The World of Isoprenes

While I was poking around the web this morning looking for some decent metabolic maps, I came upon this really excellent map of isoprenoid biosynthesis. I've seen a couple maps of similar scope, but I like how this one highlights the metabolites that people are likely to be familiar with (essential oils, vitamins) and shows how the isoprene subunit is the root of synthesis of so many disparate biological products. Isoprenes aren't just for plants - the retinal that functionalizes rhodopsin to enable us to perceive light and the cholesterol that forms the basis for the synthesis of the steroid hormones are both isoprene derivatives.

That map was put together by a real visionary, Dr. Donald Nicholson. Awardee of the ridiculously prestigious "Special Life Member" status in the IUBMB, his minimaps and animaps are changing the way people think about (and teach!) the chemistry of metabolism. His stated goal: "To Make Metabolism Meaningful, Wonderful and FUN." Bravo, sir!

For the stressed, the body-builders, the guys and gals out there who feel the effects of steroids every day: a fantastic map of steroidogenesis, courtesy Wikipedia. Bet you're glad you learned organic chemistry, right? It's never too late!

Powerpoint Magic

Powerpoint has some shortcomings, but it can be used to make some really spectacular presentations:

This was done entirely with Powerpoint; though I generated the molecular models in CN3D, the labels, the emphasis masking, everything else was Powerpoint-only (no Photoshop required!). It took me quite a while to put this slide together, but it can be done very rapidly once you know the process.

First, I pasted the molecular model image, then cropped and resized to cover the entire image. Next, I de-emphasized the area around the focus points of my image by creating a large grey oval, making it mostly transparent, and applying an edge-softening effect to the shape. The hard part was creating the focus points: Powerpoint does not have a function that allows you to 'cut holes' in shapes that you've made, so I had to devise a workaround to get the enzyme cofactors of interest to shine through the de-emphasis mask:

1. Create the 'emphasis ovals' by selecting a dashed, red outline and no fill
2. Copy the entire background molecular model image
3. Crop the background image to the area of interest, so it has exactly the same height and width as the emphasis oval
4. Select the cropped image and 'save as picture' to an easily-accessible directory
   
5. Repeat (2) and (3) for each emphasis oval
6. For each emphasis oval, switch the fill to 'picture', selecting the pictures you just cropped and saved

Next, I just added a bunch of arrows and some informative labels (again applying the 'softening' effect to the textboxes to make them blend in better) and I was done!

When you've inserted an image as a 'fill' on a shape, you can apply sorts of effects to the shape, change it to freeform, edit the defining points, and get some really neat results: link

Powerpoint is an often-abused artform... I saw some pretty horrific things on an industry internship a few years ago. It's a visual aid, so keep the text to the minimum! If your Powerpoint doesn't look like anyone else's, you're probably on the right track.

Laser Flash Photolysis

Discovering biochemistry was a big deal for me.

In highschool, I loved the systematic complexity of biology and the quantitative, mechanistic focus of chemistry. The latter won out and I headed to college in Chemical Engineering, but I made the decision near the end of my freshman year to pick up Biochemistry and Molecular Biology as a second major.

Photolyase: a light-activated enzyme that repairs UV-associated DNA damage

So many times, I came within a few minutes of dropping it. The problem: molecular biology. No offense, molecular biologists, but you ran out of fresh ideas about twenty years ago. There are a finite number of ways to do PCR, and you're really scraping the bottom of the bucket at this point (and are you still enjoying all that pipetting?). I had to wade through six credits of molecular biology of increasing irrelevance before I could break into the 400-levels, and only a mild interest in microbiology kept me at it.

Finally, BMB 401 - Introduction to Biochemistry. This is the first biology course I encountered which listed organic chemistry as a prerequisite, and it made all the difference. The chemistry, the physics, the mechanistic focus, the quantitative analysis - it was all there. The Biochemistry of Metabolism pulled me in a little further, and an excellent course in Analytical Biochemistry introduced me to the good stuff: UV-Vis, NMR, EPR, Circular Dichroism, &etc. Spectroscopy uses very basic physical interactions to 'see' the unseeable, providing an amazing look into the structure and function of the molecular machines that make biology go. Those who dislike math, physics, organic and physical chemistry need not apply.

I chose to overview an experimental technique termed "Laser Flash Photolysis" for a paper and presentation project in Graduate Chemical Kinetics. It's a pretty awesome method that's already scored two Nobel prizes in chemistry (1967 and 1999) that uses ultrafast pulses of laser light to cause and 'observe' chemical reactions on the timescales at which they actually occur (nano-, pico-, and femtoseconds).

My Laser Flash Photolysis review is available here. Definitely check out the 1967 Nobel lecture on 'Immeasurably Fast Reactions' that's referenced in the review - it's a little technical, but a good read on the initial development of the technique.

CMS for Web Design

 What is a Content Management System (CMS)?
From Wikipedia:

A Content Management System (CMS) is a collection of procedures used to manage work flow in a collaborative environment. These procedures can be manual or computer-based. The procedures are designed to:

• Allow for large number of people to contribute to and share stored data
• Control access to data, based on user roles. User roles are used to define each use as to what information they can view or edit
• Aid in easy storage and retrieval of data
• Reduce repetitive duplicate input
• Improve the ease of report writing
• Improve communication between users

In the specific example of a Web CMS, it's a tool for designing, building, and administering websites.  Many modern CMS allow you to do all of these tasks in a graphical user interface (GUI) environment that is almost entirely free of 'exposed code' - no PHP, XHTML, or CSS required (though they are still powerful tools for making your site look just the way you want it).  They offer several advantages over traditional methods of web design: because they offer friendly interfaces and a standardized way of doing things, it would be fairly easy for me to design and build a site and then hand it off to someone else (with limited web experience) to administer.

I am experimenting with a Content Management System (CMS) called 'Drupal' - it is a free, open-source platform for designing, building, and administering a website.  It's serious stuff (the White House used it for this site, for instance), and it is designed with a 'many producers, many consumers' model of web development in mind.  It requires minimal effort to set up, and the initial process of server-side installation and database creation are very similar to the steps needed to install a Wiki (covered here last week).

My favorite feature: Drupal has powerful user management built right in, with the out-of-the-box ability to create roles, define privileges for each role, and assign roles to users with ease.  The default roles are 'authenticated user', 'unauthenticated user', and 'site creator', but you can make as many roles as you'd like.  This means it's a great choice for building an intranet, a secure storage place for user-created content, or any site where you need to be able to enforce access restrictions.  It also means that you can spread out the burden of administering the site: you can create 'superuser' roles which have the ability, for instance of moderating forums and user blogs.  This feature allows you to introduce trusted users to the administration methods and interface one piece at a time, easing them into the role of site administrator.  All administration is done within the site itself on a special menu that is hidden to regular users, which new admins usually find very intuitive (though it may initially confuse users of older CMS).

Drupal is free, open-source software with lots of community support.  You can add extra functionality (forums, blogs, wikis, multimedia presentation) by installing 'modules', which are user-created add-ons (called 'nodes' or 'widgets' in other contexts) - if you can think of it, there's probably a module out there to support what you want to do.  When you assign permissions to your site's roles, you assign them by module, which allows for quite a bit of customization.

I put this demo together in a few short hours (you'll need to create an account to access any of the content).  I think that this CMS would be perfect for the creation of sites by any organization, with or without a dedicated IT department.  For educational and community projects, this format enables the recruitment of site designers, constructers, and administrators with limited scripting and coding experience, which is EXTREMELY helpful for us non-computer scientist folks.

How To Set Up a Wiki

Wikipedia has changed the way most people study and research. If you've got some spare change, they run entirely on donations.

Turns out, it's amazingly easy to set up your own wiki that looks and works just like Wikipedia. You can grab some server space for ~$0.03/day at a place like WebHostingPad, and the hosting services that they offer include everything you need to get started.

First, log into your hosting control panel (cPanel for many) and/or fire up your MySQL manager. Create a new database, then create a user and associate it with that database; make sure you give the user full control over the database. Write down the database name and the username and password associated with the managing account, in addition to the username and password that you use to administer your website (your cPanel login, for many).

Head on over to MediaWiki and download their latest software. Unpack the archive using 7zip, then FTP into your server using FileZilla and drop the archive contents into a web-accessible folder (/www/wiki, for instance). Fire up Firefox and head to http://YourSite/wiki/config/index.php; follow the onscreen prompts to get everything configured, using the database and administration information you wrote down in the previous step.

FTP back onto your serverspace, and move the 'LocalSettings.php' file from the 'config' directory into the main directory (/www/wiki).

You're done! As long as everything went well, you should be looking at something that looks a lot like this.
Customize to your heart's desire, recruit a userbase, and wiki away!

A note to potential wiki-ers: if you've never edited Wikipedia before, you might not realize that Wikipedia has its own markup syntax. While it's really, really easy to learn in no time at all, you might have trouble convincing your organization to learn it. Unfortunately, there are no simple, plug-and-play WYSIWYG (What-You-See-Is-What-You-Get, Microsoft Word-style) editors available for MediaWiki yet. Perhaps soon!