So Vietnam blocks Facebook. Fortunately I was able to find a way around that in about 2mins. It's not perfect and lacks some functionality so photos will have to wait til I return to the worLd of laptops and fully workin Internet, but it's all good. Also this next week will be mostly holiday blogging.
So yes, this week is a holiday for us so the only work I intend to do is a little reading. But really that should be interesting in itself. Usually reading of journals etc for me is a completely interrupted pasttime. It always gets shunted to the bottom of the importance pile - so holidays are a great opportunity to make up for that.
First stop will be the theoretical biology journals, then I'm going to hit the infectious diseases journals. Should be good.
Oh what have we done so far here in Saigon? Well we've been here about 24 hours now and mostly we've eaten and drunk! First stop, naturally, was pho. I had beef, Chaz had chicken and the boy had spaghetti bolognese (which oddly was very Italian tasting!). We also had some fresh pork rolls and I had some BGI beer which I didn't realize was mid strength - but it was fine. Cool and fresh as they say at cafe pp in Margaret St :P Dinner we had something different - Chaz had some noodles with beef (not sure of the name) and I had vermicelli with a beef soup which was unreal. It was both slices of beef and meatballs and the meatballs were like some magical cheetoh of cow. The soup, although simple, was probably the most amazing non hop based liquid that I've eve tasted. The people at lunch were so nice too - they gave little Dan a banana when we left and even let me take him out to the kitchen to wash his face and hands (he was very messy). Dinner was in a less touristy part of the area and nobody spoke English so the drinks we ended up with were not exactly what we wanted and it took quite a while to get some bottled water for D but we got there.
Breakfast was at the hotel which means it was pretty western. Even the fried rice reminded me a little of Ipswich ;-) but they did have some nice almond croissants. After that we went over to Cong Vien 23 Thang 9 which I think means park 23/9 which I guess refers to the district we are in. Lots of people ove there playing badminton and doing aerobics and tai chi and so forth. Very cool. I guess probably something left over from the stricter communist days. We walked up the length of the park eventually arriving at Ben Thanh market where we wandered a little showing little Dan all the fish and seafood being sold - really great. He loves this and always wants to see more "shish". I don't think he realizes what the women are doing to the frogs and eels and fish that are being gutted, but it's ok - that's how life is and I don't think he should be afraid to see that even if it isn't so normal where we live.
I just wish we had somewhere to cook because I'd love to buy some of the food and cook a heap of things. Maybe they should do that - hire out cooking stalls to whiteys looking to get their cook on! :P
On the way back we stopped at a stall on the street to get a drink. A bit pricey really at this particular place - 50000 dong only got us three drinks ($2.30) but they made up for it by moving a massive heavy umbrella to shield us from the sun. Very nice again. It was only then that I realized I was hitting the beer at 9am. Nice - gotta love holidays. We went back through the park again and I tired the little guy out by racing him up the path for about a kilometer. He's asleep now and his mum has gone for a massage. I think this will be a great week. Sorry for the lack of photos, but I haven't figured how to post from my phone - as soon as I do, they'll be here. No Facebook. :-(
Sunday, April 24, 2011
Wednesday, April 20, 2011
The gold
Ok, so as I mentioned earlier, I've struck something I think is cool. I mentioned a day or so ago that I have been doing some "modelling by sledgehammer" - ie setting up matlab to run a mountain of simulations to numerically explore the parameter space of a Chlamydia model I'm working on (with Masoum, my PhD student, Dan Simpson and also previously with Kel Heymer).
So I ran a heap of random bits and pieces and checked them out - looked good. I categorised them according to various behaviours such as cleared infection, persistent infection, oscillating infection etc. Then I realised that I had forgotten to run baselines parameters while investigating variation to a single parameter over a few orders of magnitude. So I quickly added that into the set of parameters - varying a diffusion coefficient, varying two immune response parameters and varying the rate of cell replenishment following death. These are the most speculative of the parameters in the model, so it makes sense to be looking at how changes to them alter the model behaviour.
Nothing much of interest came from the immune parameters or the cell replenishment parameter, and at first I thought the same of the diffusion parameter. Increasing the diffusion coefficient increased the speed at which a certain variable reached further along in space....duh! Then I realised that it actually had the opposite impact on the Chlamydia infection to what I expected - the upshot of all this is (after a few more "no that makes perfect sense...oh wait! no it doesn't!" moments) I have what at least on first glance and to the naive mathematical modeller, looks like a cool result from my simplish model that may have a biologically relevant, counterintuitive statement to make. That is, the results of my model seem to suggest doing something to chlamydial particles or changing them in a particular way, quite the opposite of what you'd expect, that may lead to a reduction in the length of an infection!
Awesome moment - never happened to me before. Even if it turns out to be infeasible in reality and silly, at least I had my one "Homer Simpson, whoop-whoop, spinning around on the floor in my office" moment.
So I ran a heap of random bits and pieces and checked them out - looked good. I categorised them according to various behaviours such as cleared infection, persistent infection, oscillating infection etc. Then I realised that I had forgotten to run baselines parameters while investigating variation to a single parameter over a few orders of magnitude. So I quickly added that into the set of parameters - varying a diffusion coefficient, varying two immune response parameters and varying the rate of cell replenishment following death. These are the most speculative of the parameters in the model, so it makes sense to be looking at how changes to them alter the model behaviour.
Nothing much of interest came from the immune parameters or the cell replenishment parameter, and at first I thought the same of the diffusion parameter. Increasing the diffusion coefficient increased the speed at which a certain variable reached further along in space....duh! Then I realised that it actually had the opposite impact on the Chlamydia infection to what I expected - the upshot of all this is (after a few more "no that makes perfect sense...oh wait! no it doesn't!" moments) I have what at least on first glance and to the naive mathematical modeller, looks like a cool result from my simplish model that may have a biologically relevant, counterintuitive statement to make. That is, the results of my model seem to suggest doing something to chlamydial particles or changing them in a particular way, quite the opposite of what you'd expect, that may lead to a reduction in the length of an infection!
Awesome moment - never happened to me before. Even if it turns out to be infeasible in reality and silly, at least I had my one "Homer Simpson, whoop-whoop, spinning around on the floor in my office" moment.
AHHHH!!!
Sledgehammer method pays dividends...I think I've stumbled onto a cool result that may even have some sort of biological relevance! Awesome...more on this later today.
Tuesday, April 19, 2011
Sledgehammer
This is what you call modelling by sledge hammer. We set up a model and rather than investigate the parameter space via mathematical analysis, we set up some matlab code to run the code thousands of times over with slightly varied parameters, set up a LaTeX file with a forloop and print out the results. "Analysis" involves picking the best looking pictures.
[Download] approx 2mb
Codey-code: (beware of lame coding and possible redundant packages etc)
\usepackage{calc}
\usepackage{forloop}
\usepackage{tikz,pgf,pgfplots}
\usepackage{subfigure}
\usepackage[landscape,scale=0.8]{geometry}
\setlength{\parindent}{0pt}
%Used in forloop
\newcounter{xcount}
\begin{document}
\section{Simulations of Mallet PDE model}
\forloop[1]{xcount}{1}{\value{xcount}<104}{
\subsection{Simulation \arabic{xcount}}
Parameters for this simulation are: $\input{"simulations/params\arabic{xcount}.txt"}$
\begin{figure}[htbp]
\begin{tikzpicture}
\begin{axis}
\addplot file {"simulations/data_Iprop\arabic{xcount}.txt"};
\end{axis}
\end{tikzpicture}
\caption{Caption here with call to file if you want: $\protect\input{simulations/params\arabic{xcount}.txt}$}
\end{figure}
\clearpage
}
\end{document}
[Download] approx 2mb
Codey-code: (beware of lame coding and possible redundant packages etc)
\usepackage{calc}
\usepackage{forloop}
\usepackage{tikz,pgf,pgfplots}
\usepackage{subfigure}
\usepackage[landscape,scale=0.8]{geometry}
\setlength{\parindent}{0pt}
%Used in forloop
\newcounter{xcount}
\begin{document}
\section{Simulations of Mallet PDE model}
\forloop[1]{xcount}{1}{\value{xcount}<104}{
\subsection{Simulation \arabic{xcount}}
Parameters for this simulation are: $\input{"simulations/params\arabic{xcount}.txt"}$
\begin{figure}[htbp]
\begin{tikzpicture}
\begin{axis}
\addplot file {"simulations/data_Iprop\arabic{xcount}.txt"};
\end{axis}
\end{tikzpicture}
\caption{Caption here with call to file if you want: $\protect\input{simulations/params\arabic{xcount}.txt}$}
\end{figure}
\clearpage
}
\end{document}
Wednesday, April 6, 2011
Snoop Dogg
I've like been a preacher/believer of the concept that academia is like a pyramid scheme. Kind of like selling tupperware if you will. It works like this: I start selling my tupperware (research). I take it to parties (conferences) where lots of disinterested house wives and husbands listen to me pedal my wares, then at the end a few bite and buy some (read my paper). This has a) minor benefit through the money made through purchases (citations of your paper) and b) more major benefits if the person themselves start to sell tupperware (catch on with your research and start working with you to produce more papers).
Now I'm on to a new metaphor for the research world: Rap music. You see, being a researcher is a lot like being a rapper. When you are a bottom feeding rapper (PhD student/early career researcher) you take any scrap of work that comes your way, rapping night and day (writing as many papers as you can), always on the look out for big time rappers to "feature" you on their new single (established researchers with money and a program, getting you to do all the work on a paper that they vaguely have some idea about the contents of). Then when people out there start to see "Snoop Dogg featuring Wiz Khalifa - This weed is mine" (Terence Tao and Dann Mallet, On the rap/math-research metaphor conjecture), the bottom feeder starts to grow in popularity and moves their way up the rap ladder (starts to get research grants and pick up bottom feeders of their own).
It's a twisted game... but one day I too will be singing "this weed is mine" or something like that.
Now I'm on to a new metaphor for the research world: Rap music. You see, being a researcher is a lot like being a rapper. When you are a bottom feeding rapper (PhD student/early career researcher) you take any scrap of work that comes your way, rapping night and day (writing as many papers as you can), always on the look out for big time rappers to "feature" you on their new single (established researchers with money and a program, getting you to do all the work on a paper that they vaguely have some idea about the contents of). Then when people out there start to see "Snoop Dogg featuring Wiz Khalifa - This weed is mine" (Terence Tao and Dann Mallet, On the rap/math-research metaphor conjecture), the bottom feeder starts to grow in popularity and moves their way up the rap ladder (starts to get research grants and pick up bottom feeders of their own).
It's a twisted game... but one day I too will be singing "this weed is mine" or something like that.
Sunday, April 3, 2011
PPR
PPR = Performance Planning and Review... at least it did the last time I bothered to look at what it stands for. It may have changed now. As Scott McCue says, QUT is an acronymathon.
This is a meeting all staff members have, individually, with their supervisor to discuss their performance over the last year and to plan for their work over the coming year. Traditionally I've not really worried too much about these meetings and this year was not much different. I've now had PPRs with three different bosses: Tony Pettitt, Sean McElwain and Ian Turner.
Tony was bizarre. I'm pretty sure we didn't actually follow the rules for about 3 years, but it didn't seem to matter. Sometimes you'd be in his office for the meeting and nothing would be said for about 5 minutes and then he'd walk off to a smaller side office he had back in our previous building. Not knowing what the hell was going on, I'd gradually make my way to the door presuming the meeting was over only for him to reappear asking where you are going. Odd.
Sean was much more normal and very much about the matter at hand. He was quite good actually, really hammering down on what you needed to do to make sure you did your job well and eventually got promoted.
Ian in my opinion has changed over his three years - becoming more of a "coach" in the Kaplanian sense. He tries to get you to do the talking, get you to come around to a plan that both he and you can agree on (in other words, that you are happy to do the work that needs to be done...this is "coaching"). On Friday, this didn't happen - I'm not sure what it was, perhaps he was tired, perhaps I was sharp, maybe both - Ian did most of the talking and not much of it was even about what we were there for (ie planning and review)...mostly we talked about work. He gave me a couple of great ideas though, not important here, but related to PPR. The weird thing was that he just seemed very distant. That concerned me and still is concerning me.
Anyway, I had been feeling rather concerned about my future now that I am no longer the Director of Studies (aka "Promotion in a can"), but I think it's ok... I'm ok with Associate Professor - and besides, who knows what's around the corner in our next new faculty!
This is a meeting all staff members have, individually, with their supervisor to discuss their performance over the last year and to plan for their work over the coming year. Traditionally I've not really worried too much about these meetings and this year was not much different. I've now had PPRs with three different bosses: Tony Pettitt, Sean McElwain and Ian Turner.
Tony was bizarre. I'm pretty sure we didn't actually follow the rules for about 3 years, but it didn't seem to matter. Sometimes you'd be in his office for the meeting and nothing would be said for about 5 minutes and then he'd walk off to a smaller side office he had back in our previous building. Not knowing what the hell was going on, I'd gradually make my way to the door presuming the meeting was over only for him to reappear asking where you are going. Odd.
Sean was much more normal and very much about the matter at hand. He was quite good actually, really hammering down on what you needed to do to make sure you did your job well and eventually got promoted.
Ian in my opinion has changed over his three years - becoming more of a "coach" in the Kaplanian sense. He tries to get you to do the talking, get you to come around to a plan that both he and you can agree on (in other words, that you are happy to do the work that needs to be done...this is "coaching"). On Friday, this didn't happen - I'm not sure what it was, perhaps he was tired, perhaps I was sharp, maybe both - Ian did most of the talking and not much of it was even about what we were there for (ie planning and review)...mostly we talked about work. He gave me a couple of great ideas though, not important here, but related to PPR. The weird thing was that he just seemed very distant. That concerned me and still is concerning me.
Anyway, I had been feeling rather concerned about my future now that I am no longer the Director of Studies (aka "Promotion in a can"), but I think it's ok... I'm ok with Associate Professor - and besides, who knows what's around the corner in our next new faculty!
Expert opinion
This is reasonably interesting and unusual - I'm currently acting as an expert in a court case. I'm providing expert opinion as a mathematical modeller in a divorce case. I'm not exactly sure what I can and can't, should and shouldn't talk about regarding the case or the report, so I'll stick to my experiences in doing it for the purposes of the post.
Essentially I was required to construct a mathematical model to determine financial impact of a person on a farm. The work itself was relatively simple. What was interesting was the way it has to be presented to the court. For starters, I provide opinion/advice to the court, not to the people who pay me/hire me for my services. Naturally you have to be impartial and attempt to keep any bias from your modelling and reporting. The report itself is kind of like an executive summary - I shuffled the entirety of the mathematics (only 2 pages though) to an appendix, spending the front end instead describing my credentials, the methodology itself (ie what exactly is mathematical modelling), the assumptions and how genuine I think they are, and then a simple conclusion. Most of the space was taken up by me saying that I was telling the truth, believed what I was saying etc and explaining my opinion that ANY mathematical model will only be an approximation and so forth.
Here's something exciting for the soon to be academics out there: this type of work can score you $250/hr plus. I didn't charge anything because I know the people involved in the case, but now that I know about this, I'll be on the look out for court cases, trust me :-) Court appearance, if needed, is also paid at a higher rate than that even, and includes travel, sustenance and accommodation if necessary. Indeed the consultancy work bandwagon is one I need to get on.
Essentially I was required to construct a mathematical model to determine financial impact of a person on a farm. The work itself was relatively simple. What was interesting was the way it has to be presented to the court. For starters, I provide opinion/advice to the court, not to the people who pay me/hire me for my services. Naturally you have to be impartial and attempt to keep any bias from your modelling and reporting. The report itself is kind of like an executive summary - I shuffled the entirety of the mathematics (only 2 pages though) to an appendix, spending the front end instead describing my credentials, the methodology itself (ie what exactly is mathematical modelling), the assumptions and how genuine I think they are, and then a simple conclusion. Most of the space was taken up by me saying that I was telling the truth, believed what I was saying etc and explaining my opinion that ANY mathematical model will only be an approximation and so forth.
Here's something exciting for the soon to be academics out there: this type of work can score you $250/hr plus. I didn't charge anything because I know the people involved in the case, but now that I know about this, I'll be on the look out for court cases, trust me :-) Court appearance, if needed, is also paid at a higher rate than that even, and includes travel, sustenance and accommodation if necessary. Indeed the consultancy work bandwagon is one I need to get on.
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