How to read PDFs, and other docs, offline on an iPhone using Dropbox

Shortened link for this post is http://is.gd/hlKJC

Note - there are other ways to do this, I just happen to have used this one to save files to my iPhone. 


I was inspired to dig out the draft text of this post after reading a Facebook status update from my friend David Bradley aka @sciencebase recommending the service. As far as I'm aware Dropbox works perfectly on an iPad although I don't have one of those so can't confirm.
 
General guide to using Dropbox While I can't pretend to understand the minutiae of cloud computing Dropbox is an example of this sort of thing. With a free account (which gives you 2GB of storage space) you can access your files via the internet from any networked computer. But, and this is important, your files are also stored as a local copy on your own machine - you just need an internet connection to synchronise them with the online version.

On downloading the Dropbox software (I don't think it's very big) it will create for you a Dropbox folder within your own file architecture (you can choose where it goes) and you can start putting files in there. I have Dropbox downloaded onto my home and work computer and the files that I tweak on those computers appear, miraculously ready-tweaked, when I get into work and vice versa. If your internet connection isn't working and you make changes to a file it will remain on the computer on which you edited it, but it will be unsyncrhonised with your other Dropbox.

You can tell the health status of each file and folder as there's a little green tick next to any file / folder which is up to date and syncrhonised, there's a rotating blue icon to indicate one that's being updated and when you open a file to work on it will have a red cross next to it (you need to save and close for it to update). So if you want to try this go to http://www.dropbox.com/ (they have a video there you can watch to tell you more about the service), create an account and sign up.

And now a word from our sponsors :)
Anyone can sign up for free 2GB but if you know someone who already has an account ask them for their 'referrer link' which can net you an extra 250mb - @sciencebase's referrer link is https://www.dropbox.com/referrals/NTgzNTg5MDk (Disclaimer: he isn't actually sponsoring me, I just like that phrase - my referrer link's at the end of the blog I'm just giving him top billing as he inspired me to update my post).

'MakeUseOf' have written a free guide but I confess I've not actually looked at it as I'm very familiar with Dropbox, but here it is http://sciencebase.tradepub.com/free/w_make17/prgm.cgi
Edit: Originally I mistakenly said that David had written this but he let me know that it was another company so have edited the above sentence.

You'll need an email address and a (self-created) password to log in - once you've installed the software you won't need to log in to use your files on your computer(s), only if you want to use the web interface. The web version is good - you can upload and delete files (but to edit them you'd have to download, delete and re-add so better to use your Dropbox folder for that).

A very easy way to sign up, if you don't want to start from scratch, is to ask one of your friends to send you an invite to share a folder with them - this will lead you through the process quite nicely.

Dropbox on the iPhone The iPhone Dropbox app is free from the appstore so all you need to do is download it and log in. Your files will then synchronise and you can read them online. It can open most things - I think it used to struggle with .rtf but that may have been fixed now. Most of mine are .txt, .doc, .ppt and it handles them fine. I can't remember if it cares whether it's .doc or .docx so you might want to double check.

For me, the big bonus is that you can open any file while connected to the internet and favourite it (using the star icon at the bottom of the iPhone screen). This means that if you need to access it in a low signal area you'll be able to. In the settings section (available from the app's start screen) you can set the size of your local storage (mine's 200MB but you can go up to 1GB). If you download the free PlainText app you can sync it (the default is a single PlainText folder but you can tweak it to sync with all your folders) and you can create new .txt documents on your iPhone - ie you can type something on your iPhone and then pick it up at your desk or at home. Nifty.

EDIT: I read a comment on one of Ben Goldacre's (secondary) blog posts which highlighted that this also works for .mp3 files etc. etc. Of course it does, why didn't I think of that??!!

What happens when you exceed your storage space? I once did this - don't forget that if you share Dropbox folders with other people then all of the contents you share adds towards your 2GB limit and it soon adds up. No files were deleted but I couldn't save any edits or add new files until I moved or deleted some older files. My only annoyance with Dropbox is that it didn't tell me there was a problem until I was at 2.5GB and had it mentioned it sooner I'd have pruned some files with less stress. But all was fine, but it's not a bad idea to check periodically what percentage of your allowance you're using.

Be aware though, that if you delete a file on your computer it isn't permanently deleted - this is often a good thing if you delete in error as you can undo this. As far as I can tell, 'deleted' files may actually contribute to your storage space - you can log in to your web account and choose the option to show deleted files, you'll see them in grey. You're then given the option to delete these permanently. Deleting files is a two-step process which, in the long run, I think is no bad thing - but useful to be aware of in case your storage starts to rack up.

I've been using Dropbox since January 2010 and am very pleased with it - I am not affiliated with them or anything dodgy like that :) ...and my referral link is https://www.dropbox.com/referrals/NTQwMDAxMDQ5

testing everystockphoto script

Apart from the fact that this is quite a nice photo I wanted to test this Everystockphoto widget. Seems to work OK.

Downloaded the image directly from their site and it looks like this

Tweeting - dot .@ and at @ messages

Edit 22 October 2011 - I added this info in table form (click to enlarge)

------------------------ Original post ----------------------------

(I wonder how Blogger.com will resolve the URL from this title...! )

Let's pretend I follow @HomerSimpson and @MargeSimpson and so do you.

If Homer sends an '@ message' to Marge such as

HomerSimpson: @MargeSimpson I'm hungry...

then both you and I can read it but other followers of Homer (who don't also follow Marge) won't see it unless they look at his profile page (ie the message will show up on Homer's profile page and is visible to anyone who looks at it, but it won't show up in his followers' twitter feed pages).

If Homer wants to encourage others to provide food he should write (note dot)

HomerSimpson: .@MargeSimpson I'm hungry...

and then ALL of his followers will receive it in their twitter feed.

• A profile page is what anyone will see when they look at someone's profile, eg http://twitter.com/JoBrodie
• Your twitter feed page is what YOU see when YOU log in to Twitter and look at http://twitter.com/

Note the '.' character isn't important it could be any character that 'breaks' the @ symbol being the first character.

(It used to be possible to switch off an option so that you didn't see @ messages between Homer and Marge, then Twitter stopped this - the howls of outrage brought it back, unfortunately as something from which no-one can opt out, as far as I can tell.)

Direct messages
Putting D or d as the first character will send that message only to the recipient (the @ is NOT necessary) but you can only send a D message to someone if THEY are following YOU.

HomerSimpson: d MargeSimpson I'm hungry...

will go from Homer to Marge and no-one else.

How to clean a loo bowl with vinegar or "without chemicals" for the hard of thinking

Shortened URL for this post is http://is.gd/gOFaJ

If you've got a bit of limescale in your loo bowl and you want a slightly sparklier version, try the following.

You will need

• Gloves
• Vinegar (I use distilled malt vinegar (clear in colour) from Sarson's, it's about 59p for 284ml but much cheaper stuff is available in bulk, I just get it from my local corner shop for convenience's sake).
• Loo brush and / or old toothbrush (the plastic bit at the tip with the brush on is quite good for more stubborn limescale)
• Cotton wool in strips, not the little balls but the stuff that is concertina-folded.
• Small yoghourt pot type of vessel to remove water from the bowl (I use an old M&S container which had creme fraiche in it, and a smaller one which used to contain bicarbonate of soda).
• Old sponge (optional, see point 3 below)
• Bicarbonate of soda (optional, see point 6 - use for extra science fun)
• Patience
  

The more limescale you have, the longer you'll need to leave it. For some areas you might need to do this process a couple of times or more.

Method
1. Don your gloves
2. With the larger of the two 'vessels' start bailing out the water in the bowl. You need to get the water below its natural water line (as that's where the limescale will start to build up) and if your limescale is present further down the bowl then you'll need to use a smaller container to get rid of it.
3. If you want to get rid of the maximum amount of water, use an old sponge to soak it up from the bottom.
4. Take strips of cotton wool and soak them in vinegar - I just hold them over the open bottle and upend a few times in different bits so that some vinegar can spread onto the wool pad. They don't have to be absolutely sodden (it'll only trickle out) but enough that it soaks the whole pad. You can split a pad in half to reduce its thickness but they tend to break.
5. Place the vinegar-soaked pads onto the limescaled areas pressing down firmly.
6. If you've removed all the water from the bowl and want to get limescale off its bottom then you can just pour it in neat. At this point I sometimes add bicarbonate of soda because it fizzes. I don't think it really contributes that much, but it makes it feel a bit more sciencey. Don't add too much though or the fizzing might make you worry that your bowl's about to explode ;)
7. You'll end up with a loo bowl that looks a bit like Father Christmas with a wispy white beard all around it. Leave it for as long as possible. Anything less than an hour is probably a bit pointless - a few hours is fine, overnight is better.
8. Remove and discard all the cotton wool.
9. Before flushing use the loo brush and toothbrush to rub off some of the limescale. Some will come off easily, some will need to be chipped with the plastic tip of the toothbrush and some will be very resistant to your efforts and may need a second application.
10. Flush once or twice.
11. Admire your sparklier bowl.

Nobel winner Barry Marshall and the unfriendly bacteria

This lecture took place in September 2010 and is now available online. I started typing up my notes soon after but have only got about half way through. Normally that would mean it would be ages before I finished and posted them as a blog post, but with my new 'let's serialise everything' plan I'm posting unfinished things and coming back to them later. Not sure when I'll finish it though, as I may have carelessly lost the remaining notes pages, oops.

Barry Marshall
'Past lessons and future opportunities for Helicobacter pylori'
UCL Prize Lecture, 20 September 2010

As soon as we started it was clear we were in for good-humoured fun - the audience was in a cheerful mood and I think it's safe to say we were a 'good crowd'. In number too, there was barely a spare seat in the lecture theatre. As I work at UCL I'm automatically on a list to receive information about our events - if they're public then I'll usually share them on my Posterous blog, but there's a listing of public events here. The event took place in one of the lecture theatres in the gorgeous Cruciform building, designed by the same chap (Alfred Waterhouse) who designed the Natural History Museum.

To start we had a brief introduction from someone who ran through Barry's biography, wryly admitting he'd got it from Google and Wikipedia, which got an appreciative chortle. We also saw a list of previous UCL medal winners, including a number I'd heard of.

As the introducer was about to hand over to Barry he tried to set up the presentation for him, struggling gamely with an animation of the 3D structure of the protein urease that was part of the powerpoint, and expressing amused irritation that the software wasn't yielding to his commands. Barry's 'I can do that', from his audience seat, got a welcoming giggle and he took to the stage.

Barry jokingly suggested that if you're going to make a Nobel-worthy discovery do it while you're young as it'll probably be a couple of decades before you'll get the prize. He and the team he was working with published their findings on the link between H. pylori and gastric ulcer in 1984, he won the Lasker Award in 1995 and the Nobel Prize in 2005. He showed us a rather nice cartoon slide of a couple of the bacteria - this was developed with a graphic designer and submitted to a competition at The Scientist (it's a finalist).

Around the time of the discovery there were a number of possible options for 'things that cause gastric ulcers', stress being thought to play a major role. No-one was terribly excited by the prospect of another possible cause, so the discovery seems to have arrived against a backdrop of 'meh'. Barry then put up a quote from Daniel Boorstin who said that 'the obstacle to discovery is the illusion of knowledge' - there was no particular imperative to search for other causes.

The impact on individual and public health has been notable, not to mention on lost productivity. He suggested the scenario of busy stressed executives with an ulcer being ordered by their doctors to retire early and take to a life of beach-ly leisure. More seriously, ulcers had a major cost impact and wrecked lives with several thousand deaths every year in the 1980s.

While there wasn't much impetus to find alternative causes for gastric / peptic ulcers bacteria were already low on the list of possibilities. The medical textbooks of the time held that the stomach, being highly acidic, was sterile and any bacteria introduced would be killed off. One of the reasons for acidity is to extinguish some newly met bacteria to 'sterilise' food and prevent gastroenteritis, but as we all know now the stomach contains many different bacteria which are considered essential for health. Extremophiles have also been discovered which include bacteria that can survive and thrive in conditions previously considered as unable to support life. Most bacteria are killed at pH4 and the stomach's acidity is at pH1.5 so it's not too surprising that bacterial infection wasn't considered as a likely candidate.

Barry showed us a slide of biopsies taken from 100 patients (quipping that they used 100 patients as they didn't have a computer at the time and so it made the maths easier) where 13 out of 13 patients with peptic ulcer had these twirly bacteria in their biopsies. I couldn't help but be reminded just a tiny bit of a certain struck-off someone who looked at the guts of children and drew some wrong conclusions.

He and a colleague tried to get this data into a meeting but were rejected - he showed us the rejection letter, and recommended that people kept theirs to amuse crowds in future. Apparently of 67 abstracts submitted the organisers could accept only 56 ;)

I missed an interesting aside into statistics, so forgive if this is a little bit wrong, but in the list of 100 patients they spotted that almost everyone with 'oesophagus abnormal' which is also known as acid reflux didn't have H pylori - the level of significance suggested thateliminating H pylori might increase the risk of acid reflux (but I might be wrong).

The next article he showed was 'An attempt to fulfil Koch's postulates for Campylobacter pyloridis' from Medical Journal of Australia, 1985. Koch came up with a series of tests, in the 1800s, in order to demonstrate that a condition had a bacterial cause. First catch your bacteria (from someone who has the disease you're studying), culture it, infect someone or something, wait for your disease to appear then collect evidence of bacterial infection.

This was the next step for H. pylori and Barry drank some (it turned out to be two Petri dishes' worth, someone asked at the end!) to show that they could survive and colonise in his stomach. He showed a biopsy photo which clearly illustrated an infection, and some pretty annoyed stomach lining cells. The infection was accompanied by nausea, vomiting and other gastric disturbances - I think he was fairly prompt with a course of antibiotics after though, so probably didn't have a full blown ulcer. He said he was surprised by how ill he felt - many people have asymptomatic H. pylori for (probably many) years before ulceration shows up.

His suggested explanation is that people acquire their infection in childhood, have a few days of being sick but then recover though the bacteria remain, ready to create ulcers at some future date.

It took quite a while for anyone to be particularly impressed by this and I expect that somewhere there's a seller of nonsense alternative therapies who mentions Barry Marshall in the same breath as Galileo as someone who was ultimately proved right.

In 1997 Abbott, who marketed a treatment for H. p took matters into their own hands and commissioned a cartoonist to visit Marshall's lab and create a storyboard. There was a fantastically lurid drawing of Barry holding a beaker of bubbling green liquid about to drink it saying "there's no other way" with a colleague looking on saying "you're crazy" (17m10s). The resulting cartoonified story was sent to a 150,000 doctors and was apparently very successful in convincing them that peptic ulcers should be treated with a course of antibiotics. Obviously I wondered about other uses of cartoons in communicating science, either in medical education or public engagement!

Apparently the bacterial solution was actually brown but the cartoon people had some involvement in "The Incredible Hulk" and went instead with green...



My l'esprit d'escalier question was "Why did people who had to take antibiotics for other things not notice their ulcer getting better?"