Ed's Big Plans

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.

Link: Python Crash Course Materials

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.

Link: Structural Bioinformatics A3 Hints

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.

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.

Download: Updated slides [pdf].

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 BactoHouse^MD.

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.

This is an update to this post.

It’s even easier in this version of Arclite 2.02 to throw up both a logo and title.

Edit header.php as follows…

Before:

<?php
      // logo image?
      $logo = (get_arclite_option('logo'));
if($logo): ?>
      <h1 class="logo"><a href="<?php bloginfo('url'); ?>/"><img src="<?php echo $logo; ?>
      "title="<?php bloginfo('name');  ?>" alt="<?php bloginfo('name');  ?>" /></a></h1>
<?php else: ?>
      <h1 class="logo"><a href="<?php bloginfo('url'); ?>/"><?php bloginfo('name'); ?></a></h1>
<?php endif;  ?>

After:

<?php
      // logo image?
      $logo = (get_arclite_option('logo'));
if($logo): ?>
      <h1 class="logo"><a href="<?php bloginfo('url'); ?>/"><img src="<?php echo $logo; ?>"
      title="<?php bloginfo('name');  ?>" alt="<?php bloginfo('name');  ?>"
      style="vertical-align:text-bottom;" /><?php bloginfo('name'); ?></a></h1>
<?php else: ?>
      <h1 class="logo"><a href="<?php bloginfo('url'); ?>/"><?php bloginfo('name'); ?></a></h1>
<?php endif;  ?>

That’s it!

• style="vertical-align:text-bottom;"

  • This chunk is used to keep the logo in line with the title text as last time.

• <?php bloginfo('name'); ?>

  • This chunk produces the title text.