Lightning Talks at Bioinformatics Technology Conference
When and WhereThe lightning talks are Thursday January 31 in CANYON III and IV at 2:15pm. 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.
Implementing bioinformatics algorithms in a spreadsheet
by Robert Horton, Ph.D. (California State University, Sacramento)
Bioinformatics courses often need to address a mixed audience of biologists and programmers. Using a scriptable spreadsheet (Microsoft Excel), a combination of spreadsheet formulas and scripts makes some algorithms easier to follow. Examples include dynamic programming for sequence alignment, and distance-based hierarchical clustering.
A Multi-purposes Reusable SQL Query Assignment to Share
by Meiliu Lu
One of tasks that an instructor of Bioinformatics course has is to design a set of interesting assignments to enhance learning. We developed a small web database in MySQL and PHP. Students were asked to enter on-line Bioinformatics software survey and give Summery SQL Query in MySQL+PHP. Wish more can share their great assignments.
by Djamel Medjahed (NCI-Frederick Cancer Research and Develpment Center)
This is more of a question: I have built a web-accessible, JAVA-based interactive proteomics database. I would like to incorporate buttons that are driven by CGI-scripts and will in effect produce small alterations to the underlying sequences and which reflect post-translational modifications. This will dynamically cause a slight shift in the associated protein spot.
bioperl modules for Pise Web servers
by Catherine Letondal (Pasteur Institute)
I would like to present bioperl modules for Pise (Pise is an interface generator, www-alt.pasteur.fr/~letondal/Pise). The idea is to use the information of about 300 programs (phylogeny, pattern discovery, alignment, structure prediction, EMBOSS...) that is already available in the Pise XML definitions, to generate bioperl classes for running jobs on a Pise server and getting results via a script.
Is there value in Compute Cycles?
by James McNalley
Workstations and PCs drop in price every year, but can you get enough cycles in a single package to complete your work? Does it make sense to build your own cluster?
A primer selector using Linux, Perl and Zope
by Dr Alain EMPAIN (Univ. of LIEGE (Belgium), Fac. Vet Medicine, Molecular Genetics )
An example of integration between standard UNIX tools, PERL scripts and classical bioinformatic programs like RepeatMasker or Blast. Speed is one of the main concerns because the final interface must be as interactive as possible. New sequences are inserted within the already known ones (similar sequences are clustered) to allow to choose the best primer candidates for the laboratory.
ABIPARSER, a Perl tool to explore ABI files
by Alain (EMPAIN)
ABIPARSER is an Perl tool derived from the Fortran program 'abitools.for' ( David Mathog ). It is developed to debug ABI interfaces and to provide a generic access to the various ABI fields. The field descriptions follow ABI's 'DATA DICTIONARY 3.1' and is easily extensible. One of the options is a PostScript output of selected DATA fields.
Acts of the Apostles-- The best bioinformatic novel at this gathering
by John FX Sundman (Rosalita Associates/Wetmachihe)
A synopsis and reading from my nifty bioinformatic technoparanoid novel Acts of the Apostles-- featuring soul-stealing venture capitalists, naive & good-hearted bioinformatitians, sex, chases, theories of body-building and sandstorms in the Sahel.
Teaching Bioinformatics to Biologists
by Stuart Brown (NYu School of Medicine)
This is a quick look at the course that I teach to Ph.D. students at NYU Med School. All my course notes and exercises are on the web at www.med.nyu.edu/rcr
Bioinformatics: Java's Killer App?
by Mario Wolczko (Sun Microsystems, Inc.)
The Bioinformatics field is leading the way for the large-scale use of Java for scientific computation. The kinds of bioinformatic apps being written in Java are qualitatively and quantitatively different from any other. What can platform providers do to make bioinformatics apps more efficient, scalable, etc? How can developers help?
Applying Confidence Scores to Biological Annotations
by William Ray (Children's Research Institute, The Ohio State University)
Many varieties of biological annotation are currently applied to features with no indication of the certainty of the information, which can lead to corrupted search results. The PACRAT system demonstrates that even a naive automatic qualification system can increase search result quality by rejecting obvious noise.
Sequence - structure database resource as a platform for bioinformatics research
by Katerina Michalickova (Samuel Lunenfeld Research Institute)
Description of an in-house integrated database resource which is serving bioinformatics research. It contains sequence, structure, taxonomy, gene ontology, locus link, OMIM, MEDLINE ID, conserved domain database, BLAST neighbours.....data. It supports for example BIND database.
The virtual pharmaceutical company - Infoceutics
by Martin Gollery (TimeLogic Corporation)
Here we will introduce Infoceutics Inc., which uses bioinformatics to identify sequences important in infectious disease. We'd like to show others how they could be involved in the bioinformatics and/or business side of the company. We are particularly interested in recruiting bioinformaticians/programmers.
using SWIG to make the NCBI C toolkit available from Perl et al
by Jonathan Epstein (National Institute of Child Health and Human Development)
The NCBI C toolkit is powerful, but difficult to use for the uninitiated. Using the SWIG interface language, we hope to make selected NCBI toolkit APIs available from high-level languages such as Perl, Python and Java, possibly under the auspices of BioPerl, BioPython and BioJava.
MaizeDB on a Budget
by Denis Hancock (University of Missouri -- Columbia)
Presented here is a fully-functional implementation of the Maize Genome Database using a free version of Sybase running under Linux. Such a system can serve as a low-cost alternative where funding is tight.
A Plea for Paranoia
by Andrew Dalke (Dalke Scientific Software, LLC)
Code, documentation, and databases all have errors. All too often they are silent and hidden. Just because something seems to work and has been used for years doesn't mean it's right. I'll show problems taken from bio software and suggestions for how to write and test code to make errors noisy and visible.
Send email and ask.