<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/40221?</link>
	<atom:link href="https://bioinformaticsonline.com/related/40221?" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40214/gooey-turn-almost-any-python-command-line-program-into-a-full-gui-application-with-one-line</guid>
	<pubDate>Fri, 01 Nov 2019 00:29:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40214/gooey-turn-almost-any-python-command-line-program-into-a-full-gui-application-with-one-line</link>
	<title><![CDATA[Gooey: Turn (almost) any Python command line program into a full GUI application with one line]]></title>
	<description><![CDATA[<p><span>Turn (almost) any Python command line program into a full GUI application with one line</span></p>
<p>The easiest way to install Gooey is via&nbsp;<code>pip</code></p>
<pre><code>pip install Gooey 
</code></pre>
<p>Alternatively, you can install Gooey by cloning the project to your local directory</p>
<pre><code>git clone https://github.com/chriskiehl/Gooey.git
</code></pre>
<p>run&nbsp;<code>setup.py</code></p>
<pre><code>python setup.py install</code></pre><p>Address of the bookmark: <a href="https://github.com/chriskiehl/Gooey" rel="nofollow">https://github.com/chriskiehl/Gooey</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35119/frontend-perl-web-framework-documentation-andrej-sali-lab</guid>
	<pubDate>Mon, 08 Jan 2018 22:32:03 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35119/frontend-perl-web-framework-documentation-andrej-sali-lab</link>
	<title><![CDATA[Frontend: Perl Web framework documentation - Andrej Sali Lab]]></title>
	<description><![CDATA[<p><span>The frontend is a set of Perl classes that displays the web interface, allowing a user to upload their input files, start a job, display a list of all jobs in the system, and get back job results. The main&nbsp;</span><a href="https://saliweb.readthedocs.io/en/latest/modules/frontend.html#saliwebfrontend" title="saliwebfrontend"><code><span>saliwebfrontend</span></code></a><span>&nbsp;class must be subclassed for each web service. This class is then used to display the web pages using a set of CGI scripts that are set up automatically by the build system.</span></p><p>Address of the bookmark: <a href="https://saliweb.readthedocs.io/en/latest/frontend.html" rel="nofollow">https://saliweb.readthedocs.io/en/latest/frontend.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/36605/hello-python-world</guid>
	<pubDate>Mon, 14 May 2018 16:41:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/36605/hello-python-world</link>
	<title><![CDATA[Hello Python World !]]></title>
	<description><![CDATA[<p>As I mentioned earlier, I will keep on posting one Python script per day to introduce you to Python programming. Whether you are an experienced programmer or not, this tutorial is intended for everyone who wishes to learn the Python programming language.</p><p>Python is a very simple language, and has a very straightforward syntax. The simplest directive in Python is the "print" directive - it simply prints out a line (and also includes a newline).</p><p>Create a file Hello.py</p><blockquote><p>print("Hello, Python World !.")</p></blockquote><p>Run</p><p>python3 Hello.py</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/34814/bioinformatics-web-application-development-with-perl</guid>
	<pubDate>Tue, 26 Dec 2017 18:14:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/34814/bioinformatics-web-application-development-with-perl</link>
	<title><![CDATA[Bioinformatics Web Application Development with Perl]]></title>
	<description><![CDATA[<div><p>Perl's second wave of adoption came from the growth of the world wide web. Dynamic web pages&mdash;the precursor to modern web applications&mdash;were easy to create with Perl and CGI. Thanks to Perl's ubiquity as a language for system administrators and its power to manipulate text, it was the default choice for web programming. Its presence everywhere made it popular and, in some ways, the duct tape of the Internet.</p><h4>Web Application Development</h4><p>The old days of CGI programs and the simple development style that represented seem clunky. Web pages have become web applications. Development has moved from generating static HTML to both client and server side programming, with rich client interfaces and powerful backends.</p><p>Perl is still well suited for developing modern web apps. The language grows more powerful and easier to use every year, the available libraries are wonderful and keep getting better, and the inventions and discoveries available in modern Perl are unsurpassed.</p><p>In particular, a modern Perl developer can do amazing things with modern Perl tools. If you still think of Perl web development as a&nbsp;<em>cgi-bin</em>&nbsp;directory full of messy scripts that spew warnings to STDERR, you're a decade out of date. Better yet, you can replace that mess piecemeal, thanks to the new tools and techniques of modern Perl. See, for example, the ever-growing list of technologies&nbsp;<a href="http://www.builtinperl.com/">Built in Perl</a>.</p><h4>Modern Perl Web Frameworks</h4><p>While the old wave of web development may have made the CGI.pm module central, modern Perl web programming follows a stricter separation of business logic, URL and request routing, and output. The days of slinging a string here, an array there, a Perl hash yonder, declaring every variable at the top of the program, and maybe making a subroutine are gone. The Perl world has seen the value of abstraction and ways to mechanize away boilerplate. Perl has dozens of frameworks and toolkits designed to make web development and deployment simpler.</p><p>Any of a dozen of these frameworks will help you do great things, but three in particular stand out. You can build web sites and web applications of tremendous value with all three. These are neither the only good possibilities (think of POE or Jifty or Continuity or...) nor the only mechanisms for web programming with Perl (see Mechanize or LWP or Mojo::UserAgent for more). Yet if you want three good options to choose between, start here.</p><h4>Catalyst</h4><p>The&nbsp;<a href="http://catalystframework.org/">Catalyst</a>&nbsp;framework is a flexible and powerful system for building small to large web apps. It uses the&nbsp;<a href="http://moose.perl.org/">Moose</a>&nbsp;object system to provide great APIs for extension and further development. It's the most mature of the modern top Perl web frameworks, yet it retains its flexibility and vibrancy. In particular, its plugin and extension ecosystem allows it to evolve to provide new and essential features.</p><p>Catalyst has embraced the Plack/PSGI standard for Perl web deployment and recent versions are exploring high-scalability, event-based request handling models.</p><h4>Dancer</h4><p>The&nbsp;<a href="http://perldancer.org/">Dancer</a>&nbsp;framework is deliberately minimal in syntax and scope, but it also has a vibrant plugin ecosystem. Dancer particularly excels for smaller sites and applications, though good programmers can build larger things with it.</p><p>The first version of Dancer was easy to use. Dancer 2 continues that ease while improving the internals and robustness of applications.</p><h4>Mojolicious</h4><p>The&nbsp;<a href="http://mojolicio.us/">Mojolicious</a>&nbsp;(Mojo) framework has a real-time design based on high performance event handling. Its focus is solving new and interesting problems in simple and effective ways, and the project has produced a lot of new code that does old things in better ways.</p><p>In particular, Mojolicious goes to great lengths to support new web standards, such as CSS 3, web sockets, and HTTP 2.</p><p>Where Catalyst embraces the CPAN fully, Mojolicious by design provides most of what an average app might need in a single download. It's still fully compatible with the CPAN, but the intention is to provide good working defaults in a package that's easy to start with. Mojo's fans are quick to praise it as fun to develop.</p><p>A modern Perl web developer should be familiar with at least one of these frameworks.</p><h4>Modern Perl Storage Mechanisms</h4><p>Perl's venerable&nbsp;<a href="http://search.cpan.org/perldoc?DBI">DBI</a>&nbsp;module has been the focal point of database access since its invention. Its design allows it to provide the same interface to huge relational databases and flat files alike through its DBD extension mechanism. Yet the DBI by itself isn't the be-all, end-all of data storage and access in Perl.</p><h4>DBIx::Class</h4><p><a href="http://search.cpan.org/perldoc?DBIx::Class">DBIx::Class</a>&nbsp;sits on top of DBI to provide an API to your database based on the concept of queries and results. This is often sufficient to remove all but the most complicated of SQL from your code, leaving you to manipulate your business models instead of the small details of how a relational database works. The power and maintainability you receive is well the small cost of the learning curve.</p><p>Even better, DBIC can manage (and even generate) your database schema for you.</p><p>Recent versions of DBIC have demonstrated that a well-written ORM can perform much better than even clever hand-written code. Because it builds on the Perl DBI, it scales everywhere from SQLite to PostgreSQL, MySQL, Oracle, and more.</p><h3>Rose::DB</h3><p>The lesser-known but no less powerful&nbsp;<a href="http://search.cpan.org/perldoc?Rose::DB::Object">Rose::DB::Object</a>&nbsp;builds on&nbsp;<a href="http://search.cpan.org/perldoc?Rose::DB">Rose::DB</a>&nbsp;to provide an object-relational mapper for Perl. While its high level features most directly compare to those of DBIx::Class, it's often measurably faster.</p><h4>NoSQL on the CPAN</h4><p>Of course the&nbsp;<a href="http://search.cpan.org/">CPAN</a>&nbsp;has modules for almost any NoSQL database or job queue or persistence mechanism you could name, and several you have never heard of. Everything you need is a quick CPAN or cpanm away!</p><h4>Modern Perl Deployment Strategies</h4><p>In the early days of the web, deploying a Perl web application meant putting one or more&nbsp;<em>.cgi</em>&nbsp;or&nbsp;<em>.pl</em>&nbsp;files in a special directory and hoping that your system administrator had everything configured correctly. The execution model was often slow and cumbersome, and accessing shared resources such as databases was often tricky.</p><p>Modern Perl has better choices. While deployment strategies are the source of many arguments, the return on your investment from learning the modern way is impressive.</p><h4>Plack/PSGI</h4><p>The PSGI specification (as exemplified by&nbsp;<a href="http://plackperl.org/">Plack</a>) describes a strategy for building Perl web apps independent of server and with the possibility to share custom processing behaviors.</p><p>In other words, it's a standard for writing Perl apps to take advantage of the huge ecosystem of Perl development available on the CPAN without tying yourself to a server like Apache, Apache 2, nginx, or anything else.</p><p>Any good modern Perl web framework (including those listed here) supports PSGI. Several deployment mechanisms exist to meet various business needs which also support PSGI. In particular, you can deploy the same application with a local testing server on your own machine as you can to your production server or servers without changing your application at all.</p><h4>mod_perl</h4><p>The older but still viable mod_perl Apache httpd module embeds Perl into the web server. This was the first widespread persistence mechanism for Perl web applications themselves and it's still popular to this day, though PSGI compliance is often the choice for new development. (PSGI handlers to use mod_perl as the backend are available.)</p><p>Modern Perl developers should familiarize themselves with PSGI and the wealth of available Plack middleware.</p><h4>Perl Web Development</h4><p>Of course no discussion of Perl web development would be complete without mentioning the strength of the CPAN. Almost any project will benefit from the wealth of freely available libraries built to solve real problems. These distributions run the gamut from full-blown web frameworks and content management systems to APIs for web services, development tools, testing systems, and interfaces to document formats and external resources.</p><p>For example, if you need to write a web service which accepts JSON data and produces Excel spreadsheets, you can glue together a few CPAN distributions and get the job done early. If you need to consume XML from a remote service and emit a PDF, you're in luck.</p><p>Perl's prowess as a general purpose programming language as well as its flexibility and power in managing text and gluing systems together make it a wonderful fit for web development. The community's adoption of modern Perl standards such as PSGI and Plack only enhance your power.</p><p>Web application development in Perl is still viable, and modern Perl tools and techniques and libraries make it more powerful and pleasant than ever.</p></div>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40721/efs-an-ensemble-feature-selection-tool-implemented-as-r-package-and-web-application</guid>
	<pubDate>Tue, 28 Jan 2020 05:12:23 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40721/efs-an-ensemble-feature-selection-tool-implemented-as-r-package-and-web-application</link>
	<title><![CDATA[EFS: an ensemble feature selection tool implemented as R-package and web-application]]></title>
	<description><![CDATA[<p><span>The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in EFS, which can be used separately or combined in an ensemble.</span></p>
<p><a href="https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8">https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8</a></p><p>Address of the bookmark: <a href="http://efs.heiderlab.de/" rel="nofollow">http://efs.heiderlab.de/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35148/mojolicious-a-next-generation-web-framework-for-the-perl-programming-language</guid>
	<pubDate>Fri, 12 Jan 2018 16:48:10 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35148/mojolicious-a-next-generation-web-framework-for-the-perl-programming-language</link>
	<title><![CDATA[mojolicious: a next generation web framework for the Perl programming language.]]></title>
	<description><![CDATA[<p><span>Back in the early days of the web, many people learned Perl because of a wonderful Perl library called&nbsp;</span><a href="https://metacpan.org/module/CGI" target="_blank">CGI</a><span>. It was simple enough to get started without knowing much about the language and powerful enough to keep you going, learning by doing was much fun. While most of the techniques used are outdated now, the idea behind it is not. Mojolicious is a new endeavor to implement this idea using bleeding edge technologies.</span></p>
<h2>Features</h2>
<ul>
<li>An amazing&nbsp;<strong>real-time web framework</strong>, allowing you to easily grow single file prototypes into well-structured MVC web applications.
<ul>
<li>Powerful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session management, form validation, testing framework, static file server, CGI/<a href="http://plackperl.org/" target="_blank">PSGI</a>&nbsp;detection, first class Unicode support and much more for you to discover.</li>
</ul>
</li>
<li>A powerful&nbsp;<strong>web development toolkit</strong>, that you can use for all kinds of applications, independently of the web framework.
<ul>
<li>Full stack HTTP and WebSocket client/server implementation with IPv6, TLS, SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support.</li>
<li>Built-in non-blocking I/O web server, supporting multiple event loops as well as optional pre-forking and hot deployment, perfect for building highly scalable web services.</li>
<li>JSON and HTML/XML parser with CSS selector support.</li>
</ul>
</li>
<li>Very clean, portable and object-oriented pure-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed)</li>
<li>Fresh code based upon years of experience developing&nbsp;<a href="http://catalystframework.org/" target="_blank">Catalyst</a>, free and open source.</li>
<li>Hundreds of 3rd party&nbsp;<a href="https://metacpan.org/requires/distribution/Mojolicious">extensions</a>&nbsp;and high quality spin-off projects like the&nbsp;<a href="https://metacpan.org/pod/Minion">Minion</a>&nbsp;job queue.</li>
</ul>
<p>http://mojolicious.org/</p><p>Address of the bookmark: <a href="http://mojolicious.org/" rel="nofollow">http://mojolicious.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35272/biocircosjs-is-an-open-source-interactive-javascript-library-to-interactive-display-biological-data-on-the-web</guid>
	<pubDate>Fri, 19 Jan 2018 15:03:51 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35272/biocircosjs-is-an-open-source-interactive-javascript-library-to-interactive-display-biological-data-on-the-web</link>
	<title><![CDATA[BioCircos.js is an open source interactive Javascript library to interactive display biological data on the web]]></title>
	<description><![CDATA[<p><a href="http://bioinfo.ibp.ac.cn/biocircos/index.php">BioCircos.js</a>&nbsp;is an open source interactive&nbsp;<code>Javascript</code>&nbsp;library which provides an easy way to interactive display biological data on the web. It implements a raster-based&nbsp;<code>SVG</code>&nbsp;visualization using the open source Javascript framework jquery.js. BioCircos.js is multiplatform and works in all major internet browsers (<strong>Internet Explorer</strong>,&nbsp;<strong>Mozilla Firefox</strong>,&nbsp;<strong>Google Chrome</strong>,&nbsp;<strong>Safari</strong>,&nbsp;<strong>Opera</strong>). Its speed is determined by the client&rsquo;s hardware and internet browser. For smoothest user experience, we recommend&nbsp;<strong>Google Chrome</strong>.</p>
<p>BioCircos.js provides&nbsp;<strong>SNP</strong>,&nbsp;<strong>CNV</strong>,&nbsp;<strong>HEATMAP</strong>,&nbsp;<strong>LINK</strong>,&nbsp;<strong>LINE</strong>,&nbsp;<strong>SCATTER</strong>,&nbsp;<strong>ARC</strong>,&nbsp;<strong>TEXT</strong>, and&nbsp;<strong>HISTGRAM</strong>modules to display genome-wide genetic variations (SNPs, CNVs and chromosome rearrangement), gene expression and biomolecule interactions. BioCircos.js also provides&nbsp;<strong>BACKGROUND</strong>&nbsp;module to display background and axis circles. Tooltips showing detailed information of SVG elements are also provided.</p>
<p><a href="http://bioinfo.ibp.ac.cn/biocircos/document/demo/pages/paper01.html">Demo</a></p><p>Address of the bookmark: <a href="http://bioinfo.ibp.ac.cn/biocircos/document/index.html" rel="nofollow">http://bioinfo.ibp.ac.cn/biocircos/document/index.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35108/mobyle-a-new-full-web-bioinformatics-framework</guid>
	<pubDate>Sun, 07 Jan 2018 19:33:45 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35108/mobyle-a-new-full-web-bioinformatics-framework</link>
	<title><![CDATA[Mobyle: a new full web bioinformatics framework]]></title>
	<description><![CDATA[<p><span>Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.</span></p><p>Address of the bookmark: <a href="https://academic.oup.com/bioinformatics/article/25/22/3005/179064" rel="nofollow">https://academic.oup.com/bioinformatics/article/25/22/3005/179064</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29917/gojs</guid>
	<pubDate>Tue, 22 Nov 2016 08:25:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29917/gojs</link>
	<title><![CDATA[GoJS]]></title>
	<description><![CDATA[<p><strong>GoJS</strong> is a feature-rich JavaScript library for implementing custom interactive diagrams and complex visualizations across modern web browsers and platforms. <strong>GoJS</strong> makes constructing JavaScript diagrams of complex nodes, links, and groups easy with customizable templates and layouts.</p>
<p><strong>GoJS</strong> offers many advanced features for user interactivity such as drag-and-drop, copy-and-paste, in-place text editing, tooltips, context menus, automatic layouts, templates, data binding and models, transactional state and undo management, palettes, overviews, event handlers, commands, and an extensible tool system for custom operations.</p>
<p><strong>GoJS</strong> is pure JavaScript, so users get interactivity without requiring round-trips to servers and without plugins. <strong>GoJS</strong> normally runs completely in the browser, rendering to an HTML5 Canvas element or SVG without any server-side requirements. <strong>GoJS</strong> does not depend on any JavaScript libraries or frameworks, so it should work with any HTML or JavaScript framework or with no framework at all. &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</p>
<p>More at&nbsp;http://gojs.net/latest/index.html</p><p>Address of the bookmark: <a href="http://gojs.net/latest/index.html" rel="nofollow">http://gojs.net/latest/index.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33014/synteny-portal-a-web-based-application-portal-for-synteny-block-analysis</guid>
	<pubDate>Wed, 24 May 2017 10:39:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33014/synteny-portal-a-web-based-application-portal-for-synteny-block-analysis</link>
	<title><![CDATA[Synteny Portal: a web-based application portal for synteny block analysis]]></title>
	<description><![CDATA[<p><span>Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at&nbsp;</span><a href="http://bioinfo.konkuk.ac.kr/synteny_portal" target="pmc_ext">http://bioinfo.konkuk.ac.kr/synteny_portal</a><span>.</span></p>
<p>http://bioinfo.konkuk.ac.kr/synteny_portal/</p><p>Address of the bookmark: <a href="http://bioinfo.konkuk.ac.kr/synteny_portal/" rel="nofollow">http://bioinfo.konkuk.ac.kr/synteny_portal/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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