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Industry Demos |
Learn advanced in silico high throughput bioinformatics, functional
annotation, protein homolog modeling and 3D annotation techniques
to study genomes and proteomes. Demo includes using our Discovery
Studio software to analyze the West Nile Virus genome. For more
information see http://www.accelrys.com/dstudio/.
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| The Apple Workgroup Cluster
for Bioinformatics is a turnkey computational cluster designed to
enable bench scientists to achieve greater autonomy by controlling
their own computational resources. During this session, speakers from
Apple and The BioTeam, Inc. will explore the computational challenges
that face the modern biologist, and show how the Apple Workgroup Cluster
and BioTeam's iNquiry cluster provision tool successfully address
them. The session will include live demonstrations of the hardware
and software discussed. |
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| The need for computational
power in life science computing continues to grow at a rate that,
today more than ever, requires creative approaches to resource acquisition
and management. Xgrid enables average scientists to easily harness
existing computational power into a logical resource that behaves
much like a computational cluster, but without the management complexity
and financial burden. Learn about recent announcements regarding Xgrid,
and see how you can benefit from its use, even as a non-Macintosh
user. |
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| Many biological objects
are best modeled as networks or graphs. We describe a prototype from
IBM Research that supports manipulation of biological data directly
in the form of graphs, thereby allowing bioinformaticians to manage
this data more naturally. We demonstrate its application to clustering
genes whose expression levels distinguish between two closely related
lymphoma tumor variants. |
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Bioinformaticists and researchers worldwide rely on MATLAB to
accelerate scientific discovery and reduce development time. This
software demonstration will demonstrate how to use the MATLAB
programming environment for bioinformatics applications such as
sequence alignment, microarray data analysis and visualization,
phylogenetic tree analysis, and algorithm deployment to stand-alone
executables and Excel.
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SciTegic will be introducing the bioinformatics-specific capabilities
of its successful data pipelining product, Pipeline Pilot. The
graphical user interface will be demonstrated during the composition
of analytical pipelines to search, annotate, and align sequences.
Further, these new bioinformatics capabilities can be used in
pipelines with existing cheminformatics functions for a truly
cross-domain analysis environment.
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Scotland has a number of centres of excellence in the area of
bioinformatics. The Scottish Bioinformatics forum (SBF) was set
up to increase multi-disciplinary projects in Scotland, raise
the profile of bioinformatics, attract quality people and funding,
and provide a stimulating learning environment. In this session
Scottish bioinformatics capability, and key research projects
will be demonstrated.
Scottish Enterprise demo will contain six following mini-presentations:
1. Interprobe Chemical Services Software
2. Axiope Catalyzer: How do we make it easy to database all the
other scientific data?
3. Germinate: A Plant Data Management System
4. SyntenyVista - genome visualisation software
5. PartiGene – from ESTs to partial genomes and beyond
6. Topali - Software for Detecting Recombinants in DNA Multiple
Alignments
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Sun Microsystems' CTO for Life Sciences will present a collection
of demos and information from our commercial and public partners.
These include Accelrys, BioTeam, Gene-IT, Geospiza, INCOGEN, TimeLogic
and others, APBioNet's "BioBox" collection of public
algorithms for Sun and Blueprint's comprehensive BIND database
(join us for an exciting launch by Blueprint!). Finally, Sun will
also demonstrate our technologies for secure knowlege sharing,
image and visualization management, and others that are having
high impact on life science research.
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SynaBASE is the world’s first 2nd generation database for
high-throughput genomics and proteomics. By structuring patterns
and their relationships by significance, quantum level increases
in speed and scale enable analyses that were previously impossible
or impractical; e.g. true comparative genomic comparisons in milliseconds,
real-time proteomics analysis and haplotype characterizations.
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|
Student/Non-Profit Demos |
| A wealth
of information can be mined from electron cryomircioscopy data at
intermediate resolutions. To this end, we developed AIRS, the Analysis
of Intermediate Resolution Structures toolkit. Airs is capable of
identifying secondary structure elements, localize structures and
generate ab initio and comparative models. In this demo, we will
explore AIRS using UCSF’s Chimera.
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| PATIKA
is a software framework for collaboratively constructing pathway
models based on an extensive ontology. PATIKA provides users with
different facilities such as integration, querying, analysis and
visualization, as well as microarray data analysis support.
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| We
present Wildfire, a graphical user interface for constructing and
running workflows. Wildfire borrows user interface features from
Jemboss and adds a drag-and-drop interface allowing the user to
compose workflows using EMBOSS (and other) programs. For execution,
Wildfire uses GEL, the underlying workflow execution engine, which
can exploit available parallelism on multiple cpu machines including
Beowulf-class clusters and Grids. |
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SeqHound
is a bioinformatics programming platform offering daily-updated
contents of Entrez sequences, 3-D structures, sequence redundancies
and neighbours, taxonomy, complete genomes, conserved domains, GO
terms and PubMed links. SeqHound is accessible via a remote API
(Perl, BioPerl, Java, C/C++). Source code is freely available under
GNU public license ( http://seqhound.blueprint.org). |
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The
GQL is a comprehensive tool for mining gene expression time course
data running on all systems. It is written in Python and is based
on HMMs. It allows for interactive, robust and highly visualized
analyses and supports the use of prior knowledge. The GQL is freely
available at http://ghmm.org/gql. |
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| The
Yeast Interaction Browser is a tool for network motif analysis and
exploration of cell biochemical interactions networks. It is provided
with yeast molecular interactions data: Protein-Protein interactions,
Transcriptional Regulation and Metabolic network. The web interface
provides an easy way to search for complex heterogeneous motifs,
paths and view statistics.
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Reactome
located at www.reactome.org,
describes life processes in a top-down fashion, that is useful for
didactic and data mining purposes. The web interface gives a textbook-like
view of biological processes, while the query tools allow bioinformaticists
to mine the database. The website and related tools will be demonstrated. |
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| Biozon
is a unified biological database that integrates heterogeneous data
types and the relationships between them into a single extensive
schema. This schema allows one to see each data instance in its
full biological context. More importantly it allows for complex
searches that span multiple data types and for computations on that
data.
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DisEMBL
( http://dis.embl.de) & GlobPlot
are computational tools for prediction of disordered/unstructured
regions within a protein sequence. Avoiding potentially disordered
segments in protein expression constructs can increase expression,
foldability and stability of the expressed protein. The tools are
thus useful for target selection and the design of constructs as
needed for e.g. structural biology and structural genomics projects. |
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ArrayExpress, MIAMExpress and Expression Profiler
are the EBI solution to the problem of microarray data storage,
annotation and analysis. MIAMExpress is a standalone MySQL/perl
CGI application for annotation and generation of MAGE-ML format.
ArrayExpress is a MIAME compliant data repository and Expression
Profiler is a comprehensive analysis tool.
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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 enviironment,
integration methods, and alternative interfaces, including the
use of EMBOSS in bioinformatics workflows.
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BioMart
software provides researchers the ability to perform fast, powerful
queries against voluminous biological databases. Three user interfaces
will be demonstrated: the MartView
web-based interface; MartShell, a commandline shell interface;
and the MartExplorer GUI application. These can access 5 BioMart
datasources: UniProt, Macromolecular Structure Database (MSD),
Ensembl, Vega, and dbSNP. The software is Open Source and free.
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The generation and analysis of proteome data are
now widespread. A standard way to represent proteomics data is
urgently required to facilitate its analysis, dissemination and
exchange. We present some of the work of the HUPO Proteomics Standards
Initiative: The PSI Object Model and ontology; mzData format and
associated tools..
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The EBI is a centre for research and services
in bioinformatics. This demonstration will introduce a number
of web based services that the EBI provides including sequence
similarity search tools, the protein function analysis tool InterProScan,
the multiple sequence alignment tool CLUSTALW and SOAP-based web
services.
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IntAct is a freely available, open source molecular
interaction database and analysis system. It provides manually
curated data, network visualisation in the context of GO annotation,
and dynamic PSI MI XML download. Software, data, and documentation
are available from http://www.ebi.ac.uk/intact
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EMBOSS is a free software suite encompassing over
200 applications for computational biological analysis. Jemboss
is a java-based point and click interface. We will look at sequence
retrieval from specified databases, alignment and other analyses
and will include demonstration of the Jemboss alignment and DNA
editors.
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The macromolecular structure database group at
the EBI has generated a database of 3D structure from the PDB
archive. This database contains proteins that have a biological
context plus self consistent set of ligands/Uniprot mappings.
Numerous search systems have been developed along with novel visualisation
methods for information retrieval.
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Taverna allows
users with minimal technical support to access a diverse range
of analysis tools and databases across the world, to build process
flows using these components and to manage the submission of data
into and extraction of results from these flows. It is freely
available, open source and platform neutral
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INCA
(INteractive Codon usage Analysis) provides an array of features
useful in analysis of synonymous codon usage in whole genomes. In
addition to computing common codon usage indices, INCA offers numerous
options for interactive graphical display, and clusters genes using
a neural network algorithm, the self-organizing map (SOM). Available
at http://www.bioinfo-hr.org |
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| We
show a new approach for exploration in images and associated data.
We demonstrate our Biozoom prototype on a set of marker-tagged fluorescent
cell images.We combine visual data mining in symbolic feature data
and clustering results together with advanced image inspection features.
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| DAG
Edit is an ontology management system used by the Gene Ontology(GO)
and Open Biological Ontologies (OBO) projects. Originally developed
as an editor for directed acyclic graphs (DAGs) of controlled terms
and metadata, DAG Edit can now supports many of the advanced features
of ontology languages such as OWL.
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| SPRINT,
the Side-chain PRediction INference Toolbox, represents side-chain
prediction problems as graphical models and applies various inference
algorithms to it. Specifically, it predicts the M lowest energy
configurations and characterizes the variability in configurations
(e.g. conformational entropy, free energy and rotamers’ marginal
probabilities). SPRINT main advantage over other side-chain prediction
packages is its multi-functionality while using comparable computing
resources.
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XSPAN
( www.xspan.org) supports cross-species
access to tissue-specific genetic information. It links anatomy
ontologies for human and the main model organisms (mouse, Drosophila,
C.elegans, zebrafish). Acquisition of tissue mappings is supported
by the COBrA tool and a new cell-type ontology. XSPAN can be accessed
using web service and web-based GUI interfaces. |
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| H-Invitational
Database (H-InvDB) is a human gene database with integrative annotation
of 41,118 full-length cDNA clones. H-InvDB describes their gene
structures, functions, domains, expression, diversity, and evolution.
This is a product of the H-Invitational consortium comprised of
44 research institutes worldwide, organized by Japan Biological
Information Research Center (JBIRC) and DNA Data Bank of Japan (DDBJ).
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| We
proposed a general method of directly converting concrete biochemical
networks to dynamic models, and developed CADLIVE that implements
the conversion method. The feasibility of CADLIVE has been demonstrated
by using large-scale and complicated biochemical networks, such
as nitrogen fixation, heat shock response, circadian clock, and
cell cycle systems.
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| The
FluxAnalyzer is a graphical user interface for MATLAB enabling detailed
structural analyses of large-scale metabolic networks. The powerful
collection of tools includes those for graph-theoretical calculations,
metabolic flux analysis, flux balance analysis, metabolic pathway
analysis (relying on elementary modes) and computation of minimal
cut sets.
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| MolStudio
enables you to visualize and interact with protein structures with
desktop, laptop and tablet computers. You can walk-through and hands-on
with proteins to enhance the structure-based learning and research
processes using the Virtual Reality Technology.
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| The
BRIDGES project is developing an advanced Grid based infrastructure
for use within the Wellcome Trust Cardiovascular Functional Genomics
(CFG) project. Data access and integration, security and usability
are all key issues that the BRIDGES project are addressing. This
demonstration will highlight some of the tools that the BRIDGES
team have developed for the scientists.
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| The
Rat Genome Database (RGD) curates and integrates rat genetic and
genomic data and provides access to this data to support research
using the rat as a genetic model for the study of human disease |
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The
Encyclopedia of Life (EOL) project seeks to provide annotation for
the vast number of putative protein sequences derived for genome
sequencing projects. Data from the EOL genome annotation pipeline
(iGAP) is distributed via an innovative web interface. Further information
at: http://www.eolproject.info |
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| BioInformatics
data stems from a wide variety of sources, and is serialised in
a plethora of formats, standards and conventions. Nelson's ZigZag
will be demonstrated, with a variety of information types, to illustrate
the uses of a single space for storage, viewing, analysis and representation
in a deeply interconnected manner.
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UniProt
( http://www.uniprot.org) is
a centralized resource for protein sequences and functional information.
Created by unifying the information contained in Swiss-Prot, TrEMBL,
and PIR, UniProt provides a richly annotated protein knowledgebase
(UniProt), non-redundant reference databases (UniRef) at different
levels of redundancy, and an archive database (UniParc) that reflects
the history of all protein sequences. |
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PDA
is a Web server that automatically can search for polymorphic sequences
in large databases and estimate their genetic diversity on different
functional regions. It has been applied to create the secondary
database DPDB, Drosophila Polymorphism Database. Both are
publicly available at http://pda.uab.es
and http://dpdb.uab.es. |
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| Snow
is a user-friendly interface for querying and browsing databases
of networks. Snow supports iql, a simple language enabling users
to perform complex queries knowing only the database conceptual
model. Results can be viewed as lists and graphs. For this demonstration,
Snow will be interfacing aMAZE, our database for molecular interactions
and cellular processes.
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MUSCLE
is the most accurate multiple sequence alignment program (up to
5% better than T-Coffee on benchmarks) with speed similar to CLUSTALW.
With appropriate options, MUSCLE achieves accuracy equal to T-Coffee
and aligns 5,000 sequences of length 350 in 10 minutes. MUSCLE is
a free download at http://www.drive5.com/muscle. |
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The
MAGIC Database and its associated tools provide a Modular Approach
to a Genomic, Integrated and Comprehensive resource for gene discovery
and expression. It manages and visualizes both DNA sequence and
microarray data, and is suitable for both individual research groups
and core facilities. Additional information is at http://fungen.org. |
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A
wide range of projects are pursued by the Leeds bioinformatics research
group. Those to be demonstrated include: 1, metaSHARK: a database
of automated metabolic reconstructions derived from genomic DNA
sequence. http://bioinformatics.leeds.ac.uk/shark/
, 2, TmaDB: A repository for tissue microarray data. 3, AtGATA_Base:
an Arabidopsis thaliana GATA transcription factor database for discovering
the potential regulated targets of GATA factors. 4, A 3D protein-ligand
binding site database for structure-function relationship discovery.
5, Software to predict protein-protein binding. |
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| The
Metaclinic Database System (see poster session) provides a set of
web-based tools for rapidly creating clinical research databases.
During the demonstration (about 1.5 hrs), I will start from scratch
and generate a simple research database, import data from an existing
demo, and demonstrate the built-in reporting capabilities of the
system.
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| LAMA
and CYRCA search, align, and cluster protein motif alignments (Blocks).
Together they provide a sensitive and selective approach to predict
protein function, structure and evolution. These tools improve and
complement the abilities of other advanced protein analysis methods.
The presentation will describe the methods' use, benefits, and limitations.
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