Things have been going well, as I my previous post says, I’ve gotten a job in Glasgow. I’ve now also moved into my new flat and have, finally*, got an internet connection again. (Photos to follow sometime in the near future)

Everything is going pretty well, the work is interesting and the people I’m working with are a good bunch**. For the first time in a long while I actually have money, the most of which is currently gone, and I’m getting back in touch with all the folks I know in Glasgow.

Anyway this is more of an I’m back post to say: “I’m Back!”.
- Chris

* After some very troubling times with BT Broadband
** One of whom recently had a haircut!

I’m sitting back at home after my first week on the job. I’m enjoying it so far, the work is interesting enough and the people are friendly – plus the promise of money at the end of the month is incentive enough.

I’m currently looking for a flat in Glasgow to stay in, going to look at a few on Dumbarton Road on Monday, hopefully one of those will turn up to be a good un.

Research Journal

On the MSc course at Glasgow we have all been asked to buy a hardback ledger in which we are to keep a diary of what we are doing in our research. That’s fine, but I’m a computing scientist, writing things down goes against the grain – I want a computing related solution to this problem.

After a while contemplating I concluded that alternatives to having a hardback book would be:

1. blogging software (i.e. WordPress)
2. wiki software (i.e. MediaWiki)

Blogs

Blogs lend themselves to chronological recording of data, after-all they are in necessity online diaries. Blogs can be a simple way to record ideas, dates of events and so on.

Wikis

Wikis, although not strictly ordering entries by time and date, allow for very easy addition and formatting of new content. Most wikis will allow you to create categorised or special pages. For example in MediaWiki pages can be prefixed when naming them, this can be used to categorise the pages.

Combinations

Both blogging software and wikis can be used in combination of course, blogs giving the chronological progression between different research papers and wikis showing the resulting thoughts, summaries and so on that you generate.

Why do it?

Keeping a digital version of this information means we don’t have any issue with loosing the research journal or spilling coffee over it (note: don’t spill coffee over your computer either).

Project co-ordinators can see how you are progressing, comment on what they think of your research via comment mechanisms in a blog and talk/discuss pages on a wiki.

Collaborations

Online versions of research journals can help in collaborative projects – the research journal becomes a platform for collective reasoning, interaction, and the sharing of ideas.

If you don’t want to do it electronically

The real lesson to take away from this post is that a research journal is a good thing to have, be it a bound book, wiki, blog or whatever combination.

My Wiki usage

I am currently doing research on my project for the year, which is what sparked this article, SonG. For the project I use a wiki to manage my research, post ideas, and transcribe meeting minutes to mention a few things. I thought it may be useful to share the page title formats I use for doing so.

Meetings:

• Index: Meetings
• Meeting: Meeting:[YYYY][MM][DD]
• YYYY = year, MM = month and DD = day

Papers:

• Index: Papers
• Paper: Paper:[KEY]
• KEY = the bibliography key for the paper

Project specific:

• Title: [Project]:[Title]
• I.e. SonG:Links

I hope this is useful to anyone doing a project involving any type of research, although this type of journal is not restricted to only research based projects.

- Chris

Media

First get a good .PDF or .PS copy of the paper in question. Print the document, I usually go for double sided to save space and 2-up if it’s a particularly long paper.

If the paper has a lot of pictures or diagrams take the time and expense to print it in colour. You’d be amazed at how much more a colourful document will hold your attention over a grayscale one, also detail will not be obscured due to poor colour choice from the author.

Meta

If you’re using any sort of bibliography database, and you really should be – BibTeX is my preference, then you’ll be generating keys for all the documents you enter into it. Write the paper’s key on the top of the paper along with the year it was published.

This saves time if you’re citing the paper later, rather than having to search though the database, usually a flat file, to find the title or author of the paper, you simply have to glance at the first page.

Leave space at the top of the paper for any general comments you have about the paper overall. Don’t write a critical review, just a quick note which you will be able to use to identify the contents of the paper quickly. Another useful thing to add to any paper is a list of keywords. Many conferences and journals add these to papers but your own keywords will have more meaning to you than the general ones produced by the publishers.

Once you have read the paper look through the list of references, highlight any that you think are potentially useful and try and find them, this is possibly the path your research will follow and maybe the next paper you should read. Once you have a copy and thus a key for the paper, due to your corresponding bibliography entry, note the key next to the reference. This allows you to quickly find out if you have the paper at a later date for example when rereading the paper for other research and allows you to quickly assess which paper it is.

Reading the paper

Something we’ve had knocked into us on the MSc course at Glasgow is how to read a research paper. The general consensus is a 5 stage process:

1. Read the abstract – this should roughly tell you what the paper is about, what the problem addressed is, what the authors did and what they found.
2. Read the introduction and conclusion – skipping to the end of a book usually gives away the plot, skipping to the end of a research paper will help you understand the ideas in the paper as it will contain a concise version of everything the author has said. You should have a fair idea of what’s coming from reading the abstract anyway. Reading the start and end of the paper will give a better insight into what the paper is about and help you decide if it applies to your area of research or not.
3. Read the whole paper – jumping past anything which you get stuck on. Read all the details quickly, glance at figures, tables and equations but don’t over invest time in trying to understand them. Reading the whole paper quickly will give you an overall feel for the argument put forward in the paper.
4. Re-read the paper – this time going into the fine details and trying to understand the parts of the paper which eluded you the first time round. If necessary look at some of the supporting material, consult books, websites, peers, colleagues and so forth.

   Make notes in the margins of the paper, most papers are typeset in either one or two columns, this gives space on either side of the text to annotate it – make
   notes, reference other works, point out problems e.t.c.. This is where it is useful to have a physical copy of the paper. Highlight key areas of the paper using whatever means you wish, I will go on to talk about this in the next section.

5. Summarise – write your blurb on the front page of the paper and then try and write a page summary of the whole paper. Aim to include the main points of the paper, the arguments, methodologies uses, results and conclusions which you feel relate to your research or may do in the future.

   This is useful if you need to grasp the idea of the paper quickly at a later date, don’t rely on remembering about the paper – you will forget the details.

Highlighting content

Everyone has a different method for marking parts of the paper they are reading. I prefer to use highlighter pens as they do not obscure the detail or text in the document unlike circling or underlining.

Most papers, I find, tend to break down into four main sections:

1. Introduction and related work
2. Problem definition and intended methodology
3. Experiment details and results
4. Discussion and conclusions

Each of these sections I match to a different coloured highlighter pen, the same for every paper to make it easier to find sections of the document. I use:

Yellow

Introduction

Orange

Problem definition

Green

Experiment details

Red

Conclusion

Obviously some papers don’t follow this general pattern, such as survey papers, in this case I use the yellow and red pens as before, for the introduction and conclusion. I then alternate between the orange and green highlighters for different sections or ideas within the paper body.

Storage

I urge you to keep all research papers after you’ve read them. Keep a digital copy, but also keep the printed copy which contains your annotations. It is also useful to keep a printed copy of your page summaries with the corresponding papers for a quick reference to the paper.

As the physical copy of the paper is likely to be the only annotated version of the paper you have make sure you don’t loose it. As I’ve mentioned you will forget the details and annotations can be a low cost solution to jogging the memory.

Get a box file, put the papers and summaries into it, organise them in any manner you wish but just keep them.

Re-visiting

All this seems a lot of work just for reading one research paper, but the this time is an investment which will be paid back in droves later.

Whenever you are required to cite papers or give related/supporting work sections in reports or your own papers the page summaries will provide you with the textual descriptions of the content that you will likely use. Re-writing a section on a particular paper five times, and consequently re-reading the paper five times, will take up more time than annotating and summarising the paper originally.

Enjoy!

I enjoy reading research papers, as long as they’re not too technically heavy, but reading research papers can take a long time. I’ve found that using a formulated and structured approach to reading, annotating and summarising the papers make the process easier and quicker, this is why I’m sharing my guide with you.

That’s all I have to say, if anyone has anything to add, or their own unique style for reading papers, feel free to add a comment detailing it.
- Chris

I used to do all my LaTeX writing under Windows XP, using a program called WinEdt with the MiKTeX version of LaTeX.

Since changing to Mac OS for writing LaTeX I’ve been looking around for some good tools for managing and writing anything I have to and here’s what I’ve found:

TeXShop

Good, free tool for editing and typesetting LaTeX documents. Comes complete with BibTeX integration as well as a lot of useful templates and shortcuts (a very nice feature is an automatically updating .pdf viewer), the inclusion of syntax highlighting and auto completion is very useful. I’ve been using this for the past few months and have found no flaws in it.

Here’s some speel of the site:

TeXShop is a TeX previewer for Mac OS X, written in Cocoa. Since pdf is a native file format on OS X, TeXShop uses “pdftex” and “pdflatex” rather than “tex” and “latex” to typeset; these programs in the standard teTeX distribution of TeX produce pdf output instead of dvi output.

TeXShop uses TeXLive and teTeX, standard distributions of Tex programs for Unix machines. The distributions include tex, latex, dvips, tex fonts, cyrillic fonts, and virtually all other programs and supporting files commonly used in the TeX world. These distributions are maintained for the Mac by Gerben Wierda, and available below.

The latest TeXShop release requires System 10.4 (Tiger). Users with systems 10.2 or 10.3 should use TeXShop 1.40, also available on this site. Users with systems 10.0 and 10.1 should use TeXShop 1.19, available here.

TeXShop is distributed under the GPL public license, and thus free.

Here’s the links to:

• the developer site, and
• download page

I’d recommend trying it out if you’re likely to be writing any serious documentation.

BibDesk

Another really useful tool which I’ve found for academic use. It’s basically a BibTeX organiser with a lot of addons.

As well as allowing you to add, edit and organise BibTeX entries it allows you to:

• locally link papers or articles,
• self-organises these linked articles if you wish (much like the iTunes music folder will if you ask it to),
• URL linking of articles,
• drag and drop LaTeX citation code for entry into .tex documents (in a variety of formats, i.e. \cite{Miller:2005}, \citet{Miller:2005}, …),
• auto cite key generation from BibTeX entry (based upon a user specified pattern},
• searching of BibTeX entries,
• import and export of the BibTeX file in a variety of formats (XML, RSS and Atom included among others), and
• previewing specific or ranges of entries as they would appear in a LaTeX document.

This is the kind of tool I’ve been looking for ages for, not only does it hold the details of the articles for referencing in reviews/papers, it holds and organises the articles themselves. This tool has made using BibTeX with LaTeX a hell of a lot easier for me, I’d highly recommend this to anyone who is ever going to keep a record of the papers that he/she has read.

The definition of BibDesk on this site is given as:

BibDesk is a graphical BibTeX-bibliography manager for Mac OS X. BibDesk is designed to help organize and use bibliographic databases in BibTeX .bib format. In addition to manual typing, BibDesk lets you drag & drop or cut & paste .bib files into the bibliographic database and automatically opens files downloaded from PubMed. BibDesk also keeps track of electronic copies of literature on your computer and allows for searching your database through several keys.

BibDesk integrates well with TeX for creating citations and bibliographies. This integration includes a Citation search completion service, and drag & drop (cut & paste) support for adding citations to TeX files.

Here’s the links to:

• the developer site, and
• download page

So not only can you generate nice looking, transferrable documents; but you can do so on a good OS with some great tools, making the LaTeX experience (not the rubbery kind!) much more stress free and enjoyable for all!
- Chris

I finished my job at the University over two weeks ago now, spent a week looking after the pub at home for my folks when they were on holiday and am now back at University and into my second week.

The Job

Went well, everything was finished, more or less, and all wrapped up. Steve Brewster and David McGookin colaborated and wrote a paper based upon what I did over the Summer. They’ve submitted it to CHI 2006, whether it gets accepted or not, we’ll have to see.

The Pub

An eventful week was had by all, consisting of things blowing up, throwing people out of the bar and kicking in doors. I’ll say no more.

The University

Uni is going fine, although the research readings course is a bit hefty. I’ve decided to do Information Retrieval (M), Types and Programming Languages (M) and Network Communications Technology 4.

The courses seem interesting enough, with TPL and IR both grabbing the attention quickly (Simon actually seems pleased about the class size dwindling each session. As I’ve said the Research Readings is taking up a lot of time: reading 4 papers a week and summarising 2 of them (all four for the first few weeks). Then there’s two in-depth reviews to be done throughout this term!

There’s another few courses which I am privy to, Research Methods and Techniques (M) is one which starts this Thursday and Professional Skills (M) (a sort of masters level Professional Issues) is due to start in another 3 weeks. Anyway, everything’s going well and all this reading and discussion of papers can be exciting at times. Most of the time it’s pretty boring though.

That’s the lot folks, hope everyone is having as good a time as me at their respective jobs or courses (or mid-morning TV watchings),
- Chris

P.S. I’ve now also managed to break the 3 st barrier on my diet, now having lost 3 st 2 lb (or 0.019958064 metric tonnes).

Actually it was just a drill, the deafening alarm went off, ringing in my ears. Stumbling, from the pain of the alarm, I managed to lock the PowerBook (I considered taking it with me!) and the PC (which I was definately leaving), and made my way to the nearest fire escape.

Then I went outside for a chat with David McGookin and Stephen Brewster, all very civalised. Then I came back inside. Disaster everted.

Derek had a far more interesting time of it all, he got to bread the dome of escapage:

Life in lilybank is never dull!
- Chris

I thought all the smells would be light, subtle smells that hinted towards grass, flowers, chocolate and so on. They are, in fact, the strongest artificial smells I’ve ever had the displeasure of smelling.

And that’s just to start, I’ll be working with these smells for the next month. Oh the joy,
- Chris

We’ve just this minute got a delivery of the Vortex (smell) cubes that we ordered at the start of the week, from daleair.com. This means that we are more or less set up to start people on their olfactory adventures! If anyone will be around in Glasgow next week and in around 3-4 weeks time, drop me an e-mail and I’ll get you to do the experiment (you need digital photos ~500ish).

Everything else is going fine, I’m heading off to Edinburgh for the Fringe tomorrow with Gary and Derek, it should be reminiscent of last years trip, but this time with hopefully more busses!

got my PowerBook upgraded yesterday, a gigabyte of RAM added, bringing it up to 1,536 Mb of RAM altogether. It fucking flies now!

So I’ll probably have some more photos to post soon enough and probably a few stupid stories to go with them. Until then,
- Chris

The project is as mentioned before about tagging photos with smells, something that has had little practical research done on it. The main idea is to use RFID tagged smell cubes to allow users to flag photos as being connected with any one or more smells. The tag (and smell cube) is waved across the RFID reader and this is used to tag the photos. The reverse is done to search through photos with the smell cube being used to identify the smells to isolate and the reader picking up the ID of the smells.

The first day went really well (apart from the extreeme tierdness from being up at 5:45 AM for my commute – something I will get used to I hope), with me looking into various photo browsing software and trying to isolate the appeal and faults of each for a task such as this and playing around with the Phidgets which I will be using for the RFID tags. The first four applications to come to mind (the first through Steve Brewster) are:

• Adobe Elements
• iPhoto
• Flickr
• Picassa

Both Elements and Flickr seem to be the lead runners as the other two don’t seem to have any publicly available APIs (at least none that I can find). This could lead to either an Adobe Elements plugin or an application which uses Flickr as a back end to store and organise the photos. Time will tell which will prevail.
- Chris

Nothing much has been happening at all, I’ve been sleeping a lot, playing darts and dominos, learning to play a card came called crib, drinking and the odd once and a while, playing World of Warcraft.

Uni’s finished and the graduation ball was excellent, my photos of the event are available as are a copy of Lynsey’s photos. Thanks to all the people who organised the night and all those who were there and made it an enjoyable evening, the most notable memory possibly being Rory climbing over the Sherbrooke castle roof!

So the summer is starting to plod along, I have moved back to the pub in Dumfries and have just gotten everything into my new bedroom. I’m getting settled back in and have started living healthier (after my junk food filled revision), having joined the local gym and gone on a diet (one week down and 7lbs lost, but a fair few still to go!).

Other than this I am just waiting out the remaining 8 days until I start my summer scholarship on the 1st of July, looking forward to getting back into a routine but also dreading the 4-5 hour roundtrip commute I will have to make every day. I’ve been thinking about the scholarship and trying to gather my thoughts on how to approach the problem, but there is nothing substantial as of yet to mention, I will post more when I have started the job.

Anyway, life is going fine and I’m looking forward to seeing anyone who will be around in Glasgow when I’m finally back up regularly.
- Chris

I have been hoping to work in the department after doing so last year, and heard of a scholarship that was up for grabs to do with olfactory tagging of photos.

Anyway, I applied a while ago and managed to get an interview yesterday (after my last exam and before the pubbage). I heard back earlier today and I have been offered the job, it’s a ten week scholarship in the department which pays £240 a week. The main idea is to tag photos with smells, much in the same way that flickr.com uses words to tag photos. I’m not set to start until the 1st of July but thought I would post some early details I have on the project.

Below is an extract from the outline of the project, defining exactly what it is about:

In order to investigate the use of olfaction as part of HCI, the work undertaken during the studentship will centre on the construction of an application which will be intended to both exploit the advantages of olfaction (memory and learning), and apply these advantages to a current problem in human computer interaction – the browsing of large non-textual media collections such as digital photographs. The design and construction of this application will contribute to the general aims of the studentship to improve our understanding of olfaction in HCI and the expected outcomes which are described in detail in the following sections.

The problems of browsing large collections of non-textual digital media are well known, with ineffective tools currently available for browsing and searching such collections. Most of the proposed methods to overcome the problems of browsing and searching involve the tagging of individual, or groups of photographs, with keywords which can be later used for retrieval. However, other research has found that many people find such tagging of photographs inconvenient and many do not store digital photographs in any systematic way. In any event, such a system may still break down if inconsistent labels are given to different photographs.

The application to be constructed as part of this studentship will build on existing research with Tangible User Interfaces (TUIs), to allow users to build search queries over digital photograph collections via RFID (Radio Frequency Identification) tags attached to “smell cubes” (small plastic cubes containing a fragrance impregnated in a cotton wool pad – www.daleair.com). This would allow users to associate smells easily and quickly with collections of photographs by moving the appropriate cube close to the RFID tag reader, and would help to make the process of recall easier by using the powerful memory effects of smell to remind users of the environment in which they took the photographs and thus aid their recall. For example, photographs of a holiday in India may be quickly associated with the smell of spices. In years to come the user may be looking for a particular photograph of a friend. The user can remember the friend was standing outside a building but cannot quite remember where or when the photograph was taken (such attributes being the current way in which images are tagged). To find the photograph the user would waft each smell cube under their nose. On using the spice smell cube, the user is transported back to their holiday in India and can remember where the photograph was taken. On passing the smell cube (with attached RFID tag) over the RFID sensor, the system filters the photographs on screen to show only a small subset, one of which is the photograph desired by the user – the user’s friend standing outside the building.

The work will be broken down in the 10 weeks as follows:

• Weeks 1 – 3
  The student will carry out a literature review into olfaction. Additionally the student will begin to elicit requirements for the photo browsing application. Participants will be recruited and categorisation of photographs will be undertaken.
• Weeks 4 – 7
  The student will construct the photo browsing application based on the literature review and derived requirements.
• Weeks 8 – 10
  The student will carry out an evaluation of the photo browsing application to determine the usefulness of the incorporation of olfaction. The student will produce a report on the design and evaluation of the photo browsing application that will form the basis of a paper submission to the ACM SIG CHI conference.

Anyway, I’m quite pleased with getting the scholarship and look forward to an interesting summer working on it. Sorry to the other guys who were in for it (Dave et al), I’m sure you’ll all find something soon enough.
- Chris

Matt suggested to me yesterday that we each blog at least once a day, I feel dubious about doing this as if I have nothing useful to blog I will end up writing a post about what I had for dinner or what other people had for dinner.

So everything is coming together at once, I have my newly updated site up and running now, with just a few minor changes to make before I can start properly populating it. I have, as I mentioned earlier just finished my job, after a long grueling 11 weeks (1 week more than originally intended) I have finished working on the DECS project. It feels good to be free, I can stay up as late as I want, stay in bed all day without feeling guilty, not have to clutter my computer with that hideous, hideous code anymore. Altogether it has been good working on this project, especially getting the opportunity to see what working on such a large scale legacy system (or at least the beginnings of one) is like, by the way I don’t recommend it to anyone, at least not to anyone who doesn’t like reading lots of source code.

So now I have some extra time on my hands, in fact a hell of a lot of time. I recon that it’s time to get myself a new hobby (rather than sleeping, eating and drinking as it has currently been). I intend to learn to play the guitar (properly). I have owned a guitar for years and have never been so inclined to learn to play it to any great extent. With all this free time on my hands I can hopefully aquire some sort of musical skill, if not I can probably get some cool pictures of me holding it… more likely I’ll get a whole album of pictures then get bored again. So for now it’s off to dust off the axe and try to remember the pitiful number of chords which I once knew.

Are you ready to rock?
- Chris