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Unifying Biological Image Formats with HDF5:
The biosciences need an image format capable of high performance and long-term maintenance. Is HDF5 the answer?

The biological sciences need a generic image format suitable for long-term storage and capable of handling very large images. Images convey profound ideas in biology, bridging across disciplines. Digital imagery began 50 years ago as an obscure technical phenomenon. Now it is an indispensable computational tool. It has produced a variety of incompatible image file formats, most of which are already obsolete.

by Matthew T. Dougherty, Michael J. Folk, Erez Zadok, Herbert J. Bernstein, Frances C. Bernstein, Kevin W. Eliceiri, Werner Benger, Christoph Best | October 4, 2009


The Hitchhiker’s Guide to Biomorphic Software:
The natural world may be the inspiration we need for solving our computer problems.

The natural world may be the inspiration we need for solving our computer problems. While it is certainly true that "the map is not the territory," most visitors to a foreign country do prefer to take with them at least a guidebook to help locate themselves as they begin their explorations. That is the intent of this article. Although there will not be enough time to visit all the major tourist sites, with a little effort and using the information in the article as signposts, the intrepid explorer can easily find numerous other, interesting paths to explore.

by Kenneth N Lodding | August 31, 2004


Probing Biomolecular Machines with Graphics Processors:
The evolution of GPU processors and programming tools is making advanced simulation and analysis techniques accessible to a growing community of biomedical scientists.

Computer simulation has become an integral part of the study of the structure and function of biological molecules. For years, parallel computers have been used to conduct these computationally demanding simulations and to analyze their results. These simulations function as a "computational microscope," allowing the scientist to observe details of molecular processes too small, fast, or delicate to capture with traditional instruments. Over time, commodity GPUs (graphics processing units) have evolved into massively parallel computing devices, and more recently it has become possible to program them in dialects of the popular C/C++ programming languages.

by James C Phillips, John E. Stone | October 6, 2009


Metamorphosis: the Coming Transformation of Translational Systems Biology:
In the future computers will mine patient data to deliver faster, cheaper healthcare, but how will we design them to give informative causal explanations? Ideas from philosophy, model checking, and statistical testing can pave the way for the needed translational systems biology.

One morning, as Gregorina Samsa was waking up from anxious dreams, she discovered that she had become afflicted with certain mysterious flu-like symptoms that appeared without any warning. Equally irritating, this capricious metamorphosis seemed impervious to a rational explanation in terms of causes and effects. "What’s happened to me?" she thought. Before seeing a doctor, she decided to find out more about what might ail her. She logged on to a Web site where she annotated a timeline with what she could remember. Since March, she’d had more headaches than usual, and then in April she had begun to experience more fatigue after exercise, and as of July she had also experienced occasional lapses in memory.

by Samantha Kleinberg, Bud Mishra | October 12, 2009


Computers in Patient Care: The Promise and the Challenge:
Information technology has the potential to radically transform health care. Why has progress been so slow?

A 29-year-old female from New York City comes in at 3 a.m. to an ED (emergency department) in California, complaining of severe acute abdominal pain that woke her up. She reports that she is in California attending a wedding and that she has suffered from similar abdominal pain in the recent past, most recently resulting in an appendectomy. The emergency physician performs an abdominal CAT scan and sees what he believes to be an artifact from the appendectomy in her abdominal cavity. He has no information about the patient’s past history other than what she is able to tell him; he has no access to any images taken before or after the appendectomy, nor does he have any other vital information about the surgical operative note or follow-up.

by Stephen V. Cantrill | August 12, 2010


Better Health Care Through Technology:
What can you do for aging loved ones?

Leveraging technology to support aging relatives in their homes is a cost-efficient way to maintain health and happiness and extend life. As the technology expert for my extended family, it has fallen to me to architect the infrastructure that will support my family’s aging loved ones in their homes as long as possible. Over the years, I have assisted four different senior households in achieving this goal, and although things have been bumpy at times, I have refined technical solutions and methodologies that seem to work well.

by Mache Creeger | November 10, 2006


A Conversation with David Shaw:
In a rare interview, David Shaw discusses how he’s using computer science to unravel the mysteries of biochemistry.

In this interview, Hanrahan and Shaw discuss Shaw’s latest project at D. E. Shaw Research: Anton, a special-purpose supercomputer designed to speed up molecular dynamics simulations by several orders of magnitude. Four 512-processor machines are now active and already helping scientists to understand how proteins interact with each other and with other molecules at an atomic level of detail. Shaw’s hope is that these "molecular microscopes" will help unravel some biochemical mysteries that could lead to the development of more effective drugs for cancer and other diseases.

September 16, 2009