Saturday, June 25, 2011
Paper!
Good news, bad news
So....that Australian Learning and Teaching Council Grant I applied for (with a bunch of other people)...turns out, we got it! Yay...so (unofficially at this stage as the press release is yet to be made) I'm leading the Australian Mathematical Sciences Learning and Teaching Network. Sweet. Once the news is out, I'll probably post more about it up here and maybe even the application itself.
On the other hand, I applied for a job and didn't get it... bummer.
On the other hand, I applied for a job and didn't get it... bummer.
Tuesday, June 14, 2011
I'm back!
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| Post application submission beverage and sustenance. |
Nice - so if we are super lucky, in a couple of months there will be a Commonwealth funded Australian Mathematical Sciences Learning and Teaching Network! But don't anyone hold your breath...there's not much cash and I know of 4 other applications from QUT's Faculty of Science and Technology alone (not maths...other things...although one of them is Statistics education as I found out indirectly).
Much thanks to my team members: Shaun Belward (JCU), Mark Nelson (Wollongong), Carmel Coady (UWS), Maureen Townley-Jones (Newcastle), Anne Porter (Wollongong), Irene Hudson (Newcastle) and Antony Dekkers (CQUniversity) and also to those who provided assistance including Australian Mathematical Society via Peter Taylor, Steph Beames and BUNSE, Kelly Matthews from the Quantitative Skills Network, some folks at QUT and of course my wife who dealt with my hissy fits and excessive swearing both at certain people and at Microsoft word. :P
Monday, June 13, 2011
stats
I watch my stats for this blog - they interest me greatly... I'm very interested to see who are the people reading this from various places. I know Norway, the UK, Switzerland and the US, but I've really got no idea who is in the rest of these places. See the following table for example, for this month's readers. Let me know who you are people!
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setback
So my Australian Learning and Teaching Council application is about as shot as that Council itself (it was discontinued by the feds to save -$8 million in the recent budget...yes, that's a minus there). The Aust Math Society and the Aust Math Sciences Institute basically pulled support today and yesterday...oh well. There was a waste of a week.
Saturday, June 11, 2011
On supervisors of research students
I've been thinking about supervision of research students a fair bit lately. I've obviously only been doing this for a few years now (got my first principal supervision roughly 2 years ago and had associate supervision for about 5 years now I think), but already I've changed the way I approach it quite a bit. Probably as a result of my own maturing as a researcher a fair bit. This little story will be a bit about that change. It's also about how people match with supervisors...or not.
I think that I'm a fairly laid back person most of the time and about most things (not everything: ask the scum who used to live in the apartments above and below me when we had an apartment in Brisbane City). That was how I originally took to supervision. Really laid back. Possibly because of my own nature, but also because I don't think I had any idea what I was doing, so I didn't really push any particular method or style very hard. I didn't have one to push!
Over the last couple of years, my style has become such that my expectations are a lot more focussed. I'm not so into just "rolling with the flow". This has reached such a point that a few weeks ago when a student wrote to me asking to do a coursework masters project with me (a small project really, 24cp over one semester) I responded with an email that was about 2.5 pages long explicitly outlining not only the project, but my expectations down to the level of when and where we would meet, what we would meet about and at what point of the semester, what I expected in terms of written work submitted, when it should be provided, what I would give back, oral presentation of research at regular intervals, and all of this culminating in submission of a draft of a research paper to submit to a journal following assessment etc.
Needless to say, I'm pretty sure I scared the shit out of this student and they haven't written back since. Not to worry! Obviously this student wasn't really keen on that sort of situation. It's a shame because I guarantee you that this would have given this student a research paper published in a peer reviewed journal - which they probably won't get now as part of this project unit. But that's ok.
Not that I have any reason to believe that this was the case in the above case in particular, but it's probably relevant to say now that sometimes, a student in that situation cares more about a high grade in the unit than something which is probably more useful in the long run. Not just the paper, but the actual research experience, rather than some artificial course pretending to be research.
Anyway, that's bring me to the topic of the interaction between a supervisor and a student. There is so much to this, that I had never really thought of until reasonably recently. I guess I'm a bit naive and a bit optimistic sometimes, but I kind of thought of it in the sense that there's a job to do (the PhD) and it just needs to get done by the relevant people (the student and the supervisor(s)). But it isn't really that simple. There are so many factors at play.
Sometimes, it is that simple. Even though there might be differences in style between the involved parties, sometimes they just work around each other and the job gets done. I think that this was my own experience. Graeme (my PhD supervisor) seems to be much more of a perfectionist than me and he likes to think around problems more than I do. I like to come up with an approach, use it, report on it and move on (provided it works of course). It doesn't have to be the perfect approach in my opinion...that is just scope for future work in my way of doing things. I don't think there's necessarily anything wrong with either way, but they are certainly different and for the first part of my PhD it caused me problems because I couldn't reconcile the two approaches - I was always trying to satisfy both of us. Eventually, I just satisfied me and wrote a thesis. It wasn't great (in my self-deprecating opinion, it was probably only barely good enough), but it was obviously enough...and that was what I wanted - enough to get me over the line.
Other times, the factors at play can be big problems. One of the things I remember from student days is not really knowing anything about academia. I try to keep that in mind now - I realise that my students don't necessarily know about postdoctoral life, about grants, about jobs, about research projects, about life as an academic. Sometimes they don't know about the drivers that their supervisor has - I think it's important to let students know where they fit into your life plan. The more you communicate the better. I know some people don't think of it that way and think that you should either just know or just find out yourself, but personally I think that's like having a partner and expecting them to know your feelings etc in your relationship...it just doesn't work - you have to talk or communicate in some way, or disaster ensues.
Sometimes disaster still ensues unfortunately....but I guess if it does, at least I'll realise that I wasn't being an ass and I was always trying to make it work out.
Friday, June 10, 2011
long time, no blog...again
Ok first things first, link to the promised paper preprint...feel free to check it out. I submitted it to the Journal of Theoretical Biology about a week after the previous post. It's currently under review.
Now, I've been away from the blog for a while but for good reason. I have been working my arse off on some grant applications. This is my first time doing this in any serious way. I've been third CI on an ARC discovery application a couple of years back, but didn't really contribute anything and we didn't get the grant anyway. Years back I applied for an Australian Learning and Teaching Council grant and didn't get that either...so I'm counting these last couple of weeks as my first real serious effort at getting funded. That said, I completely expect that neither of them will be funded!
ALTC - Discipline Network
The first one is an application for a national learning and teaching network for the mathematical sciences. The Australian Learning and Teaching Council has been shut down by the Commonwealth Government, but before they close completely they are splashing all these grants around in the hope that the work they've done already will continue. One scheme is to set up national, discipline based L&T networks. I'm leading an application with some folk from JCU, Newcastle, UTS, Wollongong, UWS and with support from the Australian Maths Society and Australian Mathematical Sciences Institute to set up a network for mathematics. It's only for $100,000 over 2 years, but it could see some nice initiatives for recognition and sharing of excellent teaching practice get off the ground. It's due Tuesday...almost there.
Learning experience: I'm not really one to work with other people. I hate it actually. But I went extra hard at it for this application. I essentially cold called about 30 people including the president of AustMS and Director of AMSI as well as various academics who have never heard of me. It was awkward, but worked out well in the end. Lots of support for the idea and now I have a fairly large team of interested people coming along on the journey in the hopes of getting the $$$.
US Dept of Defence - Prostate Cancer
So it turns out the the US Army funds medical research! Most of it is for clinical, experimental type stuff, but they had this one opportunity listed for "innovative" projects that "explore hypotheses". They DISCOURAGED data and/or experiments. So I put together an application based around the concept of in silico (computational/mathematical) modelling and experimentation to inform laboratory experiments prior to actually running them, or to improve them when they are already completed. I did the awkward "approach people to be involved" thing again, and it worked out pretty well again! Yay for self-improvement.
This would be for $70,000US for a one year project...basically it would hire a postdoc researcher for a little while to get some work done. Hopefully with a view to building up a more serious project that could get more, longer funding.
The learning experience here was the pain of the admin side of the application. I ended up having to make 16 separate pdf files for parts of the application as well as a fill it in as you go pdf form from the US gov't grants system which was an absolute pain in the ass.
Research postgraduate students seminar day
Yesterday we had our annual research students seminar day. From memory, way back, this used to be a day when ALL of our research students gave talks. But these days we have about twice as many students, so only a few actually get/have to speak.
I know that most of the people who read this are research students or were once, so I'll say a couple of things more about this. First I used to find it boring as hell. Now, not so much. I'm even interested in the talks from students who I can't understand the work of. Next, I know some of you worry about giving talks - don't - seriously...look around - some people give absolutely shit talks, but it doesn't matter. Chances are you are doing good work. Don't get so concerned about looking good, or people thinking you are doing something hard or easy or whatever. KNOW that you are doing something good! Then just tell everyone about it. I think some of you do this and it really shows in how relaxed you are and how the point gets across so much easier. Just talk to everyone like you are telling them your story!
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Well, less than two months to go. I need to get more papers finished.... I need to get working on a book.... and I need to help my research students more...! That's all for now.
Now, I've been away from the blog for a while but for good reason. I have been working my arse off on some grant applications. This is my first time doing this in any serious way. I've been third CI on an ARC discovery application a couple of years back, but didn't really contribute anything and we didn't get the grant anyway. Years back I applied for an Australian Learning and Teaching Council grant and didn't get that either...so I'm counting these last couple of weeks as my first real serious effort at getting funded. That said, I completely expect that neither of them will be funded!
ALTC - Discipline Network
The first one is an application for a national learning and teaching network for the mathematical sciences. The Australian Learning and Teaching Council has been shut down by the Commonwealth Government, but before they close completely they are splashing all these grants around in the hope that the work they've done already will continue. One scheme is to set up national, discipline based L&T networks. I'm leading an application with some folk from JCU, Newcastle, UTS, Wollongong, UWS and with support from the Australian Maths Society and Australian Mathematical Sciences Institute to set up a network for mathematics. It's only for $100,000 over 2 years, but it could see some nice initiatives for recognition and sharing of excellent teaching practice get off the ground. It's due Tuesday...almost there.
Learning experience: I'm not really one to work with other people. I hate it actually. But I went extra hard at it for this application. I essentially cold called about 30 people including the president of AustMS and Director of AMSI as well as various academics who have never heard of me. It was awkward, but worked out well in the end. Lots of support for the idea and now I have a fairly large team of interested people coming along on the journey in the hopes of getting the $$$.
US Dept of Defence - Prostate Cancer
So it turns out the the US Army funds medical research! Most of it is for clinical, experimental type stuff, but they had this one opportunity listed for "innovative" projects that "explore hypotheses". They DISCOURAGED data and/or experiments. So I put together an application based around the concept of in silico (computational/mathematical) modelling and experimentation to inform laboratory experiments prior to actually running them, or to improve them when they are already completed. I did the awkward "approach people to be involved" thing again, and it worked out pretty well again! Yay for self-improvement.
This would be for $70,000US for a one year project...basically it would hire a postdoc researcher for a little while to get some work done. Hopefully with a view to building up a more serious project that could get more, longer funding.
The learning experience here was the pain of the admin side of the application. I ended up having to make 16 separate pdf files for parts of the application as well as a fill it in as you go pdf form from the US gov't grants system which was an absolute pain in the ass.
Research postgraduate students seminar day
Yesterday we had our annual research students seminar day. From memory, way back, this used to be a day when ALL of our research students gave talks. But these days we have about twice as many students, so only a few actually get/have to speak.
I know that most of the people who read this are research students or were once, so I'll say a couple of things more about this. First I used to find it boring as hell. Now, not so much. I'm even interested in the talks from students who I can't understand the work of. Next, I know some of you worry about giving talks - don't - seriously...look around - some people give absolutely shit talks, but it doesn't matter. Chances are you are doing good work. Don't get so concerned about looking good, or people thinking you are doing something hard or easy or whatever. KNOW that you are doing something good! Then just tell everyone about it. I think some of you do this and it really shows in how relaxed you are and how the point gets across so much easier. Just talk to everyone like you are telling them your story!
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Well, less than two months to go. I need to get more papers finished.... I need to get working on a book.... and I need to help my research students more...! That's all for now.
Saturday, May 21, 2011
Preprint coming soon!
In the next couple of days I'll be posting a link to a preprint of a paper I am about to submit to the Journal of Theoretical Biology (with my coauthors: Masoum, Charisse, Dan and Kel). Stay tuned. :-)
Sunday, May 15, 2011
A new feeling
It is getting closer to the time when one of my PhD students will be submitted her completed thesis. This particular student is the first for whom I have been principal supervisor, so this realisation is certainly leading to a new feeling for me. I'm excited for her to be reaching this point. I'm nervous for her and myself as she will go through a rather gruelling period of judgement, first by her supervisors and then by a small panel of internationally recognised experts in the field.
It's great to see the thesis document itself starting to take shape. It really is amazing to see its transformation from a collection of loose ideas, somewhat formalised, into a story that weaves its way through a relatively unexplored topic area, adding to knowledge, tying thoughts and hypotheses together.
The way we have worked through this PhD candidature has involved now publishing journal articles along the way. Not on purpose, but that's just the way it has worked out. So now that the thesis is coming together, we are also starting to simultaneously put together numerous (well, three) journal articles. I'm kind of a sucker for this part...I just love to see work I've played a role in appearing in the formally recognised way. Most supervisors probably push their students to do the menial tasks of fixing up figures and putting the work into the template of the journal, but I love doing that part personally. So I'm having a lot of fun with this.
Still, there's more hard work to be done...so we better get back to it.
It's great to see the thesis document itself starting to take shape. It really is amazing to see its transformation from a collection of loose ideas, somewhat formalised, into a story that weaves its way through a relatively unexplored topic area, adding to knowledge, tying thoughts and hypotheses together.
The way we have worked through this PhD candidature has involved now publishing journal articles along the way. Not on purpose, but that's just the way it has worked out. So now that the thesis is coming together, we are also starting to simultaneously put together numerous (well, three) journal articles. I'm kind of a sucker for this part...I just love to see work I've played a role in appearing in the formally recognised way. Most supervisors probably push their students to do the menial tasks of fixing up figures and putting the work into the template of the journal, but I love doing that part personally. So I'm having a lot of fun with this.
Still, there's more hard work to be done...so we better get back to it.
Sunday, May 8, 2011
Lameness
I'm doing something totally cliche - cooking blog. Check it out if you are keen...else not :-)
http://hungryenough.blogspot.com/
http://hungryenough.blogspot.com/
Saturday, May 7, 2011
Losing contact
Losing contact in an email back-and-forth is embarrassing. Especially when you don't actually know the person and you start off very keen, but then die off.
This has happened to me with a contact I made serendipitously via another contact in New Zealand. I don't even really know the NZ contact. We've met once years ago at a modelling workshop. She is a pharmaceutical researcher and was trying to get some models built for what, in my opinion anyway, is a simple diffusion across a membrane issue. I think she agreed, but the rest of our group was hell bent on some differential equation based nonsense that was clearly inappropriate for something that was clearly a spatiotemporal process! Anyway, that common ground left us as occasional emailers to each other. This year I hope to visit her in NZ - probably in June.
Anyway, she introduced me to another research - a material scientist who constructs drug delivery devices - from Northern Ireland. I am really interested to work with this guy because he is interested in similar things to above, but also because he actually understands applied mathematics, probably better than me too.
I contacted him late last year and we tried to set up a phone meeting (who uses the phone anymore? honestly!)...but various things got in the way: winter storms in Belfast, Brisbane floods, then my holidays and numerous overseas trips.
I looked in my email and noticed his last email to me was February 8 - 3 months ago!!! I hastened to send a reply this morning in order to reestablish contact and set up a phone call for this coming week. Hopefully he hasn't lost interest :-)
This has happened to me with a contact I made serendipitously via another contact in New Zealand. I don't even really know the NZ contact. We've met once years ago at a modelling workshop. She is a pharmaceutical researcher and was trying to get some models built for what, in my opinion anyway, is a simple diffusion across a membrane issue. I think she agreed, but the rest of our group was hell bent on some differential equation based nonsense that was clearly inappropriate for something that was clearly a spatiotemporal process! Anyway, that common ground left us as occasional emailers to each other. This year I hope to visit her in NZ - probably in June.
Anyway, she introduced me to another research - a material scientist who constructs drug delivery devices - from Northern Ireland. I am really interested to work with this guy because he is interested in similar things to above, but also because he actually understands applied mathematics, probably better than me too.
I contacted him late last year and we tried to set up a phone meeting (who uses the phone anymore? honestly!)...but various things got in the way: winter storms in Belfast, Brisbane floods, then my holidays and numerous overseas trips.
I looked in my email and noticed his last email to me was February 8 - 3 months ago!!! I hastened to send a reply this morning in order to reestablish contact and set up a phone call for this coming week. Hopefully he hasn't lost interest :-)
Friday, April 29, 2011
Days 3-4 ho chi minh city
So here we are with some more food photos. We've been eating a lot of food here so that's mostly what you see in the photos! We ventured around the corner into an area which was a bit euro trashy if you ask me. Actually, it reminded me a lot of Amsterdam. Lots of white folk, lots of artificial Asia and tourist trap type stuff. Anyway, we went into this dodgy looking restaurant - not dodgy in the good, poor people eat here and this is good food, way, but dodgy in the we just can't be bothered because we know cheap Europeans will come in here and eat eventually. Really though it still wasn't that bad. Chaz got this lovely number - some sort of eggplant, onion and a tonne of garlic combo. Looked alright, I don't eat eggplant though so I can't say one way or the other.
I had another strange beef in tomato stuff soup stew type thing which you can see above. It tasted fine and I actually enjoyed it although most of the beef was a massive hunk of inedible fat. I'm pretty sure it messed with my stomach in a bad way though. I washed it down with a 500ml Saigon for around 55c though so that felt pretty good (shown below). We left this joint soon after though.
I think it was that night that the little guy wasn't feeling well so we actually ate room service. Below is my chicken rice soup which was quite tasty and extremely filling. Then you'll see Chaz's spaghetti bolognese. Strangely they do really good spaghetti here for some reason?
In a crazed fit of tourism we went and visited both w catholic church and the HCMC post office. I felt like a regular 60 year old retiree for a while there :P this was little Dan after triumphantly climbing the steps to some statue outside the post office. He keeps telling us how hot it was there every time he sees these.
Not a great photo I know, but I just liked this sunset the other day.
This next pic shows one of the many aerobics sessions that goes on at the park across from our hotel every day. They actually start around 5 in the morning and have a few morning sessions then start again around 5.30 in the evening. People just seem to join in. There's this flashy one where the leader stands on a big table and then there are some other smaller ones hidden away under the trees. Actually there is a lot of exercise going on over there most of the day. A little part of me likes to think romantically that this is a remnant of the more disciplined and serious communist era when maybe activity like this was compulsory. I don't know if that is true though. I also get this constant reminder of when mr burns makes all the SNPP workers start exercising at the plant. "6 hi-ya-ya". Love it. Little Dan also loves going to the park for a run. I'm sure Chaz will post some of the photos of me and Dan running through 23/9 somewhere else.
Sunday, April 24, 2011
Photos - day 1-2
This is the view out the window of our hotel (Vien Dong) across park 23/9. You can see the park itself below. Last night there were young guys playing soccer on the bitumen and lots of people doing aerobics. Today it was mostly dog walking and badminton (often without a net!).
On our walk up to the end of the park I was fortunate enough to wander along with this beautiful character often referred to as "my wife".
We ended up at the Ben Thanh market - here's some of the seafood area. Probably a redundant statement given that I grew up in Ipswich but I have never seen so many types of fish in my life. Lots of different shellfish and crabs and prawns too. The women were gutting the eels and fish in front of us - fresh as!
This was a few blocks down the road from our hotel. Crossing the road seems daunting but isn't really that bad. It actually sort of reminds me of Swiss pedestrian crossing - you need to show an element of intent, an element of fearlessness and an element of ignorance all of which need to be obvious enough for the drivers and riders to see. Then you are fine. Just walk - whenever!
Snapped this guy tapping out a text on his bike when we were driving in from the airport.
This was my first pho (with accompaniments above) in vietnam. Hopefully one of many. Yay pho!!!!
First dinner - bun cha tay ho. This was the one with the cheetoh meatballs. Yuuuummmy.
No facebook
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. :-(
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. :-(
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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