This site is archived.

Michael Caudy

Platinum and gold sponsors

mcaudy's picture
mcaudy - Thu, 02/28/2008 - 11:21pm
First Name: 
Last Name: 
United States of America
technology / bioinformatics consultant
affiliated as consultant with Cold Spring Harbor Laboratory

I am a scientist using Drupal as a web interface / portal / knowledge managment system for me to access the massive amounts of previously stored biological information and knowledge that is available online. I also use Drupal to analyse this information: to create knew knowledge by discovering previously unknown relationships in the data; and to publish that knowledge online for others to see and use.

As noted in my session proposal, I am a trained academic scientist (Ph.D. in Biophysics, from U.C. Berkeley): I study the genes that control nervous system development, using a variety of techniques: genetics; genomics; gene transcription analysis; neuronal differentiation analysis.

I am rather new to Drupal and PHP (since June, 2007). However, I have been using Perl to do genome informatics for several years. I also have studied Ruby and other programming languages - including Lisp and Python - in order to determine which is best suited for my scientific and other programming interests.. A large part of genomics research involves accessing large databases online, and I have collaborated with other programmers over the past few years to design and create custom web interfaces / portals for such databases, mostly using the Frontier web framework / CMS. I was planning to port some of our genomics software to the Ruby on Rails web framework, but several factors made me change my mind and switch recently to Drupal and PHP. What I really need most is a very powerful CMS, since so much of my work deals with accessing information in large databases containing huge amounts of genetic, molecular and DNA sequence information. I have a very good familiarity and understanding of CMS technology, and I was surprised - and very pleased - to learn that Drupal already has most of the features that I need.

I took the two day Lullabot Drupal Theming Workshop in NYC in August, 2007. I also started by working with an experienced Drupal / PHP programmer named Jacob Redding to create some very useful and powerful web interfaces for our databases, in a very short time. More recently, I took the five day Lullabot Developer Workshop in January, which focused on PHP programming for Drupal, and also more advaced Drupal API programming.

I know basic HTML/CSS, XML, JavaScript, and various other web technologies. I am very familiar with the basic concepts of web programming, web frameworks, web services, etc., as these are all central to genomics research. Most recently, I have started switching to using web services methods to access data in SQL and XML databases, and to use Flex, in combination with Drupal, for creating very powerful user interfaces for accessing data in external databases.

My plan is to to use Drupal to create custom web portals (data “mashups”) that will let me integrate large amounts of different types of scientific data. One goal is to develop software tools that will enable me and other scientists to answer important biological questions about how the genome encodes regulatory information controlling biological growth and function. I also am starting a Drupal-based consulting service that provides knowledge management technology, which will be a major area of growth in the future. I believe that Drupal, PHP, Flex and web service technologies will enable me now to achieve most of these goals.

Lodging Facility while in Boston : 
Courtyard Marriott South
Conference Resources
These fields are intended to help community members connect with one another and share resources. Please answer as many of the questions as possible. If you have suggestions for adding additional items, please post your suggestion in the forum.
I am interested in sharing a cab or vehicle for traveling to and from the conference center. : 
I can provide a video camera for recording sessions.: