http://news.bbc.co.uk/1/hi/health/7888042.stm

So at last, characterisation of the necrotic signalling pathway receptor. Now all they have to do is figure out the kinetics and I can get rid of the weighted signal proc eqn and implement something more sensible. So finally the DCs in the DCA might not resemble a NN or Linear classifier! Then maybe I'll even sleep in on a weekend.

Joking aside, its fascinating science and great news for team danger.

I cant say that the last month has been productive. In fact it has been disappointingly slow and its starting to feel like a long time since I did any serious research. As a result of a serious bout of winter flu I've been off my feet quite a bit and its been frustrating as there is so much I would have liked to have gotten done in advance of next semester. No point moping I guess, I had just better get on with it, double speed.

One of the most important skills I learnt as a PhD student was the ability to hit the ground hard and really turn up the burners when work really needs to be done. So as much as it is going to hurt, the next two weeks I am going to really ramp it up and clear the moderate backlog of things which have built up over the last month or so. This starts with the submission of the last ever Danger Project paper. Its strange that this echo of the past has lingered so long - after all its just another journal paper. But I've had a real mental block over this one, partly because I was annoyed at having to work on it in the first place but also that I think may have been clinging on to it with it being the last ever thing to happen in the project. It really is closing the book on the PhD and accepting completely that life really has moved on. I find it equally hard to believe that I was so attached to it, as it is to think of how different life was at the official close of the project nearly two years ago now.

I was an RA, without any money, esteem, students, house, direction and (strangely) cats. Now I have a real job as an academic member of staff I am finding that my perspective on life has completely changed, as have other people's perception of who I am. Does that mean that I am no longer the same person, just because of a change of job? Or is it that I have been given the reassurance by my peers that I am worthy of doing this job and doing it well, I hope , and I owe it to these people to make good on their faith in me to perform? Either way, I am feeling a little out of synch with the world.

Despite the undercurrent of apprehension I am quite looking forward to challenging myself against my most deadly opponent - my own determination. Bring it on.

Our "happenings" at AT this week have finally concluded. It was a great day today, feeling like the finish line is finally in sight. The sun came out, we did the last couple of experiments in the early afternoon, then me and stef primal screamed our hearts out the good old corkscrew. 4 days of data, umpteen research questions, first encounter of the media kind, and a serious amount of surgical tape. The participants were brilliant, our team was amazing and to cap it all off, we looked like frikin ghostbusters with the kit strapped on. Who ya gonna call?


Now if I could only get the bloody AT entrance theme tune out of my head I might finally be able to relax. Thanks stef, thanks a lot mate :P

 Research is officially amazing. Every now and again, something happens with your experiment and bang! you get hit with some unexpected results which just blow your head off. I cant be chewed with going into the details, but lets just say that electromagnets and biometric devices are not necessarily a good combination - yup, we lost the biosensor on Thril day 3, but more importantly we know why and how that can act as a hypothesis for a new stream of research. Today, well the biggest curveball was slinged at us, but we've hit this one right out of the park. I smell a paper coming on........ and no, I'm not a ghostbuster ( u wouldnt believe how many people have asked us that). 

.....now I must catch up on some sleep before I actually collapse. Back to reality with a bump tomorrow. 

Back in the late 1990's newcastle united had a team which they should have beaten but regularly didnt, namely Southampton FC - their bogey team. In a similar manner, over the years I've not had much luck with submissions to the journal associated with ICARIS - my bogey submission. The review paper we were going to submit ended up too rushed and is so far the only rejection we've had. In 2005 I wasnt invited, I dont think there was a special issue from 2006, in 2007 Bob was asked but given that we werent exactly getting along too well at the time I had no involvment in that paper either.

This year I have been asked to extend my icaris paper for the JMMA special issue on AIS. While I think it is really important to have a DCA presence in this journal, actually getting the work done at the speed I need is proving to be very difficult as I transition from RF to lecturer. I'm doing half the job of a post-doc and half the job of a lecturer. Plus, not having my co-author around to help out is proving to be a royal pain in the butt....esp as I'd scheduled this week specifically to get this work done, and it turns out he was only in the office for 2/5 days. It would have been good to know this say maybe 2 weeks ago and I could have re-prioritised things. As I was saying to Feng earlier assumption really is the mother of all f**k ups, and it was an oversight on my part not to get these things clearly scheduled in advance. And this paper is teetering on the balance of either I stress myself out to get it done or I cant make it and end up knackered in any case. Why is it always the case that I feel like I need an extra week for these things even when I try to set an earlier personal deadline?

Gotta get some results sorted else I stand no chance. But life is turning into one mahoosive balancing act atm, lets just hope I dont fall on my face.

Been getting my head around what is going to go on in the field experiment next week. I understand now what this feasibility study is all about and am looking forward to having nearly one week out of the office. Its great how its all coming together. Yet, its going to be an effort to manage my time effectively enough that I can devote some real research time to the existing and pending data and my continuing work with all things DCA. I will do it though, I will.

Been off to do some field work today for the Thrill Laboratory. Despite the rain we managed to get round 7/8 rides and test that the new kit will physically fit on the rides we want to study. The good news is that the biometric data I have is synchronised, which makes my life a lot easier. Also I managed to do a couple of studies on Oblivion, to see what the timings are and what the variability is between subjects. From kick off to the stop its a reliable number of seconds. This also lets me focus in on the potentially most adrenaline inducing stage of the data.

Roll on thrill tuesdays :)

This week I fielded a number of challenging questions about my research, through the interview process for my lecturing position. One of such questions was about the extent to which the modelling of the immune system is taken to. I stated that in contrast to previous approaches, that we had adopted an approach of rigourous modelling. This was mis-interpreted I think to imply 'simulation'. In my head at least there is a difference between being accurate and rigourous with your model, as it gives you the insight as to what is necessary to abstract. This is different to simulation, where you are going out of your way to both qualitatively and quantitatively assess the behaviour of the simulation in comparison with the data generated from the study of the original system.

I would like to stress that rigour is not the same as explicit detailed computational immunology. It simply isnt due to both the objectives and the nature of the models produced. Perhaps I should say something about this in the next pure AIS paper which I write. I have a couple in the pipeline which I want done before the new job kicks in on the 1st November.

Tomorrow I move offices. To my own office, because I'm now a lecturer in Computer Science. I've got a feeling I'm going to need to start blogging again :) I mean it this time.

Its interdisciplinary people not interdisciplinary teams which make multidisciplinary science possible.

http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.0010006

This is for why so many project teams experience difficulties. Its not that any member is incompetent in their own field, frequently quite the contrary. But each specialist speaks their own 'language' of their individual specialism. Assembling such a team would result in a committee analagous to having the united nations without any translators. It simply cannot work. For interdisciplinary research to be successful, translators have to sit right in the middle of the project and help steer it in directions which are beneficial to all.

How abundant such interdisciplinary people are.....I suspect not as many as the number of such collaborations.

Its been a long time since I did any research - we've been milking the danger project cow for a while now. I cant complain, the publications list is looking very healthy, and it must have done my citation index some good. However, there's only so many times you can talk about the same thing without repeating yourself somewhat.

I have a couple of ideas for icaris brewing in the pipeline - I'm going to make another attempt at analysing the algorithm from an OR perspective, using my new found 'power of statistics' and discrete maths skills. Its time again to silence some of the critics.

However, I have a bit of a mountain to climb before I can get to doing any new research. Paper corrections, the final danger project, a fellowship interview and moving house (amongst other things) are currently on the todo list. I've had to schedule myself in order to get any of it done.

Speaking of which, I'd better get back to it else I'll get moaned at.

In Brief:

thesis corrections - slowly slowly, but getting there chapter at a time

invited journal paper - 10 pages of magic, written one shot style; it was a blast :)

Icaris 2007 - what a trip; the conference was controversial and I got all angry at the anti-danger camp. I have results: deal with it. Brazil was amazing tho - esp the coffee!!

Flu - uuurgh, I did have a really nasty flu this week which completely knocked me off my feet

DCA - its a filter, and Bob has been able to show its filter properties in a controlled environment, which will kick some ass when he writes it up.

I'd better get some work done before I get chased down the corridor by Uwe.

Also, RIP our nespresso machine - someone kept leaving it on overnight and the pump is now busted.

Weirdness!! I've been asked to sit as a moderator on a panel of experts at Icaris - sat with Jorge Carneiro, Rob de Boer and Jon Timmis. Thats two professors, an AIS guru and me. It still freaks me out as in my little brain it weren't that long ago that I was an AIS noob and now, I'm on the freeekin panel. It might look a bit odd like, three grown ups and a fraggl :)

The technical discourse is on AIS and Immunology - how can we benefit from doin stuff together. I guess I have plenty to say on the matter, having had a foot in both camps, but its still odd. My PhD work is in Uwe's keynote, the algorithm used in Bob's presentation, and now me on this panel. And here was me thinking I was just going along for the ride.

Anyways, I think I have everything sorted for Brazil - the flights are booked and confirmed (twice now), the hotel is sorted and paid for, and Leandro is kindly sorting me out some transport from the airport. I've been scouting the area on the google maps and it looks so pretty, facing south into the atlantic. Next stop antartica. Its also my first time south of the equator: cant wait to see what the face of the moon looks like too! I might take my cheap set of binoculars to do some stargazing while I'm there. Plus there's always the dilemma of which poi to take.

Maybe I'll buy a new set....or just borrow Markus' atomballs.....

Okay, so the way in which the classification is applied to the output of the DCA so far has been pretty naive and arbitrary. Yousof has pointed out to me that it would be preferable for the problem he is trying to solve if we factor in the total number of antigen presented into the final anomaly calculation. So we came up with the following:

let:
m = mcav
a = num ag presented per process
t = total num ag presented for all processes
A = anomalousness (eek!)


so the anomalous-ness of a process is:

A = m * (a/t)

This seems to give great classn. results for his botnets stuff. I'm tempted to apply this to some of the later port scan expts and see what info that gives us, and when it can be fooled.

Cor, that felt good to do something that isnt making a graph or writing a section of the thesis! Its been a while since I've done any "computer science".

*Phew* Back from Gecco 2007, which was in London. Actually, embarrasingly enough, it was my first 'big' conference which at first was a little intimidating but I quickly got into the swing of things. I saw a couple of interesting talks, but I felt that the AIS content was a bit minimal.

However, it was a good opportunity to talk to people from the wider community about what we've done and what we're doing. I had good feedback after the talk, but alas, no best paper award this time. However, it was cool enough to be nominated - the only AIS paper on the page mind you!

The keynote speech at the natural history museum was great, and Peter B did a great job of pulling it all together. It was just a pity that it was such a long day, as I didnt get that much sleep afterwards. Still, it was good to chat to some old friends (Alex Freitas, Andy Tyrell, Steve Upton et al) and to meet some new people (Larry Bull, Rob Smith et al). I guess thats the best part of these things, being able to talk to people who give a damn about the same things as I do. Not so focused on optimising things, ahhh it was good.

Also got a chance to spend a lot of time with Uncle Steve, and he's developed a really great t-cell based extension to the danger work which hopefully will be of some use to us. All I want to do now is get these thesis corrections over with and get on with some new postdoc delights. I'd also like to make a big effort to be more organised with work because I reckon I can do better research and show these GA people that AIS are here to stay and that DCs kick ass.

Off up to Durham in a couple of hours, so I'd better split. Cant wait to get stuck in to more research tho :) Roll on monday!!

....passed the PhD with minor corrections. So thats Dr. Jools to you :)

Its V-day tomorrow. I'm as ready as I'll ever be. Its been a hard 4 years, but I've come this far. All I have to do is chill for a while, and it'll all be over soon. For the last time, once more unto the breach, dear friends, once more. Hopefully for the last time.

Its been 8 weeks since my last posting - think its the longest I've gone without posting since I started this blog 3 and a half years ago. In the last 2 months, I've completed and handed in the PhD thesis, have had the Information Fusion journal paper accepted, went on holiday to geneva, acquired a macPro at work and have been trying to prepare for my viva, which is in 8 days time.

The thesis isnt perfect: neither am I. There are areas of writing which are not as clear as I'd like it to be, and there are parts which are probably too verbose. However, on the whole, its a good thesis. I particularly like the fact that the conclusions chapter reads well, as I've never before been able to write effective conclusions. This is probably as I've never really felt like I had anything of value to conclude. Its different this time - for once I've understood what it is I've done and why. I hope that comes across.

I have two examiners for my PhD exam, and internal (Graham) and an external (Susan). As I have a journal publication and that Bob (Grahams student) has re-implemented and validated the algorithm, I think Graham will be sold on the idea. Susan however may take more convincing, as she is more experienced in both AIS and computer security. Plus, she's a scientist 'proper' and will be looking for rigour and consistency. Not exactly my strong points.

There are a number of things I can do to ensure that I dont mess this one up.

Practice explaining things clearly and concisely. No one wants to hear half an hour of discussion to get to the answer. I just have to remember to answer the question. If they want more detail, they'll ask for it.

Be well read - including brushing up on key references and the history of the info presented in the lit rev, and in the contents of the thesis and my past publications.

Have the contributions to knowledge bang on and clear in my head.

Be able to justify design choices, by first writing down which choices there are, and where the corresponding evidence in the thesis is.

Try not to be defensive when asked particulary probing questions! I do have a bit of a temper....

To make it crystal clear how methodology fits with Susan's conceptual framework, with reference to what I wrote in the lit review.

Recall of aims, hypotheses, null hypotheses (and where they are in the thesis) and results which directly back up claims.

Be able to calculate t-tests and show why they are applicable.

'Know thy self' - strengths and weaknesses.

Compile a list of practice questions and practice giving the answers again and again.

Be convincing that I am an independent researcher and that this work is mine.

Seems simple huh. Well, we shall see. All I have to do is convince Susan, and then I'll be sorted. Maybe :)

*Gasp*. Its been mental. Since the last time I posted I finished up all the DCA experiments, rennovated my lit review, completed the main implementation, done 8000 words of the last evaluation chapter, and written out the discussion on paper. Apart from the enormity of the task, which sometimes overwhelms me completely, it not been too bad. I know what needs to go where in the thesis, and now it is simply a matter of time before I get it completed. I've not made any headway on the references, and I'm going to try and write them during my CSI time on an evening. No point in doing mere formatting at any other time than when I'm already sleepy.

So the good news then. I compared the DCA to Jamie's TLR algorithm. Ok, so on some of the normal datasets we were false positive-tastic, but *i totally figured out why* which is cool. The normal datasets are tiny in terms of antigen volume, and hence not enough sampling is performed, leading to really bizzare results. Also, the signals Jamie selected work well for his binary signals, but are not so good for my real valued stuff. The most awesome thing about this data is that one of the attack scenarios is an nmap ftp-bounce scan, which the DCA was like "oi oi there's an nmap in this baby, yeah". Its a port scan detector...it just is!

And the even better news, young boB has been working on using the DCA on a pioneer robot. Its doing big gay pink object detection - using signals as the basis of classification. And guess what....it kicks ass, with like *tiny* amounts of false positives. Its great - analysis of the antingen through triangulation of coordinates not only tells you that there is an anomaly, but allows you to specify where the object is. If this data is viewed over time it can be used to track stuff. Its worked way better than I ever expected :) Its just a trivial example, but it shows that the DCA is a lightweight algorithm and can make sense of well noisy data in real time. What a result!

So the bad news, its sunny and I'm inside working on a Saturday afternoon. I cant wait until this thesis is done so I can reclaim saturdays back again! Oh well, the harder I work, the sooner I finish, so I'm going to get back to it. I've said it before and I'll say it again, Dendritic cells kick ass!!!!

On friday, we hosted the final Danger Project meeting. It was a very relaxed meeting, with a lot of smiles and a lot of good feedback for me and my work. Its been three long years since we all sat down together and figured out that DCs are the way forward, and its incredible to look back and see exactly how far we have come. Back in the day, we didnt know what antigen was and were too concerned with what exactly the danger signal are. Now its getting to the interesting stuff. Both myself and Jamie have systems up and running (he passed his viva with minor corrections, so well done there) and the lovely ladies in the lab are performing experiments with real bacteria now.

So while its the end of the project, I dont think its the end of team danger. There are so many things still to do with this algorithm, that I cant do anything but work on it. After all the effort that has gone into its development, I just couldnt run away. The immunologists are doing interesting work which ties in with us, and now I know how to conduct myself in a more competent and confident manner, I'm sure great things still lie ahead.

As with every ending, it marks the beginning of a new era. Keep watching, I assure you the best is yet to come.

P.s. thesis writing is painful, as I think I've broken my little finger...