This weekend, while I was out all day, I found myself wanting to respond to questions on my blog and for one of those I needed to check out the source code of the questioner’s website. The ability to view the source code of a web page is easy from your desktop computer, but it’s not built into mobile safari.

Searching for how to do it brought up a few options:

• A bit of a view source round up at iphoneized
  • which led me to Shaun Inman’s bookmarklet tool — this one is pretty nice because it, is reasonably easy to bookmark without computer intervention, it has line numbers, and works with copy and paste quite well; the only downside, I thought, was that the line numbers get copied when copying multiple lines
• a bookmarklet by Abe Fettig — this one is a bit more laborious to actually get into your iPhone bookmarks and also doesn’t seem to support copy/paste well (I could only get it to copy the whole page, not individual sections)
• I searched the app store for “view source” and tested all the free apps available to look at web page source code

iSource Browser

iSource was the first one I tried. It has some great ideas and features that the other apps don’t: WHOIS, DIG, and HOST lookup, as well as the ability to email debug info. Other nice (but not necessarily unique) things include browser view, open in Safari, and email source code.

My only gripes with this app are that it doesn’t use the iPhone’s browser/URL keyboard with the convenient .com button, and you have to type in http:// to the address bar: it doesn’t auto-fill that part for you when you press the x to remove the previous contents of the address bar. It also doesn’t have state saving or any bookmark feature, so you have to retype the URL every time you enter the app.

HTML Viewer

HTML Viewer is easily my favourite application of the 4 free ones that were available. It uses the iPhone URL keyboard, it has buttons to quickly switch between browser and code view, switch between line wrapped and non-wrapped code, bookmarks, search(!), and email. You can also add a bookmark in Safari to launch your current page in HTML Viewer.

It doesn’t have state saving, so remember to bookmark your current page if you want to switch to another application. The only thing that doesn’t work as well as I’d like is the copy and paste: it seems you’re stuck with copying one word or everything from the top down, because when you try to drag the select end marks (the way you do on the iPhone to change a selection) suddenly the block of code at the top of the page is selected, rather than the bit you were working with.

iHTML

iHTML is very simple, but works really well if you only need the two main features it has: code viewing and emailing the source code. If you turn the app to landscape view you get a split code/browser view (that’s the only browser view the app has). Copy and paste works smoothly in this app and, unlike the others, it remembers the web page it was on last time it was open. It also uses the URL keyboard and automatically fills in http:// for you, so typing in URLs is pretty quick.

Web Source Viewer

Web Source Viewer is the simplest app of the lot. It only uses the landscape orientation, and has no extra features other than viewing and copying the source code of a page. It does use the URL keyboard, but has no quick way to delete the URL from the address bar, it doesn’t auto-fill http:// for you, and it has no state saving.

I wouldn’t really recommend this one as it doesn’t seem to be under current development. The only reason I can see that you would pick this app over any of the others is if landscape view and copy/paste are really important at the time since iSource doesn’t do landscape view, HTML Viewer has a full landscape view, but copying is buggy, and iHTML doesn’t have a full landscape view.

This is a just a quick tip that should make your search for information a lot quicker and easier.

You can use Ctrl+F (or Cmd+F on a Mac) to find any text in a webpage.

Holding down those two keys in a browser (and indeed many applications) will usually bring up some kind of find/search bar or dialogue.

This is especially handy when a Google search has brought you to a page, which you know has the information you want (because Google showed a snippet of it), but it is really long, and you want to quickly locate the relevant section. It’s also great when a tutorial raises a question in your mind: you can quickly search for a few key words to see if anyone had that question in the comments.

The find bar might be a bit different in different browsers, but as far as I know, this shortcut works in all of them.

Firefox find bar is located at the bottom of the window, and has a few more options than other browsers

Chrome find bar is at the top right of the browser, below the tabs.

Safari find bar, like Chrome, is at the top right of the browser, below the tabs, and it has a nice way of highlighting the found words

Apologies to those accustomed to more advanced tips on this site and are slapping their forehead because they’ve known this for years, but it’s become evident to me that a lot of users of this site don’t know about this and it’s just too useful to let them continue in darkness.

No really, I’m asking!

My web host

My first (and current) web host, NearlyFreeSpeech.net, was recommended to me by my husband when I moved from Blogger to WordPress. I didn’t really know anything about servers and hosting at the time, so I trusted my software engineer’s advice implicitly. He didn’t steer me wrong; I’ve found NSF.net to be reliable, affordable and communicable when there are any server problems.

NFS.net is rather different to many other server setups: they run their servers on a custom BSD (UNIX based) operating system and they have a pre-paid account system where they charge for usage (storage, bandwidth, and MySQL processes). This might seem foreign to many of you, and you might balk at the thought of paying for usage when you can pay month for “unlimited” storage and bandwidth, but actually, for small–medium sites NFS.net is incredibly affordable (my first year on there probably only cost about $16, and my second year was about $43). I quite like their simple user interface as well. It is a lot less cluttered and complicated than most cpanels.

NFS.net might not be suitable for everyone though, since sometimes it can be a bit more hands-on. You need to access your files vis FTP or SSH, there’s no built in file editor (there is phpMyAdmin for your databases though). Also, their faster server type uses PHP safe mode, which not all WordPress plugins will play nicely with. PHP safe mode is being deprecated and I have word that NFS.net is working on solutions for fast and secure servers without it, but it did prompt me to look around at other hosts.

What’s important to you?

So, what’s important to you in a web host?

Obviously, when running WordPress, PHP and MySQL are crucial. One of the things that I find valuable is control and access of my files, including SSH access and the ability to change permissions on files. SSH access is also handy as one of the ways to access MySQL apart from phpMyAdmin, using Sequel Pro.

I guess price, security and support and probably all gimmes too, but what else?

What about these words “unlimited”? Are they really unlimited? Are they over-selling? Are they talking themselves up? What if I decide to use my server as a backup for my whole computer, will it still be unlimited?

How do you find web hosting?

Web Hosting Search was recently brought to my attention. Web Hosting Search has quite a lot of resources, reviews and articles to help you find and compare web hosts.

Have you ever wondered what the difference between Windows and Linux hosting is, how that relates to cost and what it means for you as a website manager? Or what the many different types of hosting services are? I was wondering the latter when I came across Chris Pearson’s web host recommendations (and actually, I’m still wondering how it’s possible to have VPS and cloud hosting at the same time…).

One of the best things about Web Hosting Search (I think) are the reviews. You can try to search Google for reviews on web hosts, or ask Twitter, but I’ve found that you get a bunch of one-off reviews and recommendations with no statistical significance at all and you’re no better equipped to make a decision than you were before. Web Hosting Search has quite a balanced range of reviews, and I think the reviews do a good job of identifying particular issues with hosts, which will help you decide if it’s right for you. Issues that come up include not really having “unlimited” bandwidth (may not be a problem for you if your site is small), whether they provide phone support, or efficient ticket support, or the amount of downtime.

When looking at the reviews on Web Hosting Search check out that “Show advanced features” button. It makes it so easy to see an overview of the service offerings!

I’m keen to see more reviews on there! If you have experience with web hosts then submit your reviews and get the word out—good or bad.

So, how do you choose web hosting? What’s important to you and what information do you need to make a decision? Who’s your host, do you like them, and have you left a review of them anywhere?

I bought Scrabble for the iPhone (warning: iTunes link — actually I didn’t get that exact one, I got the one in the Australian iTunes store, which includes English, French, German, Italian and Spanish) on sale last week. I was pretty impressed with the interface, the ease of play and the general enjoyment of the game, until I got to the hard level…

There are three playing levels: easy, normal and hard. Normal is pretty easy to win — easy enough that I win every time — but hard has so far been impossible to win. The computer almost doubles my score every time, and it’s not just because my vocabulary isn’t extensive enough, the bloody thing makes up words!

Check out these screenshots: I checked every one of these highlighted words in the Scrabble Dictionary and also the Oxford Dictionary.

I found the language options in the app and selected English. That part of the interface is pretty poor: there is no indication of which language is already selected, except that the menus are also in that language and since my game menus were in English I thought the computer player would be playing by the rules in English. Perhaps that was too much to assume?

Anyway, since double checking the language I’ve played one game on the hard level. It seemed like there were fewer illegal words, but there were still at least a couple.

It sucks the fun out of a game when you know you can’t win because the other playing is cheating! Also, this game really needs an in-game dictionary and possibly a “challenge” feature, because evidently the computer player can’t be trusted.

Presenting the Thesography plugin for WordPress!

Thesography allows you to display EXIF data for your photos uploaded with WordPress, and also enables the import of latitude and longitude information from your photos to the database when they’re uploaded.

You can display the EXIF information via a shortcode within your post or by a handy function in your theme template files. EXIF can also be displayed automatically in the Thesis theme.

Thesography comes with individual post options as well as options for customising the HTML output of your EXIF data. And, with your feedback and requests there will be more to come!

For more information and to download the plugin, please visit the Thesograpy plugin page.

In December I wrote about adding EXIF fields for geo locations to the image features already in WordPress. The first part of that post involved making changes to the WordPress file controlling image handling. They were simple changes, but annoying to have to change with every WP upgrade.

After several months I have finally figured out — with excellent help from Ben Barden — how to filter the read_metadata function and add EXIF fields to the WordPress database without having to edit core WordPress files.

The following function can be added to the functions.php file of your theme (or custom_functions.php if you use Thesis).

function add_geo_exif($meta,$file,$sourceImageType) {
		$exif = @exif_read_data( $file );
			if (!empty($exif['GPSLatitude']))
				$meta['latitude'] = $exif['GPSLatitude'] ;
			if (!empty($exif['GPSLatitudeRef']))
				$meta['latitude_ref'] = trim( $exif['GPSLatitudeRef'] );
			if (!empty($exif['GPSLongitude']))
				$meta['longitude'] = $exif['GPSLongitude'] ;
			if (!empty($exif['GPSLongitudeRef']))
				$meta['longitude_ref'] = trim( $exif['GPSLongitudeRef'] );

	return $meta;
}
add_filter('wp_read_image_metadata', 'add_geo_exif','',3);

The main features of the filter to note are:

• My function, add_geo_exif has 3 parameters that I don’t define, $meta, $file and $sourceImageType.
  I probably don’t need the last one because I don’t refer to it in the function, but it does no harm to leave it there. The first one is an array in the WordPress function wp_read_image_metadata, which this function adds values to. And $file is the file that is being uploaded by WordPress, defined elsewhere in the WP core files.
• The 3 at the end of add_filter means that this filter allows three parameters to be passed.
  That’s part of what took me so long to get this working, I hadn’t given that argument and the default is 1, so my function wasn’t getting $file.
• The if(!empty lines tell the function to only filter the EXIF data in if it exists in the image, so you shouldn’t get alot of extraneous stuff in the database.

After running this filter you can access the information as outlined in the geo EXIF post, in the section calling metadata from the database.

I don’t know if everyone does this total nerd out when they get an iPod Touch or an iPhone, but I did. I went looking for the best free apps I could get before I paid for any. Here’re my favourites for whoever is looking next.

These are all the apps and bookmarks I have on my phone at the moment. I haven’t used them all yet, but some of them are really cool. The only one I’ve paid for is Fieldrunners, the rest are free.

Yep, I even made a bookmark of my site on the third page there, just to see how the icon works. I’d say it works well.

My favourites are:

1. Sudoku — 10 puzzles for each of the four difficulty levels and the levels are good difficulties, the interface is very nice and it as a very nifty note feature.
2. Fieldrunners — this game is totally addictive and the graphics are way cool.
3. Calendar — okay, so this one comes with the phone, but with Google Sync Beta it is excellent.
4. Files Lite

— more than half the reason I bought a Touch is to read eBooks. Files Lite makes that possible by allowing you to copy lots of document files types onto the iPod and read them, it remembers the page you’re on too!

5. Backgammon — this works really well and is so nicely made, I just wish the computer brain had better tactics; even the hardest level (which was only introduced with the most recent version) is a push over.
6. Facebook — using this app is so much nicer than using the web interface. I use it pretty mch exclusively to check Facebook now.
7. Twitterfon — apparently Tweetie is the best Twitter app for the iPhone, but I’m still on my computer most of the time, so Twitterfon seems like a good free choice.
8. Shop Shop — I used it yesterday for my shopping list and then I looked up the recipe in Safari while cooking. Totally good.
9. WordPress — the WordPress iPhone app works really well and even has some offline writing, if like me you’ve got the iPod, so not always connected.
10. Drinks Free — very cute for a quick cocktail guide.

The rest of the games are pretty great. My least favourites are Action Bowling Free — it’s really just a preview of how well the game works, you need to buy it to get much actionI discovered last night that you can play a whole single player game, so it’s okay — and iHearts, which works, but is not too stimulating.

My winning Fieldrunners strategy

What are your favourite apps?

After almost two years of heavy daily use, my poor little MacBook was getting a bit worn out and doing some crazy things. So about a month ago I reinstalled OS X. I backed up all my files and just wiped the whole computer.

My experience doing that with Windows and Linux computers has always been pleasant. It’s refreshing to start anew. It was not so with my Mac. I think it’s because using my MacBook was normally such a pleasant experience and I’d had things set up the way I liked them for so long that I didn’t even know some things weren’t just there. I couldn’t remember everything I’d installed, such as Gutenprint and Xcode developer tools, so I couldn’t understand what went wrong when certain things didn’t work.

Anyway, all that is a bit of a tangent to what I really wanted to say, which is “Yay, for easy application installing!” or perhaps “Kudos to you intelligent developers!”

These screenshots are all for free software and all you have to do is drag one icon to the other.

Skitch

Inkscape

Darwine

It must be a reasonably simple thing to do since so many applications do it, but occasionally there’s a program that makes a fancy background for their install window and makes it difficult for you to put the program anywhere. If it were just the normal Finder window, at least it would have the shorcuts on the side, but no— it’s fancy, but not fancy enough!

Bibdesk

Not to pick on BibDesk. It’s a top program, just the most recent, nonless-friendly installer I’ve used (why do they assume the hard drive is where you want to put it?).

It was my brother’s birthday today (Happy Birthday Justin!). Naturally, he wanted to buy an iPhone.

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.

LaTeX is a document markup system, which helps you to focus on what you’re writing and reduces some of the hassle of tedious tasks like adding references and numbering sections, figures and tables. It also natively handles footnotes, table of contents, lists of figures, lists of tables, headers, footers, margin notes and probably a hundred other things. It lays documents out intelligently, for readability, and you can apply any number of styles to suit your document, be it book, journal article, letter or thesis.

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.