Lightning Talks at Bioinformatics Technology Conference

When and Where

The lightning talks are Thursday February 6 in the California Ballroom at 3:30pm. For more information about lightning talks look here. The URLs to the slides for speakers will be available here as soon as they are available.

First Half Second Half
On Validation of Scientific Algorithms
by Daniel Pick
Scalar vector graphics binary storage device
by Rex Sandwith
The OpenCD Project
by Robert Citek
BioLinux
by Wim Van Criekinge
Using Natural Keys In Databases
by Barry Dancis
J2EE, Databound Control for Bioinformatics
by Richard Xu
Bioinformatic Issues in the Risk Assessment of Genetically Modified Foods
by Steven Stelman
Grid Computing Rant
by Chris Dagdigian
3:32 On Validation of Scientific Algorithms
by Daniel Pick
Outstanding results for new ways of computing scientific quantities are frequently proposed, and even published, without being reproducible by outside researchers. This talk is meant as a cautionary tale for programmers working with scientists. Examples from personal experience of good and bad algorithms will be discussed.
Programming
3:37 The OpenCD Project
by Robert Citek - Orion Genomics, LLC and the Saint Louis UNIX Users Group
The OpenCD Project is a collection of OpenSource software (OSS) available for Windows platforms. Because the CD itself is OpenSource, I've modified it to include other OSS including Apache, MySQL, Perl/PHP/Python/Ruby.
Programming
3:42 Using Natural Keys In Databases
by Barry Dancis - Barry Dancis Consulting, Inc.
Artificial keys such as integer sequences are the SOP for designing database tables. Natural keys (e.g. the gene orf id), however, can improve clarity, speed and simplify processing. This talk will discuss the advantages and disadvantages of using natural keys
Programming
3:47 Bioinformatic Issues in the Risk Assessment of Genetically Modified Foods
by Steven Stelman
Regulation of genetically modified foods require the assessment of the potential of an introduced protein to elicit an allergic response. Available guidance from regulatory agencies is vague at best, and published protocols contain errors. Custom algorithm and database design is required to address these issues.
Biology
3:52 A Short Break
Three minutes to prepare for the second half speakers.
3:55 Scalar vector graphics binary storage device
by Rex Sandwith
If a method to extract the complex patterns in organic shapes were developed perhaps these patterns could be assembled into networks that would have unique pattern recognition capabilities. We have developed algorithms and code to generate binary scalar vector graphic representations of organic shapes in nature with a hierarchical based structure. The spatial arrangement of the original shapes is maintained for later network assembly. Once generated these binary trees can be used as data storage devices, generation of complex keys for authentication, and pattern recognition systems.
Programming
4:00 BioLinux
by Wim Van Criekinge - Biorebel
Fresh, intel optimized RPMs, just like mom used to burn
Programming
4:05 J2EE, Databound Control for Bioinformatics
by Richard Xu - Biogen Inc
The talk will cover the annotation project inside Biogen and focus on two innovations: databound control: a web component for versioned annotation. High-level reusability and configurability. J2EE: thread-safe, asynchronous messaging system for time-consuming analysis job such as BLAST.
Programming
4:10 Grid Computing Rant
by Chris Dagdigian - BioTeam LLC
  • The vision of grid computing that vendors are selling is not even close to what they are actually able to implement today.
  • Vendors eager to sell their wares have tortured the definition of "grid computing" to the point where it is now a content-free buzzword. Much of what is being described as grid computing in the life sciences is anything but.

Programming

Any Questions?

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The order of the schedule is subject to change.