There are several guides out there for running Drush on Dreamhost. Most require that you set an alias and run the drush.php file directly. However, you can do something just as easy and make it so that Drush will run via the provided shell script, which seems safer to me.

You'll want to do the following steps from the command line (skip to Step 3 if you already have Drush downloaded and just need to make it work properly):

1. Download drush to your Dreamhost home directory:
   wget http://ftp.drupal.org/files/projects/drush-7.x-4.5.zip
2. Unzip the file:
   unzip drush-7.x-4.5.zip
3. Edit your ~/.bash_profile file:
   nano ~/.bash_profile
4. Add the following line at the end:
   export DRUSH_PHP=/usr/local/php5/bin/php
5. Optional: You can also add an alias for drush in the .bash_profile so that you run just run 'drush' at the command line without typing in the full path (IE ~/drush/drush):
   alias drush=$HOME/drush_path/drush
6. From here you can either 'exit' and re-login or just run:
   source ~/.bash_profile
7. Now you can run drush via the shell script:
   drush

Other Dreamhost Guides:

• Setting up Drush on DreamHost
• Howto Install Drush on Dreamhost
• How to install Drush on Dreamhost 
• Installing Drush On Dreamhost

Ever accidentally committed a password in a file that you actually need? One of the advantages of using Git is that you can fix your horrible blunder with relative ease.

This example uses some code from Kevin van Zonneveld's helpful post and some knowledge from GitHub's guide to removing sensitive data. Kevin's example uses a new Git repo, but I used a similar process to fix an existing one.

I'm also using GitHub as my Git host, so there may be changes if you need to do this elsewhere.

WARNING: This can break your stuff. Backup and be careful.

The BioPortal Web UI is primarily built using Ruby on Rails, which is an MVC framework built for the web. The views are plain HTML with the option to include Ruby in tags. We'll walk through a quick tutorial that will enable you to add your own sections of content on top of the existing Web UI. For our example, we'll add a section that will list tools that can be used to work with the ontologies in BioPortal. The Tools section will be a simple list that includes a tool's name, a web address, and a description. This list will be stored in a database and entries can be added, edited, and deleted.

For more guides on working with Rails, see http://guides.rubyonrails.org/v2.3.10.

This tutorial assumes that you have version .4 of the NCBO Virtual Appliance running in your virtualization environment.

1. Log into Virtual Appliance with the root user
2. Run cd /srv/ncbo/rails/BioPortal/current
3. Run script/generate scaffold Tool name:string website:string description:string
4. For more information on scaffolding, see the Ruby on Rails Guides
5. You will see some output that indicates that Rails is creating files for you. Rails scaffolding will create a default set of views templates, a controller, and a model. It will also create a migration for the corresponding database table. Our example will have three columns, 'name', 'website', and 'content', all of which have string values.
6. To actually create the database table, you'll have to run the migration using rake db:migrate RAILS_ENV=production
7. Now that we have setup our new content area, we can restart the server to get the changes to show up. To do that, run ncborestart
8. Visiting http://yourappliance/tools will show an empty default page with options to create a new tool. However, it doesn't look like BioPortal and it's missing all of the links to other parts of the site. We'll need to change the layout that the section is using.
9. If we open the newly-created 'tools_controller.rb' file under app/controllers we can change the layout used by adding layout "ontology" directly under the 'class ToolsController < ApplicationController' line. If you refresh the page you can see it now shows the usual BioPortal layout. You can also read more about Rails layouts.
   
   
   • Note: You may need to run ncborestart again for these changes to take effect. To avoid this, you can run Passenger in the development environment, which will reload all controllers and templates on each request.
10. The Tools section is fully functional at this point, you can add and remove tools using the generated code. The final piece is adding a link at the top of the page for your new section.
11. The header links are contained in a sprite located here: 'public/images/layout/bp_nav_sprite.png'. This can be extended to include your own button using the original PSD file.
12. The sprite contains two images per button, one for the "normal" state (white) and one for the "rollover/active" state (gray).
13. Once you've added the two new images for the button in the sprite, export it as a png replacing the original 'bp_nav_sprite.png' file.
14. You can add the HTML for the new button in the 'app/views/layouts/_topnav.html.erb' file after the section for 'Projects' (line 50) as follows:
    
15. Edit the file 'public/stylesheets/layout/bioportal.css' and look for the section titled 'Topnav header image sprite'. Add the following CSS code to enable the new sprite (this assumes you created the two new images below the existing 'Browse' buttons):
    
16. Refreshing the page should show your changes, including the link in the top navigation

Update 11/28/11: Clarified instructions and added a screenshot of the Tools section

Barry Smith, a philosopher turned ontologist, has a two-day course that he's made available online that introduces the concept of ontology and delves into their history, practical application, and connection to computer science. For those wishing to get a firm grasp on what ontologies are and how they're used, I highly recommend that you take the time to give these lectures an in-depth listen.

I find Barry to be a captivating lecturer capable of distilling some very abstract concepts down to understandable, actionable pieces of knowledge. I saw him speak to a group of developers as a part of the National Center for Biomedical Ontology's recent meeting, where he urged all developers to at least give his course some attention. From other people in the ontology community I understand that he has a very particular viewpoint on the ontology world. But I found it useful and hope others will too. Any pointers to other educational pieces will be welcomed in the comments.

The videos, available for streaming below, are part of a two-day course that Barry teaches. Barry indicates that they are free to use in any capacity, so I took the liberty of uploading them to Viddler (the only free streaming video site I could find that would allow long videos with no special account).

Ontology as a Branch of Philosophy

http://www.viddler.com/explore/palexander/videos/1/

Ontology and Logic

http://www.viddler.com/explore/palexander/videos/2/

The Ontology of Social Reality

http://www.viddler.com/explore/palexander/videos/7/

Why I Am No Longer a Philosopher (or: Ontology Leaving the Mother Ship of Philosophy)

http://www.viddler.com/explore/palexander/videos/8/

Why Computer Science Needs Philosophy

http://www.viddler.com/explore/palexander/videos/6/

Ontology and the Semantic Web

http://www.viddler.com/explore/palexander/videos/5/

Towards a Standard Upper Level Ontology

http://www.viddler.com/explore/palexander/videos/3/

Ontology and the US Federal Government Data Integration Initiative

http://www.viddler.com/explore/palexander/videos/4/

Hopefully this will be of use for those who are deploying BioPortal on their own servers:

The BioPortal team is happy to announce some new changes that will ease the life of those who are deploying the BioPortal UI application in stand-alone instances. This should make it easier for you to upgrade BioPortal as we release new versions and lays down a framework for us to add new functionality without breaking your installations in the future. Previously, things like the autocomplete, found in the Jump To and Form Complete widgets, were hard-coded to use bioportal.bioontology.org as their AJAX back-end. That's no longer the case.

See more: BioPortal UI Now Supports Easier Deployment -- and Internationalization

I like using one email account for all of my email needs and one way I try to cut down on possible spam or unwanted emails is to use subaddressing when I sign up for a new service. It's certainly not foolproof but it does provide an easy way to filter mails when that "Unsubscribe Me" link suspiciously fails to work.

Subaddressing is simple to use, that's the main reason I like it. Gmail supports this, as it should since it's included in the email RFC. To use subaddressing, simply add a plus sign after the "local" part of your email (the section before the @domain.com). So, if you were signing up for Great Minds, you could use this email: myemail+greatminds@domain.com.

The problem comes in when people try to validate your email before allowing you to sign up. Many, many web services will not allow plus signs when you sign up, with varying degrees of success when it comes to handling a user who inputs the plus sign. Most services just reject the address as invalid and force you to try again. Some (Safeway) just strip the plus sign out without ever informing you, leaving you with an invalid email address in your account settings and, since you use your email to login, an invalid username as well.

Today I was surprised by a new response: a "helpful" employee went in and changed my email for me, thinking it was a typo.

You didn't receive an email with your decline notice and instructions to fix your [company-name] purchase because there was a typo in the email address you entered, specifically [my-email]@gmail.com (but with "[company-name]" written out in the address). I added the correct email address to your account...

I recently needed to handle some URL changes in a Rails application, basically modifying an existing route to point somewhere else. I wanted to make sure that the old route still existed so that users who might rely on it would not get left behind, not to mention search indexes that might have picked up the old location. I used the method outlined by Andrew Bruce, then tweaked it to make sure that params that were being passed by the user remained intact.

Basically you can follow his technique and use the code below in the controller.

Pretty simple, and very effective when you need to move things around but still provide access to the deprecated URLs.

The following code will allow you to pull a search term and its context out of a larger string. It can be modified to use offsets as the start/finish points for the term rather than looking for the term itself. I'll end up doing this myself as the actual application this will be used in is semantic-based and the term a user searches for could have synonyms or relationships to other words which will also produce results. In this case it would be dangerous to highlight the original search term.

I recently needed to use Thickbox functionality in a place where I wanted the Thickbox to appear without user interaction. This was mainly to keep the appearance of the dialog in line with what we use elsewhere. To do this, it's possible to create a url that will never be called and use Thickbox's built-in functionality for handling inline content.

The variable should store a url just as you would normally create for use with Thickbox links. This can include various options, including height, width, modal state, and the id for the div that holds the inline content.

The first step was to create the HTML portion that would be displayed in the modal Thickbox. For some reason Thickbox wouldn't display the text unless it was contained within paragraph elements.

Next we can use jQuery to create an event trigger for after the document is ready. I found that the Thickbox invocation didn't work, at least not reliably, without waiting for the document ready event, which makes sense if the DOM hadn't been built out yet.

Pretty simple, and very effective for my needs.