Biocurious

/ a biophysics blog

Semi-digital lab notebooks

Posted 17 January 2009 by PhilipJ under

Going on a year ago, I talked a bit about digital lab notebooks and their use as a potential replacement for the paper notebooks we all carry around. The idea of a digital notebook is very appealing: searchable, easily archived, portable (if you wanted to place it on the internet), etc. The downsides, however, are also obvious: having a computer next to you on the bench to write is not always ideal, since spilling a solvent on paper causes relatively little harm compared to frying the electronics of a laptop. It is also much slower to do a quick sketch on a computer than on a piece of paper.

When I first tried to “go digital”, I set up a wiki on my group’s server and would try to include information in it as I was going about my day. I found it, unfortunately, quite cumbersome. When the kinds of things you are doing at the optical table are alignment, position readings, power measurements, etc, I found it crucial to keep my paper notebook with me to quickly record these numbers and make sketches of the optical elements, and I was loathe to transcribe this information into the wiki later, mostly because scanning or redrawing the figures digitally takes too long.

When it comes to data analysis, however, everything has to be done on a computer, as it is just not feasible to plot thousands of data points by hand in a paper notebook. My computer algebra system of choice is Mathematica, and because of Mathematica’s notebook system, it became extremely straightforward to include sufficient commentary among the analysis and calculations. The important “working” details of my day are recorded on paper that is heavy on scribbles, numbers, and comments on the minutiae of a particular instrument or measurement, followed by references to specific data files collected that day. The Mathematica notebooks where I visualize and analyze data are then filled with the relevant comments about the data collection and subsequent analysis, but not usually the random scribbles that you need to keep on paper while leading-up to and actually taking a measurement. Having everything organized by date makes it simple to correlate between paper and digital notebooks.

All this is to say that I’ve found a happy medium between analog and digital data retention. The paper notebooks will remain as a permanent record of the day-to-day activities in the laboratory, while digital notebooks are used to flesh out important collected data. The only downside is that Mathematica is not an open platform, but as long as there are free Notebook readers available, I’ll try not to get too worried.

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Micropipettes and the shakes

Posted 8 November 2008 by PhilipJ under

Dr./Mrs. Jekyll/Hyde has been teaching a new laboratory tech the tricks of the trade (or, as it turns out, some basic algebra), and in one of the posts mentioned something that we often don’t think about in science education but is critically important when you’re actually in a lab: having good hands.

This is important for a variety of reasons: pipetting solutions, filling the wells of a gel before running electrophoresis experiments, or even simpler things like not stabbing yourself with a needle or not dropping expensive samples. The shakes can be the difference between having to do experiments only once and wasting an entire week repeating them, with questionable results each time.

Not drinking coffee is, for me at least, not an option. Thankfully, my Ph.D. work involves very little that explicitly requires extremely good hands (mind you, pipetting solutions in a dark room under dim red lights* is annoying no matter how good your hands are…). I was not so lucky for my Master’s work, where, you may recall, I dealt with micropipettes.

Making the micropipettes was annoying for consistency reasons, but actually getting a micropipette into a flow chamber was the real fun part. Our flow chambers looked like this:

flow chamber

Brown tubing, having an outer diameter of ~160 microns, and an inner diameter about half that, was squished between melted Nescofilm between two No.1 coverslips, and was the means of inserting micropipettes into the active flow area.

pipette tipThe micropipettes, shown on the right, were tapered to ~1 micron at the very tip (the polystyrene bead held by suction at the tip is 2 microns in diameter), and for practical reasons were usually 3-5 cm long. They were connected to a length of thin tubing so as to allow for easy connection to a syringe, and the whole contraption was mounted on an aluminum clamp, with a separate clamp specifically to hold the micropipette in place.

As I mentioned above, I drink a lot of coffee, and while I don’t have a serious case of the shakes, I don’t have a particularly steady hand. Despite this, I would insert the micropipettes into the brown tubing by hand. We had a 20x optical microscope with two-dimensional motion on the microscope stage. I would mount the flow chamber to the stage, centre everything such that it was all in focus, bring a micropipette tip into the field of view by hand, and, once also focussed, try to move the stage so that the pipette tip ended up in the brown tubing.

This would (obviously) often result in disaster, as any time the tip of the pipette would touch the brown tubing it would be ruined, no matter how incidental the contact. For a while I was keeping a log of successful tips to ruined ones in my lab book, and the ratio got so depressing I had to stop. By the end of my Master’s though, despite my regular multiple cups per day, I had developed a couple of tricks to raise
the success rate. The most useful of which was to introduce water into the system.

Flushing the flow chamber with water would produce a large (under the microscope, anyway) bead at the opening aperture of the brown tubing, which, after Kimwiping it away, would leave a slight meniscus of water right at the entrance. When the tip of a micropipette was nearing the entrance to the brown tubing, the pressure difference in the pipette tip would result in rapid suction of water from the meniscus into the pipette. With much practice, rapidly moving the stage once observing water in the pipette led to, near the end anyway, maybe as high as a 50% success rate in getting tips into chambers.

While my Ph.D. work has it’s own series of issues (this week’s: overlap two 200 femtosecond pulses focused into a ~100 micron diameter area. Spatially is simple, temporally, less so), I am very happy I don’t have to do anything like that anymore. I think I’ll have another espresso to celebrate!

* I’m working on the most-obviously-photoactive protein you can imagine. Take a guess which!

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We need to stop pigeon-holing science

Posted 4 May 2008 by PhilipJ under &

My brief anxiety over what kind of scientist I am was initially posted as a bit of a joke. As the resident wet lab junkie (scary!) in what is primarily an ultrafast optics group, having spent at least as twice as much time on sample prep over the past 8 months as I have on aligning lasers to do fancy nonlinear optics, it gets harder and harder to say things like “I’m a physicist“ with the same kind of certainty that I once would.

And you know what? That’s okay. The more I play in other sandboxes (or as the case has been, dark rooms*), the more I realise my own sandbox of physics is no “better” than anyone else’s. We’re just asking, and trying to answer, different questions.

This is all coming to mind because we just finished holding the annual Chemical Biophysics Symposium again, and on the first evening of every symposium there is a panel discussion on some interesting topic. Something that keeps coming up at these kinds of discussions is the “us” versus “them” comments, wherein “us” is invariably physicists (or physical chemists), who are the majority of the audience at the symposium, and “them” are those nebulous biologists who never seem to be around to offer a biologists viewpoint on science.

I have news for physicists who have woken up to find lots of fun problems in biology: most of us are solving physics problems in biological systems. We are nowhere near addressing most biological problems. It is flashier and more exciting to say we’re working on cancer, or drug deliver, or what have you, but in most cases we really aren’t working with biologists to help solve biological problems, despite claims that we are now starting to study biology the “right way”.

It is useful to recall Bob Austin’s take on the interesting problems in biology:

I want to do the big problems: I want to understand energy flow in biomolecules; I want to understand how genes are turned on and off; I want to understand the collective processes in cell growth; I want to understand how the brain works; I want to understand the origins of consciousness. […]

Nowhere above does he say “the physics of …”. It is great that physicists are turning to biology for new problems to solve, but I grow a little tired of the physics vs biology mentality. If we truly want to make great strides in understanding biological phenomena, we need to stop pigeon-holing disciplines. There is no “us” or “them”, “they” aren’t doing things incorrectly, we’re all simply using the tools we were trained to use to solve the problems we find interesting. What we really need to do is find better ways to share ideas, so that everyone understands exactly what they can contribute. We can’t be afraid to learn from each other, and in the case of biology, it is most certainly a two way street.

* More on this soon.

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Identity crisis

Posted 17 April 2008 by PhilipJ under

I just used ChemDraw for the first time! What does this mean???

Also, I’m studying for a biological chemistry final. It could hardly be more different than studying for a physics course. Blurring the line between the sciences in research is awesome, taking the other side of the line’s courses can be… tricky. Biology isn’t harder than physics, it’s just different.

Come on May 1st.

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SciBarCamp report: Digital lab notebooks

Posted 16 March 2008 by PhilipJ under &

The first SciBarCamp is going on this weekend at Hart House at the University of Toronto. The basic idea of SciBarCamp is that of “a gathering of scientists, artists, and technologists for a weekend of talks and discussions.” The kinds of things that have been discussed this weekend are the forefront of science (quantum gravity, synthetic biology, open access, scientific software), and the interactions with science and technology and art. There’s an extremely interesting mix of people here today, from quantum information theorists from the Perimeter Institute to social scientists from OCAD, grad students, science writers, musicians, etc. Quite the eclectic group.

The “un“conference opened up with what was perhaps the most interesting discussion for me. It was by Corie Lok from Nature Networks and John Dupuis from York University on “Science 2.0”, or basically how technology is changing first the way we do science, and then how we publish and track science. Things like Connotea and del.icio.us were discussed as ways to keep track of relevant journal articles, but the discussion was dominated by discussion about keeping track of your experiments, and how this is changing in laboratory environments.

Many labs are moving to an all-digital lab notebook. Gone are pens and paper as the primary means of keeping track of your experiments, and they are instead being replaced by digital equivalents, such as wikis or some other, commercial software (which I unfortunately didn’t catch any names, but a google search brings up all kinds of examples). The advantages of such a “notebook” are clear: entirely searchable, easily referenced with hyperlinks, the ability to keep digital images and snippets of code, etc. There is also an advantage which hadn’t been discussed, but is something I’ve long thought about: legibility! If you’ve ever looked in another scientists notebook, you will quickly find that their writing may be atrocious (guilty as charged), and it quickly becomes an exercise in frustrating trying to interpret what was written.

Perhaps not surprisingly, this is being embraced in a big way by the big pharma companies, where it is crucial to have detailed records, and to keep them for a long time (something like the lifetime of a drug being sold + ten years). But there’s an advantage to graduate students in academic laboratories that hadn’t been addressed in the discussion, that came to me as I was talking about this to another grad student friend. It’s that of the copies. I graduated from SFU with my Master’s less than a year ago, but I could tell you basically no specific details on some of the more mundane, day to day experiments that I carried out. I’m sure the same thing happens to those who graduate with a PhD, and leave their lab notebooks behind. I’ve decided I want to keep this kind of information, and I’m still early enough in my PhD that it won’t be too hard to change.

To the other scientists reading this blog: have you changed to a digital lab notebook? Have you tried the switch and failed, or have things gone smoothly? What software did you decide on? I’m leaning towards a wiki, and I’ve decided it will be necessary to keep a paper notebook as well, but to make it degenerate information which will, at the end of every day, always end up in the digital notebook as well.

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Repoll: Windows in your office?

Posted 19 October 2007 by PhilipJ under &

I have some exciting news.

Well, it isn’t exactly new, since I’ve been in Toronto for three months now. But it’s still exciting to me.

Last year I asked if there were windows in your office. Now I can happily change my answer to yes!

Yes, that is natural light saturating my digital camera! Now, I’m in a chemistry building, so the windows don’t open, but this is still significantly better than the concrete bunker I used to call an office.

How about you, has your situation changed?

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