>p>Long-term:/p>ul>li>… endless/li>/ul>p> /p>h3>Now, let us take a quick dive into the mechanics/h3>p>The first class diagram (a hrefhttps://github.com/Taoffi/covid5ync.git target_blank>updated source code/a> with such documentation is @github)/p>p>img src/image.axd?picture030320_1103_covid5yncdn2.png alt />/p>p>That seems quite basic(!), actually, as the reality of DNA, and that is one reason it is also fascinating!/p>ul>li>A sequence (iDnaSequence) is composed of nodes (iDnaNode)/li>li>A node is noted as a char. It refers to a base./li>li>Commonly a set of 4 bases is used (a, t, g and c). There may be more, but we can easily handle this when needed./li>li>Each individual base has a complementary Pair. A is pairable with T, C with G/li>li>The standard set of bases (iDnaBaseNucleotides) is a (singleton) list of the 4 bases. It sits as the main reference for nodes. It provides answers to important questions like: is c a valid base?... what the complementary of X?... what is the complementary sequence of the string span stylecolor: red;>atgccca/span>? and so on./li>/ul>p> /p>h3>Visual presentation: a start point/h3>p>There are many ways to present a DNA sequence. To start with something, let us assign a color to each base. The user can later change this to obtain a view according to his or her work area. Technically speaking, we have some constraints:/p>ul>li>The number of nucleotides of a sequence can be important. For coronavirus, that is roughly 29000. We therefor need paging to display and interact with a sequence./li>li>Using identification colors for nucleotides can also help to visually identify meaningful regions of the sequence on hand. For this to be useful, we need to implement zoom-in/out on the displayed sequence./li>/ul>p> /p>h3>Paging/h3>p>I simply used the solution exposed in a a href/post/2020/02/15/doc5ync-Trie-integration-tool-UI-Tag-cloud-paging-and-navigation>previous post/a> about doc5ync./p>p> /p>h3>Zoom-in / out/h3>p>I found a good solution through a discussion on Stack Overflowbr /> (credit: a hrefhttps://stackoverflow.com/users/967254/almulo target_blank>https://stackoverflow.com/users/967254/almulo/a>)./p>ul>li>Find the scroll viewer of the ListView./li>li>Handle zoom events as required/li>/ul>div>table styleborder-collapse: collapse; border0>colgroup>col stylewidth: 626px; />/colgroup>tbody valigntop>tr>td stylepadding-left: 7px; padding-right: 7px; border: solid 0.5pt;>pre classbrush:csharp;auto-links:false;toolbar:false contenteditablefalse>var presenter UiHelpers.FindChild<ScrollContentPresenter>(listItems, null);var mouseWheelZoom new MouseWheelZoom(presenter);PreviewMouseWheel + mouseWheelZoom.Zoom;/pre>/td>/tr>/tbody>/table>/div>p> /p>p>Sample screen shots of a zoom-out / in/p>p>img src/image.axd?picture030320_1103_covid5yncdn3.png alt />/p>p>img src/image.axd?picture030320_1103_covid5yncdn4.png alt />/p>p>More details later in a future post./p>p>Please send your remarks, suggestions and contributions on github./p>p>Hope all that will be useful in some way… Time is running… Humanity will prevail/p> /section> /article>/div>div idpostPaging styledisplay: none> a idctl00_cphBody_PostList1_hlPrev stylefloat:left><< Older posts/a> a idctl00_cphBody_PostList1_hlNext stylefloat:right>Newer posts >>/a>/div>div styleclear:both; display:block> ul idPostPager>li classPagerLinkDisabled>Newer posts/li>li classPagerLinkCurrent>1/li>li classPagerLink>a href/?page2>2/a>/li>li classPagerLink>a href/?page3>3/a>/li>li classPagerLink>a href/?page4>4/a>/li>li classPagerLink>a href/?page5>5/a>/li>li classPagerLink>a href/?page6>6/a>/li>li classPagerLink>a href/?page7>7/a>/li>li 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