Monday, August 7, 10:30 a.m. - 11:20 a.m.

Website: img.jgi.doe.gov

Short Description: The Integrated Microbial Genomes (IMG) system (img.jgi.doe.gov) provides support for comparative analysis of microbial genomes sequenced at the Joint Genome Institute in an integrated genome data context. Since its initial release in March 2005, IMG’s data content and analytical tools have been substantially extended via quarterly updates.

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Monday, August 7, 10:30 a.m. - 11:20 a.m.

Short Description: A demonstration of the SSAHA2 package, briefly describing the algorithm and demonstrating its unrivalled speed. Applications to EST alignment and polymorphism detection will be shown, followed by a demonstration of the distributed implementation used to search our trace archive. Examples will show this to be an invaluable research tool.

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Monday, August 7, 10:30 a.m. - 11:20 a.m.

Website: www.ebi.ac.uk/arrayexpress

Short Description: ArrayExpress is a public repository for microarray data developed and maintained at the EBI. ArrayExpress supports the minimum information about a microarray experiment (MIAME) standard for content, and utilises MAGE-ML, a format standard which allows microarray data to be shared unambiguously. Since going online in 2002 the database has grown to contain data for over 40,000 hybridizations from a variety of experiment types, such as gene expression, CGH and chromatin IP.

This presentation will cover how well-annotated, MIAME compliant data is acquired and stored, and how this information can then be used to enable further data analysis in the online tool Expression Profiler.

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Monday, August 7, 10:30 a.m. - 11:20 a.m.

Website: http://gin.univ-mrs.fr/GINsim

Short Description: GINsim is a software implementing a qualitative formalism to model and analyse essential dynamical properties of genetic regulatory networks. GINsim allows the user to specify a model in terms of asynchronous, multivalued logical functions, and to simulate or analyse its dynamical behaviour.

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Monday, August 7, 11:45 a.m. - 12:35 p.m.

Website: http://bioinfo.mbi.ucla.edu/pygr

Short Description: Pygr, the Python Graph Database Framework for Bioinfomatics, makes it easy to do comparative genomics analyses of huge multigenome sequence alignments, using a disk-based query algorithm that is 5- 500x faster (100-300 microseconds/query) than other indexing methods such as MySQL, binning, or R-Trees. Benefits: simplicity; speed; documentation; many features.

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Monday, August 7, 11:45 a.m. - 12:35 p.m.

Website: http://www.ebi.ac.uk/Tools/webservices

Short Description: Web Services technology brings into the bioinformatics community a new development concept in which users can access all data and applications hosted in the European Bioinformatics Institute as if they were installed in their local machines, providing seamless integration between disparate services and allowing the construction of workflows to perform complex tasks such as genome annotation, protein function prediction or microarray data analysis.

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Monday, August 7, 11:45 a.m. - 12:35 p.m.

Websites: www.synamatix.com, www.mgrc.com.my

Short Description: Three modules designed to enhance and accelerate genome assembly are presented. SynaMer identifies all unique overlapping 96-mers within a genome in 1/100th of the time taken by conventional software. SynaSearch was used to map Elephant genome reads to the Human Genome 219 fold faster and with 17% more true positives than BLASTz. Lastly, SXPet was used to identify all contaminating vector sequences without reference to Univec by filtering over-represented patterns in SynaBASE

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Monday, August 7, 2:25 p.m. - 3:15 p.m.

Website: http://www.bioinformatics.nl/tools/treedom/

Short Description: TreeDomViewer is a biological web-based visualization tool that combines a phylogenetic tree, sequence alignment and InterProScan analysis of sequences and generates a phylogenetic tree projecting the predicted protein domains onto the multiple sequence alignment. TreeDomViewer is a valuable addition to the annotation pipeline of unknown gene or gene product.

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Monday, August 7, 2:25 p.m. - 3:15 p.m.

Website: http://www.cs.bilkent.edu.tr/~patikaweb

Short Description: PATIKAweb provides a Web service for retrieving and analyzing biological pathways in the PATIKA database, currently containing data integrated from many prominent pathway databases. It features a user-friendly interface, dynamic visualization, advanced graph-theoretic queries, microarray data analysis tools and exporting facilities to various exchange formats as well as static images.

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Monday, August 7, 2:25 p.m. - 3:15 p.m.

Website: www.ebi.ac.uk

Short Description: BioModels Database is an effort to develop a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.

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Monday, August 7, 2:25 p.m. - 3:15 p.m.

Website: www.ebi.ac.uk

Short Description: EBI provides Text Mining services for document retrieval and information extraction based on Medline (EBIMed, PCorral) as well as scripted access to EBI’s TM servers for any type of textual data (e.g. Http request, SOAP Web services). All services will be explained and online tools will be demonstrated.

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Monday, August 7, 3:40 p.m. - 4:30 p.m.

Website: http://pir.georgetown.edu/

Short Description: The PIRSF Protein Classification System (PCS) allows classification of proteins into a family hierarchy using on-the-fly curator-guided clustering and other built-in tools. We will demonstrate how PCS facilitates large scale-functional annotation by classifying proteins belonging to i) a specific metabolic pathway and ii) a specific genome.

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Monday, August 7, 3:40 p.m. - 4:30 p.m.

Website: http://genepro.ccb.sickkids.ca

Short Description: A demonstration of GenePro, a plugin to Cytoscape, featuring multi-resolution display of interaction networks as weighted graphs at both cluster and protein/gene level. GenePro also allows mapping between any two groupings of proteins based on different attributes.

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Monday, August 7, 3:40 p.m. - 4:30 p.m.

Website: http://www.biozentrum.uni-wuerzburg.de/bioinformatik/

Short Description: GEPAT, http://bioapps.biozentrum.uni-wuerzburg.de/GEPAT/, is a web-based platform for annotation, analysis and visualization of microarray gene expression data. Analysis and visualization methods under genomic, proteomic and metabolic context are integrated in an easy to use, interactive graphical user interface. The session will include a live demonstration of microarray data analysis with GEPAT.

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Tuesday, August 8, 10:50 a.m. – 11:40 a.m.

Website: www.nationalgeographic.com/genographic

Short Description: An overivew of a study completed at IBM Research in preparation for the expected mtDNA and Y Chromosome data from the Genographic Project. We applied PCA and Robust Consensus Ensemble Clustering on 1737 complete mtDNA sequences to identify robust phylogeny markers, cluster samples into haplogroups and infer the evolutionary tree. We find 6 new subgroups of MD, two distinct migrations out of Africa and an N clade subtree that divides European and Eurasian haplogroups into a West-East split on the tree, in agreement with their geographic location but in disagreement with the currently accepted mtDNA tree. In particular, we place the B haplogroup close to A and not in the R megahaplogroup, in spite of SNP12705.

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Tuesday, August 8, 10:50 a.m. – 11:40 a.m.

Website: http://arrayanalysis.mbni.med.umich.edu/draw/

Short Description: Biological Concept Diagram Editor (BCDE) is a tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes. Besides standard diagramming functions, it has powerful data capture and annotation capabilities. BCDE is compatible with BioPax and it also exports to PowerPoint and Visio.

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Tuesday, August 8, 10:50 a.m. – 11:40 a.m.

Short Description: A demonstration of both myGrid and ToolBus/PathPort towards a specific biological problem will be presented. These are two bioinformatics software suites built on standards from Web services, which allows them to interoperate at multiple levels. Both tools will be introduced and then used jointly thus demonstrating the power of standards-based infrastructure for bioinformatic analyses.

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Tuesday, August 8, 10:50 a.m. – 11:40 a.m.

Website: http://www-bs.informatik.uni-tuebingen.de/

Short Description: OpenMS is a C++ platform for data analysis applications in the field of shotgun proteomics. It offers data structures and algorithms for data preprocessing, protein identification, quantitation, alignment of samples, statistical analysis and visualization. Most functionality is already turned into tools which can be combined to powerful analysis pipelines. (www.OpenMS.de)

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Tuesday, August 8, 2:00 p.m. – 2:50 p.m.

Website: http://arrayanalysis.mbni.med.umich.edu/arrayanalysis.html

Short Description: The Web-based GeneChip Analysis System (WGAS) incorporates popular probe-, gene- and function category-level analysis methods through straightforward web interface. It natively supports custom GeneChip probe set definition files for more accurate data interpretation. Users can also access to any Cel files deposited in NCBI GEO database for re-analysis and comparison.

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Tuesday, August 8, 2:00 p.m. – 2:50 p.m.

Website: www.accelrys.com

Short Description: Simplify your analyses and save time using Pipeline Pilot™, an integrative workflow pipelining environment for automating and improving your bioinformatics efforts in many application areas. The integration of new algorithms and data sources within Pipeline Pilot greatly expands the bioinformatics capabilities by working with other applications and extending bioinformatics into new areas.

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Tuesday, August 8, 2:00 p.m. – 2:50 p.m.

Website: http://compbio.mcs.anl.gov/gnare

Short Description: GNARE supports automated and interactive analysis of user sequence data including function prediction and development of metabolic reconstructions. It provides a framework for comparative and evolutionary analysis and annotation of genomes and metabolic networks. The Grid-based computational backend can analyze an average prokaryotic genome in less than five hours.

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Tuesday, August 8, 2:00 p.m. – 2:50 p.m.

Website: http://www.cnptia.embrapa.br/

Short Description: STING_RDB is a relational database composed of structural parameters for protein analysis operating with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Currently, STING_DB has over 300 parameters compiled at the single site and was implemented using free software.

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Tuesday, August 8, 2:50 p.m. – 3:40 p.m.

Website: http://www.biopostgres.org/GObase/

Short Description: GObase is an open-source graph database for Gene Ontology by extending PostgreSQL with a graph datatype and operators. It also includes an interactive graphical user interface which displays selected sub-hierarchies of the ontology, facilitates queries over GO annotation data and automatically initiates searches in relevant databases. (Genbank, Pubmed, etc).

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Tuesday, August 8, 2:50 p.m. – 3:40 p.m.

Website: http://brainarray.mhri.med.umich.edu/brainarray/datamining/MarkerInfoFinder

Short Description: MarkerInfoFinder is a novel web-based Medline search engine that supports the use of various genetic marker IDs and flexible positional/linkage disequilibrium criteria. It incorporates natural language processing methods and integrates information from multiple databases. MarkerInfoFinder greatly facilitates the understanding of the pathophysiological significance of SNPs derived from genome-wide scanning.

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Tuesday, August 8, 4:05 p.m. – 4:55 p.m.

Website: http://www.cbi.cnptia.embrapa.br/SMS/

Short Description: Accessing STING features: identification of active sites and folding essential residues by STING; Sting key components: JavaProtein Dossier and STING Report; Local file submission to STING server: generating 310 different structure/function parameters; 3D and 2D related parameter plots for multiple structures.

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Tuesday, August 8, 4:05 p.m. – 4:55 p.m.

Website: http://www.kurnikov.org/harlem_main.html

Short Description: HARLEM (Hamiltonians to Research LargE Molecules) has functionality that includes: Pathways for electron transfer, continuum electrostatics, PNP, replica-exchange-rigid-body-Monte-Carlo etc; interfaces AMBER, GAUSSIAN, FIRST etc.; maintains several levels of coarse-graining; parallelizable C++ program for windows and Linux with a versatile menu-driven GUI, xml and xml-like file formats, interfaced with python.

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Tuesday, August 8, 4:05 p.m. – 4:55 p.m.

Website: http://www.ebi.ac.uk

Short Description: PRIDE is a repository of mass spectrometry based proteomics identifications. The PRIDE data model makes considerable use of controlled vocabularies, supported by the Ontology Lookup Service (OLS) that has become an important service in its own right. Both services will be described and demonstrated.

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Tuesday, August 8, 4:05 p.m. – 4:55 p.m.

Websites: www.sun.com/edu/commofinterest/compbio, www.sun.com/lifesciences, www.exludus.com

Short Description: Sun Microsystems is synonymous with innovation in hardware and software, like the Sun Fire x64 server family, Coolthreads, Solaris 10 and Utility Computing. Open standards, extensive technology sharing, and Computational Biology community support lead to successful collaborations like the data-activated-processing by N1 Grid Engine and eXludus RepliCator.

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Wednesday, August 9, 9:50 a.m. – 10:40 a.m.

Website: img.jgi.doe.gov/m

Short Description: IMG/M is an experimental data management and analysis system that extends the Integrated Microbial Genomes (IMG) system by integrating IMG’s isolate genomes with microbial community metagenomes. In addition to IMG’s analytical capabilities, IMG/M tools allow examining functional profiles across genomes and metagenomes, and strain-level heterogeneity within a species population.

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Wednesday, August 9, 9:50 a.m. – 10:40 a.m.

Website: http://vision.lbl.gov/People/ddas/

Short Description: High-throughput expression profiling technologies have raised the possibility of a global understanding of gene regulation in multifarious biological systems. The MARSMotif suite of tools based on regression splines, which identify the active cis-regulatory motif combinations and their associated target genes from microarray data will be demonstrated. They do not require gene-clustering and have proven very effective in deciphering transcriptional subnetworks in both lower eukaryotes and mammals, in contrast to many comparable approaches.

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Wednesday, August 9, 9:50 a.m. – 10:40 a.m.

Website: http://string.embl.de

Short Description: The web-based STRING database of known and predicted protein interactions will be demonstrated. Known interactions are integrated from several protein interaction and pathway databases. Additional functional associations are obtained through literature mining and analysis of microarray expression data and genomic context. The STRING database is available at http://string.embl.de/.

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Wednesday, August 9, 9:50 a.m. – 10:40 a.m.

Website: http://www.scmbb.ulb.ac.be/

Short Description: The BioMAZE System is a workbench for the representation and analysis of networks of molecular interactions and cellular processes, genetic expression and regulation, enzymatic transformations and regulation, metabolic pathways, signal transduction. The BioMAZE system integrates the aMAZE database and various tools for analyzing and visualizing the stored information.

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Thursday, August 10, 9:50 a.m. – 10:40 a.m.

Website: http://www.ebi.ac.uk/

Short Description: This demonstration explores the wealth of information in UniProtKB and InterPro, two major proteomics databases at EMBL-EBI. UniProtKB (SwissProt, TrEMBL, PIR) is a central repository of protein sequence and function, while InterPro provides functional and structural annotation/classification for proteins by integrating information from ten major signature and five structural databases.

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