Short Description:
An industry standard, Discovery Studio GCG, formally
known as the Wisconsin Package, contains over
100 programs and utilities covering the cross-disciplinary
needs of today‚s research environment. New
and updated programs enable greater depth and
breadth of analyses within a program architecture
that enhances flexibility.
Short Description:
High performance computing is now a critical component
of the research workflow. Clusters, while no longer
exotic, are nonetheless cumbersome to set up,
manage and use. In this session, you'll see how
Apple and its partners have simplified computational
clustering. Scientists and IT managers alike will
benefit from this innovative approach to clustering
in the life sciences.
Apple
Computer, Inc.: Mac OS X v10.4 'Tiger' for the
Life Sciences
Short Description:
The latest version of Mac OS X, dubbed 'Tiger,'
brings 64-bit computing, incredible search capabilities,
and other productivity enhancements to both desktop
and high performance computing. In this session,
you'll hear from Apple customers whose day-to-day
work has been improved by their use of Tiger.
The session will include live demonstrations of
real-life scientific workflows.
Ariadne
Genomics Inc.: Software for the Analysis of
Molecular Networks
Short Description: PathwayStudio
Central is a client-server software application
developed for navigation and analysis of biological
pathways, gene regulation networks and protein
interaction maps. It comes with the build-in natural
language processing (NLP) module MedScan and the
comprehensive database describing more than 500,000
events of regulation, interaction and modification
between proteins, cell processes and small molecules.
Biobase
Corporation: Pathway Analysis with Curated Protein
Databases
Short
Description: This demo will walk you
through a pathway analysis case study, all the
way from microarray data through signaling pathways
and gene regulation to the target genes and their
associated diseases. You will learn how to use
the databases Proteome BKL, TRANSPATH, and TRANSFAC
as a newly integrated solution.
CSIRO:
GeneRave and New Statistical Algorithms for p>n
Data
Short Description: Many
biological data capture platforms result in vastly
more measurements than available samples. CSIRO
has been developing tools to model phenotypic
endpoints in terms of expression (or other p>n)
data. The distinguishing features of these algorithms
are that they are: multivariate, parsimonious,
general (survival analysis, ordered classes, etc),
and scalable.
Gene
Logic Inc.: Biomarker Discovery Using an Extensive
Clinical Microarray Gene Expression Database
Short Description: Gene
Logic's BioExpress® System expression database
and Genesis Enterprise System® Software are
powerful tools for the identification of biomarkers
of human disease and response to therapy. Case
examples of the discovery of biomarkers in autoimmune
disease and cancer using blood and tissue samples
will be demonstrated.
Presenters: Eric
Kaldjian, MD, Senior Scientific Director Pharmacogenomics
and Oncology; William Craven, Ph.D., Systems Engineer
Hewlett
Packard: Build and Execute Genomics Pipelines
with HP and TimeLogic
Short Description: Learn
how to build and process sophisticated genomic
analysis pipelines on
an accelerated biocomputing workstation powered
by TimeLogic and HP. The PipeWorks™ interface
features drag-and-drop pipeline creation and the
DeCypher Engine™ drives routine searches
at the speed of a large cluster. Researchers now
have access to powerful bioinformatics capabilities
within a single HP xw8200 workstation without
having to master Perl programming.
IBM:
From Biological Networks to Web Services: The
Latest IBM Technologies for Querying Biological
Data
Short Description: IBM's
technology for querying biological networks and
other graph structures was demoed at ISMB 2004.
We present an update on this technology and show
its power in the context of SQL queries over a
variety of sources, such as NCBI Entrez Web Services.
We present the latest WebSphere Information Integrator
technologies and demonstrate their usefulness
for bioinformatics research.
SciTegic:
Pipeline Pilot: Providing Informatics Tools
and Integration Choices
for the Life Sciences
Short Description: Pipeline
Pilot offers the indispensable informatics tools
for creating custom analysis pipelines that complement
any research environment. Scientists can combine
components that address such areas as sequence
analysis, text analytics, R statistics, chemistry,
and reporting. This demo will show how you can
create unique pipelines all within a single interface.
Sun
Microsystems: Discovery to Development Demos:
How to Save Time, Money & Hassels With 6 Solutions
Short Description: Sun,
AMD and partners will demonstrate: 1) Monitoring
your cluster with a New XML enabled qstat for
N1GE6 - The BioTeam; 2) high-throughput
BLAST and patentability - Gene-IT; 3) Use-case:
mechanism for APAP induced toxicity - integrating
microarray and clinical data – Gene Logic;
4) a developer's toolkit to create a custom apps
- Genvea Bioscience; 5) bioinformatics workflow
tied to proteomics – INCOGEN; 6) SeqHound
in DogBox – Unleashed Informatics.
Synamatix:
Applications of a Novel Structured Network Database
in Ultra-high-throughput Genomics Analysis
Short Description: SynaBASE
is a novel database platform that stores genomics
data in a "Structured Network" derived
from the inter-relationships between sub-sequences.
The network structure enables ultra fast searching
and efficient management of genomes. Applications
built upon SynaBASE that enable multi-genome scale
comparative genomics, chip design and genome assembly
will be demonstrated.
Non-Profit/Academic Demos Links after each demo title will take you to
each demo's corresponding General Session day on
the detailed agenda. Demos not yet listed on the
ISMB 2005 agenda will be scheduled in May.
Short Description: Protégé
is an open-source tool that uses an extensible
plug-in architecture that allows developers to
create and to use ontologies in intelligent applications.
There are over 25,000 registered users of Protégé
who have used the system to manage ontologies
in many domains. Protégé provides
an intuitive graphical user interface for building
ontologies and data acquisition tools that use
them. There are over 90 Protégé
plug-ins providing advanced capabilities such
as reasoning and inference support and visualization
of large ontologies. In this presentation, we
will demonstrate Protégé's features
and its particular advantages in the creation,
maintenance, and use of biomedical ontologies.
Short Description: OligoWiz
2.0 facilitates probe selection according to a
series of probe quality scores: cross-hybridization,
Delta-Tm, position in transcript, probe folding
and low-complexity. The program has a graphical
user interface which assist the probe designer
in getting an overview over these scores by presenting
them as graphs along the input sequences. In addition,
OligoWiz 2.0 allows for integration of sequence
annotation such as exon/intron structure, UTR
regions, intergenic regions, transcription start
site etc. Microarray probes can be placed automatically
according to both quality scores and sequence
annotation. Availability: http://www.cbs.dtu.dk/services/OligoWiz2
Short Description: Collaboration
of bioinformatics researchers with experimental
life-science groups often involves functional
prediction for uncharacterized proteins. In-depth
sequence analysis of even a single target with
dozens of prediction tools can easily generate
~100 MB of ASCII-text. Studying of multiple targets
creates an impossible workload that requires automated
solutions. The ANNOTATOR accepts query sequence
sets from the user, analyses them with all major
academic sequence-analytic tools, parses the outputs
and presents the results in a user-friendly way
both at the sequence and query set levels. Thus,
the ANNOTATOR greatly enhances the productivity
of applied sequence analysis.
Short Description: Apollo is
an interactive genome browser and editor written
in Java and available as an Open Source tool under
the BSD license. It allows researchers to explore
genomic annotations at many levels of detail,
and to perform expert annotation curation, all
in a graphical environment. We will demonstrate
how to read data of various formats into Apollo,
view the computational evidence, create and edit
detailed annotations, and customize the visual
display.
Short Description: It is not
straightforward to manually trace metabolic pathways,
because molecular structures of substrates are
rearranged into products in each reaction step;
a beginner may easily lose the track by not noticing
molecular symmetry or chirality. To aid such atomic
analysis in metabolic networks, Atomic Reconstruction
of Metabolism (ARM) software is designed to explore
and visualize logical traces of arbitrary metabolic
pathways in a defined network. The search engine
can output atomic-level traces (i.e. tracer result)
of any reaction steps and the visualizer can graphically
display searched pathways through drag-and-drop
manipulations.
Short Description: Whole-genome
tiling arrays are powerful tools for the discovery
of new genes. We introduce a program named ARTADE
that estimates the exon/intron structure of a
structurally unknown gene by maximizing the likelihood
of observed array-signal intensities and nucleic-acid
sequences based on the combined model of a threshold-based
intensity likelihood, a bi-directional Markov
model and length likelihood of exons and introns.
We applied it to the Arabidopsis thaliana whole-genome
array data analysis. The predicted results can
be browsed through our integrated genome browser
GPS (http://omicspace.riken.jp).
Short Description: We present
the Biochemical ALgorithms Library (BALL), a framework
for rapid
application development in molecular modeling
and structural bioinformatics. BALL provides an
extensive set of datastructures as well as classes
for molecular mechanics, advanced solvation methods,
comparison and analysis of protein structures,
file import/export, and visualization. Its extensibility
resulting from an object-oriented and generic
programming approach distinguishing it from other
software packages. BALLView, our stand-alone molecular
visualization tool gives access to the broad functionality
of BALL. BALL and BALLView are distributed under
a free license and are available For Linux, Windows
and MacOs. http://ball-project.org
Short Description: The rapid
accumulation of microarray data translates into
an urgent need for methods and software to effectively
integrate data generated with different platforms.
We have developed the software package BioArrayMiner
to address this need. BioArrayMiner is data mining
and visualization software for the integrative
analysis of cross-platform microarray data, and
in particular, the discovery of expression patterns
recurrent in multiple data sets. It can also be
used to identify conserved expression patterns
across different species. The power of BioArrayMiner
comes from its efficient graph mining algorithm,
its interactive graph visualization interface,
and its functional analysis tools.
Short Description: Short
Description: BioDASH is a demonstration of
Semantic Web technologies as part of a life
science drug discovery application (www.w3.org/2005/04/swls/BioDash/Demo).
It will introduce students and scientists to
the technologies that create the Semantic Web,
including RDF, the Web Ontology Language (OWL)
and the Uniform Resource Indicator (URI) with
a particular focus on how Semantic Web can
impact querying across multiple distributed
heterogenous databases (molecular biology,
chemstry, biopathways, and polymorphisms),
enterprise knowledge aggregation and elements
of scientific inferencing. The demo will touch
upon:
Content creation applications that utilize
metadata
Short Description: Publicly
available Biological resources form a complex
maze of highly heterogeneous data sources, connected
by navigational capabilities and applications.
This makes it difficult for scientists to select
the best resources for their tasks. We developed
the BioNavigation system which provides scientists
with a two level modeling of resources: an ontology
of scientific objects and relationships, and a
corresponding physical graph representing the
maze of resources. Scientists can express their
queries at the ontology level, whereas a sophisticated
algorithm, ESearch, determines the best path to
evaluate the query through the physical graph,
thus providing valuable guidance in the selection
of resources.
Short Description: In order
to analyze large-scale, genome-wide datasets,
efficient data management and the ability to integrate
important biological tools are required. Traditional
relational databases, though widely used, lack
support for native biological datatypes (such
as location and its index) and important functionalities
(such as BLAST sequence alignment), causing performance
deterioration, inconsistent data representation
and a hindrance to large-scale automation. We
also created BLASTgres, an extension of the PostgreSQL
database system to support location datatype and
BLAST alignment. Large-scale data analysis tasks
have been conducted in BLASTgres and showed great
advantages of this extension over traditional
database systems.
Short Description: Array database
is a standards based open source data management
system that features MIAME 1.1 compliant data
annotation forms, controlled vocabularies (MGED
ontology), and MAGE-ML import and export. caArray
also provides defined interfaces for programmatic
access to microarray data. caArray works with
statistical and biological analysis tools that
connect to the NCICB's cancer Bioinformatics Infrastructure
Objects, permitting access to variety of biomedical
information. caArray datasets and open source
tools are publicly available, and can be accessed
at http://caArray.nci.nih.gov;
caArray source code is available for local installations
at http://ncicb.nci.nih.gov/download.
Short Description: Performing
hierarchical analysis of protein domains requires
integration of knowledge from various sources
such as structure-guided multiple sequence alignments,
phylogenetic analysis, profile-recognition comparisons,
and domain architectures. While algorithms or
databases exist to allow for these analyses, no
application has been reported to effectively integrate
all the necessary analysis. We have developed
the CDTree software to fill this void. CDTree
is an interactive graphical application designed
to discover and create hierarchical relationships
among domain families in a coherent fashion. Consistent
and extensible GUI-based interfaces allow one
to perform the aforementioned analysis and correlate
different sources of information.
Short Description: Key amino
acid positions that are important for the maintenance
of the 3D structure of a protein and/or its function(s),
e.g., catalytic activity, are often under strong
evolutionary constraints. Thus, the biological
importance of an amino acid often correlates with
its evolutionary conservation level within the
protein family. ConSurf (http://consurf.tau.ac.il)
is a web-based tool for mapping residues' evolutionary
conservation on protein structures via the Protein
Explorer interface. Functionally important regions
in the protein typically appear as patches of
evolutionarily conserved residues that are spatially
close to each other on the protein surface.
Short Description: We introduce
a framework of tools, standards and libraries
to identify and analyze genomic regulatory patters,
and to simplify and streamline the development
of new pattern discovery and analysis tools. Framework
tools are proven to contribute to computational
molecular biology and are practical and efficient.
We hope that an open-source framework of standards
and libraries will aid in the development of easy
to use and easy to access pattern discovery tools
that share common libraries, interfaces and data
formats.
Short Description: DAMBE is
an integrated software package for data analysis
in molecular biology and evolution at the Windows
platform. It features many functions for sequence
input/output including extraction of annotated
sequence segments such as CDS, intron, exon, rRNA,
tRNA, etc., in GenBank format, sequence format
conversion, contig assembly, routine sequence
alignment and aligning protein-coding nucleotide
sequences against aligned amino acid sequences,
descriptive and comparative sequence analysis,
molecular phylogenetics and evolution, graphic
functions for visualizing results of analysis
and extensive online help. DAMBE is easy to use
and freely available at http://aix1.uottawa.ca/~xxia/software/software.htm.
Short Description: CTD (http://ctd.mdibl.org)
advances understanding of the effects of environmental
chemicals on human health. CTD integrates sequence,
chemical, reference, taxonomy and Gene Ontology
data to identify gene-chemical interactions and
to annotate genes of toxicological significance
in vertebrates and invertebrates. CTD also curates
"Gene Sets," which place sequences in
a unique, comparative context by grouping all
sequences from vertebrates and invertebrates for
a gene or related genes. Hierarchical controlled
vocabularies present interesting data model, user
interface and data integration challenges. This
presentation will demonstrate the benefits and
methods of integrating these controlled vocabularies
in CTD.
Development
of a Microarray Data Analysis Software (MicroArrayWare)
with a Calibration Step for Automatic Selection
of Optimal Analysis Methods and Parameters (view
scheduled time/location on the detailed agenda)
Short Description: MicroArrayWare
is a tool for analyzing microarray data using
optimal methods. There are a number of data analysis
methods and even more microarray analysis tools.
However, those tools cannot automatically select
the optimal analysis methods and parameters and
thus, require users to select the analysis methods
which they may not understand. In our approach,
the microarray analysis workflow consisting of
preprocessing, normalization and identification
of differentially expressed genes, is integrated
with an additional process called calibration
to select the optimal methods and parameters.
Using this calibration step prior to data analysis,
MicroArrayWare ensures high-quality data analysis
at each step.
Short Description: SMID-BLAST
(http://smid.blueprint.org)
is a new, freely available multi-purpose tool
for the annotation and prediction of protein-small
molecule interactions and binding sites. This
is done by using NCBI's RPS-BLAST tool to identify
domains in the query sequence then look them up
in SMID, a database of domain-small molecule interactions
generated from the PDB. We will demonstrate several
possible uses of the tool including drug design/screening,
protein annotation, and studying evolutionary
relationships. We will also illustrate how to
set SMID-BLAST up to run locally on your own servers,
and how to keep the data up to date.
Short Description: EMBOSS is
an open source sequence analysis project. EMBOSS
programs can be automatically integrated under
many interfaces, and be used for in-house development
of utilities. The demonstration will cover an
overview of EMBOSS, the programming environment,
integration methods, and alternative interfaces,
including the JEMBOSS GUI and the use of EMBOSS
in bioinformatics workflows.
Short Description: SplitsTree4
is a new program for estimating phylogenetic trees
and networks. It provides methods for constructing
splits networks, such as the consensus network
or super network of a set of (partial) trees,
distance methods such as Neighbor-Net and split
decomposition, and direct methods such as median
networks and spectral analysis. SplitsTree4 is
currently the only available program for computing
hybridization networks from gene trees and recombination
networks from binary sequences. The program also
provides distance transformations and methods
for trees, and interfaces to external programs
such ClustalW or Phylip. It is freely available
for Linux, Windows and MacOS from: www.splitstree.org
Short Description: Friend is
a standalone, multimodule, web related application,
designed to be a front-end interface for visual
and analytical analysis of multiple sequences
and structures of biomolecules in real time on
a personal computer. Both structure and sequence
data are linked to local and remote databases
providing researchers with a comprehensive picture
about related proteins. Friend allows users to
visualize and manipulate hundreds of spatial protein
structures and protein or DNA/RNA sequences. An
extensive GUI and possibility to add user-defined
menus and libraries make usage of the application
comfortable and effective for scientists with
any level of programming experience.
Short Description: FUZEBASE
is a publicly available online platform that provides
tools for exploration and analysis of biomedical
informatics data. Recent advances in biomedical
informatics emphasize the need for tools that
perform information fusion based analysis of heterogeneous
data sets such as patient demographics, clinical
and pathology data, as well as genomic data such
as gene expression. Results from such tools could
help better disease diagnosis, treatment, and
drug discovery. FUZEBASE offers tools that provide
these functionalities using various information
fusion and integration techniques. The prototype
platform is available online at http://biogeowarehouse.cse.psu.edu.
Short Description: In this software
demo we present the two genome annotation systems
GenDB and the SEED. While GenDB is focused on
annotating the genes and other regions of interest
on one genome as detailed as possible, the SEED
system aims at annotating homologous regions across
all genomes known so far. We will briefly describe
the design and the basic features of both systems
and introduce the two web frontends. The major
part of this demo will be dedicated to our latest
developments towards integrating the two systems
and we will illustrate how both applications complement
each other for enhancing genome annotation.
Short Description: GeneNotes
is the first application that allows users to
collect and manage multimedia biological information
about genes/ESTs. It provides an integrated environment
for researchers to surf the Internet, collect
notes, and retrieve notes. It is supported by
a server that integrates gene annotations from
many major databases (e.g., HGNC, MGI, RGD, FlyBase,
WormBase, etc.). GeneNotes also serves a platform
for studying users' behavior when seeking and
manipulating biological information. The results
of such study can lead to innovation of more intelligent
human-computer interfaces that greatly shorten
the cycle of biology research.
Short Description: Similarity
Plot or S-plot provides large-scale comparison
and visualization of genomic sequences in just
seconds. While existing tools for genomic sequence
comparison are computationally impractical for
genomes over 10 Mbp, S-plot can quickly perform
comparisons for a vast range of genomic sizes,
from complete viral or microbial genomes to entire
mammalian chromosomes. S-plot uses the correlation
between the distributions of short subsequences
to obtain a measure of statistical similarity
between genomic regions. S-plot is effective in
detecting regions with unusual statistical properties
within a single genome and highly similar regions
between genomes.
Short Description: Gene Expression
Open Source System (GEOSS) software incorporates
a web-interface, a relational database backend,
and a variety of bioinformatics modules for archiving
and analyzing Affymetrix GeneChip(r) and other
microarray data. It provides an integrated framework
for the management, publication (in support of
MIAME standards), and analysis of microarray data
for individual researchers and institutional microarray
facilities. Innovative GEOSS analysis interface
allows users to construct customized analysis
trees for microarray data investigation. Users
without access to their own GEOSS installation
may use our public server to analyze their and
other public data sets at http://biostat.virginia.edu/geoss/site.
