We’re looking at a major expansion of the diseasescape for Autworks coming soon.

We recently designed a short, but effective behavioral questionnaire to diagnose autism. We have wrapped that questionnaire into an online survey in hopes that the entire community of caregivers will help us to validate the accuracy. So far, over 250 people have participated! We hope to bring that number to 500 by the end of the week – April 1, 2011. Please help us spread the word.

More information:

Autism can be diagnosed through the use of a behavioral exam named the “Autism Diagnostic Interview – Revised” or ADI-R (Western Psychological Services). However, because this survey is long – it has 93 questions and can take up to 2.5 hours to complete – the diagnosis process can be prohibitive. We have designed a substantially shorter exam of 7 questions that we believe may be as effective as the ADI-R at diagnosing autistic children. Should this prove to be true, our exam would help healthcare providers diagnose autistic children more rapidly and enable children to receive valuable therapy that is more in tune with the timing of their development and more likely to have a positive outcome. One big way to determine if our abbreviated exam is effective is to get your help.

If you are a care provider for a person with autism, your answers to the few questions in the following survey will tell us whether our exam actually works. Please click here to load the survey and get started. It will take no more than 10 minutes of your time.

Our article on how to use the cloud for high performance computing has been accessed more than 1050 times since it’s publication late in December 2010. You may view it here here. Briefly, we created a model to estimate cloud runtime based on the size and complexity of the genomes being compared that determines in advance the optimal order of the jobs to be submitted. Using that, we computed orthologous relationships for 245,323 genome-to-genome comparisons on Amazon’s computing cloud, a computation that required just over 200 hours and cost $8,000 USD, at least 40% less than expected under a strategy in which genome comparisons were submitted to the cloud randomly with respect to runtime. Our cost savings projections were based on a model that not only demonstrates the optimal strategy for deploying RSD to the cloud, but also finds the optimal cluster size to minimize waste and maximize usage. Our cost-reduction model is readily adaptable for other comparative genomics tools and potentially of significant benefit to labs seeking to take advantage of the cloud as an alternative to local computing infrastructure.

We have a job opening for a project manager to help orchestrate efforts associated with our autism research, in particular the Autworks web portal. Please contact us if you are interested. Competitive salary, great working environment, and an opportunity to contribute to an important cause – the search for the genetic causes of autism.

Transforming “personalized genomics” from party hype into clinical action requires disruptive computational innovation that is based within the heart of the health care enterprise. That is why I recently elected to join the Department of Pathology at Beth Israel Deaconess Medical Center to help launch a new program in Genomic Pathology.

There my colleagues and I are focused on a national revamp of hospital Pathology to ensure that modern genomic practices are deeply integrated with and regulated by the same standards as any other clinical test in primary care. Our vision is to embed high-powered computational analysis and clinical assessment of human genomes directly into the pipeline of primary care testing.

We believe that this may be the only way to guarantee that the “thousand dollar genome” achieves its potential to make personalized medicine a ubiquitous reality. This move to Pathology is an important one for me and hopefully for medicine, but I want to stress that I am also remaining at the Center of Biomedical Informatics to ensure that my focus on autism remains primary. Check back later for more details on what I’m doing for personalized genomics and for understanding the genetics of autism.