Tag Archives: comparison

MATLab and Biology

I made a bold prediction today. I predicted that Biology, as a discipline, would adopt MATLab as its computing environment. That may have been overstating things, but still, here’s why I think so:

 

1. Marketing: There are plenty of development environments out there. I’m looking at this from the perspective of a non-programmer. And non-programmers think in terms of “what program do I have to buy to do this?”

Anybody can code in a text editor in C and compile with a free compiler. But it’s not a complete development environment with a box, a price tag, and a user-friendly GUI. Biologists won’t use it. In terms of a packaged development environment, there’s MS Visual Studio, Mathematica, MATLab, Maple, Mathcad and some Open Source projects like SAGE.

2. Function Library. I’ve played with all of those but Maple. In terms of large, pre-made scientific funciton libraries, Mathematica and MATLab come out ahead. And they have a similar learning curve.

3. Math. Mathematica definitely has its advantages. But I don’t think that biologists think in terms of solving boundary value problems symbolically. They think more in terms of Finite Element simulations. Discrete math. That leans toward MATLab.

4. Social network. I suspect that the biologists will turn to their biochemist, chemist and engineer friends for adivce on computing, and they will hear MATLab overwhelmingly. I doubt they will go to
the physicists and mathematicians, where they might hear more about Mathematica.

OK, so MATLab’s the way of the future… what can you do with MATLab?

You can do everything that Excel does (including much nicer graphing options). Plus you can analyze images, spectra, or any other data. Most importantly, when you’ve gone to all that trouble, you can apply it as a loop to other inputs.

Take this for instance. Say you have a fluorescence image of cells. You go to all the trouble of figuring out three data values from that image. Maybe you measure cell count, average cell area, average cell fluorescence brightness. The trouble is that you probably have 100 images. Or you would like to in order to have a publishable result. That will take forever. If you “train” your PC to do that with MATLab, you can just run the program on a whole directory of images and have it spit the results out as an Excel file (if you insist on using Excel). Or a nice graph (it will look better if MATLab makes it).Or you can make a little GUI for your friends. I worked out how to do that in about 3 hours. Next time, 15 minutes.

Quantification is the future, and it is now.

Cheers,
Peter

Getting Things Done (GTD) vs. First Things First (FTF)

Stephen Covey’s First Things First (FTF) will help you examine priorities and focus on what is important. It won’t help you end procrastination when it comes to lots of important things vying for your time. David Allen’s Getting Things Done (GTD) is a more systematic approach to task fulfillment when there are a myriad of important but not urgent projects on your plate.

FTF sets out two really good principles of time management. The first is the idea of the Ladder. We’ve all heard about the corporate ladder – the stages of professional advancement in the world of corporate executives and lawyers. There are equivalent “ladders” in other professions, of course. The academic world has a ladder toward tenure; the political world has a ladder toward elected position; the list goes on. The ladder is the set of steps leading to a particular kind of success. FTF stresses that the First Thing should be to determine if the ladder is “leaning against the right wall.” That is to say, the success at the top of the ladder is not necessarily the best life for any given person. Since it takes a lot of time and effort to climb such a ladder, the success at the end had better be of the right kind.

The second thing that FTF does really well is to split all activities according to a 4 part matrix. Tasks are split according to their importance and according to their urgency. FTF points out that most people get focused on urgent things, sometimes at the expense of important things. An approach to life that will have an effect consistent with a person’s goals is one that focuses on things that are important to those goals. That’s sort-of a tautology. But what’s frustrating is that lots of times tasks and interruptions present themselves as urgent and critical even though doing them won’t actually create progress. Getting focused on important things is the most important message of FTF.

So, assuming you have found an appropriate goal and you are prepared to focus on things that are important to achieving those goals, how do you actually go about the day-to-day business of that? There are a few suggestions in FTF, like setting aside scheduled time for non-urgent tasks on a weekly basis. I can certainly see that being useful for a manager or executive with lots of interruptions. Setting aside an hour for private time to work through a strategic plan might be the only way he could actually have time to do that. For those of us in more free-form enterprises (like science or studying) that’s not so relevant. In a life filled with urgency, I’m sure setting time for non-urgent activities is critical, but my life is not filled with urgency.

I have 6 hours a day to do whatever I feel is important. There are not schedules, no interruptions. That’s great, but writing down in my planner that I want to spend an hour on strategic work during those 6 unscheduled hours seems arbitrary and I seldom make good on the plan. It’s a lot easier to procrastinate when there are no obligations than when there are. When I had classes, I would demand that I plan out the time between them so I could use it effectively. Now I have no classes, and such plans tend to get pushed aside for the importance of the moment (as opposed to the urgency of the moment). Now, that’s not great, because it means I’m not working from pre-planned priorities. I’m “winging it.”

The FTF mentality doesn’t help avoid procrastination when there is no urgency and many important tasks are doomed to failure. That’s science in a nutshell. Often there’s no hard deadline, since we all know it’s impossible to predict how an experiment will go. Although scientists know that it’s important to do the next experiment, without a deadline or any particular assurance of success, it’s a motivational nightmare. Science is all about the Q2 activities, but among Q2 activities it can be hard to discriminate. Reading the Literature, having ideas, surfing the ‘net looking for motivation all can conceivably be classed as Q2 activities, so how do we get pumped to actually get the experiments done?

This is where GTD shines. It won’t help you put the ladder against the right wall. It won’t help you cut out the Q3 distractions. But if you have those issues more-or-less settled, then you can get a lot from the GTD mentality.

The GTD mentality is a lot like a Virtual Assistant. The idea in hiring a Virtual Assistant is that this person will take care of certain things so you don’t have to stress about them any more and can really focus on the tasks at hand. What kinds of a things could a virtual Assistant take care of? Well, he could call you to make sure that you got to appointments on time. He could go through your inbox and make sure that all of the appointments to which you were committed were in the list of appointments about which he would remind you. He could parse emails and phone calls into the bare bones questions and flag them for you to answer. And he could tell you what was the next thing to do between right now and your next appointment so that you could use that time effectively and make progress on longer term projects.

Hiring a person to do all of that for you all the time is rather expensive (though with the connected nature of the world, you can hire a person to do the job at a long distance for a lot less than a personal executive assistant). GTD lets you do all of that efficiently for yourself.

The system works like this (or at least this is my boiled down version): you put everything in a trusted receptacle (like email inbox, phone, Thunderbird Task List, etc.). Call this your “bucket.” You have to make putting things in your bucket a really consistent habit or you won’t trust your bucket. If you don’t trust it, you might as well not waste time creating it. But once you trust it to have everything important inside, start the following loop:

When there is a lull (as when you have completed a task) check the bucket

Look for upcoming time critical appointments and set a timer (unless your bucket beeps at you, like my phone does)

Do any task you can do in 5 min immediately, this includes things like delegating, filing away for long term, short emails, or triaging a task as no longer mission-critical.

Do the thing on the top of the list until your next time critical appointment, or until it is done as much as it can be at the time. Add the next step in this project (and only the next step) to the bucket.

Repeat

The most important thing about this is that you must trust your bucket to have everything in it. If it is a trustworthy bucket (if your habit of adding things to the bucket is good enough) then you will never be blindsided by an appointment you forgot about or a deadline that came out of nowhere.

Both the GTD and FTF systems remind their readers to re-center once a week. Process everything, prioritize, decide if projects are worth continuing. FTF organizes this according to “roles and goals” which is a fine way to do it, maybe a little more systematic than the “altitude analogy” treatment in GTD.

Hope that’s useful to you all.
-Peter

P.S. David Allen did a Google talk where he talked about his method. That might explain it better if you have 45 min. Alas, he’s not as polished a speaker as S. Covey, but it’s still a fine talk.