1 day until Boss M goes on leave

I've still got a week ahead of me of official university days. But Boss M will be on leave for the rest of the year starting this Saturday, so I won't be seeing him until January. Tomorrow will be our last research meeting. Our last lab lunch didn't pan out as I blogged previously, but I was able to chat a little with M and F(V) for lunch today. It was a surprise but M did manage to go to work today despite being under the weather. He still looked a tad bit tired though, I hope he's fine. Surely he'll get his much-deserved rest come Saturday when his leave starts.

In other news F(V) will be going home to Belgium with his family for the holidays. Won't be seeing him 'til February next year.

* * * * * *

So before M went home he popped his head into our room to say goodbye. We ended up somehow talking about drinks on Friday. So looks like we will have our last lab drinks for the year after all :)

Black ants in my bedroom, and their bites sting!

Well, not really looking like an academic post today hey, but that's just the title. Some ants were socialising on my bedroom floor, and I thought nothing of it. Coz black ants really don't cause any trouble as far as I knew. Boy was I wrong! My feet stung a few moment after seeing that first ant. It hurt!!! So I've cleared out the lollies I had in my bag for fear that there was a social group there. I was right :(


* * * * * * *

Today, the lab (M, A, Z, Y and myself) was supposed to meet up for a lunch. I was going to bring my camera in to take a photo, the last one for the year. Unfortunately, M felt ill this morning and sent out an email he won't be able to make it. He still encouraged us (the students, so basically no A) to go out without him. An hour and 5 minutes later since M's email, no one has reacted. I've sent out an email to Z and Y to follow up. Maybe they're still sleeping, or they might have not checked their email so early in the morning yet. I hope they do reply soon as I have no intention of doing the 1.5 hour commute if they aren't up to it.

I was disappointed to miss M and A today, as we were supposed to talk about something important for one of the upcoming projects. And of course I'm worried for M, as he's been swamped with work (recently, and most of the time) and now he is ill. Poor guy. I hope I still see him on Friday for out last meeting for the year before he goes away on leave.

Conferences and alcohol.

I had not blogged about the conferences we've been to the last month or so. In late October I was in Canberra with Z and Boss M at the Evolution meeting. That was a fun one. A big conference, with mostly Aussies, but a handful of big international names too. My favorites were the Helsinki plenary and Simon Ho (of course), who's recently moved back to University of Sydney. Another special thing about this conference is more time spent drinking alcohol with the lab and other scientists. After getting lost for a time Boss M and I found the famed 'Wig and Pen' in Canberra Centre. That night was possibly the most amount of beer I've drank. 3 bottles, a singapore sling and 2 glasses of wine. Good times.

I went to New Zealand by myself just last week to attend another conference. NZ is still cold this summer season down under, and of course alcohol consumption is still a central part like any conference :P It wasn't as much fun to attend conferences by myself than it is when it is with the lab. But I did meet some interesting people there. And I wouldn't mind living in NZ too, now I've been there twice (once in the South Island and now in the North Island) . I really like the climate.

99 days, and then I'll have a good beer spree

I've set the deadline for myself on the 18th of March to submit my thesis. Officially I have until the 31st of March, but I figured I'd leave a few days slack... just in case.

I had a very good, long "chat" with Le Boss yesterday, which gave me a good boost of confidence on finishing. In case I forget, I am going to breathe a thankful noise of acknowledgment to my mentor out into the ether. I really owe him a lot, and he deserves lot of good karma his way.

In other news, my scholarship has been reinstated. Well, it never really went away, but I lost a considerable portion of it after an administrative issue about the source of funds. Apparently, the contract for the other source had expired. It meant I had to live on half the amount in one of the most expensive cities in the world. Le Boss had a big hand in me getting more funding. After having a row at all the people responsible, he was not getting any positive responses for months. Ultimately, he asked the administration to dip into his own funds to append to my scholarship. That was excellent, and will help me heaps. Thank you <3 :) Clears my worries greatly, and makes me focus more at the tasks at hand.

The holiday break is coming up shortly, and I will not be seeing Boss M until January 2010. He invited me to stay in contact over the break, but I figured since he is going on leave early, he'd appreciate the silence. Though he insisted so, since it's quite important to us both that I finish on time, and do a good job of it. For now he has told me to focus on the thesis, and shelf the other projects for now, until I submit.

I am lucky I get these encouraging exchanges with him. From some other students I hear they are not in good terms with their supervisor and get very little time to talk to them. Or even if they do get the time to chat, it sometimes still amounts to them feeling confused and as if they've wasted time.

With only a few weeks left in my official enrolment in this degree, I feel more pressure and actually have more appreciation for this chance to work with Boss M. Even today I feel sad that the time is to end soon. It's not always that you spend a lot of time working on problems and have a brilliant mind to help you work it out. After this stint, it's going to be more about me doing all the thinking and driving on projects, with other scholars considered on level ground. Technically at least.

I hope the community of scholars do welcome me and grant me the award. With Boss M's signature, I think I have a pretty good chance. When I do get awarded, I will not accept his refusal for that sampler of beers, and he MUST have a beer spree with me!

Seven months later... and Four months until submission

I've got four months left... FOUR months. It doesn't sound like much at all.

I'm doing my best to keep working at a steady pace, or faster. At this point I am scared to the core, so I have a lot of adrenaline every day. I wonder when I will hit a wall? I imagine I will, but I am hoping it doesn't come at an inopportune time.

So what's going on now?

I've got 2 papers being written, hopefully ready for journal submission before December. I've got one project that needs writing up, and one other that hasn't even started.

Thesis writing has been put on hold, but I have to produce a good "complete" draft by first week of December. I've enlisted a couple of friends to do some editing/proofreading for me next week, so I ought to work on it this weekend. I can't do anything else in the next couple of days since I'm busy with work and writing for the other two papers lined up for submission.

That's all I've got at the moment. Hope to sound less somber in my next update.

An article shared by a friend.

Insights on working to get a PhD http://bit.ly/4thX7G

Another episode of writer's bloc

phd041309s.gif

http://www.phdcomics.com/comics/archive.php?comicid=1159

This is exactly the point I am in my writing. I've got my existing and about-to-be-submitted papers, and I've been moving text around, inserting bits here and there. I've gotta get my act together and actually make it look like a thesis and not a series of publications.

I stumble upon two situations which cause me grief: (1) the writing and rewriting of sentences that I already understand, but have trouble communicating an idea in a concise manner, and (2) just not knowing what else to say.

Situation (1) is not a fun place to be in. I get lost in time sometimes and get stuck on a sentence/paragraph for hours. Situation (2) isn't too bad, cause it clearly is a signal that I should stop writing, and work things out on a whiteboard, or hunt down articles and do more reading.

I mention grief, but it's not that I don't enjoy this process. Sure there are non-fun periods of time. But that's part of it. Overall, I have a vision in my brain how I expect things to turn out.

But my main adversary is TIME. I resent the calendar as the days are whizzing by now. I've got so much I still want to do, but there must be a point where I just have to stop the ideas and get the writing done.

Whiteboard frenzy

Thought that it would be productive to have my own whiteboard at home, and I will hence be able to save paper with my doodling. And I'll be able to take photos of them without embarrassing myself! (Coz I take photos of whiteboard stuff we discuss in my supervisor's office, lest I forget anything. He used to find it odd, but now he uses his new iMac to do the same thing!)

Papers, papers, papers... !!!

Thinking aloud on which papers I actually do have lined up... Let's see which's sure and which's possible:

(1) Work with F. Review on methods. I'll need to write and collect more literature. Should finish a draft in 2-3 weeks.

(2) Work with boss M. Proposal of a new model. Running experiments which will last for another 3 weeks. I can't say how long the writing will take for this yet. Since this is first-hand work with boss M, he's keeping a close eye on the model, algorithm and code, and that in itself makes it take time as the feedback loop is more frequent. Not that this is a bad thing, it actually makes the work validate itself, though I keep rewriting code more often.

(3) Work with boss M and Z. Estimation of parameters from new model applied to current methods. Just yesterday, boss M pointed out that there is another possible paper out of our work in (2) that can be piped into Z's work. No time frame for this yet as it largely depends on (2).

(4) My own work. Validation of our previously-published method. A project that is on stand-by soon as I can find time for it. Should be open and shut as I've got the framework done.

(5) Possible work with R. Proposed new method for different organism. I've not met with R for a while (since last year). This is all up in the air, and I'm not sure I can think this up in time for the PhD to end.

Ok... now, what are the chances I finish at least ONE before September?!

A conference and a little competition

A conference

I'd been mumbling a while back about not being able to afford attending conferences this year, especially with the "downscaling" of scholarship top-ups (meaning there would be none). Added to that, I've got to save some money for A's application for a visa this midyear.

Good news is, boss M announced that he is setting aside some money for all of us in the lab to attend a conference in late September. The catch is we have to present work there. No big deal, we always expect to give talks in meetings/seminars, so this is actually good!

At least I am sure I'll have at least one more conference to add to my CV without spending too much.

Publishing papers and funding

Every year, we used to receive a constant top-up to our scholarship from boss M. Since the money is scarce, he's set rules on how he's going to allocate it. In fact, he's set up a sort of "competition" amongst us.

So how it goes, is that for every paper we publish, we'll get an *award* for it. Each paper is worth half of the top-up I used to receive yearly. The paper has to be work accomplished with the lab.

The thing is, if we get productive and publish papers more, he's actually going to have more problems with money. That was funny, but he welcomed the challenge and opened even his own pool of money (for his own funding) to us, should we publish more. He's more than happy to oblige. So what came forth from here is not really a solution to the money being scarce. But it turned out to be a better set-up I should say.

I've got at least a couple of papers lined up. Let's see how it goes!

A successful talk

In our most recent lab meeting, I gave a presentation on my work. I'm happy to report that it went very well. It certainly cleared my doubts that what I was doing made sense to other people. For a while I had been worried that the simulations I had designed and my plans for reporting the results in a specific manner would be undecipherable to others. After yesterday, I'm glad that they understood what I was doing.

And as a bonus, big boss seems happy and excited with it. He thinks I should hurry and get it published.

So back to work!

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I have some stories to tell as well about conferences and scholarships and such... But I'll save those for another time.

Updates

Since the beginning of the month, I've commenced tutorials at the School of Maths. I've met with all the groups, they seem like polite and able students. It takes a while to break the ice, especially in a course like Linear Algebra and Calculus. So with the rolls still not finalised and the session just started, and as I usually say, let's see how it pans out as time passes.

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So I've officially ditched C.

I decided my multi-dimension array issues is just not worth troubleshooting anymore. I've since migrated all my code to PERL now. Speed is not so much an issue anymore. So the more pressing issue is to get the code working, and working correctly.

======

One thing that I still have to implement is the sampling in the simulations. The current structure of my arrays, hashes and variables changed when I migrated to PERL. This makes the sampling different, and I have to re-implement it. When I was using C, I had a code snippet (from my supervisor) that accomplishes this. It's a bit different now with my new structures, so I'm having a think through how to write my loops and distribution arrays.

Another demo

Looks like I'm being eyed to teach another course in Maths. I was asked to do a demo for Stats for Life Sciences on Wednesday. My name was forwarded to the course handler/lecturer after the demos I gave for Linear Algebra and Calculus. I'm not as experienced in Stats as in the other courses, so this makes me a bit nervous. I wouldn't mind not doing it, but the course handler knows me from the lab. It'll be embarrassing if I mess it up.

I'm grabbing a library book on the way home today to spruce up my Stats.

Goodbye Fevrier

Clock continues to tick. No way around that fact eh?

Today is the last "work" day of February. I had been productive today, surprisingly, despite the bloc I've been experiencing the past two weeks. I've got an idea for the last part of the thesis that resembles a blood clot in a brain. In fact, at this point I believe there is a manifestation of a blood clot in MY brain by the way my thoughts are getting constipated.

I foresee my last February weekend to be a busy one; I need to get something interesting to pass up as a RESULT by Tuesday. I had not impressed boss M last Tuesday with what I showed him in our brainstorming.

I've got ONE graph to show him so far. At least I've got that. The precious one. But I expect to have a few more by MARCH, which is on Monday.

Codeword: CODEMONKEY.

Maths demo tomorrow.

Tomorrow is the schedule I have for the tutorial demo at maths. If I do well, I can be looking at at least 4 hours a week of teaching.

I'm not sure I want the added workload, and I've been advised against it. Though I do need the money, and the diversion from thesis work can sometimes help. I also did note the last week that attempting to prepare a class lesson was enjoyable.

So here's hoping I do well. I can still decide not to push through with the gig should I get it. And there's also the chance I won't be given a schedule, or I'm not wanted at all.

Scholarship and a Postdoc.

(Source: http://www.phdcomics.com/comics/archive/phd020209s.gif)

Of course, I hope the deviation is not as wide as his. At least I know it's not an option for me to finish AFTER a year, coz the money runs out by then ;)

Thank goodness for the scholarship. Otherwise, I'm pretty sure I can't afford this degree. The amount to spend for tuition is incomprehensible to me.

In other news, boss M forwarded an email to me regarding a postdoc opportunity... in Canada. First off, I'm happy he suggested it. Second of all, Canada. I would love to go, but it's another 2 years of solitude should the husband and I not jive in our plans. Anyhow, it's another thing to think about. The list can only get longer ;)

On writing the thesis

From Joe Wolfe (School of Physics, UNSW)-- One anonymous postdoc told me: "You should tell everyone that it's going to be unpleasant, that it will mess up their lives, that they will have to give up their friends and their social lives for a while. It's a tough period..." It certainly is hard work, stressful and you will have to adapt your rhythm to it. It is also an important rite of passage and the satisfaction you will feel afterwards is wonderful."

Lecture and tutorial demos

This week there were lecture demos for the search for a replacement for boss M's position as Genetics lecturer. I went to sit for some. So I heard the sickle-cell and malaria example and Hardy-Weinberg law several times (as well as koalas, kookaburas and possums, very Australian hehe). Not bad, I need to be reminded about teaching styles as I might give demos in the next few weeks myself.

Yesterday afternoon I started to write up answers for sample problems for two undergraduate courses: Vector Calculus and Complex Variables. I found myself breezing through the first few problems, but later on got stumped on several ones. On some items I knew how to answer them, but the theory got lost.

Went to the library to harvest dusty textbooks to backtrack on theorems to justify my solutions in these problems. I suddenly felt nostalgic, felt how much I missed teaching, and the process of preparation for lectures.

I am certain I want to teach in a university again.

Couples, partners, incest and such.

(Source: http://www.phdcomics.com/comics/archive/phd012809s.gif)

This blog is turning out to be a commentary/reaction on phdcomics.com. What can I do, almost each comic strip strikes a chord.

I suppose "incestuous departments" occur not just in academia. But, having hardly worked (less than a year) outside academia I haven't enough data to support that claim hehe.

I met my husband in the university, and we both became instructors there. Some (if not most) of our colleagues in the department also met their spouses in the university or in the department. So I can say that our department is also incestuous.

I only know of one couple in my current university who work in the same department. Yep, they are also in Maths. Fancy that. Ah, there is also another couple in Biological Sciences, but they started out as a professor-student relationship. There are also a number of those from all over I'd imagine. I know I've seen a lot.

I've met some couples in a conference, who work in the same university. It's kinda tricky spotting them. I find out only after speaking with them that they are partners, coz they say so. I've met only one couple so far who share the same surname. It's not something I'm accustomed to, coz most couples in my country take their husband's surname.

It's interesting to note that some universities encourage couples to work "together", meaning that if they hire one of them, the university would try to hire the partner. Even not in the same department. It like a "hire one, get two" situation.

A blue form

So about item (3) in this list, I'm being summoned to the other school to fill out a blue form. Ok so that other school is the Maths and Stats school. It gets me excited to think that I can experience tutoring in an actual Maths school here. Two reasons:

(1) I'm not in a maths school at the moment. Though I am sorta doing maths-related research.
(2) I used to teach maths. In fact I taught maths for a while after graduating from a maths degree.

I'll stop counting eggs before they hatch for now. No jinxing!!

A dilemma of priorities

(Source: http://www.phdcomics.com/comics/archive/phd012609s.gif)

Ah, Jorge Cham continues to write the story of my life. This strip shall be me in our next research meeting, scheduled for February.

I need to come up with my plan for a last paper to publish. One agreement I have with boss M is to publish one more, and I haven't quite decided which idea I'm going to pursue for it.

At the moment I have three options:

(1) An extension of a previous paper, entailing that I design and perform synthetic experiments. This will enable me to perform tests on a methodology I had presented before, and report an evaluation on its performance. Difficulty: relatively easy. Publication probability: not likely for a really good journal, likely for a journal of lesser impact factor.

(2) The simulations in option (1) can be used for a different report altogether. This means using the same code I can write for (1), but keep track of different quantities for analysis. The analysis would require me to learn some more theories. Difficulty: moderately hard. Publication probability: less likely to get published soon coz of the fewer options for theoretical journals.

(3) A different methodology that I have yet to finish developing. This would be the most interesting of all options, as I expect most of our peers in the field to find it useful. Difficulty: Very hard. Publication probability: Very likely in a nice journal.

With only months to go, I am left with a prioritisation problem. I want to do all three plans (and some other side projects that merit attention) but I also have to think which will help me best for the thesis.

Less than two weeks to think long and hard about this.

Whip-crackin'

I admit I had been procrastinating on writing for my thesis for the past months. I've not been totally unproductive. I've managed to push some papers out in the past year. But I still think I can do better. I know I could. And I hope I will.

It's far from being the home stretch, as I don't hand in the thesis 'til late this year. But I do feel the enormous pressure now that time is dwindling away so fast.

If I'm cranky at some times, I apologise. If I am neurotic, know that I could also be normal, when I try. And most of all, if I fail in many respects to be present as a friend, please understand that this is my childhood dream I'm hoping to fulfill. I take it to be my last shot for the moon.

There's something I ask: I'm gonna need a lot of support to keep me sane.

January at an end.

It's almost February, and I have not done anything significant for the thesis. I've done a little reading, but there are more urgent things to attend to before I can get my foot into the door of motivation:

(1) Debug code. There has been a flurry of emails from users of our website, and how there are errors arising.

(2) Answer emails. Aside from those websiteusers, there are some emails I have yet to reply to.

(3) Apply for tutoring position. Despite boss M's discouraging, I think I'll push through with this one. I have yet to speak again to the admin in the other school, but I have a couple of weeks to decide.

(4) Organise. I have a wall calendar for 2009 now in my bedroom. I've been marking important dates the other night, but the deadlines for myself are still unclear until I get to speak with boss M again.

(5) Read. I've got a pile of papers (articles) I have yet to read AGAIN. I've gone through them once last November 2008, but I have to go over them again to refresh my memory.

(6) Contact F. I have plans to work on a project with this person this first quarter of 2009. I haven't made contact since I came back yet. I'm not ready. Have to read material and compile some ideas first.

Sheesh, even this list is not well-written. I have so much to think and write about, that even this list needs overhauling next time.

Blogging about the last year of my phd.

Started this blog, to chronicle my journey towards the end of my degree. I am set to finish before February of 2010. Let's see how far I go, and if I can pull this off.