Showing posts with label work. Show all posts
Showing posts with label work. Show all posts

Thursday, October 21, 2010

Update on Makita's life

I haven't been posting much lately. Things have generally been going well, so there isn't much to complain about. Exceptions:

1. Our beloved cat had to be euthanized last week. A big hit for the entire family, she was a fairly young (6 years) kitty and she was a valuable member of our household. We're all devastated.

2. My plans to get the new Leaf feel through when my 12-year old car developed problems that would require large sums of money to fix. Unwilling to invest any more into the old car, I had to get another one, and I just couldn't wait for the Leaf. I did decide to lease the new car, so in 3 years I'll be back on the car market, and by that time the Leaf will be in it's 2nd generation or so.

3. F1-1 who is particularly saddened by the demise of our kitty has taken his apathy to new lows, and is struggling to keep his grades up. No amount of positive or negative incentives have worked so far. We'll keep on dragging on, but it gets tiring.

4. My marriage to P1 is going through a bit of a low spot right now. Nothing serious. We're just over-worked, don't get to spend enough time together, always have kids around, you know the drill. We'll be ok, I'm sure, we go through ups and downs like any other couple, but right now, we're definitely in a down. The reason I think we'll be ok is that we genuinely are crazy about each other, and we see eye-to-eye on the most important things. The reason we struggle sometimes is that we're both incredibly stubborn, and a bit self-righteous, so when we do disagree on something, it poses some problems.

There is also some good news. My temporary (3-year) car isn't exactly horrible. I'm driving a brand-new 2010 Prius, and it's fa.bu.lous. What a pleasure to drive, what clever, modern design, what great gas mileage. I can go on and on, but you get the idea.

In more good news, it looks like my boss managed to secure funding for me for another 2 years, starting in January. Yeah! I love working here, so I've turned down two other job offers with better benefits to stay here. I'm so happy I stuck around. It's not cast in stone yet, but it's looking pretty good right now.

Edit: More good news, I almost forgot! Since about mid-Summer I've been trying to lose some weight. Simply eating a little better, and switching one meal a day to cereal (usually something oat-based) with fruit, I lost a whopping 18 lbs! I still have the same breakfast as always, I eat whatever I would normally eat for either lunch or dinner, and switch the other one to a modest oat-meal based meal. Today I'm wearing a pair of jeans that I couldn't fit in for the past few years. Not bad, eh?

Sunday, August 1, 2010

WTF?

A postdoc (PD) in our lab was using another lab to do a particular technique that we're not well-equipped for. Such lab-sharing is not uncommon. PD asked a postdoc (SH) in the other lab to point out the location of the hazardous waste container. SH asked if s/he would be made co-author on the paper if s/he did so. PD stared at SH, turned around and returned to our lab.

I had worked briefly with SH in a lab some years ago, so PD asked me if SH is a very funny person. The answer was no, SH definitely did not strike me as funny. PD told me what had happened and asked again, if this was simply a display of dry humor. I again told her I didn't think so.

PD went to the SH's boss to ask the same questions. The boss apologized for SH's behavior. Apparently SH is been having some trouble getting data published lately. I understand that SH is desperate, but authorship to point out the waste container? That's got to be some kind of record.

Friday, July 23, 2010

Conversations in the lab

One of the post-docs in our lab says to our boss:

"I'm going to be in this other lab around the corner. I'm going to fix my tissue"

The boss (never missing a beat): "Why? Is it broken?"

Monday, March 22, 2010

Panic mode!

Hi, I'm back! Remember how I didn't post much because I didn't have anything to complain about? Ok, here's a post. Well, not really a complaint, but I'm officially in panic mode, and it's my own fault.

I love, love, love my postdoc job. And I love, love, love my boss. In a he's the smartest-most-dedicated-best boss in the world kind of way. Of all the things I like about him, I think his best feature is that he very quickly realizes your strengths in the lab, and he tailors (as much as possible) your project to match with your talents. This results in a happy cycle of liking-what-you-do -> doing-it-well -> liking-what-you-do. I've always told him that the one thing that's missing from my job is a teaching component. Add that in, and I'll be in science heaven.

Be careful what you wish for, eh?

My boss is leaving for a few days, and has asked me to teach his classes while he's gone. Of course, I immediately said "yes!" Thinking: woohoo! Then it occurred to me to ask what he was teaching. "Piece of cake" he says. "Topic A, really basic stuff, and topic P, kind of related to topic A, and then a third topic, I don't really remember what it is. But you'll be great!" Sigh... I wish I had his confidence in me. I haven't really kept up with topics A and P over the last, uhm, 7 years. And I dread to think what the third topic might be.

Anyway, so I took a deep breath. How bad can it be? So I said (hoping that I sounded calm and collected): "Oh, ok, sounds good. These are undergrads, right?" My boss, casually: "No, this is the graduate class." Do you think he could see my heart sinking? Because I could feel it beating in my feet. I answered: "Oh, ok. No problem."

Excuse me for a sec.
"Aaaaaaaaaaaaaaaaaaaaaahhhhhhhhhhhhhhhhhhhhhhhh".
Now there, that's much better.

I had a wee bit of imposter-syndrome when I graduated. But having to teach graduate-level classes on topics A, P, and who-the-hells-knows-what-else is bringing that to new heights. What if there are 5 students from professor So-and-so in that class? You see, that lab works on this topic, and they'll know far more than I do, and will be more up-to-date.

I have no one to blame for this but myself. I got *exactly* what I asked for. Part of me is also a bit excited. I have a book on topic A. It's 16 years old, but it covers the basics. I dug it up, and since I'm home with a sick little F1-2 today, I've been reading a bit, and trying to refresh my memory. There is not better way to learn something than having to teach it. I like learning, I want to learn about these topics. I just wish the students were a little less advanced, and I was a little more advanced. That'd be nice. I would feel a little more confident.

My boss has very graciously offered me his class notes, and will go over them with me this week. I have time to prepare. And I have time to get over this nervousness. I sure hope I do, otherwise my stuttering may not get me past the first 2 sentences.

Normally, I perform well under performance pressure, and hopefully that'll proof to be the case here too. Just having written this post makes me feel better. That's what blogging's all about for me. I'll let you know how it turned out. Or not. In which case I probably dug a hole for myself in the backyard, crawled in it, and closed it up above me.

Thursday, January 14, 2010

Karma

First of all.... Happy New Year!! I know, the year is two weeks old already, but I figured I had to say it.

I've had this coffee mug for almost 9 years. It's been with me through my MS, my job in between, my entire PhD program, and a year of post-doc. I like it. I've used it every day I've been in this building since I got it through some kind of graduate student event I helped organize back in '01. So when I dropped it on the floor this morning, and it shattered into a thousand pieces, I was a little sad. It's just some ceramic, but it's been with me for a long time. You know, emotional ties and all that.

To top it off, it shattered so thoroughly that it required me to sweep out the entire storage room. Shards were everywhere on the floor. It took me about 10 minutes to clean up the floor. And while I'm crouched on the floor, sweeping with the hand broom to get every last shard, I just barely notice this little tube underneath the -80 degree freezer. I pull it out to throw it away, but then I look at the label.

It's a tube I had taken out of the freezer this morning and needed desperately. I would never have found it if it wasn't for the fact I had dropped that mug. That tube was important. I figure, that's worth my 9-year old mug. Thank you mug. For many happy years of warm coffee, and your sacrifice for my tube of DNA.

Wednesday, August 5, 2009

Job offer

Did I mention that I love, love, love my job? If I didn't, I should have. I can hardly wait to get to work in the morning, and if it wasn't for the family, I'd have to be chased out at the end of the day.

Of, course, when you're not looking for it, you get all these job offers. I already declined a rather attractive job offer. It wasn't an easy decision. The week after I declined that offer, I received another one. The principal investigator (PI) who made the offer is relatively new to the department, and wanted a presence in the lab, to make sure the lab space wasn't lost because of lack of use. The research subject wasn't quite my thing, and I didn't think it fair to accept the job for three reasons:

1. Being a new faculty member, the PI really needed a post-doc who could get results soon. Since it wasn't my exact field of expertise, I would face too steep a learning curve to satisfy those requirements.
2. I can't guarantee being in the lab early in the morning to late afternoon. With 3 kids, at some frequency I'm going to be called out for picking up children that are ill, and I'll have to stay home with them until they get better. I wasn't about to make promises I knew for a fact I couldn't keep.
3. Points 1 and 2 would end up disappointing the PI who I like and respect.

So,I declined. Again, it wasn't easy. After benefits, the job would have paid $11,000 more than what I currently make. That's not insignificant, and I've wondered whether I made the right decision ever since.

Meanwhile the PI hired someone else, and has been wondering the same thing, whether the right decision was made. I suppose I'm a known evil, compared to the unknown evil of the incoming post-doc. Now the PI seems determined to hire me one way or the other. E-mailing other researchers to try to come up with joint research proposals that would fund my position, and even asking me if we should maybe write a proposal together.

I must say, I'm flattered. In my dreams, I had always imagined a position that would allow me to visit home once a year or so. The most recent ideas would involve me being *required* to go home for work at least once a year. I can live with that.

Really, I love, love, love my job. But as I've discovered, there are limits to my loyalty. $11k wasn't enough. But $11k with mandatory trips back home, might be impossible to resist.

Monday, June 15, 2009

Decision

As some of you may remember, I had to decide whether to change labs and projects at this point. I wrote about that before. I got to read the project proposal and went back and forth a number of times over the weeks. Sometimes closer to staying, other times closer to leaving. If I decided to leave and join the other lab, I had to make myself available for an all-day meeting tomorrow.

For the past 2 weeks I've also been embroiled in legal battles more disgusting than you can imagine. It's not over yet, so I can't go into it, but it's not pretty. So this morning I made my choice: I'm staying.

Ultimately, the working conditions in this lab are so good, that it's hard to leave, even if it means turning down health benefits. Also, my current adviser has many different projects, each with a different funding source. If need be, I can be shifted around from one project to the other. As a post-doc I don't care particularly which actual project I'm on.

Now that I've made my decision, and I've notified both PI's involved, I feel much, much better. I think my potential employer was quite disappointed. I wish I could take both jobs, but I can't. And I haven't been this happy in a long time. I'm sticking around.

Monday, April 27, 2009

Dilemma

Ok, the dilemma has arrived. Now that it has, I realize that I was hoping the decision would be made for me by default. But it wasn't meant to be. Help!!

A position that I had applied for in another lab has become available. My current position is listed is technically as an hourly-wage position, even though I get paid for 40 hours a week no matter how much time I put in. It doesn't have health benefits though and that is a wee bit of a problem. The pay isn't fabulous, but it's average.

The position that has become available would be a regular post-doc position with health benefits. So even if the base pay is the same I get now, it would in real terms be better-paying. It involves research on a topic I worked on a few years ago, so presumably the learning curve is minimal. My current job is (at least on paper) not quite in line with the work I did for my PhD, but that hasn't stopped me from producing good-quality work. For immigration purposes it might be a good idea to take on the new position, because that one is more in line of what I studied for. It'll be easier to make the argument that I'm this indispensable scientist int he field.

The big thing is I absolutely *love* my current job. The lab I work in is large compared to the lab where I'm offered a job now. I don't think I can stress enough how incredibly happy I am here. It is so much fun to be in a large lab, with lots of great people, a fantastic PI. I get up in the morning eager to rush into the lab to get to hang out with cool people, and do cool research. I've had to learn some new things in the past 3 months, and I think I've gotten quite good at it. My boss told me the other day he has another small project using the same principles in another crop that he got funding for. I could polish that off in no time.

This is really hard. I'll be putting up a pros and cons list in the next day or so, and everyone can help me decide. I had sort of hoped that the other position would wither away, maybe not be available anymore, or whatever. At the same time it would be a good opportunity to get back into the work that I did in the past. I would actually be very good at it. Would that be satisfying in and of itself? You help me decide!

Wednesday, April 8, 2009

Celebration!

Tonight I'm in such a good mood! For all intents and purposes I've finished my first project in my new lab as a post-doc. I've never actually had a project that was just finished. There was always something else that had to be done, a slew of experiments that could/should be done. None of that. A few minor holes to be plugged, and I've already done those experiments and sent them off, just waiting for results. There is nothing left to do but write the paper.

Did I mention how much I like my boss? He's *the* best. Really. He gave me an easy project and nothing but great feedback. He is always encouraging to everyone in the lab. He's wonderful!

I'm so happy and relaxed right now. A couple of glasses of red wine certainly didn't hurt, but I was already feeling like this on my way home from work. Did I mention that I absolutely loooove being a post-doc? If I had known how much fun it would be, I would have graduated ages ago.

I wish I had a babysitter, so I could grab P-1 and go have fun somewhere downtown. And get him drunk, take him home and ..... you don't want to know the rest. I haven't felt this good in a long time. Just wanted to share.

Friday, March 20, 2009

Update

In the good news department, I'm love being a post-doc. It's really nice to do research and not have to worry about classes and such. More good news: A paper I submitted in December was accepted with some minor modifications. Not half bad. But wait! There's more! I'm submitting another paper today, and hopefully wrapping up the modifications to the first this weekend. And it doesn't stop there either. I'm also finishing up my first post-doc project and I'll be writing that paper in the next little while. I simply cannot be stopped.

On the not so good news department, The dementor (father of F1-1) served me with legal documents, asserting that whatever problems F1-1 is facing are entirely my fault, and therefore it would be in F1-1's best interest to go live with his father. In addition, his father ought to be the only person to make decisions about F1-1's medical care, education, and religion.

Yep, you read that right, he should decide the kid's religion. It's pretty clear he does not think F1-1 (who is 13 by the way), ought to have any say in the matter. It's not going to be pretty, and it will drag out for many moons. But such is life. I refuse to have my life turned upside down by the dementor. He can't possibly have any evidence to substantiate his allegations, because they're simply not true, but that does not make it a happy situation.

However, knowing me, I'll focus on the good stuff. Remember all those publications? And that I like my job.. a lot? That is determining my current state of mind, and I am positively jubilant!

Friday, January 30, 2009

Happy

At the end of my first week in my new lab, I must say... I'm ecstatic. I love it! After having done much more applied than molecular work over the past few years for my PhD, I'm back to more molecular work. And I can't believe how much I've missed it. I've been home from work for about 3 hours now, and I can hardly wait to get back!

I still have to finish a couple of papers from my PhD work. I'd better get on those out quickly, before I get completely buried in this work.

The lab is fair-sized, roughly 15 people. That includes the principal investigator, undergraduate and graduate students, post-docs, and technicians. All sorts of backgrounds, nationalities, and personalities, but all very, very nice. I think I fit right in, although a week of work may not be enough to come to that conclusion.

I've made a fair bit of progress, and hope to get a paper out of this work in the next month or so. It's supposed to be pretty straightforward. I guess I'll find out for sure when I get a better handle on the data analysis. Right now, I'm filling in the gaps, figuring out what those who came before me have done, and analyzing some data. I'm almost sad it's Friday, I'll be up at the crack of dawn on Monday to get back into it.

Tuesday, January 20, 2009

Update

Has it really been 3 weeks since I last posted? I thought it was a couple of days ago. I guess I'd better get everyone caught up.

I've taken a nice break. From (almost) everything. The holidays were relaxed, although it was a bit challenging to entertain 3 kids with ages varying from 3 t0 13. I've had to take care of my plants for the experiment I'm trying to wrap up for publication purposes, and I did finish writing a paper by mid-December. I did a lot of little projects around the house that had been accumulating for more than a year. It's been nice to go from room to room through the house and do some of that.

I searched for a job by (literally) going from door to door (but being selective when it came to choosing specific doors) offering my services. On the first day I scored two maybe's not bad.

Job 1 is related to the research I did for my MS. I suppose the learning curve is somewhat smaller. But the funding isn't certain for several more weeks, and I couldn't afford to wait, largely because of immigration issues.

Job 2 is with a really high-energy professor in a neighboring department. It's less than ideal in that it's not a full post-doc with (health) benefits. However, the PI has agreed that if I make some decent progress on the two projects I'm assigned I can leave to pursue other options (presumably Job 1). Fair enough.

The really good news was that I could start today at Job 2, which I did. So technically I was unemployed for 20 days. Not bad, eh?

I got so caught up in science that I totally forgot to feed the parking meter all day. Luckily the parking police didn't stop by, and I got away with it. I'd better not try that again.

I really, really like the lab. There are 14 or 15 very friendly people in the lab, the PI works at the bench regularly, they have regular lab meetings (lacking in the previous lab I was in, which I didn't like at all), and one of the projects is in such an advanced state, I ought to be able to get a paper out of it in a couple of months. It might be hard to leave the lab for another job (with a higher salary and/or benefits). I was never in this for the money anyway. But the benefits account for a lot. I need health benefits badly, and cannot justify turning down a job with health benefits simply because I'm having so much fun.

Anyway, now everyone is back up-to-date. Dr Makita is employed!

Monday, January 5, 2009

Post-doc for hire

Aahhhhh!
The break is over. For the first time since, well...., since eh, forever, did I have a real break. No deadlines, nothing to do that would make or break my life. Just getting reacquainted with the husband and the kids. It was good.

It was also challenging to keep the kids happy and occupied throughout their vacation. Every day we had to figure out something to do to get the kids out of the house and active. We made lots of trip to the many parks this town has. We even took them to the mall one afternoon, the museum, walks around the neighborhoods, you name it.

So, now they're all back in school and daycare, and the race is back on. I must say I was happy to get back to the lab, take care of some cultures. And now....


The Job Hunt

Yuck! Not going so well. A job that I had high hopes for received funding, but the budget was cut so much, that the principal investigator cannot hire a post-doc and has to get a graduate student instead. I do have another job offer, but it's 4 hours away, and because it's not really practical for me to move far away from here, I had to decline. Sadly.

No jobs are posted within driving distance from here. Now, I'm literally going door-to-door talking to people trying to find something to do. I would hate to become a stay-at-home mom. Don't get me wrong, I love my kids. I just think it's better for them and me if I work. Really.

The situation is rather desperate. If I don't find a job at the university in a couple of weeks, I'll have to pull F1-3 out of daycare. If I don't find a job within a couple of months, I'll lose immigration status. Consequently, I'll take anything. I'd rather be very excited, but I'm also very flexible. I can get excited about things I've never heard of before. In fact, following up on a distant possibility, I've downloaded some papers to read over tonight.

On the bright side, I should have more time for blogging for a while.

It's both scary and exciting to start up this new phase of my life.

Friday, October 3, 2008

Oh no!

In my experiments I test whether an additive to the soil does good things to the plants. We'll call it RGS (Really Good Stuff) for now. When I add RGS, I also add (because it's part of the chemical) something we'll call ES (Extra Stuff). To verify that the observations are due to RGS and not ES, I have a control to which I add only ES. This is a negative control.

A while ago, I analyzed my plant material and noticed that the plants that had only gotten ES, tested positive for RGS. I had already seen that the observations weren't as expected. ES plants were behaving too much like RGS plants.

The next experiment had the same problem. As I was writing this up for the past few weeks, I had a real problem explaining my data, because the ES plants were doing weird things. I did some tests last night, and more detailed ones this morning. And the verdict is: someone must have mixed up the labels on the container and put a form of RGS in the container labeled ES. All the while I though I was putting in ES as a negative control, I was simply adding another RGS treatment.

When I started noticing these problems with my plants, I added another negative control to my experiments, to which I didn't add anything at all (no ES or RGS). Those experiments are still salvageable, because at least I have a negative control. The ones where ES was my only negative control are useless.

I now have to re-do the entire statistical analysis and go back over all my data, trying to figure out when exactly this problem occurred. On the bright side: my data makes much more sense now. ES plants were behaving like RGS plants, because that's exactly what they were. It's easier to explain, but I really didn't need to spend more time analyzing data, thank you.

I'll spend the rest of the day working on statistics, and making new graphs and tables for the chapter in question, and sadly, tossing out a bunch of experiments.

This is exactly what the negative control is supposed to do, though. Science did do it's job here, and let me know that something was up. At least I figured it out now, and not after the paper was published. I would have had a hard time explaining my data.

I also have to notify all the other people in the lab that might have used ES as a negative control. They're likely to run into problems too. If I ever get my hands on the person that mislabeled those containers....

Tuesday, September 30, 2008

Deadlines looming

I have been told that finishing your PhD is anti-climatic, because there is no single deadline. There are bunches of them. For example:

My first submission deadline is in 2 weeks. That means I have to submit the manuscript to the university for review of formatting issues and such. It will be incredibly difficult (if not impossible) for me to meet that deadline. There is no way I can put all my data in, and I don't have time to work on my data right now. All I can do is write. So I will hopefully submit the first draft to my adviser next week, so that he can sign off on that. This is necessary for me to do the first submission.

Once I've killed nearly myself meeting that deadline, I have to go back to the lab, gather more data, and revise the manuscript in about 2 weeks, so that I can submit the revised version to the rest of my committee too. More killing of myself to get it to them on time.

Time to sit back and relax? Hell, no! Of course, I will not manage to get all the data in on time, so there will be more crunching of data, statistics, quick repeats of experiments that need confirmation, and putting in the final data as I go along. Oh yeah, and prepare to defend. That would be the next deadline. In the third week of November I'm scheduled to defend my work. That means I have to convince a group of 5 or 6 faculty members that I am worthy of carrying the same degree they have. How am I going to fool these people into thinking that I am worthy?

Big sigh and a break after that? Hell, no! My committee members will give me a list of things to change in the final document, and I will work for a full week to implement those. There might even be some last minute data to be added. I would be surprised if there will not be any of that. The final submission deadline is in early December.

So you see, it's not one final burst of activity, culminating in this big sense of freedom. Right now, the road is blocked by 4 major hurdles, with hardly any time to breathe in between. Who ever thought this was a good idea?

Adding insult to injury, P1 is leaving for the weekend. As in: going out of town, and I'm stuck at home with a couple of little kids when I'm supposed to be working on this. Anybody want some kids for the weekend?

Friday, August 15, 2008

go, Go, GO!!

That is the chant that's been going through my mind this week. It's the inner voice that is telling me that time is running out for real. This week, time has turned critical, and my inner voice is now so loud, I can no longer ignore it.
go, go, go!!

I walk through the hallways, to the greenhouse, up the driveway, in the parking lot. And every step my mind screams "go". The results of the experiments I'm setting up now will not come in time for the dissertation deadline. They are contingency experiments, in case the other ones don't turn out right. In case I can't make it on time for a December graduation. Time is really up. I can hardly believe it.

On the one hand, if I had worked at the rate I'm going now all along, I would have been finished a year ago. On the other hand, there is no way anyone can sustain this for any length of time. Every minute in the lab is spent near the greenhouse. Every one of my plant shelves will be filled to capacity after today. Every minute at home is spent either writing, or thinking about writing. It's this all-consuming drive that hopefully will provide the final push necessary. It will have to.

Anyway, enough time spent typing this blog post. It's been hard to take my raging mind away from work, but maybe it will refresh and reset me too. Another cup of coffee for the day, and the race continues. Hang on to your hats folks! The finish line is in sight.

Tuesday, July 15, 2008

Silence

Why is Makita so silent these days? Has she had enough of blogging?

Well, here it is guys and gals. I'm hoping that this is the home stretch, and is it ever torture!

1. My adviser is leaving at the end of this month, and although I have a co-adviser for the Fall semester it will not be the same.
2. I have to prepare and present two posters at a meeting at the end of July.
3. My first dissertation draft is due in early October. That is 3 months from now!
4. I'm still frantically doing experiments to get the necessary data. I just harvested one yesterday. While I'm processing those samples (plants, soil, and disease data), I have to set up the next experiment.

To prepare the posters for the meeting I've been up until 3-4 am in the morning almost every day for the past 2 weeks. There isn't enough coffee in the world to keep me awake anymore.

So you see, I hardly have time to read blogs (and I miss doing that dearly!), so writing blog posts myself right now is a bit tough, But I'll try to do better.

By the time October comes along it will be clear where I stand. Whether my work will be deemed good enough to graduate or not. December is the ultimate deadline for me. In terms of immigration status and funding. If I don't graduate by December, I will not graduate at all. And that would be a shame. So I suppose this means more sleepless nights, and less blogging for the foreseeable future. I will put up a post in the near future to introduce the newest addition to our family, so stay tuned!

Friday, May 23, 2008

Shocker of the day

My boss has been really busy lately. I just figured there was another grant proposal deadline coming up. He's been hiding in his office, keeping the door closed and such. Finally he crawled out yesterday and called a lab meeting for today. To break the news: he's leaving! As in, he's quitting his job and moving to greener pastures. In 3 months! I'm shocked, shocked, I tell you.

I may have mentioned this before, but my adviser is just the nicest, most decent human being, and he certainly deserves good things happening to him. I suppose this is a good thing for him. And I've really tried very hard to show my support for him, and to wish him luck in his endeavors. I've tried not to be selfish, but the truth is: I'm worried sick.

He has done some of his homework already and he has lined up alternate advisers and placement for his students. He has another adviser in mind for me, and under the circumstances, I think I agree with his choice. I have to think it over, and talk some more to him about this. For now, I'm going back to being shocked!

Tuesday, May 20, 2008

Arrays again

Considering the fact that I'm supposed to present a poster later this summer on the microarray data that my adviser has collected in collaboration with another lab, I figured it was time to brush the old data off again. I must admit that I've been so busy that I haven't taken a look at the data in about a year.

My research has taken off in a different direction, then I got busy taking written and oral qualifying exams, and currently I'm furiously trying to finish up research by the end of the summer to hopefully graduate in the Fall. In addition I had gotten a bit frustrated by my inability to find software that would allow me to look at the data, maybe suggest some biological pathways involved, without taking one or more courses in how to work the software. That dilemma hasn't changed yet, but the date of my poster presentation is creeping ever closer. If you know of any good idea for affordable microarray analysis software, don't be shy, tell me about it.

I'm currently looking into an online package called Expression Profiler. Wish me luck.

Sunday, April 20, 2008

Managing references 2: The search

This is part 2 on managing references. Here is part 1.

So I needed to find some software to manage my references and citations that would overcome some of the recent changes in my computing preferences. The change to MAC and my adviser's and university's preferences resulted in a switch to Office for MAC, and this made reference manager obsolete.

I searched the internet, and eventually came on a Wikipedia site that compared several reference managers. I found this very useful, because it provided a lot of information on a single webpage, allowing me to narrow it down pretty quickly.

I first made a list of managers that would work on my MAC:
1. 2Collab
2. Aigaion
3. BibDesk
4. BibSonomy
5. Bibus
6. CitULike
7. Connotea
8. Endnote
9. JabRef
10. Papers
11. RefBase
12. RefDB
13. Zotero

Moving on to the next table on the page, I realized that I wanted to be able to share my database with my adviser and colleagues. This might not be necessary but I don't like to be restricted. The boss uses EndNote, so the software needs to export to EndNote. This cut the following options from the list: 2Collab, Aigaion, BibDesk and CiteULike. The import format options did not remove any additional programs. Nine programs left.

Citation styles. In my field several different styles for in-document-citations and lists of references are used. I'm not entirely sure which one I'd like to use, but again, more options are better than less. And if my style is unavailable, being able to define my own might help. BibSonomy, Connotea, and JabRef were scrapped. Because Bibus still allows user-defined styles, it's hanging in there. Down to 6.

1. Bibus
2. Endnote
3. Papers
4. RefBase
5. RefDB
6. Zotero

Not all of the table provide useful information for the elimination process. The next one that will help me bring down the number of choices is wordprocessor integration. That is a BIG plus.

The restriction that EndNote does not work on the 64-bit versions of Windows, is of no consequence to me, there is no information on Papers, and I'm too lazy to go find that out right now. If Papers becomes a serious option, I'll have to go back and look at that. But at this point we say goodbye to RefBase and RefDB. We have the following left:

1. Bibus
2. Endnote
3. Papers (keeping this Word-integration thing in mind)
4. Zotero

The next set of tables don't change anything to this list, so we go back to the first table where the prices are listed. Price is important, but I'm willing to pay some for great functionality. And as a student, I do often get deep discounts. That is why price only now comes into play.

1. Bibus-free
2. Endnote-Academic version roughly $100
3. Papers-$24-42
4. Zotero- free

I was really interested in taking a closer look at Zotero at this point. Free sounds great, but m ore than anything, the integration in FireFox, the browser I already use anyway, sounded intriguing. Clicking on the Bibus link, I read that Bibus' functionality of MAC is limited. It should probably have been eliminated quite a while ago based on this. Bibus is out. Papers was 29 Euro, not unreasonable, if it's good I'd be happy to pay that. Endnote, being the most expensive of the options, even as a student, was eliminated. So this left me with Zotero. I'm trying it out right now, and I reserve the right to hate it, and go back to the list to choose something else. But with free you can't go too far wrong. If it doesn't work out, I can simply remove it, nothing lost but some time, right?

To be continued....