Thesis has excellent SEO, and with it you can choose the number of sidebars that you want and their position, you can adjust the widths of content and sidebars, and you can change fonts across the webpage… all from dropdown options in the admin area. There are a bunch of other options allowing you to change the nav menu, size of gravatars, comment count, author link, category, date and tag display, and more. If you’re not a coder you can receive assistance with custom CSS and PHP hooks on the forum.

For those reasons and a few others I am now using Thesis. The new full page framework makes it fairly easy to have full-width headers and footers. In this post is a how-to on customising your header.

Full page framework

The first step of making a full-width header and footer is to choose the Full-width framework from the Design Options page.
NB if you have done the coloured background thing with the page framework, selecting full-width will mess it up. You’ll need to rearrange your CSS a bit. The following assumes you haven’t modified much of your design yet.

Prepare header and navigation

The easiest way to swap the positions of the header and navigation is as described in the Thesis documentation, by adding code to custom_functions.php.

remove_action('thesis_hook_before_header', 'thesis_nav_menu');
add_action('thesis_hook_after_header', 'thesis_nav_menu');

Swap header and navigation

Doing that makes the header area structure,

• div#header_area
• div.page
• div#header
• ul#tabs

Which basically means that div#header_area spans the full width of the page and everything else is inside that.

On the Tip’d blog Chris has created new divs, which make it easier to give the header and nav different backgrounds. If you do that with custom_functions.php I don’t think it’s possible to remove the #header_area. However, for this demonstration I’m going to do it anyway and just hide #header_area with CSS.

Place the following at the very bottom of custom_functions.php.

remove_action('thesis_hook_before_header', 'thesis_nav_menu');
remove_action('thesis_hook_header', 'thesis_default_header');

function full_width_header() { ?>
	<div id="nav_area" class="full_width">
		<div class="page">
			<?php thesis_nav_menu(); ?>
		</div>
	</div>
	<div id="title_area" class="full_width">
		<div class="page">
			<div id="header">
				<?php thesis_default_header(); ?>
			</div>
		</div>
	</div>
<?php }
add_action('thesis_hook_before_html', 'full_width_header');

This adds the nav above the title, or you can take the whole nav_area and move it below the title and before <?php }, to have the nav below the header.

Replace header with new title and navigation

Styling the header with CSS

All your CSS should go in custom.css.

Remove unwanted styles

There are a bunch of borders and related styles that we don’t necessarily want in our new header, so I’m going to remove them. I’ve done it in a specific way that should allow you to add some back in if you want to.

.custom #header_area{display:none;}

.custom #nav_area ul {border-bottom:none; border-left:none;}
	.custom #nav_area ul li {border-width:0; margin-bottom:0; padding-bottom:0; background:none;}

.custom #header {border-bottom:none;}

These styles hide the original header (unfortunately the empty div is still in the markup); remove borders, padding and margin from the nav that were mainly related to current page styles; remove the header double border.

Remove unwanted styles

Add some new styles

Now we’re set to add some backgrounds and some more space for the nav, which feels a bit squished up the top, as well as some borders, which just make things feel much more complete. Building on the previous CSS:

.custom #header_area{display:none;}

.custom #nav_area {background:#c3d9d6; padding:0.5em 0; border-bottom:1px solid #ddf;}
	.custom #nav_area ul {border-bottom:none; border-left:none;}
		.custom #nav_area ul li {border-width:0; margin-bottom:0; padding-bottom:0; background:none;}

.custom #title_area {background:#de6a61; padding:1em 0; border-bottom:1px solid #c55;}
	.custom #header {border-bottom:none;}

Background colours and borders

I like to use background images to spruce things up, then hide the title and description. In thesis you can opt not to show them, but I like to leave them in and hide them in case someone loads the page without CSS and because Google bots don’t care about CSS.

.custom #title_area {background:#de6a61; padding:1em 0 0.5em; border-bottom:1px solid #c55;}
	.custom #header {border-bottom:none; height:150px; padding-top:0; padding-bottom:0; background:url(images/header.png) center left no-repeat;}
		.custom #header #logo {display:none;}
		.custom #header #tagline {display:none;}

Title & description hidden, background image added

Coffee cup is from OpenClipart.org.

The other option is to replace the default title and description in custom_functions.php.

<div id="title_area" class="full_width">
	<div class="page">
		<div id="header">
			<p id="logo"><img src="<?php bloginfo('template_directory') ?>/custom/images/header.png" alt="<?php bloginfo('name') ?>" /></p>
		</div>
	</div>
</div>

The process to customise your footer is similar, but even easier since there is only the one footer element, as opposed to both the title and nav bar. I’ll follow up with a post about footers in due course.

Questions?

If you have any questions, ask away! There is a forum thread so other thesis users can discuss it too.

Although my Dad probably feels like my li’l bro is frivolous in his technological purchases, he does take time to research them. He went into the Telstra shop on two different occasions to ask the price of an iPhone outright. He also called Telstra to make sure his GSM SIM card would work in the iPhone 3G until he wanted to upgrade to a NextG SIM.

So, he gathered his money together and went to the Telstra shop, where they fetched an iPhone and faffed around for a while. They told us that it was taking a while because they couldn’t find the form that is required to sell an iPhone outright; apparently Telstra changed the website and the link to the form didn’t work anymore (reassuring for a telecommunications company don’t you think?).

We went to a movie (Burn After Reading, not nearly as funny as the trailer, don’t even bother) and came back about two and a half hours later. They still hadn’t found the form (surely it would only take one phone call and an email?!), so instead we asked for the price to be written down, which we would then take to JB Hifi for a price match. The price was $762.30. Not the $726 that Justin had been told on two separate occasions, which apparently is the staff price.

So, we went to JB Hifi, told the mobile phone girlie the story of Telstra’s incompetence and she happened to be on the phone to a manager who said Justin could have the phone for $726! They didn’t have to wait for a form, or spend time being snarky about Justin’s requests. They were friendly and just did it.

It’s not new news, but further evidence that JB Hifi is cool and Telstra bites.

So far the GSM SIM card isn’t working… not sure whose fault that is yet.

I used TeXShop to edit the .tex files and typeset (render) the document. I also used BibDesk to manage my references (just as easy, if not easier, to use as Endnote). Both of these programs are for Mac OS X; for Windows you might be able to try LaTeX Editor, or TeXnicCenter looks very nice. I’m not sure what you would want to use on Windows for managing references though.

Dave’s thesis in a box

For my thesis I needed something a little more complicated than the standard document template. So I started with Dave’s thesis in a box. It’s basically a collection of files that get compiled together to create your document. It has a separate file for each chapter, which makes writing simpler and reduces the load on your computer (imagine trying to save 70 pages of writing in Word!).

There are other thesis templates floating around if you don’t think this one suits you.

Useful things LaTeX can do

Defining new terms

If you have to type something a lot, you could use TextExpander (which I did for a while), or you could just define some shorthand. Somewhere near the start of your document you put \def\Mf{Methanogenium frigidum} and then whenever you type \Mf in your document, it will output “Methanogenium frigidum” instead.

Math mode & equations

LaTeX has a math mode that you can begin using a dollar sign ($) and also an equation environment using \begin{equation}. It is very useful for typing Greek letters (you need quite a few in biology), writing simple equations, or writing large complex equations. It typesets them very nicely.

Hyphen in math mode

Conveniently, hyphens are automatically changed to minus signs when you’re in math mode. Less convenient when you actually want a hyphen. You can do it with \mbox{-}.

Long tables

You can make a table span multiple pages by using the longtable package and using \begin{longtable} instead of \begin{table}. I used that for my list of abbreviations, which I formatted as a table because I thought it was a bit nicer.

Rotating tables and figures

Apart from placing figures pretty much any way you like, you can use the rotating package to create sideways figures and tables. Very good for wide figures and tables that you don’t want to shrink to unreadable proportions.

Stuff I couldn’t do and had to work around

Table descriptions

It seems like the standard format for tables in biology has the table number and title above the table, whereas figures have the number, title and legend beneath. I wanted to add a small legend/description underneath the table, but there was no standard way to do it. The normal title and legend would be inserted with \caption{Title. Description goes here.}, but if you put another one of those in it creates another table number.

I ended up hacking a solution by adding
\linebreak[4]
\linebreak[4]
{\footnotesize Sequence alignment scores calculated by Clustal 2.0.1.0.}
underneath the tabular environment.

Bottom line

The long and the short of it is that LaTeX is huge in its versatility and well worth learning. However, it does take a bit of learning and I recommend trying it out on smaller projects before venturing into a huge one. However, if you are venturing into a thesis, even if you haven’t tried LaTeX on something smaller it could well be worth learning. It may save you much time in referencing, cross-referencing and document layout. If worst comes to worst you could just copy your text into Word, OpenOffice or Pages and reformat it, which I’m sure you’d be doing several times working in those editors anyway. So give it a go!

If you need to find a specific function for LaTeX I suggest using Google and searching for “latex” plus a description of what you want to do. I usually found the answer quite quickly.

Hope you had a good Halloween, or lack there of (as I did). Just a short note to say w00t! I handed in my thesis yesterday. I am now free to do stuff I enjoy, plus some cooking and cleaning and real life stuff. Sweet.

Also, last month was Breast Cancer Awareness month. This month is Movember for men’s health. Mat Packer has shaved off his enormous beard to grow a moustache and raise some money, and raise some awareness of men’s health issues… that’s right, they’re not as unbreakable as we all like to pretend.

Have a great Movember! Good luck with the election America!

Shot out of the plane window when I flew to San Francisco in February.

Shot out of the plane window when I flew to San Francisco in February.

There is one last photo contest for this month and the word is bra.

Taken at the pink ribbon brunch I went to.

Please take care of yourselves and don’t find yourself having to pad your bra one day!

Shot out of the plane window when I flew to San Francisco in February.

Candid photos are always better!

An update on my previous post Gender Fail. I got another email from Australia Post. It looks like they’ve FiXed the issue!

Who’s baby is that anyway?

I was on Facebook and spied this advert on the side of the page.

Is this what your baby starts to look like when you give them enough free stuff? Is this free stuff some kind of consumer testing?

Just looking at that kid cracks me up!

Four’N Twenty Magic Salad Plate

I was driving home listening to the radio and I heard a rather extended advert, perhaps radio’s answer to the info-mercial. It was for the Four’N Twenty Magic Salad Plate. By the end of the ad I thought that it might have been a joke. Definitely up the alley of some Aussies.

Have a look at their FAQ though: