A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education Oleksyk, Taras K.; Pombert, Jean-Francois; Siu, Daniel; Mazo-Vargas, Anyimilehidi; Ramos, Brian; Guiblet, Wilfried; Afanador, Yashira; Ruiz-Rodriguez, Christina T.; Nickerson, Michael L.; Logue, David M.; Dean, Michael; Figueroa, Luis; Valentin, Ricardo; Martinez-Cruzado, Juan-Carlos Background: Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings: In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50=6,983 bp, longest=75,003 bp), which was further scaffolded into 148,255 fragments (N50=19,470, longest=206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions: The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts. Sherpa Romeo green journal. Open access article. Creative Commons Attribution 2.0 (CC BY 2.0) applies

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What I meant was scanning the DOM of a page for text equivalents and showing the actual parts of the page, as well as hiding the irrelevant ones. I came up with the technique when I was designing Readerrr’s FAQ page. Take a look at the example:

I have also implemented the solution here on my blog.

How it works

All simple. Let’s take the FAQ page as an example. Here’s a typical markup:

<h1>FAQ</h1>
<div class="faq">
	<input type="search" value="" placeholder="Type some keywords (e.g. giza, babylon, colossus)" />
	<ul>
		<li id="faq-1">
			<h2><a href="#faq-1">Great Pyramid of Giza</a></h2>
			<div>
				<p>The Great Pyramid of Giza <!-- ... --></p>
				<!-- ... -->
			</div>
		</li>
		<li id="faq-2">
			<h2><a href="#faq-2">Hanging Gardens of Babylon</a></h2>
			<div>
				<p>The Hanging Gardens of Babylon <!-- ... --></p>
				<!-- ... -->
			</div>
		</li>
		<!-- ... -->
	</ul>
	<div class="faq__notfound"><p>No matches were found.</p></div>
</div>

I wrote a tiny piece of JavaScript code to handle the interaction and this is how it works:

1. When the page loads, the script indexes the content of all li’s into browser’s memory.
2. When a user types text into the search field, the script searches for equivalents among the indexed data and hides the corresponding li’s where no equivalents were found. If nothing found, a message is shown.
3. The script highlights the text equivalents by replacing phases, for example, babylon becomes <span class="highlight">babylon</span>.

Now, try it yourself:

Demo

Taking it further

Since I chose FAQ page as an example, there are some issues to deal with.

Toggling the answers

It is a good practice to hide the answers by default and show them only when user needs them, that is to say when they press the question:

.faq > ul > li:not( .is-active ) > div
{
	display: none;
}

$( document ).on( 'click', '.faq h2 a', function( e )
{
	e.preventDefault();
	$( this ).parents( 'li' ).toggleClass( 'is-active' );
});

In the CSS part I use child combinator selector > because I don’t want to select and, therefore, to hide the elements of an answer, which may contain lists and div’s.

What if JavaScript is disabled

The user won’t be able to see the answers. Unless you show them by default or develop a JavaScript-less solution. To do this, take a closer look at these fragments of the markup:

• <li id="faq-1">
• <a href="#faq-1">

The usage of fragment identifiers enables us to take the advantage of CSS’s pseudo selector :target:

.faq > ul > li:not( :target ) > div
{
	display: none;
}

Furthermore, the real-time search is not possible as well. But you can either provide a sever-side search possibility or hide the search field and so as not to confuse the user:

<html class="no-js">
	<head>
		<!-- remove this if you use Modernizr -->
		<script>(function(e,t,n){var r=e.querySelectorAll("html")[0];r.className=r.className.replace(/(^|s)no-js(s|$)/,"$1$2")})(document,window,0);</script>
	</head>
</html>

I added a class name no-js to <html> element. The <script> part removes that class name. If JavaScript support is disabled in a browser, the class name won’t be removed; therefore:

.no-js .faq input
{
	display: none;
}

The no-js is a very handy technique, you can use it site-wide.

Improving UX

If there is only one list item that matches user’s query, it is a good practice to automatically show the content of that item, without requiring to press the title. To see what I mean, head over the GIF at the beginning of the post.

Hidden keywords

Here on my blog I have a filterable list of blog post titles only. Each post has some related keywords assigned. So, during the search, how do I make an item discoverable even if the title does not consist of a particular keyword? For example, how can I make the entry “Real-Time Search in JavaScript” visible if a user entered “jquery”? Yes, exactly, that is adding keywords and hiding them with CSS:

<li>
	<h2><a href="/real-time-search-in-javascript">Real-Time Search in JavaScript</a></h2>
	<p class="hidden-keywords" aria-hidden="true">jquery filter input html css</p>
</li>

.hidden-keywords
{
	display: none;
}

A simple trick but not always that obvious.

You will find two versions of the code in the source of the demo: without dependencies and jQuery-dependent. These versions are also divided into three groups of code so you can adapt only what your project needs.

Demo

Hayden Library - TP248.25.N35 M46 2013

Barker Library - T174.7.M63 2011

Hayden Library - T174.7.C459 2011

Barker Library - TP248.25.N35 H93 2012

Hayden Library - T174.7.B88 2012

Online Resource

Hayden Library - T174.7.C456 2013

Hayden Library - T174.7.C46 2013

Barker Library - T174.7.S64 2014

Barker Library - T174.7.I59 2014

Hayden Library - T174.7.C459 2012

Hayden Library - T174.7.M523 2015

Barker Library - TK7874.85

Online Resource

Barker Library - T174.7.A38 2015

Dewey Library - T174.7.L379 2017

Online Resource

A housewife has moved the Madras High Court seeking Rs 1 crore as compensation and a public apology from the Tamil Nadu AIDS Control Society.

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