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3:38 pm by admin in life
My daughter, nine, sleeps in; I like to get up and be in front of the computer working by four or five a.m. Last weekend when I was putting her to bed she looked at me and said "Dad, I want to get up really early tomorrow morning like you and we can go for a walk—I’ve never seen what it’s like outside that early." Then she told me she knew that when the morning came she would be asleep and I would decide not to disturb her, so she made me promise to wake her up no matter what.
Six-thirty the next morning, I gently nudge her shoulder as she sleeps. Her eyes open and she hits the ground running—the next thing I know she’s got her coat on. "Hurry up, Dad, it’s getting light!"
So we step outside, and she’s amazed, first of all, that there aren’t any cars, except a few taxis, and hardly any people. We live in the West End of Vancouver so we decide to walk down to the water at English Bay and along the seawall for a bit. I’m amused that she’s so amazed at the difference between this time of the day and when she’s normally up, so I start making up lies: "Do you know that early in the morning like this the animals can talk?". I proceed to give a crow sitting on a lamppost a jaunty "Good Morning to you, Sir!" as we pass. This gets an eye roll, because it’s not like she’s five and is just going to believe everything I say. Then I start making up tales about people on the seawall handing out free porridge to all the early risers. Another eye roll, but she is, as usual, moderately amused by her old man.
Then she stops and stands on the seawall, still and quiet, then says she can’t believe "how smooth the water is." I agree and try to make up some kind of lie to fit the situation but nothing comes.
Next thing we know this huge, and I mean huge—it must have been forty pounds—raccoon streaks across the grass in front of us. And there are about five crows chasing it, making a hell of a racket, and they’re taking turns dive-bombing it. Must be some thing that happens between crows and raccoons, but I’ve never seen anything like it. They chase the raccoon, who’s running like hell, to the road and across it; a car screeches to a halt, narrowly missing it. The raccoon disappears into the alley behind a hotel.
She looks at me, and I look at her. "See?" I tell her casually, "I told you things were different in the morning."
7:40 am by admin in Uncategorized
Hmm…only three months since the last post…not bad, I guess. I actually haven’t given up on this, despite a number of tribulations that have cropped up.
What I realized, sometime in November, is this: my plan to revolutionize science in one fell swoop was ridiculously naiive. Science is by its very nature a conservative enterprise. Scientists—good ones, anyway—are visionary and daring with ideas, but extremely careful about the way they actually carry out lab research. The person who sees a neat Nature paper on drosophila developmental genetics and decides that tomorrow the whole lab is switching over from mouse work, including all the techniques the lab has taken years to get up and reliably running and, more important, fixable when something goes wrong, is not going to stay in business very long. So approaching them with a grand plan to revolutionize the most basic of their research activitiies, record keeping, was doomed to failure.
I’m still convinced that over the next ten years more and more scientific record keeping will move to computer databases, where it can enjoy all the benefits inherent in that. It’s inevitable. What I’m concerned about is that this will be done piecemeal, such that the final system will be a hash of hastily implemented solutions meant more for business then being designed for the very different structure of the free-form but intricately connected data that lab research generates. Let’s say an "electronic notebook" in the form in which they are emerging today, which in my mind appear more like a gigantic Word document that data can be pasted into than a set of databases intelligently designed to match the unique character of this data.
After a great deal of thought I realized that, rather than a "top-down" approach ("I’m going to change everything! Why aren’t you excited about this?") I need to pursue and sell this idea from the bottom up. In other words, to offer scientists tools that will accompany their traditional methods (namely the handwritten notebook) but help them start organizing things better. For example, a system that would allow them to label every sample produced, record its storage location, and, most important, link it permanently and unambiguously to the notebook page where its creation is described. Even if that person left the lab ten years ago. Wouldn’t it be nice to come across a frosty microfuge tube in a hoary old box in the back of the freezer, give it a quick rub and a swipe of the barcode, and be able to look up in seconds not only what it was but what page of whose notebook it came from?
The beauty of this system is that, as I’ve designed it, it will take a few minutes at the end of every day to put the pre-printed label on the tube and enter a bit of data into the computer. I can also make it viable using free software at a cost of a few dollars per sample. But the real beauty is that this data, limited as it will initially be to assure acceptance, will be stored in the format I’ve devised to ultimately link everything in the lab: protocols, experiments, sample-to-sample-to-sample lineages, all searchable. By using my system you’ll be able not only to solve a ubiquitous and vexing problem in your lab—"Can I trust that this poorly labelled sample is really what I think it is?"—but start laying down the foundations of a much more comprehensive system of dedicated lab database software.
Slowly…slowly.
10:26 am by admin in Development
Well, this is it: time to put together all the components of the lab data management software I’ve been working on for the past five or so years. It’s taken this long because when I started I didn’t know where I’d end up. I had a general idea of what I wanted: the software would handle any kind of data, from mice to DNA samples to digital images; it would be scalable so as to be able to accommodate the vast amount of data accumulated in a lab over the years; it would be simple, robust, and able to be installed by the user without the help of IT; and it would include a means to create a series of higher order data summaries automatically. But it turned out to be the sort of thing where you don’t know where you’re going until you start, and once you gain a clearer realization of your objective you sometimes need to backtrack and start over.
Creating a data model that would handle the variety of data generated in a lab has been challenging. I approached it by breaking down the data into categories, which ultimately revealed themselves to be samples, procedures, measurements, and a single higher order category, experiments. Then I had to look at each category and come up with a system of data storage and access that would not only fit the different data types but also work in accordance with the more general objectives such as usability and scalability. There’s some work to be done on that yet–I haven’t nailed down how to store and access measurements, and I haven’t really thought about experiments yet other than to conceive of them very generally as a patterned array of samples, procedures measurements. But that can come later.
I’m going to start with samples and procedures, which are the backbone of the whole enterprise. Every day in the lab you start with one or more samples of some type and do something to them in an experiment. The ‘doing something’ part I’m calling a procedure. Details on the first steps next post.
9:53 am by admin in life
…in which Rob is revealed as a cynical smartass.
Friday afternoon: still no notice of payment from the monolithic BRI. I spend another hour on hold as the triumphant elevator music clip is burned into my brain, then give up when I am finally convinced by the repeated announcement:
"Your call is important to us. Really. But just between you and me, you’re going to be waiting a long time. A long, long time. In fact, I don’t even know if there’s anyone answering these phones. And if there is, can you imagine how pissed off they’re going to be after listening to complaints from people like you all week? No, if I were you I would just relax and hang up that phone. Make it easier on everybody. Just put it down, now…you can do it…nice and easy…there you go."
As I sit at my desk with the dead phone in my hand, wondering how I got here, inspiration strikes. I remember that I actually got through to a real human at one point (the Angry Lady). Maybe this time if I try really hard to be nice I can get her to help me.
I dial the number and wait as it rings, preparing myself for the little stutter that tells me the call has been transferred to voice mail. Then: "Hello?". Success! From her accent I know it is the Angry Lady. I (verbally) throw myself prostrate in front of her and beg her to look up my p.o. number. She does! Then she tells me that she doesn’t handle this "type of number" (what, it’s got too many sevens?), but if I call another phone number I will get through to someone who does.
And here’s where my cynical crappy attitude is revealed as just that. I get a very nice lady on the line, and tell her what my problem is. She tries several ways to find my invoice but can’t and asks me to resend it to her because she is ‘going to make sure she takes care of me’ and ‘would feel a lot better just having the invoice in her hand’. I promise to do this and she says, in a worried tone, that it’s 4:00 on a Friday afternoon so she’s going to try to get down to the mailroom on time but they sometimes leave early there so… it might be Monday morning before she can send the payment.
Monday morning? Monday morning is great! I tell her this and thank her effusively. As I hang up I realize I’ve found my gal—I just had to look for her.
12:04 pm by admin in life
Back in June I made a very nice sale of Big Bench Mouse to an investigator at a very large US government research institute; let’s call it Big Research Institute. When I sent my invoice I was delighted to be informed that they were to pay by direct transfer of funds to my bank account. Hallelujah! No waiting for a cheque! No usurious cut taken by the company holding my credit card merchant account!
It didn’t work out quite that simply. I found out that in order to be entered into the BRI accounting system I had to be registered as a US Government Contractor. This involved applying for three different numbers in three different places, filling out and faxing myriad forms, registering with Dun and Bradstreet and, most excellent of all, registering with the Canadian Armed Services.
Anyway, on August 20th I received notice of the last required registration (my Trading Partner Identification Number). Jubilantly I submitted my invoice, assuming payment was just a few days away. Then I reconsidered:
Dear Barbara,
I’ve faxed my invoice to the number you gave me.
Now, I don’t want to be cynical but I have this sneaking suspicion that this is not the end of the process. Well, that’s not entirely true. When I faxed the invoice I visualized the cheerful gang at BRI headquarters passing a pleasant afternoon at their desks as they conducted the nation’s business. One in particular, a quietly beautiful young lady, modestly but stylishly attired, would have been sitting at her desk, perhaps eating an orange. Suddenly her ears would perk up. "What’s that?," she’d wonder to herself, before the realization hit her, "By God, I think it’s the fax machine." Unfortunately, by this time others in the office would have picked up the telltale sound and each would have jumped from their chairs in a race to be the first to arrive at the machine and snatch the still-warm facsimile as it emerged from the rollers.
My gal, though, would have been the first. She would briefly scan the cover page before triumphantly holding her prize aloft and shouting "It’s the Scientifica order from Rob in Canada." Suddenly a cloud of worry would pass across her face as she glanced at the clock. "Ohmigod, it’s already three o’clock on a Friday. We’re going to have to hustle if we’re going to get this money to Canada by the weekend!"
Fortunately all the BRI’ers would be eager to pitch in and do whatever they could to ensure that the Canadian was paid promptly. After all, they understood the challenges that had been placed before him, and which he had hurdled with commendable aplomb. "He even had to register with the Canadian military!" one would exclaim. "Does Canada even have a military?" would question a second. "I don’t know anything about that," BRI’er number three would muse, "but I do know that if I want to find out anything about his company, Scientifica Software, or any of its pending orders, I need only visit the Central Contractor Registration Site (small/female/minority -owned business subdivision) and enter his Official US Government Alien Corporation Doing Business in America Registration Number. I have it on reliable authority that this task should take no more than thirteen and a half minutes to complete!"Alas, Barbara, I fear something has gone awry. The funds have not yet arrived in my account, which leads me to suspect that your eager colleagues have hit a snag and are right now engaged in an agony of worry and mutual recrimination as to who is ultimately responsible for this unforgiveable lapse. I fear that in the meantime the BRI will have been diverted from its critical disease curing mission. So I beseech you, Barbara, how can I help and get the BRI back on track?
With humble thanks,
I remain yr obed’t servant,Rob
Barbara-not-her-real-name writes back to me and very matter-of-factly explains I’m not the only one not getting paid, as the BRI has undergone a wholesale change of their purchasing and accounting system—which is so far totally not working—and none of their other orders are going through either. I sense that her proximity to the problem is making it somewhat more difficult for her to find humour in my situation. But hell, she doesn’t have a bunch of money tied up in it either, does she?
Anyway, she gives me two numbers I can call for further information ("hint hint never email me again"). I cleverly decide that the rest of the chumps are going to go straight for the first one so I should have the second number all to myself. This turns out to be true, as I immediately get a human on the line. The bad news is that this human is a very Angry Lady. She begins to grill me as to who gave me her personal phone number, with the clear implication that if she finds out who it is they are very quickly going to find themselves escorted out the front door of BRI Headquarters with a security guard on one arm and a hastily packed box of possessions in the other. I mumble a bit and manage to keep Barabara’s identity a secret, and then set myself to the task of getting Angry Lady to put my invoice through. Now, I can usually turn on my natural charm and get phone ladies, even angry ones, to cooperate, but this one is a pro and is having none of it. She insists that I will have to call the "Customer Service Line" if I wanted to see anything happen.
I have an uneasy feeling that "Customer Service" is one of those NewSpeak terms that mean precisely the opposite of what they purport to. But I call, and wait for the canned "We’re so happy to be taking your important call!" messages to finish. The next message is by a woman who, in contrast to canned Ms Happy, obviously actually works there. The tone of her voice, tired and frustrated, makes it immediately apparent that recording the hold announcement is not something she cheerfully volunteered for. As I wonder what she is being punished for—Grievous Assault on a Customer from the sound of it—I hear her tell me that the BRI had recently undergone a "massive technological restructuring" and that I "should be prepared for extremely long wait times." Then the canned happy voice again. "We are experiencing abnormally high call volumes. Please remain on the line as your call will be answered in priority sequence! Estimated wait time is…EIGHT!…MINUTES!"
After an hour and a half I give up.