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Bioinformatics Journal
SIGSIM: Systems Biology of E.coli

Software Demonstrations - Abstracts

Industry Demos
Apple Computer

Presented by Apple Computers Australia's Dr Des Muller and Stephen Atherton

The Macintosh is not new to the molecular biosciences where it has been a workhorse for both research and teaching since the advent of the polymerase chain reaction. Indeed, large institutes such as this conferences' host, the IMB, are predominantly "Mac camps". With the introduction of our UNIX based operating system - Mac OS X- colleagues in mathematics, statistics and computer science are now opening their eyes to the possibilities. Bioinformatics is at this junction of these physical sciences and biological science and this talk will examine Apple's operating system evolution - in particular its' open source code "Darwin". Work in the area of clustering with Apples' xServer technology will be discussed and an overview of the innovative work of the Boston based BioTeam ( will be explored. Imagine- a cluster being installed in 30 minutes using Apples' MP3 player... the iPod! With UNIX comes access to true and tested command line applications. With the elegance of Macintosh comes ease of use and power:

"The result (of the installation of xServers and BioTeam's"InQuiry" product) was well beyond expectations, a truly multifunctional web portal including not only BLAST, FASTA and HMMER but the full EMBOSS suite running on top of a Sun Grid Engine managed cluster" (David Adelson, Associate Professor Animal Genomics Texas A&M University)

Attendees of this session will be in the draw for an iPod to use on their PC or Macintosh.

Hewlett Packard with geneticXchange Pty Ltd

To date, scientists and bioinformaticists have been forced to hand code data access and integration tools in order to conduct scientific queries and research. This has created huge IT inefficiencies and has slowed the discovery process. The result is a limited set of data that rapidly becomes out of date as data sources change and expand. geneticXchange has architected a solution from the ground up that supports virtually any scientific data sources and offers an open, embeddable architecture, for the ultimate flexibility and performance in any environment.

With discoveryHub, scientists and their IT support organization get a complete biological data integration platform with a familiar SQL interface. On the back-end, discoveryHub provides a powerful engine that efficiently collects, transforms, integrates and loads scientific data from both internal and external sources in a secure and private manner.

Visit our demonstration session to find out more about our product and where discoveryHub version 6 is heading.

Queensland Parallel Supercomputing Foundation (QPSF) - Bio-portal demonstration

QPSF is developing a web based 'Bio-Portal' interface to a suite of phylogenetic codes. The environment will allow users to submit and track jobs, retrieve results and enter appropriate meta-data for subsequent retrieval. We are presenting here a portal and workflow environment that is suited to phylogenetic activities, the concept is largely generic in molecular biology, and easily extendible to other domain areas. In addition discrete modules can be accessed by uses when needed. The back-end system uses the open source PBS queuing system, enabling jobs to be run on the full range of QPSF compute servers and is extensible to grid computing models.

The QPSF, a consortium of six universities, was formed in 2000 from an existing joint venture to act as the state's peak strategic body for high performance computing and communications.

Sun Microsystems
Sun Microsystems is synonymous with vast compute power robust hardware and software, best exemplified through our SunONE & N1 architectures for data management. Sun supports the life science community's goal of developing solutions and sharing and open standards.
Student/Non-Profit Demos
The Blueprint Initiative - Tools for investigating biomolecular interaction data
We will demonstrate freely available tools and data for investigating biomolecular interactions. Topics include the Biomolecular Interaction Network Database (BIND), BIND-BLAST, the tab-delimited BIND index, literature-mining with PreBIND, the Pajek graph tool, molecular complex detection using MCODE,and retrieving sequence and sequence annotation data using the seqHound remote API
EMBL Biocomputing Unit - ELM Consortium (ELM Consortium) - ELM - The Eukaryotic Linear Motif Database
ELM is a resource for finding linear functional motifs in eukaryotic proteins. Functional motifs are identified by patterns or HMM models. To improve predictions, context-based rules and logical filters are applied to reduce the amount of false positives. Currently we provide basic filtering by cell compartment and globular domain clash.
European Bioinformatics Institute - Sequence Services at the EBI
The EBI offers the scientific community a wide range of services, notably those revolving around nucleotide and protein sequences. The demo will provide a tour of the EMBL nucleotide and Swiss-Prot/TrEMBL protein sequence databases, as well as secondary databases like InterPro and others available through SRS at the EBI.
German Cancer Reserach Center - Management and Analysis System for Molecular Genetic and Annotation Data
We will present our array informatics system which integrates management and analysis of heterogeneous molecular and clinical data and is intended to support and integrate RNA expression data with other kinds of genomics data.
Kyushu Institute of Technology - CADLIVE for constructing and simulating biochemical networks
CADLIVE (renamed from BIOCAD) is a powerful software suit with GUI for constructing a large-scale map of complicated biochemical reaction networks, and for converting the map to a mathematical model according to various conversion methods including TPP and CMA, which enables us to understand the dynamic features of the network.
Protein Data Bank - The Reengineered PDB
The PDB team is pleased to introduce you to the reengineered PDB web site and query system. An overview of this new system's capabilities will be presented, and sample queries will be demonstrated at this session. We invite you to visit the PDB's exhibit at booth #42 to preview the new PDB.
Technical University of Denmark - OligoWiz: A powerful, flexible yet easy-to-use tool for designing oligonucleotides for DNA microarrays
This demonstration will give an introduction to the ideas behind oligo design, and show how to use OligoWiz for designing hi-quality oligos. OligoWiz is build to be useful to both the "lab-biologist" and the bioinformatician. Details:
University of Auckland - The PEBBLE Application
PEBBLE is an extensible application for performing phylogentic analysis. Currently functionality includes serially sampled analysis, general cluster analysis, coalescent simulation, alignment simulation, and a powerful alignment editor. The demonstration will examine the philosophy behind PEBBLE, general usage, useful tricks, and advanced features.
University of Manitoba - BIRCH - A portable and comprehensive bioinformatics platform
BIRCH is a  resource of integrated programs and databases for molecular biology, unified through the GDE graphic interface. The BIRCH framework is designed for semi-automated installation and customization on Unix systems, and integration of locally-installed software and databases into BIRCH.
University of Melbourne - XNAfold - a Window program: computing secondary structures of a RNA sequence and computing a RNA seq

XNAfold is a Window application for predicting RNA secondary structure and computing a sequence that can fold into a predefined structure. It is a JAVA-C hybrid program that uses a Java Application Programming Interface and the C-based RNA folding routines in the ViennaRNA library. It is freely available at