David Woolford

A programmer disguised as a Post Doc.

See my old project: SwarmPS

What is Single Particle Reconstruction?

If you want to figure out where all of the atoms of a protein are arranged in space, how do you do it? There are several techniques for doing this, the one we use is called single particle reconstruction.

spr_overview.jpg

Overview of single particle reconstruction

In this flow diagram my primary role is the development of EMAN2, which is an large suite of image processing algorithms and interfaces.

C++

Some of my work in EMAN2

Here are a few of the C++ classes that I wrote in EMAN2

Patterns in EMAN2

We use a nifty Factory for just about everything.

We have an object that can be of "any" type, sometimes referred to as the Variant pattern. We pass it around in Dictionaries, specifically for communicating to and from Python and C++. The use of the EMObject and the Dict is all-pervasive in EMAN2.

Extensive use of the Strategy pattern, for alignment, projection, comparison, processing, and orientation generation, to name a few.

C++ is sometimes like what you call the name of a song...

A friend once told me that this is exert, taken from Alice in Wonderland, reminded him of C++

You are sad, the Knight said in an anxious tone: let me sing you a song to comfort you.

Is it very long? Alice asked, for she had heard a good deal of poetry that day.

It's long, said the Knight, but very, very beautiful. Everybody that hears me sing it -- either it brings the tears into their eyes, or else --

Or else what? said Alice, for the Knight had made a sudden pause.

Or else it doesn't, you know. The name of the song is called "Haddocks' Eyes."

Oh, that's the name of the song, is it? Alice said, trying to feel interested.

No, you don't understand, the Knight said, looking a little vexed. That's what the name is called. The name really is "The Aged Aged Man."

Then I ought to have said "That's what the song is called"? Alice corrected herself.

No, you oughtn't: that's quite another thing! The song is called "Ways and Means": but that's only what it's called, you know!

Well, what is the song, then? said Alice, who was by this time completely bewildered.

I was coming to that, the Knight said. The song really is "A-sitting On A Gate": and the tune's my own invention.

Python

PyQt and PyOpenGL and the weapons of choice for the EMAN2 interfaces. Have a look at a gallery that I made as I wrote some of the PyOpenGL widgets, and another one.

Here is a figure depicting the workflow, which was for a poster. The workflow is a fairly large body of Python code designed to be very user friendly.

e2boxer is gaining popularity.

Cuda

You can't see the CUDA on the web because the machine which builds this documentation does not have the CUDA_FLAG on. But here is some EMAN2 code that is already cuda enabled.

Why many calls to cudaFree/cudaMalloc seems to cause havoc

Why cudaMemcpyDeviceToDevice seems to fail

Does MathML work ?

$$sqrt(a^2+b^2)$$

Let's try some interesting formulas:

E=m c2

and ei pi=-1

and AA x in CC (sin2x +cos2x=1)

and one more: sum_(i=1)n i3=((n(n+1))/2)2

Trivial examples.

First, using asciimath formatting. `a+b`

Then, using latex format.

$$\frac{d}{dx}f(x)=\lim_{h\to 0}\frac{f(x+h)-f(x)}{h}$$

Email: <woolford AT SPAMFREE bcm DOT edu>

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