ACM Queue - Bioscience

Computers in Patient Care: The Promise and the Challenge

Stephen V. Cantrill — Thu, 12 Aug 2010 16:22:44 GMT

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. The physician is left with nothing more than what he can see in front of him. The woman is held overnight for observation and released the following morning symptomatically improved, but essentially undiagnosed.

Metamorphosis: the Coming Transformation of Translational Systems Biology

Samantha Kleinberg, Bud Mishra — Mon, 12 Oct 2009 17:17:51 GMT

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. "Why don't I go back to sleep for a little while longer and forget all this foolishness," she thought. As she was about to abandon this errand, the system came back to life with a barrage of questions: Is she female? Had she experienced any significant stress in the past few months? Had she noticed any joint or muscle pain? It also obtained her permission to download her genomic profile.

Probing Biomolecular Machines with Graphics Processors

James C Phillips, John E. Stone — Tue, 06 Oct 2009 12:47:58 GMT

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.

Unifying Biological Image Formats with HDF5

Sun, 04 Oct 2009 17:39:42 GMT

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.

A Conversation with David Shaw

Wed, 16 Sep 2009 14:52:13 GMT

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. If his track record is any indication, the world has a lot to be hopeful for.

The Hitchhiker's Guide to Biomorphic Software

Kenneth N Lodding — Tue, 31 Aug 2004 11:47:32 GMT

Hitchhiker's Guide to Biomorphic Software

The natural world may be the inspiration we need for solving our computer problems.

Kenneth N. Lodding, Nasa

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.