http://mndoci.disqus.com/At the interface of science and computingenMon, 07 Jul 2008 18:24:18 -0000http://mndoci.com/2008/07/06/a-middle-out-web-services-infrastructure-for-systems-biology/#comment-830921<p>Good find! I enjoyed the read of both your blog and the original PDF too.</p><p>One thing that I want to point out is that REST and SOAP are not mutually exclusive technologies, but can play together quite well. Matter of fact, I3 (Systems biology driven software design for the research enterprise, page 11) uses REST combined with SOAP as one mechanism for browsing and querying an image repository, or LSID can be used for a more direct access to the data: "Once the experiment information is available… it can be browsed and queried using two different mechanisms: a SOAP/REST based interface …; and an LSID endpoint … ."</p><p>Just as John Boyle, et al, points out that the field of life sciences is a highly dynamic and evolving field; I tend to feel the same way about computer science on a whole with its use of evolving technology and associated methodologies. Given a few years, hot buzzwords (and their associated technological counterparts to which they refer) tend to drop to the wayside; either through complete obsolescence or through an acceptance to where the newer technologies build upon them. If they are lucky, they may become the defacto standard, but even if they do not, their contribution to the newer technology can be upstaged or even obscured altogether.</p><p>The point that is interesting is that even though a project may adopt a bottom-up or middle-out approach, which may cause some water-fall purest to cringe, the final application can be very stable. I feel that generally the attributed stability of these projects arise from building blocks that find their roots in mature and stable open source projects and/or a clearly defined and adopted set of standards. These two key components, open source and standards, give the final application stability that even a top-down approach 3 to 5 years ago would have had great difficulty in matching. On a whole, I feel that open source and the wide adoption of standards has contributed to the functional reality of bottom-up and middle-out programming models.</p><p>With all this said, the next major challenge in the computer science and life science application development will be the move to support parallel processing, of which the industry on a whole is scrambling to find a solution that will scale nicely and insulate the applications from developer's limitations. The search for the new parallel holy-grail will most likely lead to a highbred blend of current parallel programming techniques along with novel advancements from both the software and hardware camps. Many corporations and organizations project that in the next 3 to 5 years that the multi-core processors will require a new approach so that tomorrow's software can just keep up with Moore's Law. This is evident in both the flood of announcements of these new endeavors, and by the millions of dollars that are going in to research within just the last six months. This new paradigm may cause yet another shift in programming in ways in which we can neither foresee nor predict today, but it will undoubtedly lead to the continuing evolution in both hardware and software.<br></p>Scott TabarMon, 07 Jul 2008 18:24:18 -0000