Monday, September 11, 2000

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Bioinform Lincoln Stein Makes Annotation Easy
"Hanging out at the University of California, San Diego watering hole one evening during the Bioinformatics Open Source Conference, a young researcher from the Berkeley Drosophila Genome Project turned to his colleague and whispered with the kind of reverence generally reserved for rock stars, “Hey, that’s Lincoln Stein.”

Although Stein isn’t known for playing in a rock ‘n roll band, he has achieved celebrity status among bioinformaticists. The revolutionary CGI.pm Perl module he created for the Common Gateway Interface is considered one of the most widely used programs for creating Web applications.

These days Stein is working on a new project at the Cold Spring Harbor Laboratory that he said will enable researchers increased access to and understanding of genomic annotations."

redux [08.09.00]
PC Magazine New Apps Exploit Connectivity
"A natural complement to distributed file-sharing capabilities is distributed computation. The idea behind distributed computation is that a really big problem gets split into discrete, independent chunks, which are then parceled out to individual computers whose owners have volunteered their idle processor time to the cause. In aggregate, the users' computers form a sort of distributed supercomputer. The concept was first popularized by U.C. Berkeley's SETI@Home project, a 1999 PC Magazine Technical Excellence finalist that's now been downloaded by more than 2 million users. Though SETI@Home is a single-purpose tool designed solely to scour radio-telescope signals for signs of extraterrestrial transmissions, you can expect to see general-purpose mechanisms for distributing all kinds of massive computations. United Devices, for example, is a company that will use distributed computing for projects in areas such as bioinformatics research, drug design, and climate studies."

redux [07.22.00]
The Standard Distributed Computing Goes Commercial
"The distributed-computing model could be one of those rare cases where capitalism and pure scientific research mesh. Not every lab can afford to pay $200,000 for an eight-processor Origin 2000 SGI supercomputer, much less $1 million for a 40-processor machine, says David Fenstermacher, director of scientific computing for the medical school at the University of North Carolina at Chapel Hill. (Fenstermacher is also acting director of the campus' Center for Bioinformatics and a United Devices adviser.) And even the most powerful supercomputers need time to process data.

A project that would take several months on a supercomputer – creating a 3D model of a protein's linear be accomplished in much less time using thousands of distributed computers"

redux [04.05.00]
Wired Researcher Borrows from Napster
"A researcher working on the Human Genome Project is using Napster technology, and he's not looking for T3 connections to download Moby.

Dr. Lincoln Stein, an associate professor of bioinformatics at the Cold Spring Harbor Lab in New York, is investigating ways to use Napster-type technology to allow scientists to share their discoveries of the genome.

"I was very interested when I saw Napster," Stein said. "It has a similar architecture (to what we use now), but it allows for 'peer-to-peer' data exchange and it dawned on me that it would be marvelous for our annotation system.""

Stein Laboratory Distributed Sequence Annotation System (DAS)
"The pace of human genomic sequencing has outstripped the ability of sequencing centers to annotate and understand the sequence prior to submitting it to the archival databases. Multiple third-party groups have stepped into the breach and are currently annotating the human sequence with a combination of computational and experimental methods. Their analytic tools, data models, and visualization methods are diverse, and it is self-evident that this diversity enhances, rather than diminishes, the value of their work."

"The solution that we advocate allows sequence annotation to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. A single server is designated the "reference server." It serves essential structural information about the genome: the physical map which relates one entry to another (where an "entry" is an arbitrary segment of the sequence, such as a sequenced BAC or a contig), the DNA sequence for each entry, and the standard authorship information. Multiple sites then act as third-party "annotation servers." Using a web browser-like application, researchers can interrogate one or more annotation servers to retrieve features in a region of interest. The servers return the results using a standard data format, allowing the sequence browser to integrate the annotations and display them in graphical or tabular form. No attempt is made to automatically resolve contradictions between different third-party annotations. Indeed, it is the ability to facilitate comparison among different centers' annotations that distinguish this proposal. We currently have a working prototype of this system based on ACeDB servers and CGI scripts, and are now generalizing this architecture to support other client and server combinations."

egroups : Decentralization Description
"* Is decentralization ever a good idea? If so, when? Is there non-anecdotal evidence on costs and benefits?
* What protocol issues are there? Can we begin assembling a good protocol for decentralized messaging? To what degree do the protocols for Freenet, Gnutella or WorldOS meet the need? Do we need an application protocol or something lower level? Can HTTP do the job? Can we implement peer routing as an add-on to existing protocols? Is there a call to develop an IETF working group?
* Given that authoring and versioning are critical but hard in a decentralized environment, how can we approach the job? Is it possible to integrate WebDAV with peer networking?
* What are the business issues? Who are the players? Who else stands to win or lose, and why?

At present many people and groups are working on the issues in isolation, some for competitive reasons and some for lack of an alternative. My belief is that a communal approach will be more productive."