Demonstrations
posted 18 Jun 2007
Demo Number: 01
geWorkbench: An Open-Source Platform for Integrated Genomics
Sunday, July 22
9:30 a.m. – 9:55 a.m.
Room: L
Presented by: Aris Floratos, Columbia University, USA
Abstract:
We demonstrate geWorkbench (http://www.geworkbench.org), an innovative open-source software platform for genomic data analysis that brings together gene expression, sequence and pathway-related information and tools. It gives scientists transparent access to a number of external data sources and algorithmic services, combining these with many built-in tools for analysis and visualization.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/ismb07/floratos200506.pdf
Demo Number: 02
Demonstration of The Pathway Tools Software
Sunday, July 22
10:00 a.m. – 10:25 a.m.
Room: L
Presented by: Peter Karp, SRI International, USA
Abstract:
The Pathway Tools software system integrates metabolic, genomic, and regulatory information. This demonstration will cover new aspects of Pathway Tools including a display of the transcriptional regulatory network, a new genome browser, a new tool for interactively constructing complex database queries, depiction and editing of protein features, and a facility for interactive tracing of metabolites through the metabolic network.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/ismb07/pkarp113451.pdf
Sunday, July 22
10:50 a.m. – 11:15 a.m.
Room: L
Presented by: Oscar Serrano, Advanced Computer Vision GmbH, Austria
Abstract:
SpotRobot is a robust, quick and highly reliable microarray image analysis tool providing fully automatic spot finding, batch image analysis and accurate spot quantification in an extremely intuitive interface. Configurable multiformat outputs (GPR and XML) and a command line mode facilitate its integration with other tools.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/ismb07/oscar.serrano022732.pdf
Demo Number: 04
The Phylogeny Cafe
Sunday, July 22
11:20 a.m. – 11:45 a.m.
Room: L
Presented by: Istvan Miklos, Eotvos Lorand University of Sciences, Hungary
Abstract:
Phylogeny Cafe is a software package written in Java for doing phylogenetic analysis based on the mutation of biological-genomical units. The possible units are sequences, gene orders and gene copy numbers. The possible mutations are insertions, deletions, substitutions, genome rearrangements of gene orders, gene duplications, deletions and horisontal gene transfers.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/miklosi_20070510001129.pdf
Demo Number: 05
ENDEAVOUR, an application to prioritize candidate disease genes
Sunday, July 22
11:50 a.m. – 12:15 p.m.
Room: L
Presented by: Leon-Charles Tranchevent, Katholieke Universiteit Leuven, Belgium
Abstract:
Genome-wide experimental methods to identify disease / pathway genes often generate large list of candidates from which only a few are interesting. Using multiple data sources, ENDEAVOUR is able to prioritize such a list, i.e., give a rank to each gene according to its similarity with the process of interest.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/ltranche_20070510030829.pdf
Demo Number: 06
CADLIVE: Computer-Aided Design of Living Systems
Sunday, July 22
2:30 p.m. – 2:55 p.m.
Room: L
Presented by: Hiroyuki Kurata, Kyushu Institute of Technology, Japan
Abstract:
CADLIVE is a comprehensive computational tool that rationally designs large-scale biochemical networks at the molecular interaction level. It consists of a GUI network constructor, database, a pathway search module for knockout mutants, a network layout module, and the dynamic simulator that automatically converts biochemical network maps into mathematical models.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/kurata_20070510074653.pdf
Sunday, July 22
3:00 p.m. – 3:25 p.m.
Room: L
Presented by: Esther Schmidt, EMBL-EBI, UK
Abstract:
Reactome is a manually curated human pathway knowledgebase (2040 reactions, 1921 proteins). Electronically inferred reactions are provided for 22 other species. Data are linked to other resources and available in multiple export formats. A “SkyPainter” tool supports high-throughput data analysis, and a Mart tool supports query submission and data retrieval.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/eschmidt_20070510080340.pdf
Demo Number: 08
The European Molecular Biology Open Software Suite (EMBOSS)
Sunday, July 22
3:50 p.m. – 4:15 p.m.
Room: L
Presented by: Peter Rice, EMBL – European Bioinformatics Institute, UK
Abstract:
The European Molecular Biology Open Software Suite (EMBOSS) is a mature package of software tools developed for the molecular biology community. The demonstration will summarise the well established key features and also new features in EMBOSS 5.0.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/jison_20070511034848.pdf
Demo Number: 09
Exploring Ensembl beyond the Genome Browser
Sunday, July 22
4:20 p.m. – 4:45 p.m.
Room: L
Presented by: Michael Schuster, EMBL-EBI, UK
Abstract:
Ensembl is a system providing automated genome analysis. This software demo will focus on programmatic access to the set of relational databases via an object-oriented Perl API. High-level concepts like genome sequence slices, features and the assembly mapper, as well as selected Ensembl Perl objects will be introduced.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/michael.schuster_20070511035320.pdf
Demo Number: 10
MADMAX-MicroArray Database Management and Analysis of eXperiments
Sunday, July 22
4:50 p.m. – 5:15 p.m.
Room: L
Presented by: Anand Gavai, Wageningen University and Research Centre, The Netherlands
Abstract:
Madmax is an Oracle database facilitating any kind of microarray data storage and analysis. It has a MIAMI compliant LIMS extended with a controlled vocabulary. The quality control and analysis pipelines (t-statistics, ermineJ, GSEA) are independently executed via webservices on a dedicated R-server (Bioconductor) and the results are automatically imported.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/anand.gavai_20070511062746.pdf
Demo Number: 11
The EMBL Nucleotide Sequence Database (EMBL-Bank): Submission methods to the repository, data curation and innovative solutions to the handling of large datasets.
Sunday, July 22
5:20 p.m. – 5:45 p.m.
Room: L
Presented by: Gaurab Mukherjee, EMBL – European Bioinformatics Institute, UK
Abstract:
The EMBL Nucleotide database has developed new methods for submission of nucleotide sequence data, both improving existing tools and supplying new tools to speed submission itself and value-added curation. These tools allow the rapid submission of large and complex datasets, focusing on the needs of groups within the scientific community.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/gaurab_20070511063103.pdf
Demo Number: 12/13
Improving Scientific Intelligence through Integration
Monday, July 23
9:30 a.m. – 10:25 a.m
Room: L
Presented by: Scott Markel, Accelrys, USA
Abstract:
Many biological science organizations experience the problem of data and application integration. Pipeline Pilot® provides a software environment where algorithms and data come together easily into a single data-pipelining model that allows quick and customizable application integration, data analysis and reporting of results. Pipeline Pilot already integrates chemistry, text analytics, statistics and bioinformatics sequence analysis. Gene expression microarray analysis has become commonplace with standard processes being employed. The ability to seamlessly process microarray data and integrate the results with other data and applications for analysis is part of the new functionality being added to Pipeline Pilot.
Demo PDF:
Demo Number: 14/16
Genomics Acceleration using the FPGA based BLAST appliance by SGI and Mitrionics.
Monday, July 23
10:50 a.m. – 11:45 a.m.
Room: L
Presented by: Dr. Matthias Fouquet-Lapar
Abstract:
As the amount of data collected grows, fully understanding and leveraging data to advance research has become the bottleneck in R&D productivity. Learn how organizations can leverage the latest technologies such as FPGAs in biotech and drug discovery to remove bottlenecks and achieve insights faster. BLAST acceleration case studies discussed.
Demo PDF:
Demo Number: 15
Pedro: A Model Driven Data Entry Tool for Bioinformatics
Monday, July 23
10:50 a.m. – 11:15 a.m.
Room: M
Presented by: Kevin Garwood, University of Manchester, UK
Abstract:
The demo will showcase Pedro, a model-driven data entry tool which has been developed to service bioinformatics use cases at the University of Manchester.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/zaredbaron_20070507044919.pdf
Demo Number: 17
Semantic Web for Healthcare and Life Sciences
Monday, July 23
11:20 a.m. – 11:45 a.m.
Room: M
Presented by: Eric Neumann, W3C, USA
Abstract:
We use the Semantic Web to provide data sources in RDF or OWL, the Standard languages of the Semantic Web. Existing RDF databases and OWL reasoners can be used to query and analyse the data. The benefits of the illustrated include knowledge representation, knowledge integration, and knowledge discovery.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/eneumann_20070518140643.pdf
Demo Number: 18
beta.uniprot.org: a preview of the new Web site of the UniProt consortium
Monday, July 23
11:50 a.m. – 12:15 p.m.
Room: L
Presented by: Eric Jain, Swiss Institute of Bioinformatics, Switzerland
Abstract:
This demo is an in-depth tour through beta.uniprot.org, the new Web site of the UniProt consortium. Our aim is to demonstrate how common tasks that used to be difficult to accomplish have become straightforward, and how the new Web site allows users to get the most out of UniProt.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/eric.jain_20070510120802.pdf
Demo Number: 19
BioModels Database, a curated resource of annotated published models
Monday, July 23
11:50 a.m. – 12:15 p.m.
Room: M
Presented by: Nicolas Le Novere, EMBL-EBI, UK
Abstract:
BioModels Database is the reference resource that distributes curated quantitative models of biological interest. We will demonstrate how to submit new models, search relevant models, download them in various formats, and give examples on how to use them.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/lenov_20070424111202.pdf
Demo Number: 20/21
Pattern Discovery in Bioinformatics: Theory and Algorithms
Monday, July 23
2:30 p.m. – 3:25 p.m.
Room: L
Presented by: Laxmi Parida. IBM T. J. Watson Research Center
Abstract:
The Computational Biology Center at IBM Research pursues basic and exploratory research at the interface of information technology and biology. Information technology plays a vital role in enabling new science and discovery in biology. Advances in high throughput and platform technologies in biology present an unprecedented challenge in scale, management, and analysis of biological data. We will discuss the theoretical and algorithmic challenges in some of these problem areas and how we study and tackle them.
Demo PDF:
Demo Number: 22
E-Cell Simulation Environment and E-Cell 3D visualization front-end
Monday, July 23
3:50 p.m. – 4:15 p.m.
Room: L
Presented by: Kazuharu Arakawa, Keio University, Japan
Abstract:
We demonstrate the new 3-dimensional visualization front-end for the E-Cell Simulation Environment, a generic cell simulation platform for systems biology researches. E-Cell is compatible with SBML model description language, and the new visualization platform as well as the simulator itself can load existing models in SBML.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/gaou_20070510114717.pdf
Demo Number: 23
Visualisation and Analysis of Molecular Sequences, Alignments and Structures Software Demo: Interoperable analysis applications
Monday, July 23
4:20 p.m. – 4:45 p.m.
Room: L
Presented by: James Procter, University of Dundee, UK
Abstract:
TOPALi (evolutionary analysis), Jalview (sequence alignment and visualizaion), and AstexViewer@MSD-EBI (protein structure visualization and datamining) are widely used applications for local and web service based analysis. Their combined use for bioinformatics analysis will be demonstrated and the ‘Visualization and Analysis of Molecular Sequences, Alignments, and Structures’ (VAMSAS) communication mechanisms described.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/jimp_20070511022359.pdf
Demo Number: 24/25
Apple Workgroup Server for Next-Generation Sequencing
Tuesday, July 24
9:30 a.m. – 10:25 a.m.
Room: M
Presented by: William Van Etten, Apple Inc., USA
Abstract:
Next-generation DNA sequencing instruments produce data at a thousand-fold greater throughput at a thousand-fold lesser cost than today’s methods without providing a clear strategy for the necessary data storage and analysis. In this talk Apple and The BioTeam present a simple and affordable solution to this complex problem.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/steven_20070623132256.pdf
Demo Number: 26/27
Exploring Ensembl beyond the Genome Browser
Tuesday, July 24
10:50 a.m. – 11:45 a.m.
Room: M
Presented by: William Van Etten, Apple Inc., USA
Abstract:
The Apple Workgroup Server for BioInformatics combines the Mac Pro workstation (3TBs of storage and 8 cores of processing power) with BioTeam’s iNquiry to provide the shared high-throughput and high-performance computing capability of a small cluster to a department or workgroup without the complexity.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/steven_20070623132444.pdf
Demo Number: 28
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
Tuesday, July 24
11:50 a.m. – 12:15 p.m.
Room: M
Presented by: Shoba Ranganathan, Macquarie University, Australia
Abstract:
ESTExplorer (http://estexplorer.biolinfo.org) is a web server to assemble and annotate expressed sequence tags (ESTs) at DNA and protein levels. ESTExplorer accepts ESTs as input, runs several programs and outputs gene ontologies, mappings to protein domains/motifs and metabolic pathways. Examples with parasitic nematodes have demonstrated ESTExplorer to be an invaluable research tool.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/shoba.ranganathan_20070530232611.pdf
Demo Number: 29
The Next Generation Biology Workbench
Tuesday, July 24
1:30 p.m. – 1:55 p.m.
Room: M
Presented by: Mark Miller, San Diego Supercomputer Center, USA
Abstract:
The demonstration will focus on use of the Next Generation Biology Workbench, a web application that provides tools databases access, and storage at no charge. We will walk users through account creation, data uploading, assembly, and staging, data searching and staging, tool running, and linking individual tools in workflows.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/mmiller_20070511085133.pdf
Demo Number: 30
Symphony: An Open Source Framework for Lab Information and Data Management
Tuesday, July 24
2:00 p.m. – 2:25 p.m.
Room: M
Presented by: Mark Miller, San Diego Supercomputer Center, USA
Abstract:
The Symphony Framework is a flexible open source laboratory data management system with enterprise class stability. We will provide a user-focused overview of the Framework and several of its applications, including laboratory workflow management, acquisition of laboratory data, presentation of results, integration of multiple structured and unstructured data sources.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/mmiller_20070511091102.pdf
Demo Number: 31
My BioAID: personalised text mining with web services from the AIDA toolbox
Tuesday, July 24
2:30 p.m. – 2:55 p.m.
Room: M
Presented by: Marco Roos, University of Amsterdam, The Netherlands
Abstract:
We demonstrate applications of our Adaptive Information Disclosure Application (AIDA) toolbox, which contains web services for ontology alignment, ontology-supported query construction, named entity recognition and concept learning. We show personalized text mining workflows, built in Taverna, that support hypothesis construction for research on the relationship between diseases and epigenetic factors.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/roos_20070511110510.pdf
Demo Number: 32
NCIBI Suite of Tools
Wednesday, July 25
9:45 a.m. – 10:10 a.m.
Room: L
Presented by: Timothy Wiggin, NCIBI, USA
Abstract:
The NCIBI suite of tools provides end-to-end analysis for finding, describing and annotating cellular networks. This demonstration will show how to use Bayesian networks, MiMI, Cytoscape, SAGA and natural language processing and to analyze high-throughput gene expression data. The content is suitable for both biologists and computer scientists.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/twiggin_20070511122302.pdf
Demo Number: 33/35
ExPlain(TM): ExPlaining Gene Expression Data
Wednesday, July 25
9:45 a.m. – 10:40 a.m.
Room: M
Presented by: Alexander Kel, BIOBASE GmbH, Germany
Abstract:
Mice were infected by leukemia viruses, either by neurovirulent FrCasE or by non- neurovirulent Fr75E;
Aim of the analysis (demo) to find specific changes resulting from infection of microglia cells;
Comparison of gene expression in FrCasE-infected versus Fr75E-infected microglia cells will be done in the following example to identify key molecules that might provide coordinated regulation of the selected TFs, at 1,2,3,4 steps upstream of TFs;
To suggest at least two promising key nodes (adaptor proteins Hgs and TRAF2) to be involved in response to viral infection in microglia cells. Suggested key nodes are mapped on pathways, and we concluded what pathways might be affected upon viral infection of microglia cells.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/alexander.kel_20070601073404.pdf
Demo Number: 34
GALAXY: a simple web application for the analysis of enormous datasets
Wednesday, July 25
10:15 a.m. – 10:40 a.m.
Room: L
Presented by: Anton Nekrutenko, Penn State University, USA
Abstract:
Galaxy links large datasets with analysis tools and provides an environment where experimental biologists can perform complex analyses of very large datasets without even knowing of scalability or format compatibility issues.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/anton_20070511135103.pdf
Demo Number: 36
Effortless integration of tools into simple, scalable, multiuser, pythonic framework
Wednesday, July 25
11:10 a.m. – 11:35 a.m.
Room: L
Presented by: James Taylor, New York University, USA
Abstract:
I will show how to integrate any command line tool into a simple, scalable framework that takes care of all housekeeping and provides uniform interface for heterogeneous tools.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/james_20070511141628.pdf
Demo Number: 37
Multi-Scale Cellular Modeling with Simmune
Wednesday, July 25
11:10 a.m. – 11:35 a.m.
Room: M
Presented by: Martin Meier-Schellersheim, NIH, USA
Abstract:
The modeling tool Simmune offers an intuitive GUI for the definition of detailed models of cell biological processes ranging from interactions between molecular binding sites to the behavior of populations of cells. It provides numerous ways for visualization of and wetlab-like interaction with the simulated systems.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/mms_20070511145953.pdf
Demo Number: 38
AMAP–Fast and accurate multiple alignment using posterior decoding and sequence annealing
Wednesday, July 25
11:40 a.m. – 12:05 p.m.
Room: L
Presented by: Ariel Schwartz, University of California, San Diego, USA
Abstract:
We present AMAP, a fast and accurate multiple sequence alignment program. AMAP is based on a sequence annealing algorithm, which improves significantly on the standard progressive alignment approach. AMAP allows for adjustment of the sensitivity/PPV tradeoff and can reliably identify homologous regions among protein sequences. AMAP is freely available at http://baboon.math.berkeley.edu/amap/.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/sariel_20070511155148.pdf
Demo Number: 39
Revised Title – YASARA View – free molecular modeling environment – now in Python!
Wednesday, July 25
11:40 a.m. – 12:05 p.m.
Room: M
Presented by: Elmar Krieger, Radboud University
Abstract:
Accelerate your research in structural bioinformatics with the molecular modeling and visualization platform YASARA View, freely available for Linux, Windows and MacOSX with 24 hour support. Today’s fastest OpenGL graphics including surfaces, combined with extensive structure analysis made easily accessible, now also as a new open source Python module.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/elmar_20070530130102.pdf
Demo Number: 40
H-Invitational Database:an integrated database of all human genes and transcripts
Wednesday, July 25
12:10 p.m. – 12:35 p.m.
Room: L
Presented by: Tadashi Imanishi, AIST, Japan
Abstract:
H-Invitational Database (H-InvDB; http://www.h-invitational.jp/) is an integrated database of all human genes and transcripts. The latest release of H-InvDB (release_4.0, March 2007) contains detailed annotation of gene structure, alternative splicing, protein function, diversity, expression pattern and evolution for a total of 173,690 human transcripts that define 34,701 human genes.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/imanishi_20070531235242.pdf
Demo Number: 41
Online Resource Center for Biodefense Proteomics Research
Wednesday, July 25
12:10 p.m. – 12:35 p.m.
Room: M
Presented by: Raja Mazumder, Georgetown University, USA
Abstract:
The National Institute for Allergy and Infectious Diseases has created a biodefense proteomics research program to identify targets for vaccines, therapeutics, and diagnostics targets for select pathogens. The data generated from this program is available at www.proteomicsresource.org. We will demonstrate how to use the website and the associated bioinformatics tools.
Demo PDF:
http://www.iscb.org/cms_addon/conferences/uploaded/css/wuc_20070509123606.pdf
