So I'm really trying to defend and graduate this semester, hence the lack of blog posts. And now, here it is, 3:30 am on Saturday morning, and I can't sleep. Why not? My brain won't stop. What's going through my running brain? What will I say if my committee asks me "What's next?" (I know, that should really be what I'm worrying about when I'm still analyzing data and my thesis is due in 1.5 weeks). But in any case, here's what I've come up with.
I'm seriously considering two completely different routes. I like research, so I'm definitely considering continuing in research. I've also very much enjoyed any teaching I've been able to do. However, I think I would rather choose one or the other. I think trying to teach and do high-level research, i.e. being a research professor at a research university, would not be right for me.
So, for research, I'm interested in national labs and industry positions. (I could name several national labs that do interesting research, including 2-3 in the area where I live. I could name several (2,3,4?) biotech companies I've been researching. I could even forward my resume to a contact I have in the area where I live, and then I could say I'd done that.)
For teaching, I'm interested in undergraduate-level teaching positions where I could focus on teaching, and potentially do some undergrad-friendly research. However, I have very little teaching experience, and these types of positions are few and far between and hard to get. My plan is to continue looking for these types of positions while also applying for national lab and industry research positions. I'm considering anything from a teaching postdoc (or any postdoc where I could spend a good amount of time teaching), to any kind of undergrad-level teaching position (tenure-track, visiting or temporary faculty). Lectureships are also a possibility.
Not that I have to tell my committee this, but in thinking about my plans, I realized two things: 1) with my seemingly undecided teaching vs. research interests, most people have advised me to do a typical postdoc, and 2) a typical post doc is not what I want or need. My problem is not that I need more time to decide which path to take or more research experience to make me a good job candidate, but that I either need experience teaching to determine if I like it and get on the path toward a good teaching position, or if I'm not going to be getting teaching experience, I need to plunge into the type of research position I might have long term to see if I can be happy there. Not to mention that if I'm not getting teaching experience, I should at least get a research position that pays well. A typical low-paid post doc would get me no closer to a potential teaching position, and it would be a low-paid means of getting more research experience.
So, what's next? My goals are an undergrad-level teaching position or a national lab/industry (i.e. well-paid) research position.
Hopefully now I can sleep.
Saturday, November 20, 2010
Thursday, September 16, 2010
The perfect pair of heels - and other thoughts on shoes
So, I'm back on fashion again. In my previous post about my dream wardrobe, I determined I only needed 6 pairs of shoes: ballet flats, running shoes, flip flops, hiking boots, snow-boarding boots, and the "perfect" pair of heels. Maybe for guys, 6 pairs of shoes sounds like plenty, but for girls, that's really extreme. Especially when 1 pair of the 6 is ski boots. With only those 6 pairs of shoes, the shoes listed have to be mega-versatile. The ballet flats have to work with jeans and casual t-shirts, as well as with black pants and dressy shirts. And they have to be mega-comfortable for walking. And those "perfect" heels, well, that's the topic of this post.
I dream of the "perfect" heels. Heels that are sexy as hell, that you can also run a mile in. I know that doesn't exist, but I really *want* it to. So instead, the closest to the single pair of perfect heels would be a classic leather pump, not too round of a toe, but not too pointy either; not too high of a heel (for comfort), but not too low (for attractiveness); and as comfortable as is physically possible. That heel could be worn with jeans and dressy tops, with black pants, with a suit, and with black and non-black dresses. That heel could be worn year-round, fall-winter-spring-summer.
And yet, I still want other shoes. I want a wedge summer sandal, to wear in the summer and spring with a dress or pants. Because summer sandals feel so much fresher in spring and summer than closed-toe shoes, and wedges are sooo much more comfortable than other styles of heels. And I want a wedge fall-winter shoe, to wear when I want to wear a heel, but I want be more comfortable than is possible in the classic pumps. And I want a strappy summer version of the perfect heel, because it's so much sexier and summer appropriate. And I want a city-sneaker, because it looks better with casual t-shirts and is still more comfortable than any ballet flats I've tried.
And I want boots. Oh, how I want boots. I used to just want heeled boots, but now I want more. I want heeled, knee high boots, to tuck my jeans into and wear with dressy tops. I want flat, knee high boots, again to tuck my jeans into and wear with casual and dressy tops. Now I even want heeled booties, to be super-sexy and trendy, to wear with jeans and dressy tops, black pants, dresses.
Oh, and did I mention that I want all of the above in both black and brown?
I really must rein myself in. Really I must.
First, I must say no to the black and brown. I need to limit myself to clothes that go with black. If I buy brown, taupe, or some other color I need to be okay with it going with black. Sometimes that can work really nicely.
Second, I must say no to the boots craziness. Partly because boots are *expensive*! But I like the idea of one pair of boots. Should it be a heeled or a flat boot? Heeled is more dressy, flat is more comfy. But really, for the comfort of flats, I should just wear the ballet flat. So the one pair of boots should be heeled. Should it be a knee-high boot or a bootie? Well, knee high is so cute over jeans, but that's a trend that will come and go. In truth, either length looks the same if it's underneath pants. But if pants stay slim, it's hard to pull them over a tall boot. So maybe it should be a bootie, which just looks like a classic boot if the pants cover the top. So the one pair of boots should be a heeled bootie, as comfortable as possible. And I could wear them with jeans, black pants, and even a dress as the current trend stands.
As for the other shoes, maybe it wouldn't be so bad to just say yes. So I increase my ideal list of shoes from 6 (ballet flats, running shoes, flip flops, hiking boots, ski boots, and the "perfect" pair of heels) to 11 (strappy summer heels, wedge summer sandals, wedge fall-winter shoes, city-sneakers, and heeled booties). That's really not so bad, is it?
I dream of the "perfect" heels. Heels that are sexy as hell, that you can also run a mile in. I know that doesn't exist, but I really *want* it to. So instead, the closest to the single pair of perfect heels would be a classic leather pump, not too round of a toe, but not too pointy either; not too high of a heel (for comfort), but not too low (for attractiveness); and as comfortable as is physically possible. That heel could be worn with jeans and dressy tops, with black pants, with a suit, and with black and non-black dresses. That heel could be worn year-round, fall-winter-spring-summer.
And yet, I still want other shoes. I want a wedge summer sandal, to wear in the summer and spring with a dress or pants. Because summer sandals feel so much fresher in spring and summer than closed-toe shoes, and wedges are sooo much more comfortable than other styles of heels. And I want a wedge fall-winter shoe, to wear when I want to wear a heel, but I want be more comfortable than is possible in the classic pumps. And I want a strappy summer version of the perfect heel, because it's so much sexier and summer appropriate. And I want a city-sneaker, because it looks better with casual t-shirts and is still more comfortable than any ballet flats I've tried.
And I want boots. Oh, how I want boots. I used to just want heeled boots, but now I want more. I want heeled, knee high boots, to tuck my jeans into and wear with dressy tops. I want flat, knee high boots, again to tuck my jeans into and wear with casual and dressy tops. Now I even want heeled booties, to be super-sexy and trendy, to wear with jeans and dressy tops, black pants, dresses.
Oh, and did I mention that I want all of the above in both black and brown?
I really must rein myself in. Really I must.
First, I must say no to the black and brown. I need to limit myself to clothes that go with black. If I buy brown, taupe, or some other color I need to be okay with it going with black. Sometimes that can work really nicely.
Second, I must say no to the boots craziness. Partly because boots are *expensive*! But I like the idea of one pair of boots. Should it be a heeled or a flat boot? Heeled is more dressy, flat is more comfy. But really, for the comfort of flats, I should just wear the ballet flat. So the one pair of boots should be heeled. Should it be a knee-high boot or a bootie? Well, knee high is so cute over jeans, but that's a trend that will come and go. In truth, either length looks the same if it's underneath pants. But if pants stay slim, it's hard to pull them over a tall boot. So maybe it should be a bootie, which just looks like a classic boot if the pants cover the top. So the one pair of boots should be a heeled bootie, as comfortable as possible. And I could wear them with jeans, black pants, and even a dress as the current trend stands.
As for the other shoes, maybe it wouldn't be so bad to just say yes. So I increase my ideal list of shoes from 6 (ballet flats, running shoes, flip flops, hiking boots, ski boots, and the "perfect" pair of heels) to 11 (strappy summer heels, wedge summer sandals, wedge fall-winter shoes, city-sneakers, and heeled booties). That's really not so bad, is it?
Tuesday, August 31, 2010
Why do I suck?
I'm trying to write my thesis. I really am. I just keep getting stuck, so it's going super slowly, and I'm plagued with guilt about being slow. But every time I try to push myself, to give myself deadlines, to increase the pressure on myself, it just backfires, and I get less done.
I think about what I want to do next. I imagine when I defend my thesis, my committee members may ask me what I plan to do next, and I dream about various answers. I think about telling them that I've realized research is just not for me, and I imagine telling them reasons why I think that. I imagine they might be able to offer some insight into whether I'm right, or whether they might tell me how I could learn to be good at and like research.
But the thing is, my committee, my mentors, anyone who might actually be able to offer me insiders' insight when I say I don't think I'm cut out to deal with failing 99.9% of the time, I don't think I have the vision to seek out the paths that lead to good results, and I don't know how to gain that vision, all the people who might be able to say something to help me are also the people who I need to be references for my future jobs. So I need them to think I've never had a doubt in my life about doing anything, and I certainly don't need to help them come up with a list of my weaknesses. They need to think I'm confident, brilliant, passionate about my career (whatever I eventually decide to pursue).
I've wanted to be good at this. I've wanted to bolster my strengths and improve where I have weaknesses. I've just never really figured out what they are. When everything you do is met with negative feedback, you just change random variables all the time. All you know is, that didn't work; I'll try something else.
I did eventually gain some insight over the years, but I feel like I had to learn everything in the hardest way possible: by doing it wrong in a million different ways. But I continued to evaluate myself, and examine what I could see working (or not working) for other people, and I did eventually improve. But now I just feel too tired of it all, and like it's too late.
I started this game as a smart girl, capable of working very hard. As we all did.
But I was naive, and my whole life, all that had been demanded of me was to do what I was told, the way I was told to do it. And my advisor was a micromanager, so he told me what to do, and how to do it, and how to think about it, and I tried to do it.
But lab work doesn't work that way. What my advisor really wanted was publishable results. And with research, no one knows a priori how to get there.
And anyway, a Ph.D. isn't about that. It's not about just doing what someone else wants you to do. It's yours, your work, your thesis, your Ph.D. But damn if standing up to my advisor doesn't result in insults and threats and extreme unpleasantness. But it's what had to be done to make progress, rather than circling the same microproblem forever. So, difficult Lesson 1 - You can't be a people-pleaser, and Lesson 2 - You may have to endure unpleasantness, insults, and threats and you have to try not to let it get to you.
And then there's Lesson 3, that I'm still trying to wrap my head around. How to choose the right paths to pursue. You see, I'm a plodder. I like to do things once, correctly, and double-check my work along the way. It seemed to work for me in school. But it doesn't work for me in the lab.
I used to do homework with a friend, and I used to say we were perfectly matched as homework partners. He was a racer, and I'm a plodder. He could take our ideas, race through the steps, and see that we were on the right path. I could then plod along and make sure we got all the steps just right. I was not good at the half-assedly racing through to see that it was going to work; he wasn't as good at the details of to plodding along to get all the steps right. It was a great partnership.
But it turns out that the skill he had is much more important to getting stuff done in the lab. And I still suck at it. I've tried. But I feel like I race through the wrong way, choose the wrong steps to gloss over, the wrong results to follow. I race through, choose the path, and then the path is wrong. I do this over and over. How the fuck can I get better at it??? Still don't know.
Over and out.
I think about what I want to do next. I imagine when I defend my thesis, my committee members may ask me what I plan to do next, and I dream about various answers. I think about telling them that I've realized research is just not for me, and I imagine telling them reasons why I think that. I imagine they might be able to offer some insight into whether I'm right, or whether they might tell me how I could learn to be good at and like research.
But the thing is, my committee, my mentors, anyone who might actually be able to offer me insiders' insight when I say I don't think I'm cut out to deal with failing 99.9% of the time, I don't think I have the vision to seek out the paths that lead to good results, and I don't know how to gain that vision, all the people who might be able to say something to help me are also the people who I need to be references for my future jobs. So I need them to think I've never had a doubt in my life about doing anything, and I certainly don't need to help them come up with a list of my weaknesses. They need to think I'm confident, brilliant, passionate about my career (whatever I eventually decide to pursue).
I've wanted to be good at this. I've wanted to bolster my strengths and improve where I have weaknesses. I've just never really figured out what they are. When everything you do is met with negative feedback, you just change random variables all the time. All you know is, that didn't work; I'll try something else.
I did eventually gain some insight over the years, but I feel like I had to learn everything in the hardest way possible: by doing it wrong in a million different ways. But I continued to evaluate myself, and examine what I could see working (or not working) for other people, and I did eventually improve. But now I just feel too tired of it all, and like it's too late.
I started this game as a smart girl, capable of working very hard. As we all did.
But I was naive, and my whole life, all that had been demanded of me was to do what I was told, the way I was told to do it. And my advisor was a micromanager, so he told me what to do, and how to do it, and how to think about it, and I tried to do it.
But lab work doesn't work that way. What my advisor really wanted was publishable results. And with research, no one knows a priori how to get there.
And anyway, a Ph.D. isn't about that. It's not about just doing what someone else wants you to do. It's yours, your work, your thesis, your Ph.D. But damn if standing up to my advisor doesn't result in insults and threats and extreme unpleasantness. But it's what had to be done to make progress, rather than circling the same microproblem forever. So, difficult Lesson 1 - You can't be a people-pleaser, and Lesson 2 - You may have to endure unpleasantness, insults, and threats and you have to try not to let it get to you.
And then there's Lesson 3, that I'm still trying to wrap my head around. How to choose the right paths to pursue. You see, I'm a plodder. I like to do things once, correctly, and double-check my work along the way. It seemed to work for me in school. But it doesn't work for me in the lab.
I used to do homework with a friend, and I used to say we were perfectly matched as homework partners. He was a racer, and I'm a plodder. He could take our ideas, race through the steps, and see that we were on the right path. I could then plod along and make sure we got all the steps just right. I was not good at the half-assedly racing through to see that it was going to work; he wasn't as good at the details of to plodding along to get all the steps right. It was a great partnership.
But it turns out that the skill he had is much more important to getting stuff done in the lab. And I still suck at it. I've tried. But I feel like I race through the wrong way, choose the wrong steps to gloss over, the wrong results to follow. I race through, choose the path, and then the path is wrong. I do this over and over. How the fuck can I get better at it??? Still don't know.
Over and out.
Wednesday, August 25, 2010
The catch-22 of the unsupportive advisor
Some advisors are universally unsupportive. Others are more selective. The result seems to generally be the same: failure of the unsupported. So the question is:
Do we fail due to lack of support?
Or do we not get support because we are failures?
Do we fail due to lack of support?
Or do we not get support because we are failures?
Wednesday, August 18, 2010
My dream wardrobe
Ok, I know that wardrobes aren't exactly science-talk, but hear me out - this is a minimization problem.
I've never had a lot of money to spend on clothing. I generally don't have a lot of closet space to devote to clothing. And I seem to travel and move around fairly often. I always thought these three conditions were what drove me towards a minimal wardrobe (i.e. a wardrobe that would keep me reasonably clothed while being as small as possible). I realized recently that there's another factor driving me towards this minimal wardrobe: I don't like to have to think too hard about what I wear each day. I don't want an entire department store worth of clothing and accessories to choose from each morning. I want a small, carefully selected number of items. I want my wardrobe to be small so I have fewer choices, and it's easier to get dressed in the morning.
Now, don't get me wrong. I like clothes. And accessories. And shoes. Especially shoes. I like to play around with outfits and looks sometimes, either in my own closet or in clothing stores. But for the everyday grind, I just want go-to outfits that are comfortable and make me feel and look good.
So, my minimization problem is this: what is the minimum amount of clothing a person can own and clothe themselves nicely for a year? That means they have enough clothing in quantity and style to wear for 1-2 typical weeks (time between laundry sessions), clothing for all seasons, and clothing to cover the usual special occasions.
First, I need to define some terms. What kinds of clothing do I need in 1-2 typical weeks? I need clothing for work, for weekends, for work-outs, and for sleeping. For work, I must have comfortable clothing - comfortable closed-toe shoes, outfits I can bend and move around in, some layers for buildings with poor climate control, and nothing that's going to dangle into the dangerous elements of my experiments. For weekends, I do a lot of walking, a lot of indoor and outdoor activities, so I need to be cute and comfortable. For work-outs, I sweat! I need good clothes to sweat in and do tough work-outs. For sleeping, I must have loose shorts and comfy tops. So there we go - my needs for 1-2 typical weeks.
Next, I need to define the typical special occasions. Let's see...We have weddings and funerals, job interviews and presentations. dressy parties and social outings. I also like to swim, ski, and hike. I think that covers the special occasions category for me.
So we have the requirements for typical 1-2 weeks, the usual special occasions. The requirements for four seasons varies by region, but I'd say appropriate shoes, coat, hat, scarf, gloves, light layers and short sleeves for summer, heavier layers including sweaters and long-sleeves for winter. Those seasonal requirements can be fairly universal. So here we go, my minimal wardrobe, below.
For work and weekends:
-1 pair Cute, comfy ballet flats
-1 pair of Dark, straight leg jeans
-1 pair of black pants
-7 casual tops for summer - camisoles, ribbed tanks, short-sleeved T's, graphic T's
-7 dressier tops for summer - dressier short-sleeved and sleeveless blouses
-7 casual tops for winter - long-sleeved t's
-7 dressier tops for winter - thick sweaters, thin sweaters, button downs, blouses
-1 cardigan
-1 blazer/jacket
-1 coat
-scarf, hat, gloves
-14 pairs comfy, no show undies
-2-3 good bras (1 black, 1 nude)
-socks for ballet flats
-belt
-handbag
-sunglasses
For workouts
-Running shoes
-Fleece
-1 pair each of work-out pants: shorts, capris, and long
-1 short-sleeved and 1 long sleeved work-out shirt
-1 great sports bra
-1 pair of great socks
-If these items are the right fabrics, I can rinse them after each work-out and hang dry. If I want to be less gross, I could up the numbers to 3-5 of each item.
For sleeping
-2 pairs of loose fitting shorts
-2 comfy tank tops
-1-2 robes (preferably 1 light-weight for summer, 1 heavy-weight for winter)
For special occasions - dressy
-1 little black dress - sexy but classy
-1 pair of perfect heels
-1 non-black dress
-1-2 wraps/shrugs to go with dresses
-1 suit (can be black pants and blazer from work-wear)
For special occasions - sporty
-flip-flops, swimsuit, swim cover-up, sun hat
-can wear work-out tops for skiing and hiking
-ski boots, socks, thermals, pants, fleece, waterproof shell, gloves, helmet, muffler
-hiking boots, pants (can wear same socks, fleece, shell as for skiing)
There you have it, my minimal wardrobe. So, is this wardrobe what I own? Of course not. But a girl can have dreams, can't she?
I've never had a lot of money to spend on clothing. I generally don't have a lot of closet space to devote to clothing. And I seem to travel and move around fairly often. I always thought these three conditions were what drove me towards a minimal wardrobe (i.e. a wardrobe that would keep me reasonably clothed while being as small as possible). I realized recently that there's another factor driving me towards this minimal wardrobe: I don't like to have to think too hard about what I wear each day. I don't want an entire department store worth of clothing and accessories to choose from each morning. I want a small, carefully selected number of items. I want my wardrobe to be small so I have fewer choices, and it's easier to get dressed in the morning.
Now, don't get me wrong. I like clothes. And accessories. And shoes. Especially shoes. I like to play around with outfits and looks sometimes, either in my own closet or in clothing stores. But for the everyday grind, I just want go-to outfits that are comfortable and make me feel and look good.
So, my minimization problem is this: what is the minimum amount of clothing a person can own and clothe themselves nicely for a year? That means they have enough clothing in quantity and style to wear for 1-2 typical weeks (time between laundry sessions), clothing for all seasons, and clothing to cover the usual special occasions.
First, I need to define some terms. What kinds of clothing do I need in 1-2 typical weeks? I need clothing for work, for weekends, for work-outs, and for sleeping. For work, I must have comfortable clothing - comfortable closed-toe shoes, outfits I can bend and move around in, some layers for buildings with poor climate control, and nothing that's going to dangle into the dangerous elements of my experiments. For weekends, I do a lot of walking, a lot of indoor and outdoor activities, so I need to be cute and comfortable. For work-outs, I sweat! I need good clothes to sweat in and do tough work-outs. For sleeping, I must have loose shorts and comfy tops. So there we go - my needs for 1-2 typical weeks.
Next, I need to define the typical special occasions. Let's see...We have weddings and funerals, job interviews and presentations. dressy parties and social outings. I also like to swim, ski, and hike. I think that covers the special occasions category for me.
So we have the requirements for typical 1-2 weeks, the usual special occasions. The requirements for four seasons varies by region, but I'd say appropriate shoes, coat, hat, scarf, gloves, light layers and short sleeves for summer, heavier layers including sweaters and long-sleeves for winter. Those seasonal requirements can be fairly universal. So here we go, my minimal wardrobe, below.
For work and weekends:
-1 pair Cute, comfy ballet flats
-1 pair of Dark, straight leg jeans
-1 pair of black pants
-7 casual tops for summer - camisoles, ribbed tanks, short-sleeved T's, graphic T's
-7 dressier tops for summer - dressier short-sleeved and sleeveless blouses
-7 casual tops for winter - long-sleeved t's
-7 dressier tops for winter - thick sweaters, thin sweaters, button downs, blouses
-1 cardigan
-1 blazer/jacket
-1 coat
-scarf, hat, gloves
-14 pairs comfy, no show undies
-2-3 good bras (1 black, 1 nude)
-socks for ballet flats
-belt
-handbag
-sunglasses
For workouts
-Running shoes
-Fleece
-1 pair each of work-out pants: shorts, capris, and long
-1 short-sleeved and 1 long sleeved work-out shirt
-1 great sports bra
-1 pair of great socks
-If these items are the right fabrics, I can rinse them after each work-out and hang dry. If I want to be less gross, I could up the numbers to 3-5 of each item.
For sleeping
-2 pairs of loose fitting shorts
-2 comfy tank tops
-1-2 robes (preferably 1 light-weight for summer, 1 heavy-weight for winter)
For special occasions - dressy
-1 little black dress - sexy but classy
-1 pair of perfect heels
-1 non-black dress
-1-2 wraps/shrugs to go with dresses
-1 suit (can be black pants and blazer from work-wear)
For special occasions - sporty
-flip-flops, swimsuit, swim cover-up, sun hat
-can wear work-out tops for skiing and hiking
-ski boots, socks, thermals, pants, fleece, waterproof shell, gloves, helmet, muffler
-hiking boots, pants (can wear same socks, fleece, shell as for skiing)
There you have it, my minimal wardrobe. So, is this wardrobe what I own? Of course not. But a girl can have dreams, can't she?
Tuesday, August 10, 2010
Wednesday, August 4, 2010
Notes, organization, and reproducibility
How do you keep notes and records on your experimental methods, data, analysis, and journal articles? What do you keep on file, and where, and how do you organize it? As scientists, we all face the record-keeping problem, and I'm interested in how others deal with it. Over the course of grad school, I've developed my own system in fits and starts, and I'll describe what's working for me.
What to keep, what to keep? There's essentially one reason for keeping things on file: because you might need it later! I know, obvious. But I'd like to break it down a little further, to four reasons you might need it later: 1) it's a result, 2) it's information needed to reproduce a result, 3) it's information that may help with interpretation of a result, or 4) it's information that may lead to a future result. So, as for what I keep on file, I try to keep everything on file that falls into one of those four categories. That's a lot of stuff. How the heck to you organize this stuff so you can find it later when you need to?
How to organize? In the beginning of a project, starting a system of organization is difficult because you don't have a feeling yet for the number of different sub-projects, the scale of those projects, and all of the variables that will change along the way. But, there are categories that will be important when it comes time for publishing and ensuring that you have all the information needed to reproduce your work. For me, those categories are experimental methods, data, analysis, and references.
Where to keep it? I have 3 places. I have lab notebooks - the daily record of what I've done. I have a physical filing cabinet - keeper of everything from written notes and hand-drawings to printouts of journal articles, hardware specifications, and data. And I have a computer (and backup!) - keeper of essentially everything that's not handwritten and a few things that were scanned in. The computer can really get you in trouble with it's infinite space and the myriad bad ways of organizing and naming files. But what I've outlined below works for me, and perhaps could work for others.
References/Journal Articles
I like to keep lots of pdfs of journal articles, and print lots, but not all. I generally make file folders (both physical and on the computer) that represent some general topic and file lots of papers in each folder. For computer files, I like to name the files "(first author's last name)_(Journal)_(pub year)_(2-3 key words)". This system works...okay. I can easily find the papers again when I need to, and it's nice to have hard copies with notes and soft copies for easy access when I'm away from my filing cabinet. However, now that I'm writing, I've started using EndNote, which may cause me to completely overhaul my system. We'll see.
Experimental methods
Experimental methods has been one of the most troublesome categories for me to organize. Methods can be a very diverse category, particularly in biophysics where methods may range from biochemistry to instrumentation to automation. Developing the methods may be a major component of a research project, or even if it's not, methods may change over time. Figuring out how to deal with diverse, evolving methods has been challenging.
Eventually, I determined two keys to organizing my notes and files on experimental methods: subcategorizing, and organizing by date. Over time, I found I generally had three categories of methods: sample preparation, instrumentation, and data acquisition.
For sample preparation, I found it best to type up a protocol, date it, and paste it in my lab notebook on that date. Then I could refer back to that protocol by date and lab notebook page number each time I performed the protocol. As I modified the protocol, I would still refer back to the same protocol, but note the modifications. Eventually, enough modifications would be added that I'd type a new copy, date it, and paste it in my notebook. Eventually, the protocols were fairly settled and each day I prepared a sample, I could just refer back to that date and page. And it worked well for some items I made and stored. Typically we write the date on anything bio-y that we store, and when I used it, or ran out and needed to make more, I could just refer back to that date in my lab notebook. Convenient. Plus, if a labmate wanted to do something similar, they could also look it up and not need me to "remember" exactly how I'd done or made something.
For instrumentation, I had several subcategories that required various forms of organization. I had designs, part specifications, optimization and characterization techniques, calibrations techniques, automation software. I wasn't the best about organizing these things as I went, but hindsight being 20/20, I've learned what I should have done.
1) Keep an accordion of files and a notebook dedicated entirely to your instrument.
2) Design involves a lot of notes, hand-drawings, calculations, references to articles. Date these things and keep them in a folder.
3) Part specifications become impossible to find later. Keep them on file, hard and soft copies if at all possible. (Also, determining what parts are in an instrument is really hard after the fact. Keep records of what you put in your instrument!) 4) Optimization and characterization techniques evolve, and the instrument evolves with them. Write down and date what you do in a notebook dedicated to the instrument (or at least make notes in the instrument notebook referring to where it is written down).
5)Calibrations are very important. Keep good notes on them, by date, in that instrument notebook.
6)Automation software is still a toughy for me. Ideally, it would change rarely, you would carefully track changes by date, and you would keep old copies. Our automation software is all custom written, in a very large suite of software that all works together. I tried to keep notes on major changes, and I tried to keep old copies, but ultimately, I didn't do it that well.
With hindsight, I eventually found the above guidelines to be a good means of organizing instrumentation techniques.
Data acquisition, was generally a combination of the above sample preparation and instrumentation techniques. Generally I prepared a sample and used the instrument in it's present status with the current calibrations to acquire data. And I used some of the automation software I had written to acquire that data. I usually made notes to this affect in my daily record in my lab notebook, with any modifications or variables noted. Those variables are one of the places where things can get tricky, as you often don't even know what the important variables are until you start changing them. But nevertheless, the lab notebook was generally where I noted the details of data acquisition.
Data
Data was actually the simplest thing for me to organize. Our lab had already established a system of organizing computer files by date and time stamp, with a descriptive base file name and different file extensions representing different types of data. I followed that system and found it works pretty well, as long as you follow it. Keeping notes in my lab notebook about the individual files was also key to knowing which files were what. Also helpful: a description somewhere of what's in the different files, and how to load the files for analysis.
Analysis
Analysis was another doozy of an organizational challenge. My raw data files were all nicely organized by date and time stamp, but for analysis, it took awhile to decide how to organize. Did I organize by date, like the data? But then, what about when I wanted to analyze data from several dates together? Did I organize by type of data? By date I performed the analysis? By type of analysis? And how did I organize the analysis programming itself? And what, if anything, did I write about it in my notebook? Or print anything out? Analysis organization definitely presented it's own set of challenges.
Eventually I decided to organize the analysis by date of the data and purpose of the analysis. If I analyzed several days of data together, I just titled it by the multiple dates and grouped it in the applicable month or year. I generally didn't write notes in my lab notebook about analysis, though I wish I had. I often printed plots, and put them in a 3-ring binder organized by data acquisition date and type of data. I wish I had more notes about my data analysis, and eventually I discovered notes about the analysis itself were very important (see below).
Even more important than the top-level organization of the analysis files was putting notes and organization into the analysis files themselves. My analysis software allows data folders, so that I could arrange data within the file by date, timestamp, and type. I also could make notes within the analysis files. I found keeping notes in the form of "date of analysis, goal of analysis, methods of analysis, and results of analysis" were very useful to making the analysis useful to myself later.
A couple more key points
Following the general rules above, I established a pretty decent filing system for myself. I have a lot of files, hard copy in my filing cabinet, soft copy on my computer, and lots of lab notebooks. In keeping this stuff useful, I have a few more key points:
1)Back up your computer files! In at least 2 places, 3 places ideally.
2)Organize your hard copy files. Filing cabinet, tabbed files.
3)Index your lab notebooks. Our labnotebooks had pages at the front for indexing. I liked to list a major category (sample prep, instrumentation, data, analysis, notes), then the specific task of the day.
Also, I found that the more information that was available on computer, the better. Lugging around lab notebooks and file folders sucks. I like to have soft copies whenever possible. Short of scanning in your lab notebooks (or typing all the entries), I found it useful to make an Excel spread sheet, organized by date, that listed what I did on each day that I acquired data. On this spread sheet, I also added in all the important changes made in the instrumentation, sample prep, and data acquisition. I color-coded it in subcategories. It's made finding data sooooo much easier.
Some final notes on file organization for publication
As I write up my work, I've found it very helpful to make a folder for each paper, and within that folder, to have subfolders for each figure or significant result. Each figure or significant result has it's own 1)analysis file, 2)final figure file, 3)data caption file, and 4)data source file. The analysis file has all the relevant data, from raw to fully analyzed. The source file has where the data came from, how and when it was acquired, how it was analyzed, and any important quantifications. The final figure file is the .jpg, and the caption is a caption that would be appropriate for the figure. With this information, I have everything necessary to include the figure or significant result in the the paper.
And that's it. That's my system. What's your system?
What to keep, what to keep? There's essentially one reason for keeping things on file: because you might need it later! I know, obvious. But I'd like to break it down a little further, to four reasons you might need it later: 1) it's a result, 2) it's information needed to reproduce a result, 3) it's information that may help with interpretation of a result, or 4) it's information that may lead to a future result. So, as for what I keep on file, I try to keep everything on file that falls into one of those four categories. That's a lot of stuff. How the heck to you organize this stuff so you can find it later when you need to?
How to organize? In the beginning of a project, starting a system of organization is difficult because you don't have a feeling yet for the number of different sub-projects, the scale of those projects, and all of the variables that will change along the way. But, there are categories that will be important when it comes time for publishing and ensuring that you have all the information needed to reproduce your work. For me, those categories are experimental methods, data, analysis, and references.
Where to keep it? I have 3 places. I have lab notebooks - the daily record of what I've done. I have a physical filing cabinet - keeper of everything from written notes and hand-drawings to printouts of journal articles, hardware specifications, and data. And I have a computer (and backup!) - keeper of essentially everything that's not handwritten and a few things that were scanned in. The computer can really get you in trouble with it's infinite space and the myriad bad ways of organizing and naming files. But what I've outlined below works for me, and perhaps could work for others.
References/Journal Articles
I like to keep lots of pdfs of journal articles, and print lots, but not all. I generally make file folders (both physical and on the computer) that represent some general topic and file lots of papers in each folder. For computer files, I like to name the files "(first author's last name)_(Journal)_(pub year)_(2-3 key words)". This system works...okay. I can easily find the papers again when I need to, and it's nice to have hard copies with notes and soft copies for easy access when I'm away from my filing cabinet. However, now that I'm writing, I've started using EndNote, which may cause me to completely overhaul my system. We'll see.
Experimental methods
Experimental methods has been one of the most troublesome categories for me to organize. Methods can be a very diverse category, particularly in biophysics where methods may range from biochemistry to instrumentation to automation. Developing the methods may be a major component of a research project, or even if it's not, methods may change over time. Figuring out how to deal with diverse, evolving methods has been challenging.
Eventually, I determined two keys to organizing my notes and files on experimental methods: subcategorizing, and organizing by date. Over time, I found I generally had three categories of methods: sample preparation, instrumentation, and data acquisition.
For sample preparation, I found it best to type up a protocol, date it, and paste it in my lab notebook on that date. Then I could refer back to that protocol by date and lab notebook page number each time I performed the protocol. As I modified the protocol, I would still refer back to the same protocol, but note the modifications. Eventually, enough modifications would be added that I'd type a new copy, date it, and paste it in my notebook. Eventually, the protocols were fairly settled and each day I prepared a sample, I could just refer back to that date and page. And it worked well for some items I made and stored. Typically we write the date on anything bio-y that we store, and when I used it, or ran out and needed to make more, I could just refer back to that date in my lab notebook. Convenient. Plus, if a labmate wanted to do something similar, they could also look it up and not need me to "remember" exactly how I'd done or made something.
For instrumentation, I had several subcategories that required various forms of organization. I had designs, part specifications, optimization and characterization techniques, calibrations techniques, automation software. I wasn't the best about organizing these things as I went, but hindsight being 20/20, I've learned what I should have done.
1) Keep an accordion of files and a notebook dedicated entirely to your instrument.
2) Design involves a lot of notes, hand-drawings, calculations, references to articles. Date these things and keep them in a folder.
3) Part specifications become impossible to find later. Keep them on file, hard and soft copies if at all possible. (Also, determining what parts are in an instrument is really hard after the fact. Keep records of what you put in your instrument!) 4) Optimization and characterization techniques evolve, and the instrument evolves with them. Write down and date what you do in a notebook dedicated to the instrument (or at least make notes in the instrument notebook referring to where it is written down).
5)Calibrations are very important. Keep good notes on them, by date, in that instrument notebook.
6)Automation software is still a toughy for me. Ideally, it would change rarely, you would carefully track changes by date, and you would keep old copies. Our automation software is all custom written, in a very large suite of software that all works together. I tried to keep notes on major changes, and I tried to keep old copies, but ultimately, I didn't do it that well.
With hindsight, I eventually found the above guidelines to be a good means of organizing instrumentation techniques.
Data acquisition, was generally a combination of the above sample preparation and instrumentation techniques. Generally I prepared a sample and used the instrument in it's present status with the current calibrations to acquire data. And I used some of the automation software I had written to acquire that data. I usually made notes to this affect in my daily record in my lab notebook, with any modifications or variables noted. Those variables are one of the places where things can get tricky, as you often don't even know what the important variables are until you start changing them. But nevertheless, the lab notebook was generally where I noted the details of data acquisition.
Data
Data was actually the simplest thing for me to organize. Our lab had already established a system of organizing computer files by date and time stamp, with a descriptive base file name and different file extensions representing different types of data. I followed that system and found it works pretty well, as long as you follow it. Keeping notes in my lab notebook about the individual files was also key to knowing which files were what. Also helpful: a description somewhere of what's in the different files, and how to load the files for analysis.
Analysis
Analysis was another doozy of an organizational challenge. My raw data files were all nicely organized by date and time stamp, but for analysis, it took awhile to decide how to organize. Did I organize by date, like the data? But then, what about when I wanted to analyze data from several dates together? Did I organize by type of data? By date I performed the analysis? By type of analysis? And how did I organize the analysis programming itself? And what, if anything, did I write about it in my notebook? Or print anything out? Analysis organization definitely presented it's own set of challenges.
Eventually I decided to organize the analysis by date of the data and purpose of the analysis. If I analyzed several days of data together, I just titled it by the multiple dates and grouped it in the applicable month or year. I generally didn't write notes in my lab notebook about analysis, though I wish I had. I often printed plots, and put them in a 3-ring binder organized by data acquisition date and type of data. I wish I had more notes about my data analysis, and eventually I discovered notes about the analysis itself were very important (see below).
Even more important than the top-level organization of the analysis files was putting notes and organization into the analysis files themselves. My analysis software allows data folders, so that I could arrange data within the file by date, timestamp, and type. I also could make notes within the analysis files. I found keeping notes in the form of "date of analysis, goal of analysis, methods of analysis, and results of analysis" were very useful to making the analysis useful to myself later.
A couple more key points
Following the general rules above, I established a pretty decent filing system for myself. I have a lot of files, hard copy in my filing cabinet, soft copy on my computer, and lots of lab notebooks. In keeping this stuff useful, I have a few more key points:
1)Back up your computer files! In at least 2 places, 3 places ideally.
2)Organize your hard copy files. Filing cabinet, tabbed files.
3)Index your lab notebooks. Our labnotebooks had pages at the front for indexing. I liked to list a major category (sample prep, instrumentation, data, analysis, notes), then the specific task of the day.
Also, I found that the more information that was available on computer, the better. Lugging around lab notebooks and file folders sucks. I like to have soft copies whenever possible. Short of scanning in your lab notebooks (or typing all the entries), I found it useful to make an Excel spread sheet, organized by date, that listed what I did on each day that I acquired data. On this spread sheet, I also added in all the important changes made in the instrumentation, sample prep, and data acquisition. I color-coded it in subcategories. It's made finding data sooooo much easier.
Some final notes on file organization for publication
As I write up my work, I've found it very helpful to make a folder for each paper, and within that folder, to have subfolders for each figure or significant result. Each figure or significant result has it's own 1)analysis file, 2)final figure file, 3)data caption file, and 4)data source file. The analysis file has all the relevant data, from raw to fully analyzed. The source file has where the data came from, how and when it was acquired, how it was analyzed, and any important quantifications. The final figure file is the .jpg, and the caption is a caption that would be appropriate for the figure. With this information, I have everything necessary to include the figure or significant result in the the paper.
And that's it. That's my system. What's your system?
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