# Ed's Big Plans

## An Old Physiology Project — Operation Spinny Chair :D

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I discovered this ancient report in my repository about three months ago– I’ve finally decided to put it up because it made my day reading the abstract again. This is definitely one of my prouder albeit sillier projects from the days of my undergrad.

Independent Research Project Acute centripetal acceleration is correlated with increased heart rate and R-wave amplitude

Matthew Boyle, Bryan Chung, Eddie Ma

Abstract

In the present study, we set out to discover the correlation between the exposure of acute centripetal acceleration in human subjects and cardiovascular function across the following three dimensions: Heart rate, R-wave amplitude and QRS interval. This was accomplished by measuring the above properties via Lead II Bipolar ECG trace, after having spun the subject at 0.8 revolutions per second in an office chair for successively, 30, 60 and 90 seconds. It was determined that heart rate showed strong positive correlation (n = 3, average increase between trials of increasing duration, 3.2 beats per minute, s = 1.8). R-wave amplitude showed positive correlation in all subjects up until and including the 60 second trial. There was no systemic correlation between duration of spin and the length of the QRS interval in any of the subjects. The heart is therefore an important effector in response to centripetal acceleration in the human model.

Key Words: electrocardiogram, QRS interval, centripetal force, R-wave amplitude, spinning office chair.

Thumbnails of pages 5, 7 and 11.

Written by Eddie Ma

March 12th, 2010 at 5:07 pm

## Idea: Delaunay Simplex Graph Grammar

The Structural Bioinformatics course I’m auditing comes with an independent project for graduate students. I’ve decided to see how feasible and meaningful it is to create a graph rewriting grammar for proteins that have been re-expressed as a Delauney Tessellation.

I was first introduced to the Delauney Tessellation about half a year ago. Such a tessellation is composed of irregular three dimensional tetrahedrons where each vertex corresponds to an amino acid. A hypothetical sphere that is defined by the four points of such a tetrahedron cannot be crossed by a line segment that does not belong to said tetrahedron.

An alphabet in formal languages is a finite set of arbitrarily irreducible tokens that composes the inputs of a language. In this project, I want to see if I can discover a grammar for the language of Delauney protein simplex graphs. Graph rewriting is likened to the collapse of neighbouring tetrahedrons. The tetrahedrons selected are either functionally important, stability important or have a strangely high probability of occurrence. This definition is recursively applied so that previously collapsed points are subject to further collapse in future passes of the algorithm.

When a subgraph is rewritten, two things happen. Some meaning is lost from the original representation of the protein, but that same meaning is captured on a stack of the changes made to the representation. In this way, the protein graph is iteratively simplified, while a stack that records the simplifications indicates all of the salient grammatical productions that have been used.

This stack is what my project is really after. Can a stack based on grammatical production rules for frequency of occurrence render any real information, or is it just noise? I can’t even create a solid angle to drive my hypothesis at this point. … “Yes … ?” …

I’ve seen a lot of weird machine learning algorithms in my line of work… and I attest that it’s hard for a novice to look at a description and decide whether or not it derives anything useful. Keep in mind that the literature is chuck full of things that DO work, and none of the things that didn’t make it. I conjecture that this representation has made me optimistically biased.

This method however IS feasible to deploy on short notice in the scope of an independent project

Written by Eddie Ma

March 8th, 2010 at 6:31 pm

## Arclite Theme – Invisible Text in Submenu Fix

with one comment

Brief: The Arclite WordPress Theme is great, but the default CSS for the submenu causes the text to be almost completely invisible when moused over. The fix is an easy edit in style.css.

ul#nav ul a:hover, ul#nav ul a:hover span,
ul#nav a.active ul a:hover span,
ul#nav li.current_page_item ul a:hover span,
ul#nav li.current_page_ancestor ul a:hover span,
ul#nav ul li.current_page_parent a:hover span,
ul#nav ul li.current_page_item a:hover span,
ul#nav ul li.current_page_parent li.current_page_item a:hover span{
//color: #fff;
color: #2d83d5;
background: #CCCCFF;
}

To make the text look like a deep blue on light blue, I changed the default white colour for a:hover in the sub-menus section to match the text colour of the blue in the rest of the theme plus a lighter blue as its background.

Written by Eddie Ma

March 5th, 2010 at 7:51 pm

Posted in Web Programming

Tagged with , , ,

## Python Crash Course & CS[64]83 Next Directions

Python Crash Course

Having completed teaching that Python Crash Course before reading week, I can say that I’m probably not going to teach it again any time soon for its time commitment! It was a good experience for me since I’ve figured out how to balance content for time and also how to talk to a crowd of heterogeneous experience levels in programming.

There’s going to be a PERL one-off course offered by BIC on this week that I think I’ll attend to figure out what the general style is for one-session courses– it was previously offered by Edgar and is offered this time by Anna and James.

I definitely need to clean up the course materials, but Andre thinks we should have my course packaged along with the Biology for Engineers course he offered. These two packages will eventually be shipped off to oGEM & iGEM HQ as per their recent interest in local workshops.

CS [64]83 Structural Bioinformatics

I threw up a hints page some time two weeks ago to coordinate help for assignment three for the structural bioinformatics course I’ve been auditing. I’ll probably take it down from the main menu when it becomes completely irrelevant. For the mean time, I’ll leave it up or replace it with assignment four hints when that gets underway.

I think I’ll eventually consolidate all of my one-off pages as a single page linked in the menu to reduce clutter. I’ll probably put all of my slide shows in there too.

Written by Eddie Ma

February 28th, 2010 at 4:18 pm

## Oh, right! Newick format for tree representation.

Update: I cover how to parse the Newick format with recursive descent here.

Brief: The Newick format offers a nice flat representation of a tree. This is done by performing a depth-first (prefix) traversal on the tree and documenting each of the nodes and lengths of edges as they occur during that traversal. Note that this representation is only valid for directed acyclic graphs and inherently preserves the parent-child relationships between the nodes. While there is no restriction on where a root node is for a particular set of data, the format indirectly specifies a root node as the last node to be visited in the traversal. The Newick format is used in phylogenetic trees, and is inherited by MUSCLE through compatibility with PHYLIP. The format does not state a particular arity, although the culture of phylogenetics has made the binary tree the most common flavour. Finally, due to the regular nature of its encoding, Newick format strings are just as regular to convert back to their in-memory representations.

Written by Eddie Ma

February 26th, 2010 at 4:10 pm

## iGEM*BIC — An Awesome Meeting

About two weeks ago (Feb. 11th), we had an iGEM*BIC meeting where five iGEM members showed up and roughly a dozen BIC members showed up. I expected a few more from iGEM but they ended up with illnesses or midterm exams that week.

We started the meeting with a nice description of BIC from Anna, followed by a nice description of iGEM at large then iGEM at home from Andre. I then finished with a collaborative projects presentation.

I’ve attached the slides I presented (actually, I’ve updated them since then)– just like the very last set of slides for the Python Crash Course, I ended up using iWork Pages this time around instead of NeoOffice.

The meeting was designed to go for half an hour because of its proximity to midterms. We ended up discussing for about two hours about all of the projects we wanted to try this term– everything from the now defunct Bunny Buddy to BactoBones to BactoHouseMD.

Anna had remarked earlier that iGEM isn’t well marketed to CS students or BIC– so this will certainly be a recurring thing at the beginning of each semester. This is particularly important summer because the next stream of BIC students are returning from co-op.

The general consensus is that everyone was interested in doing *something* in iGEM which is a real bonus. This Wednesday, we’re going to have a modeling meeting that’s punctuated with John’s mini-project talk. I’m hoping that many BIC members will show up to carry over their interest.

My original assessment that most BIC students would want to do in silico modeling and software development was far off. As it turns out, BIC students showed interest in every facet of iGEM from wet lab to software development to outreach and public relations.

A direct consequence of the iGEM*BIC meeting is that we had a much larger design meeting the next day (Feb. 12th)– thirteen showed up.

Finally, the feeling of the group is that the next crossover meeting should be more social. I think that’s something we can shoot for, for early summer.

Written by Eddie Ma

February 21st, 2010 at 3:54 pm