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.
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.
Short Description: We demonstrate GMAP, a standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without the use of probabilistic splice site models. Additional features of the program include: identification of microexons and chimeras; relative alignment of ESTs; efficient lookup of genomic map information; and handling of genomes with alternate assemblies or strains.
Short Description: This demonstration will describe the use of several immunological relevant web tools available at the Center for Biological Sequence Analysis (CBS). The tools described are: NetChop-3.0; a proteasomal cleavage site predictor, NetMHC-2.0; a predictor of MHC class I peptide binding, NetCTL; a CTL-epitope predictor, and BebiPred; a tool predicting linear B-cell epitopes. Furthermore we will present other bioinformatics web-tools, that are very useful in immunological studies, including a general motif predictor, EasyGibbs, which can be used for, e.g., MHC class II binding-motif establishment, and a specialized 9mer motif predictor builder, EasyPred.
Short Description: INDUS is a federated, query-centric system for knowledge acquisition from semantically heterogeneous, distributed and autonomous data sources. INDUS employs ontologies and inter-ontology mappings to enable a user or an application to view a collection of such data sources as though they were a single data source structured according to a user ontology. INDUS and the associated collection of software tools support: editing of ontologies and specification of semantic relationships between ontologies through a graphical user interface, query answering and construction of predictive classifiers from semantically heterogeneous data sources, without having to assemble all of the data at a central location.
Short Description: INOH is a human curated signal transduction pathway database of model organisms including human, mouse, rat and others. The aim of INOH project is to provide pathway knowledge that resides in the scientific literature in a machine-accessible form. To that end, every pathway component in INOH (events, proteins, chemicals, etc.) is annotated by a biological ontology and these ontological knowledge can be utilized during a pathway query. The ontologies and the system are freely available at http://www.inoh.org.
Short Description: Integrated Microbial Genomes (IMG) system (http://img.jgi.doe.gov) provides a framework for comparative analysis of genomes sequenced by the Joint Genome Institute. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective. IMG aims at providing high levels of data diversity in terms of integrated genomes, data coherence in terms of gene annotation quality, data completeness in terms of breadth of functional annotations, and system comprehensibility in terms of documenting its structural and operational semantics. IMG was released in March 2005 and is updated on a quarterly basis.
Short Description: This demonstration illustrates how text mining web services can be integrated into a workflow environment to provide a flexible system whereby research biologists can have relevant literature delivered, clustered and annotated. Initiated from within a biomedical workflow, text mining web services are used to automatically retrieve, cluster and annotate document collections based on information from resources such as UMLS, HUGO and Uniprot amongst others. The results are presented to the user via a client interface designed for efficient browsing and navigation. The Integration of workflows, services and user interface is supported by a portal framework with customisation and reusability functionalities.
Short Description: LARALink(Loci Analysis for Rearrangement Link) is a database driven web application that utilizes several public datasets to analyze clinical cytogenetic data to identify candidate genes. LARALink allows UniGene clusters or SNPs (Single Nucleotide Polymorphisms) to be queried for multiple patients by cytoband, chromosome marker or base pair. The results can be refined with the use of an expression filter. Once a set of UniGene clusters has been identified, the expression distribution profile, EST's, NCBI Map View, OMIM or NCBI GEO entries are displayed.LARALink is a public resource available at: http://laralink.bioinformatics.wayne.edu:8080/unigene.
Short Description: M-GCAT is a genome comparison software package that can quickly analyze, cluster and align multiple genomes. M-GCAT is similar in speed to MUMmer, and, in several cases, generates alignments consistent with BLAST. M-GCAT has a user interface that allows the user to efficiently analyze and compare various regions of the genomes. This visualization tool is robust and easy-to-use, allowing for interactive multiple genome comparison to aide in detecting biological patterns such as evolution and mutations among the genomes. M-GCAT is available at http://alggen.lsi.upc.es, under the Research link, in Align Tools.
Short Description: The MAPPER platform (http://bio.chip.org/mapper) consists of a library of over a thousand HMM models abstracting binding site characteristics for several hundred transcription factors, a search engine for the retrieval of putative transcription factor binding sites in a known gene or uploaded sequence, and a large database of such sites identified in the upstream sequences of all human, mouse and Drosophila genes. The demonstration will present the powerful visualization, selection and export options offered by the system and, given its many possible applications, will provide practical guidance regarding the most appropriate tool and choice of parameters for a given task.
Short Description: Michigan Molecular Interactions (MiMI) assists scientists digging through an overwhelming amount of protein interaction data. MiMI gathers data from well-known protein interaction databases and merges the information. Since these datasets often contain contradictory information, the merge is performed in such a way that all information is retained. A provenance model has been developed that tracks where each piece of data came from, and what processes have been performed upon it. A simple yet powerful user interface aids users in their queries. Thus, MiMI allows scientists to query all data, whether corroborative, or contradictory, and specify which sources to utilize.
Short Description: MSight is a package to construct, manipulate and analyse images from liquid chromatography (LC) - mass spectrometry (MS) experiments. Exploiting the correlations that exist within LC-MS datasets allows for the extraction of information otherwise not visible when looking at a single spectrum at a time. Image processing of these data is extremely useful for quality control, experimental monitoring, quantitation and more generally knowledge extraction in high-throughput proteomics studies.
Short Description: myGrid offers a collection of services used to develop applications for creating, running and recording the results of in silico experiments. We will demonstrate the myGrid middleware through its use in the Taverna workflow environment. We cater for both expert bioinformaticians and working biologists. We will show support for both groups by showing a complex bioinformatics analysis being constructed, enacted and verified through use of the rich, semantically annotated provenance data automatically captured by myGrid. These two linked demonstrations will show how myGrid services can be used to rapidly create in silico experiments that will change how bioinformatics is performed.
Short Description: Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes. Phylogenetic algorithms and software that incorporate both processes are needed. We present Notung 2.0, a software tool that offers a unified framework for incorporating macroevolutionary information into phylogenetic tasks, including new methods for gene treereconstruction and the analysis of gene duplication and loss.
Short Description: OncoTCap integrates a cancer knowledge base with an agent-based simulation engine. It synthesizes heterogeneous information to create and calculate a model. OncoTCap supports building and validating multi-scale models integrating submodels from the molecular network up to the clinical trial. One criterion is to facilitate the work of people with a diverse set of skills and goals, to encourage team science. Another is extreme modularity of ideas, to achieve re-use. A third is iconoclast support, to facilitate new ways of thinking. This demo will step through the workflows and execute a model combining mitosis, mutation, and apoptosis.
Short Description: Pathway Tools is a software environment for creating, querying, visualizing, and analyzing Pathway/Genome Databases (PGDBs). PGDBs integrate information about the genes, proteins, metabolic network, and genetic network of an organism. This demonstration will cover two Pathway Tools modalities for interacting with a PGDB: a graphical environment for visualizing the contents of a PGDB and interactively updating a PGDB; and a sophisticated ontology and database API that allows programs to perform complex queries, symbolic computations, and data mining on the contents of a PGDB. Those APIs allow users to query the 165 PGDBs within SRI's BioCyc database collection.
Short Description: PATIKAweb provides a Web service for retrieving and analyzing biological pathways in the PATIKA database, which currently contains data integrated from popular public pathway databases such as Reactome. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena and exporting facilities to various exchange formats as well as static images.
Short Description: PIR (http://pir.georgetown.edu) provides a comprehensive resource for bioinformatics analysis of protein sequences and families, facilitating accurate and rich functional annotation of UniProt Knowledgebase. The resource framework couples PIRSF protein family classification with the iProClass integrated protein database, thereby allowing associative analysis using information on protein sequence, structure, function, and other systems biology information. The integrative approach supports novel functional predictions for uncharacterized proteins, correction of annotation errors, and understanding of structure, function, and evolutionary relationships. We will demonstrate, with case studies, how to use web-based PIR databases and software tools for knowledge discovery on protein sequences.
Short Description: High-throughput proteomics techniques are enabling the generation of mass-spectrometry derived protein identifications at an ever increasing pace. As almost all of this data is published solely in PDF format, it is not readily accessible to other researchers. We here present PRIDE, a publicly available protein identifications database, that can alleviate these needs by storing protein identifications and the spectra that gave rise to them in a structured and queryable online repository.
Short Description: HHpred is the first server for protein homology detection based on the pairwise comparison of profile hidden Markov models (HMMs). HHpred is interactive and designed to offer maximum flexibility and speed. It allows users to search a wide choice of databases (PDB, SCOP, Pfam, SMART, COG/KOG, CDD). HHsearch is the program package that underlies HHpred. It has been shown to be the fastest and most sensitive publicly available profile-profile comparison program. We will explore the possiblities offered by HHpred and HHsearch by analysing several proteins recently investigated in our lab. Availability: http://protevo.eb.tuebingen.mpg.de/hhpred
Short Description: POSE is an interactive graphical environment for the design, modeling, and optimization of protein structures. It permits manipulation of protein structures with pinpoint control using concepts from robotics. Its features include: 1. automatic generation of 3D structures from sequence, 2. manipulation of parts of a protein with respect to its other parts without breaking its chemical structure, 3. real-time energy visualization to facilitate comparison and analysis of structures, 4. calculation of low-energy configurations by applying local optimizations, 5. automatic creation of a variety of low-energy beta-sheet configurations according to high-probability beta topologies and beta pairings.
Short Description: We will demonstrate the functionality and utility of PUMA2 - an integrated Grid technology-based computational environment for high-throughput genetic sequence analysis and evolutionary analysis of metabolism. PUMA2 contains sequence data, annotations and results of analyses for over 1050 organisms. It allows interactive analysis of data by variety of bioinformatics tools, including tools developed by our group (e.g. Chisel, PhyloBlocks) in a framework of metabolic and phenotypic information. The following capabilities will be discussed:
Environment for high-resolution comparative analysis of genomes,
Representation of metabolic pathways in PUMA2,
Automated Grid-technology based computational infrastructure for analysis of genomic data.
Short Description: We will demonstrate how to use Pygr to write simple but powerful graph queries; store and query multiple sequence alignments in a form that can scale to alignments of whole genomes; provide a simple but powerful interface to large sequence databases and automation of tools like BLAST; provide both container and graph interfaces to existing data in relational databases such as MySQL and Postgres; store and query multi-genome alignments such as the UCSC BLASTZ alignments of many animal genomes; and facilitate development of visualization tools (we will use alternative splicing graphs as a tutorial example).
Short Description: We propose to demonstrate an algorithm to find common spatial motifs from multiple protein structures. The motifs are sequence order independent and may occur in every member of a group of proteins or a significant fraction of them (as specified by a threshold parameter). The spatial motif matching process accommodates variation inherent in structure determination. With our current software we expect to be able to provide real time responses (tens of seconds of processing time) for queries submitted by users in the ISMB demo session.
Our command line and simple Graphics User Interface (GUI) are shown in our demo proposal and is being extended. We intend to present a web-based interface with a fully integrated GUI to our server that implements our algorithms and provides access to PDB structures and previously determined spatial motifs.
Short Description: The Rat Genome Database (RGD, http://rgd.mcw.edu) curates and integrates rat, mouse, and human 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 diseases. This demo will show tools including ones that use multiple ontologies to map biology onto the genome:
GBrowse - the open source GMOD genome browsing tool
Gviewer - a novel genome-wide viewer for gene, pathway, phenotype, and disease data
VCMap - a multi-species comparative mapping tool
RGD Advanced Search Tool - a comprehensive database searching tool that uses multiple ontologies
Short Description: Reactome, located at http://www.reactome.org, is an expert-authored and peer-reviewed database of biochemical reactions and cellular processes/pathways in human. Reactome contains information on both metabolic and signal transduction pathways/network as well as various other processes. The demonstration will cover Reactome web site, Reactome data entry tool and programmatic access to Reactome data. Reactome tools and data are freely available.
Short Description: The mission of the National Cancer Institute Center for Bioinformatics (NCICB) is to provide informatics infrastructure and applications that support advanced translational research in cancer biology. Rembrandt (Repository for Molecular BRAin Neoplasia DaTa) is one such informatics effort that leverages data warehousing technology and an N-tiered architecture to host and integrate clinical and functional genomics data from various cancer clinical and molecular trials. The goal of this initiative is to integrate gene expression patterns with genetic aberrations and clinical observations for classifying tumors into biologically meaningful and clinically useful categories.
Short Description: SeqHound is a bioinformatics programming platform offering daily-updated contents of Entrez sequences, 3-D structures, sequence redundancies and neighbours, taxonomy, complete genomes, Entrez Gene contents, conserved domains, Gene Ontology annotations, database cross-references, interaction data, PubMed links and literature co-occurrence data. SeqHound may be set up locally using a freely available user manual and software. SeqHound is ODBC compliant and employs the MySQL database engine. SeqHound is also accessible via a remote API (Perl, BioPerl, Java, C/C++). Source code is freely available under GNU public license (http://www.blueprint.org/seqhound).
Short Description: The Short Time-series Expression Miner (STEM) is a Java application with a graphical user interface for the analysis of short time-series microarray data. The package uses a novel clustering technique specifically designed for such data that allows researchers to determine the statistical significance of gene clusters, even when very few (<8) time points are measured. The software is integrated with the Gene Ontology database allowing direct assessment of the biological significance of clusters. The software is available for free to academic and non-profit users. For further information see http://www.cs.cmu.edu/~jernst/st/st.html.
Short Description: Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in wide variety of eukaryote species. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations. The recent application of random shotgun sequencing to environmental samples makes possible extensive SNP analysis of co-occurring and co-evolving microbial populations. We present an interactive visualization tool, SNP-VISTA, to aid in analyses of large-scale resequence data of disease-related genes for discovery of associated and/or causative alleles and massive amounts of ecogenomics data for studying homologous recombination in microbial populations.
Short Description: STING is a program that has the capability to present the largest number of descriptors for the sequence, structure, function, stability and binding in a concise and visually compelling way, as well as the capability to select those residues which satisfy a user defined parameter/descriptor values. This feature allows that some very interesting and important questions can be answered, such as: Is there a set of parameters (protein structure descriptors) which can define UNIQUELY an amino acid ensemble coinciding with the active site of a given protein or coinciding with amino acids identified experimentally as crucial for folding/stability.
Short Description: We have developed SynBrowse, a synteny browser for visualizing and analyzing microsynteny, macrosynteny, homologous genes both within and between species. SynBrowse is a GBrowse family software tool that runs on top of the open source Bioperl modules. It consists of two components: a web-based front end and a set of relational database back ends. Each database stores pre-computed comparative alignments from a focus sequence to reference sequences and genome annotations of the focus sequence. The user interface lets end users search for syntenic blocks between two sequences and zoom in to view the detailed comparisons.
Short Description: Chimera is a program for interactive molecular graphics and modeling. Chimera provides standard graphics features as well as more unique tools for working with sequence alignments (with information flow to and from associated structures), volume data, docking results, molecular dynamics trajectories, and large molecular assemblies. Menu and command-line interfaces provide a rich and overlapping set of functionality. Chimera includes detailed user documentation and is available for Windows, Linux, Mac OS X (with X11), IRIX, and Tru64 Unix. Chimera is free for academic, government, and non-profit use and can be downloaded from http://www.cgl.ucsf.edu/chimera.
Short Description: In this demonstration, we introduce a system GEMS for automated development and evaluation of high-quality cancer diagnostic models and biomarker discovery from microarray gene expression data. The development of GEMS was informed by an extensive algorithmic evaluation using 11 microarray datasets. The system was further evaluated in cross-dataset applications and using 5 microarray datasets. The performance of models produced by GEMS is comparable or better than the results by human analysts, and these models generalize well to independent samples in cross-dataset applications. The system is freely available for non-commercial use from http://www.gems-system.org.
Short Description: The Generic Model Organism Database project has created a suite of software for creating a MOD. This demo will focus on the software to create, edit, and browse genome features using open source tools, including GBrowse, Apollo, and CMap running on top of a modular genomics schema, chado.
Short Description: Biozon is a knowledge resource that integrates and materializes interrelated biological data on proteins, DNA, interactions, pathways and more, onto a unified graph schema. We will discuss the graph structure and demonstrate how each entity can be viewed in its broad biological context. We will explain the unique web interface to create complex queries (that span multiple data types and their relationships), and "fuzzy" searches (using similarity data). We will demonstrate materializing search results and ranking using the Biozon equivalent of Google's PageRank. Additional topics include Biozon's analysis tools, including domain prediction and protein and EST sequence analysis.
Short Description: Vigyaan (http://www.vigyaanCD.org) is an integrated software workbench for bioinformatics and computational biology. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software. It is being distributed as free ISO image under GNU General Public License (GPL). Vigyaan includes applications for genome analysis, biomolecular structural visualization/manipulation and molecular. Vigyaan is suitable for booting a collection of PCs as a cluster, enabling high-throughput analysis of genome and sequence data and detailed molecular modeling. Early view of a more advanced integrated workbench, BiLab, will also be presented.
Short Description: VisANT is a web-based software framework for visualizing, analyzing and interpreting networks of biological interactions and associations. It provides a workbench interface for combining and annotating network data in the context of sequence, pathway, structure, and associated annotations for different genomes, such as those from Gene Ontology and KEGG databases, and provides statistical and analytical tools needed for extracting topological properties of the user-defined networks. Users can customize, modify, save and share network views with other users, and import basic network data representations from their own data sources, and from standard exchange formats such as PSI and BioPAX. RemarksThanks for considering our proposed demonstration at ISMB. If you have any questions or problems regarding the demo, please feel free to email us (firstname.lastname@example.org or email@example.com).
Short Description: Cytoscape is open-source bioinformatics software for visualizing and analyzing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Cytoscape is written in Java, and provides a rich framework for bioinformatic analysis. Cytoscape is extensible through a plugin architecture, allowing rapid development of additional computational analyses and features. Plugins are available for biological network analyses, layout, data format support, and database and web resource access. A diverse set of plugins are being developed by the user community using Cytoscape's open Java software architecture.
Short Description: VitaPad is an open-source cross-platform application that allows users to create and modify biological pathway diagrams and map microarray data to them. It uses an intuitive interface and high resolution graphics to create visually appealing graphs that are stored in an open XML format that allows for easy integration with other software tools. Pathway graphs can also be created dynamically with force-directed layout alogithms. VitaPad is built upon a database design that separates the pathway's biological details from its rendering details, allowing for new classes of data to be readily incorporated into the schema.
Short Description: Searching and collecting data from online resources can be automated using scripts but these require programming and customization. WinAgent offers a convenient way to automate repetitive data collection processes by enabling biomedical researchers to build customized agents that collect information from web-accessible databases. The WinAgent tool is based on a mapping-by-example method; new agents are created by recording a users' natural browsing, highlighting and tagging actions within their web browser. Agents can be invoked to replay users' navigation actions and to automate information collection. Agents store the collected data in XML format, for use in other applications.