ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.
[A Charity Event held at the Ghana National Science Museum, with Kwame Yeboah and the OBY Band (Ohia Behe Ya Band). Reviving this essential and beloved part of Ghana's musical history.]
. . . Rains that the clouds spewed dropped on the soft edge of dignity
We enjoyed games in the market 'cause there was key soup
Elders greeted each other - you could feel the serenity
The football that we played didn't know stadiums like the Bundesliga
We were both players and referees - back then we didn't know FIFA . . .
Update (March 8, 2014):
From "The Atenteben and Odurugya Flutes" by J. H. Kwabena Nketia:
"The interpretation of the tunes should be guided by traditional practice. Short pieces may be repeated as a whole or in appropriate contrasts e.g. solo/chorus alterations, alterations between atenteben and odurugya solos, alternations between flutes and voices (humming, singing to a nonsense syllable etc.) A number of them could also be played in a cycle, or arranged in the form of a suite. Pieces with similar modal structure or similar rhythmic foundation can be easily combined. It is our hope, therefore, that creative performers will find this book useful as a source material for building up their repertoire of flute pieces."
Physics at RMC: The First 125 Years
pages 82-85 As part of setting up the new Science and Engineering program at Royal Military College in 1957, we (Tom Hutchison and David Baird) embarked on preparing a Third Year physics laboratory course. As with all the laboratory courses in the preceding junior year, the course was constructed to follow the traditional pattern in which the students, working in pairs, were provided with detailed instructions for every step of their experiment. These instructions included all the relevant theory, the setting up of the apparatus (including if necessary, circuit diagrams), the schedule of the measurements, the drawing of graphs and the calculation of final answers. Nothing was left to the skill or imagination of the student. The purpose in these ritualized exercises was not clear. Such was the unquestioned practice that was almost universally followed in those days.
At the end of the 1957-58 academic year, Tom and I decided to pay homage to our stern Scottish heritage of laboratory education and give the students, for the first time, a laboratory examination. Without thinking, we apparently assumed that in the laboratory courses that were part of all their physics courses in the preceding three years, the students must have learned something of how to actually do experiments. In addition, thinking to let the students down gently, we chose a simple experiment. We gave the students a dish-shaped glass "watch glass", a steel ball bearing that could roll in the watch glass, and appropriate measuring equipment for dimensions and time. A small piece of paper stated that the requirement for the examination was to derive an expression for the period of oscillation as the ball rolled back and forth and make the necessary measurements to derive a value for the acceleration of gravity.
At the time appointed for the examination, the students were admitted and Tom and I confidently strolled around the laboratory, innocently expecting to supervise the busy activity of the students. Instead, there was complete stillness and profound silence. After half and hour of total inactivity it finally dawned on us that after three whole years of traditional laboratory courses the students still did not have even the most remote idea of how to conduct an experiment. Eventually, we wrote the necessary formulae on the blackboard and coaxed the students through their "exam." It was an enlightening experience for Tom and me. For the students, it was sufficiently traumatic that one senior retired officer (an ex-Commandant of the RMC) recently accusingly mentioned it to me.
Tom and I were forced to recognize that almost all time spent in our earlier highly structured laboratory classes had been wasted. The students had no idea of the nature of measurements and their uncertainty, the nature of theoretical models, the significance of graphical analysis of the experimental results, or the nature of the final statement one could make about the experiment or the results.
For the 1958-59 school year, I attempted to construct a syllabus for the Third Year laboratory class to address this. It was a dismal failure. After two whole years of following recipes in the preceding labs, the students had no intension whatsoever of actually working to acquire something as esoteric as experimental independence. It was clear that, like learning a foreign language, experimenting involved basic mental attitudes that would have to be acquired at the earliest possible stages.
I asked Tom if I could have the First Year lab. This had traditionally contained nothing but experiments that consisted of a series of illustrations of the lecture course material in "recipe book" style. This we now totally discarded. The new program consisted of a mixture of lecture material and experimental procedures chosen specifically to illustrate the various aspects of measurement uncertainty, measurement statistics, graphical analysis and the analysis of experimental results.
Reference: Experimentation, An Introduction to Measurement Theory and Experiment Design (Link)
Some of you, if you've been reading this blog recently, will know that I went to a military college. Yes, well, how did a Vancouver granola kid end up at the Royal Military College of Canada (RMC)?
In fact, I had grown up in Vancouver (British Columbia) and even volunteered for a bit at the Greenpeace office in the 70s (before it became an international going concern.) It had occurred to me that, like most of my other classmates at Magee Secondary School, I would probably end up going to the University of British Columbia. There was only one problem. I had a private pilot license and I really wanted to be a commercial pilot. In Canada, at that time, there were pretty much only two ways that you could become a commercial pilot: (a) become a bush pilot or (b) join the Air Force.
As it happened, as I was considering my options, for the very first time, RMC, under pressure from Canada's Prime Minister Pierre Trudeau, had decided to accept women.
I was also quite interested in science and I heard that RMC had a pretty good science program.
Finally, I also wanted to escape the west coast, at least for a while.
And that is how I ended up standing there in first year physics lab, in my damn uniform, trying to remember what I should write under "Method" and whether or not I should have separate sections for "Discussion" and "Conclusion". So here comes Professor Hutchison. At this time, he was several years before retiring. I'm sure he thought I was a complete novelty and I distinctly had the impression that he thought I should be taking English Literature or Anthropology at Queen's or U of T not Physics at RMC. In spite of this, I think he took me on as a special case. He would come to where I was rushing to throw my "Experiment" together and try to give me a few suggestions. He had a Scottish drawl and a very dry wit which, at the time, I did not fully appreciate. I somehow survived the first year Experimentation lab in part due to his patient attention. Dr. Baird was also a professor in the Experimentation lab.
I took a class in solid state physics from him in second year which was very good.
He would often try to talk to me about golf. Golf! "We are not running a country club here, Professor Hutchison." My chosen sports were cross country running and track and I was usually in no mood to discuss golf. I did tell him one time that my Dad liked golf. I could tell that he made the point of writing that in his mental notebook.
In third year, I ran across him at a social function. By this time, my class load was particularly heavy and my formerly very dedicated running schedule had been down graded a bit. I had figured out that I could use the after class "training" to instead escape (jog) to Kingston in order to hang out with some of the students at Queens University. Hutchinson was chiding me about not being a very dedicated athlete. Misunderstanding him, I quietly vowed not to speak to him again.
And I never did. I graduated a year later. I never said goodbye. He retired. He died in the mid-nineties.
I found out quite recently that he had told David Baird that he knew what I was up to. He knew that I had been escaping to Queens. He apparently thought it was funny and was delighted for me.
I was talking to David and Margaret, his wife, a few days ago. Now both in their eighties, they are currently helping a poor neighborhood forestall the building of a cell phone tower too close to a low income residence. When I visited them last year, they were more than busy working to preserve the beautiful traditional architecture of Kingston, Ontario. They have many friends, a number of whom are current and former faculty members of both the Royal Military College and Queen's University, including Agnes Hertzberg.
David is the former head of the Physics Department of the Royal Military College of Canada (RMC) where I obtained my first undergraduate degree (Honours Math and Physics). He was my professor for a first year lab in experimentation. He also taught me in a class on quantum and statistical physics. So, about the picture. David loved to use natural phenomena to teach his classes. My first exposure to Young's Double Slit Experiment was with David putting up photos showing the interference of waves on Lake Ontario. He had managed to find a spot where a river (the Cataraqui) interacted with "The Lake", resulting in a beautiful demonstration of double slit induced constructive and destructive interference. The above photo approximates the delicious pictures that David used to introduce this concept.
I also clearly remember David introducing Fourier series and Gibb's phenonoma toward the construction of a square wave. Another favorite was the visual representation of the sinc function and the squared sinc function. He had an artistic flair in the presentation in his classes, a genuine warmth and a great sense of humor. He was also a very rigorous scientist. I never really understood just how rigorous until many years later. I just remember really getting nailed when I had missed some concept like not getting the proper calculation of uncertainty. There was a gravity to it.
Recently, David wrote a book on the history of RMC. I'm currently reading it. The book has some surprises such as these:
"At a time when personal contact between east and west was carefully supervised and rare, three prominent Russian physicists were authorized to make a closely monitored visit to Toronto to attend the 1960 International Conference on Low Temperature Physics. They were B.N. Samoilov, V.P. Peshkov, celebrated as the discoverer in 1944 of second sound in liquid helium II, and B.I.Verkin after whom the low termperature laboratory of the National Academy of Sciences of Ukraine was named as the B. Verkin Institute for Low Temperature Physics and Engineering." David and another professor hosted them in Kingston and even drove them to the Thousand Islands Bridge "so they could, at least, look across the international border at their Cold War adversary."
"The French-language teaching in the Physics Department had actually started in 1974. Mukherjee, who since 1969 had been a Research Associate with Wiederick and Baird, was the only department member fluent in French (his early education in India had taken place in Pondicherry where the European language was French), and in the 1974-75 academic year he taught in French the entire set of Third Year physics courses in the Engineering Physics program - no mean feat for one's debut in professional duties." [Mukherjee and Wiederick would eventually together focus their research on the characterization of dielectric and piezoelectric properties of materials.] [With extensive hiring from 1975 to 1977, the extension of French language teaching in the Physics Department to all four years was accomplished by 1977.]
David's official bio reads as follows:
David Carr Baird was born in Edinburgh where he attended George Watson's Boys' College and the University of Edinburgh. His early interests included music, astronomy, researching historical sites for the Society of Antiquaries of Scotland, archaeological excavations, and mountain climbing. While studying for his Ph.D. at St. Andrews University, he developed a lifelong love of flying while flying Tiger Moths as a member of the RAFVR Air Squadron at Leuchars.
In 1952 he joined the Physics Department at RMC to continue his research in superconductivity, and to participate actively in the development of physics curriculum at all levels from elementary to post-secondary. He is the author of several physics texts that include Experimentation which has been in print since 1962.
Following his term as Head of the Department, he was appointed Dean of Science during a period of considerable change from 1980 to 1990. During this decade the introduction of Space Science resulted in the creation of new research areas and educational programs. In 1981 he became Director of an interdisciplinary team which constructed the first model in Canada of a superconducting motor for ship propulsion.
His early interest in archaeology was renewed when he undertook research as Visiting Scientist at the Laboratory for Archaeological Science and the History of Art at Oxford University (1980-95).
He encouraged his children [and his students] to follow their individual interests.
One day at Princeton I was sitting in the lounge and overheard some mathematicians talking about the series for e^x, which is 1 + x + x^2/2! + x^3/3! + ... Each term you get by multiplying the preceding term by x and dividing by the next number. For example, to get the next term after x^4/4! you multiply that term by x and divide by 5. It's very simple.
When I was a kid I was excited by series, and had played with this thing. I had computed e using that series, and had seen how quickly the new terms became very small.
I mumbled something about how it was easy to calculate e to any power using that series (you just substitute the power for x).
"Oh yeah?" they said, "Well, then, what's e to the 3.3" said some joker - I think it was Tukey.
I say, "That's easy. It's 27.11."
Tukey knows it isn't so easy to compute all that in your head. "Hey, How'd you do that?"
Another guy says, "You know Feynman, he's just faking it. It's not really right."
They go to get a table, and while they're doing that, I put on a few more figures: "27.1126," I say.
They find it in the table. "It's right! But how'd you do it!"
"I just summed the series."
"Nobody can sum the series that fast. You must just happen to know that one. How about e to the 3?"
"Look," I say, "It's hard work! Only one a day!"
"Hay! It's a fake!" they say, happily.
"All right," I say, "It's 20.085."
They look in the book as I put a few more figures on. They're all excited now, because I got another one right.
Here are these great mathematicians of the day, puzzled at how I can compute e to any power! One of them says, "He just can't by substituting and summing - it's too hard. There's some trick. You couldn't do just any old number like e to the 1.4."
I say, "It's hard work, but for you, OK. It's 4.05."
As they're looking it up, I put on a few more digits and say, "And that's the last one for the day!" and walk out.
What happened was this: I happened to know three numbers - the logarithm of 10 to the base e (needed to convert numbers from base 10 to base e), which is 2.3026 (so I know that e to the 2.3 is very close to 10), and because of radioactivity (mean-live and half-life), I knew the log of 2 to the base e, which is 0.69315 (so I also knew that e to the 0.7 is nearly equal to 2). I also knew e (to the 1), which is 2.71828.
The first number they gave me was e to the 3.3, which is e to the 2.3 - ten - times e, or 27.18. While they were sweating about how I was doing it, I was correcting for the extra 0.0026 - 2.3026 is a little high.
I knew I couldn't do another one; that was sheer luck. But then the guy said e to the 3: that's e to the 2.3 times e to the 0.7, or ten times two. So I knew it was 20.something, and while they were worrying how I did it, I adjusted for the 0.693.
Now I was sure I couldn't do another one, because the last one was again by sheer luck. But the guy said e to the 1.4, which is e to the 0.7 times itself. So all I had to do is fix up 4 a little bit!
They never did figure out how I did it.
When I was at Los Alamos I found out that Hans Bethe was absolutely topnotch at calculating. For example, one time we were putting some numbers into a formula, and got to 48 squared. I reach for the Marchant calculator, and he says, "That's 2300." I begin to push the buttons, and he says, "If you want it exactly, it's 2304."
The machine says 2304. "Gee! That's pretty remarkable!" I say.
"Don't you know how to square numbers near 50?" he says. "You square 50 - that's 2500 - and subtract 100 times the difference of your number from 50 (in this case it's 2), so you have 2300. If you want the correction, square the difference and add it on. That makes 2304."
A few minutes later we need to take the cube root of 2 1/2. Now to take cube roots on the Marchant you had to use a table for the first approximation. I open the drawer to get the table - it takes a little longer this time - and he says, "It's about 1.35."
I try it out on the Marchant and it's right. "How did you do that one?" I ask. "Do you have a secret for taking cube roots of numbers?"
"Oh." he says, "the log of 2 1/2 is so-and-so. Now one-third of that log is between the logs of 1.3, which is this, and 1.4, which is that, so I interpolated."
So I found out something: first, he knows the log tables; second, the amount of arithmetic he did to make the interpolation alone would have to taken me longer to do than reach for the table and punch the buttons on the calculator. I was very impressed.
After that, I tried to do those things. I memorized a few logs, and began to notice things. For instance, if somebody says "What is 28 squared?" you notice that the square root of 2 is 1.4, and 28 is 20 times 1.4, so the square of 28 must be around 400 times 2, or 800.
If somebody comes along and wants to divide 1 by 1.73, you can tell them immediately that it's 0.577, because you notice that 1.73 is nearly the square root of 3, so 1/1.73 must be one-third of the square root of 3. And if it's 1/1.75, that's equal to the inverse of 7/4, and you've memorized the repeating decimals for sevenths: 0.571428 . . .
I had a lot of fun trying to do arithmetic fast, by tricks, with Hans. It was very rare that I'd see something he didn't see and beat him to the answer, and he'd laugh his hearty laugh when I'd get one. He was nearly always able to get the answer to any problem within a percent. It was easy for him - every number was near something he knew.
One day I was feeling my oats. It was lunch time in the technical area, and I don't know how I got the idea, but I announced "I can work out in sixty seconds the answer to any problem that anybody can state in ten seconds, to 10 percent!"
People started giving me problems they thought were difficult, such as integrating a function like 1/(1+x^4), which hardly changed over the range they gave me. The hardest one somebody gave me was the binomial coefficient of x^10 in (1+x)^20; I got that just in time.
They were all giving me problems and I was feeling great, when Paul Olum walked by in the hall. Paul had worked with me for a while at Princeton before coming out to Los Alamos, and he was cleverer than I was. For instance, one day I was absent-mindedly playing with one of those measuring tapes that snap back into your hand when you push a button. The tape would always slap over and hit my hand, and it hurt a little bit. "Geez!" I exclaimed. "What a dope I am. I keep playing with this thing, and it hurts me every time."
He said, "You don't hold it right," and took the damn thing, pulled out the tape, pushed the button, and it came right back. No hurt.
"Wow! How do you do that?" I exclaimed.
"Figure it out!"
For the next two weeks I'm walking all around Princeton, snapping this tape back until my hand is absolutely raw. Finally I can't take it any longer. "Paul! I give up! How do you hold it so it doesn't hurt?"
"Who says it doesn't hurt? It hurts me too!"
I felt so stupid. He had gotten me to go around and hurt my hand for two weeks!
So Paul is walking past the lunch place and these guys are all excited. "Hey, Paul!" they call out. "Feynman's terrific! We give him a problem that can be stated in ten seconds, and in a minute he gets the answer to 10 percent. Why don't you give him one?"
Without hardly stopping, he says, "The tangent of 10 to the 100th."
I was sunk: you have to divide by pi to 100 decimal places! It was hopeless.
One time I boasted, "I can do by other methods any integral anybody else needs contour integration to do."
So Paul puts up this tremendous damn integral he had obtained by starting out with a complex function that he knew the answer to, taking out the real part of it and leaving only the complex part. He had unwrapped it so it was only possible by contour integration! He was always deflating me like that. He was a very smart fellow.
"Les voyages à l'étranger se multiplient. Paris exerce toute l'attraction. Trop étendu dans le temps et dans l'espace, trop mobile pour nos âmes timorées, il n'est souvent que l'occasion d'une vacance employée à parfaire une éducation sexuelle retardataire et à acquérir, du fait d'un séjour en France, l'autorité facile en vue de l'exploitation améliorée de la foule au retour. À bien peu d'exceptions près, nos médecins, par exemple, (qu'ils aient ou non voyagé) adoptent une conduite scandaleuse (il-faut-bien-n'est-ce-pas-payer-ces-longues-années-d'études!)
"Des oeuvres révolutionnaires, quand par hasard elles tombent sous la main, paraissent les fruits amers d'un groupe d'excentriques. L'activité académique a un autre prestige à notre manque de jugement.
"Ces voyages sont aussi dans le nombre l'exceptionnelle occasion d'un réveil.
"L'inviable s'infiltre partout. Les lectures défendues se répandent. Elles apportent un peu de baume et d'espoir.
"Des consciences s'éclairent au contact vivifiant des poètes maudits: ces hommes qui, sans être des monstres, osent exprimer haut et net ce que les plus malheureux d'entre nous étouffent tout bas dans la honte de soi et de la terreur d'être engloutis vivants. Un peu de lumière se fait à l'exemple de ces hommes qui acceptent les premiers les inquiétudes présentes, si douleureuses, si filles perdues. Les réponses qu'ils apportent ont une autre valeur de trouble, de précision, de fraîcheur que les sempiternelles rengaines proposées au pays du Québec et dans tous les séminaires du globe.
"Les frontières de nos rêves ne sont plus les memes . . ."