20th Annual International Conference on
Intelligent Systems for Molecular Biology
PDF Print E-mail

Technology Track Schedule


TT01 - GRIDBase: A platform for scientific data integration, curation, and dissemination
Date: Sunday, July 15: 10:45 a.m. - 11:40 a.m.Room: 201A

Presenting author: Jeff Milton, Genentech, United States

Presentation Overview: Show/Hide
Capturing bioinformatics workflows in a web framework that highlight collaborative efforts.

Integrating heterogeneous environments: MySQL, Oracle, Excel etc... web accessible curation platform and exporting into any environment.

Presentation PDF:Download Abstract
TOP


TT02 - MISO: An open-source LIMS for next-generation sequencing centres
Date: Sunday, July 15: 10:45 a.m. - 11:10 a.m.Room: 201B

Presenting author: Robert Davey, The Genome Analysis Centre, United Kingdom

Presentation Overview: Show/Hide
We will present MISO (Managing Information for Sequencing Operations), a freely available open-source LIMS for recording next-generation sequencing (NGS) metadata. The presentation will focus on the core areas of data tracking within MISO, avenues for downloading, installing and developing the system, and give an insight into future new features.

Presentation PDF:Download Abstract
TOP


TT03 - Jalview 2.8: Including new JABAWS 2 Alignment, Conservation and Disorder prediction webservices and support for RNA secondary structure
Date: Sunday, July 15: 11:15 a.m. - 11:40 a.m.Room: 201B

Presenting author: Jim Procter, College of Life Sciences, United Kingdom

Presentation Overview: Show/Hide
Jalview is an open source platform for multiple sequence alignment, editing and analysis. We will demonstrate Jalview v2.8, which includes new web services for protein disorder and alignment conservation provided by JABAWS 2, and supports DAS 1.6/2.0 via JDAS, and the visualization of RNA secondary structure and base-pair conservation.

Presentation PDF:Download Abstract
TOP


TT04 - Providing Bioinformatics Services with the StratusLab Cloud
Date: Sunday, July 15: 11:45 a.m. - 12:10 p.m.Room: 201A

Presenting author: Christophe Blanchet, IDB - IBCP, France

Presentation Overview: Show/Hide
Improvements of experimental technologies forces biologists to face a deluge of data that require relevant tools and sufficient resources to be analyzed. The StratusLab cloud helps bioinformatics experts to define virtual appliances with pre-installed tools and workflows, and helps scientists to deploy them, on demand, on research infrastructures.

Presentation PDF:Download Abstract
TOP


TT05 - BioJS for representing biological information
Date: Sunday, July 15: 11:45 a.m. - 12:10 p.m.Room: 201B

Presenting author: Rafael Jimenez, EMBL-EBI, United Kingdom

Presentation Overview: Show/Hide
BioJS is an open source JavaScript library of graphical components to represent biological information. BioJS as project encourages developing standard components that can be easily reused and shared by the bioinformatics community. This demo will present and demonstrate how to use and develop graphical components with BioJS.

Presentation PDF:Download Abstract
TOP


TT06 - The Taverna Server: Executing Scientific Workflows Remotely
Date: Sunday, July 15: 12:15 p.m. - 12:40 p.m.Room: 201A

Presenting author: Katy Wolstencroft, University of Manchester, United Kingdom

Presentation Overview: Show/Hide
The Taverna Server allows workflows to be deployed and enacted on remote computational resources, allowing workflow execution through web portals and third-party software. The Taverna server is used for high throughput experiments, e.g. analysing whole genome SNP data on the Amazon Cloud, and workflow interoperability, running Taverna workflows through Galaxy.

Presentation PDF:Download Abstract
TOP


TT07 - PSI-Search: iterative HOE-reduced profile SSEARCH searching
Date: Sunday, July 15: 12:15 p.m. - 12:40 p.m.Room: 201B

Presenting author: Andrew Cowley, EMBL-EBI, United Kingdom

Presentation Overview: Show/Hide
PSI-Search combines a Smith-Waterman sequence search and the PSI-BLAST profile construction strategy, along with a technique to reduce homologous over-extension errors. As a result, PSI-Search achieves better sensitivity than PSI-BLAST, whilst giving many times fewer false positives. This talk will demonstrate how to use PSI-Search at the EMBL-EBI website.

Presentation PDF:Download Abstract
TOP


TT08 - Interactive Visual Analysis of NGS Data using Trackster and Galaxy
Date: Sunday, July 15: 2:30 p.m. - 2:55 p.m.Room: 201A

Presenting author: Jeremy Goecks, Emory University, United States

Presentation Overview: Show/Hide
The Trackster visual analysis environment couples visualization and next-generation sequencing (NGS) analysis tools to enable interactive, user-friendly experimentation on NGS data. We will demonstrate how Trackster can be used for interactive RNA-seq analysis, real-time SNP calling, and other common NGS analyses.

Presentation PDF:Download Abstract
TOP


TT09 - Persephone: a GUI to Genomic Data
Date: Sunday, July 15: 2:30 p.m. - 3:25 p.m.Room: 201B

Presenting author: Maxim Troukhan, Ceres, Inc., United States

Presentation Overview: Show/Hide
A stand-alone graphical application visualizes genomic data of different kinds: genetic maps, genomic sequences, gene models, QTLs, RNA-seq, synteny, SNPs, etc. Data is stored in an Oracle database and presented by a high-performance graphical engine in a smooth, intuitive way.

Presentation PDF:Download Abstract
TOP


TT10 - The first biomedical AppStore: Galaxy Tool Shed
Date: Sunday, July 15: 3:00 p.m. - 3:25 p.m.Room: 201A

Presenting author: Greg Von Kuster, The Pennsylvania State University, United States

Presentation Overview: Show/Hide
Demonstrate the interaction of the Galaxy environment with a Galaxy tool shed. Tools and related components will be installed from the tool shed into the Galaxy environment, providing a rich visual demonstration of the ease with which Galaxy can be manipulated using the tool shed.

Presentation PDF:Download Abstract
TOP


TT11 - Zooma2 – A repository of annotation knowledge and curation API
Date: Sunday, July 15: 3:30 p.m. - 3:55 p.m.Room: 201A

Presenting author: Tony Burdett, EMBL-EBI, United Kingdom

Presentation Overview: Show/Hide
We present Zooma2, a linked data repository and API of annotation knowledge and highly annotated data. Zooma2 offers a useful ontology annotation service that makes it possible to integrate annotation data from a variety of different sources, and share this knowledge between applications.

Presentation PDF:Download Abstract
TOP


TT12 - Efficient Searching and Mining of the RCSB Protein Data Bank
Date: Sunday, July 15: 3:30 p.m. - 3:55 p.m.Room: 201B

Presenting author: Peter Rose, University of California San Diego, United States

Presentation Overview: Show/Hide
The Protein Data Bank, the worldwide repository of the 3D structures of proteins, nucleic acids, and their complexes, is growing rapidly and now exceeds 80,000 structures. We will demonstrate the latest features of the comprehensive website and provide tips for how to effectively use the RCSB PDB website and web services.

Presentation PDF:Download Abstract
TOP


TT13 - VisANT: Integrative network platform to connect genes, drugs, diseases and therapies
Date: Sunday, July 15: 4:00 p.m. - 4:25 p.m.Room: 201A

Presenting author: Zhenjun Hu, Bioinformatics Program, United States

Presentation Overview: Show/Hide
VisANT is a web-based systems biology workbench for integrative analysis of biological networks. It provides rich functionalities for network visualization, analysis and inference with integrated biological knowledge. New features in VisANT allow easy navigation and networking between genes, drugs and their targets, diseases and therapies. VisANT is available at http://visant.bu.edu

Presentation PDF:Download Abstract
TOP


TT14 - HH-suite for sensitive protein sequence searching based on HMM-HMM alignment
Date: Sunday, July 15: 4:00 p.m. - 4:25 p.m.Room: 201B

Presenting author: Markus Meier, LMU, Germany

Presentation Overview: Show/Hide
HHsuite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models. We will demonstrate HHblits and HHsearch with practical examples. We will also present recent developments, such as a set of sequence-structure scores that improve template selection and alignments for homology modeling.

Presentation PDF:Download Abstract
TOP


TT15 - GenomeSpace: An environment for frictionless bioinformatics
Date: Monday, July 16: 10:45 a.m. - 11:10 a.m.Room: 202B/C

Presenting author: Michael Reich, Broad Institute, United States

Presentation Overview: Show/Hide
GenomeSpace is a connectivity layer between genomics analysis tools. Using GenomeSpace, researchers can construct analyses requiring data transfer between diverse tools such as Web applications, desktop packages, and scripts. GenomeSpace provides cloud-based storage and handles file-format compatibility automatically. The GenomeSpace community includes Cytoscape, Galaxy, GenePattern, Genomica, IGV, UCSC, and others.

Presentation PDF:Download Abstract
TOP


TT16 - Vector NTI – Sequence Analysis & Design in Synthetic Biology
Date: Monday, July 16: 10:45 a.m. - 11:40 a.m.Room: 201A

Presenting author: Raymond Tecotzky, Life Technologies, Inc., United States

Presentation Overview: Show/Hide
Vector NTI® software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publicize diverse types of molecular biology data, all within one graphically rich analysis environment.

Presentation PDF:Download Abstract
TOP


TT17 - Better Computing for Better Bioinformatics
Date: Monday, July 16: 10:45 a.m. - 11:40 a.m.Room: 201B

Presenting author: George Vacek, Convey Computer, United States

Presentation Overview: Show/Hide
Convey’s Hybrid-Core computing architecture, which combines a traditional x86 environment with a reconfigurable coprocessor, delivers extremely high-performance for genomic data analysis workflows including reference mapping, de novo assembly, functional annotation, variant analysis and RNA expression profiling. Comparative performance for a range of bioinformatics application workflows will be presented.

Presentation PDF:Download Abstract
TOP


TT18 - Using CATH-Gene3D to study the evolution of your protein and find its function
Date: Monday, July 16: 11:15 a.m. - 11:40 a.m.Room: 202B/C

Presenting author: Christine Orengo, University College London, United Kingdom

Presentation Overview: Show/Hide
we will describe the CATH-Gene3D classification of domain structure superfamilies and demonstrate all the major features accessible via the web ie evolutionary classifications, phylogenetic analyses, evolution of functions within superfamilies and prediction of domain contexts and interactions. We will also introduce Genome3D integrating CATH with other major structural resources.

Presentation PDF:Download Abstract
TOP


TT19 - GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens
Date: Monday, July 16: 11:45 a.m. - 12:10 p.m.Room: 202B/C

Presenting author: Esther Schmidt, German Cancer Research Center (DKFZ), Germany

Presentation Overview: Show/Hide
RNA interference (RNAi) allows systematic screening for loss-of-function phenotypes on a genome-wide scale, providing a rich source of functional annotation. The GenomeRNAi database (www.genomernai.org) holds RNAi-induced phenotype data from published screens for human and drosophila. Data on RNAi reagents are provided, as well as phenotype download options and DAS-enabled visualization.

Presentation PDF:Download Abstract
TOP


TT20 - Use of Genome-scale Metabolic Reconstruction coupled with Characterized Parts to enable Synthetic Engineering of Organisms
Date: Monday, July 16: 11:45 a.m. - 12:40 p.m.Room: 201A

Presenting author: Kevin Clancy, Life Technologies, United States

Presentation Overview: Show/Hide
Rational engineering of organisms requires a genome-wide understanding of the organism’s physiology. We have applied a combination of genome sequencing, assembly and annotation, metabolic modeling, and synthetic biology methods to engineer the algal strain Synechococcus elongatus PCC7942. This approach can be readily used for engineering known and novel organisms.

Presentation PDF:Download Abstract
TOP


TT21 - Sensitive metagenomics searches against reduced libraries with FASTA
Date: Monday, July 16: 11:45 a.m. - 12:10 p.m.Room: 201B

Presenting author: William Pearson, EMBL-EBI, United Kingdom

Presentation Overview: Show/Hide
Metagenomics studies are challenged as both the volume of metagenomic data and the size of protein databases increases. Improvements to the FASTA programs, including FASTX, allow searches against representative databases that recover 90% or more of the sequences found in complete sequence searches from representative sets that are 100-fold smaller.

Presentation PDF:Download Abstract
TOP


TT22 - Efficient key pathway mining – Combining networks and OMICS data
Date: Monday, July 16: 12:15 p.m. - 12:40 p.m.Room: 202B/C

Presenting author: Jan Baumbach, Max Planck Institute for Informatics, Germany

Presentation Overview: Show/Hide
We present KeyPathwayMiner 3.0, a set of integrated methods for extracting and visualizing expressed key-networks where most genes are dysregulated due to specific diseases, treatments or perturbations. We will investigate Huntington’s disease and colorectal cancer by connecting the human interactome with gene expression data and genome-wide methylation profiles, respectively.

Presentation PDF:Download Abstract
TOP


TT23 - MOPED and SPIRE: Proteomics data to knowledge to action
Date: Monday, July 16: 12:15 p.m. - 12:40 p.m.Room: 201B

Presenting author: Winston Haynes, Seattle Children's, United States

Presentation Overview: Show/Hide
We present two web-based, publicly available proteomics resources: MOPED (http://moped.proteinspire.org), a new and expanding protein data resource that enables rapid browsing of expression information from publicly available studies on humans and model organisms; and SPIRE (https://www. proteinspire.org), a mass spectrometry proteomics analysis platform.

Presentation PDF:Download Abstract
TOP


TT24 - MONGKIE: Modular Network Generation and Visualization Platform with Knowledge Integration Environment
Date: Monday, July 16: 2:30 p.m. - 3:25 p.m.Room: 201B

Presenting author: Sanghyuk Lee, Korean Bioinformation Center (KOBIC), Korea, Rep

Presentation Overview: Show/Hide
MONGKIE is an integrated network visualization platform which allow exploring and analyzing inter-connected biological data in an interactive manner with knowledge integration environment. It incorporates various network analysis methods into the visualization platform, such as Interaction Manager, Gene ID Conversion, Expression Overlay, Network Clustering, Gene Set Enrichment Analysis, Pathway Visualization.

Presentation PDF:Download Abstract
TOP


TT25 - EMBL-EBI Industry Engagement
Date: Monday, July 16: 3:30 p.m. - 3:55 p.m.Room: 201B

Presenting author: Dominic Clark, EMBL-EBI, United Kingdom

Presentation Overview: Show/Hide
This presentation will provide an overview and demonstration of some of the means by which EMBL-EBI interacts with industry stakeholders. Industry users already comprise a significant proportion of the EBI services user-base and will continue to grow.

Presentation PDF:Download Abstract
TOP


TT26 - Overview of The Universal Protein Resource (UniProt)
Date: Monday, July 16: 4:00 p.m. - 4:25 p.m.Room: 201B

Presenting author: Benoit BELY, EBI (European Bioinformatics Institut), United Kingdom

Presentation Overview: Show/Hide
1- A description of the UniProt.
2- New developments, functionalities and design.
3- Accessing UniProt using simple query syntax. The user will be presented with helpful suggestions and hints.
4- Exploration of sequence similarity searches, alignments and ID mapping tools provided.

This demonstration will also encourage user interaction and feedback.

Presentation PDF:Download Abstract
TOP


TT27 - The Immune Epitope Database and Analysis Resource (IEDB)
Date: Tuesday, July 17: 10:45 a.m. - 11:10 a.m.Room: 201B

Presenting author: Nima Salimi, The Immune Epitope Database and Analysis Resource, United States

Presentation Overview: Show/Hide
The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. It also hosts tools to analyze data and predict epitopes. The workshop will present an introduction to the website’s features and highlights of the latest IEDB release.

Presentation PDF:Download Abstract
TOP


TT28 - MaGnET and BaGET: Intuitive “Exploration-Style Analysis” of Functional Genomic Data for Malarial and Bacterial Infectious Disease Agents
Date: Tuesday, July 17: 11:15 a.m. - 11:40 a.m.Room: 201B

Presenting author: Dietlind Gerloff, University of California, Santa Cruz, United States

Presentation Overview: Show/Hide
Our free "exploration tools" facilitate innovative intuitive analysis of different types of functional genomic data for Plasmodium falciparum (MaGnET), and 13 species of oral disease bacteria (BaGET). Through interactively modifiable selections, simple visual and integrated displays, we want to allow bench biologists to take data “browsing” to a next level.

Presentation PDF:Download Abstract
TOP


TT29 - Recent Developments in the Pathway Tools Software and BioCyc Databases
Date: Tuesday, July 17: 11:45 a.m. - 12:10 p.m.Room: 201B

Presenting author: Mario Latendresse, SRI International, United States

Presentation Overview: Show/Hide
Pathway Tools: Recent developments include growth of the MetaCyc database to 1,800 pathways and 10,300 reactions, the ability of Pathway Tools to automatically generate flux-balance models from its Pathway/Genome databases in a manner that drastically reduces model-development time, and development of web services for Pathway Tools.

Presentation PDF:Download Abstract
TOP


TT30 - Export Genomic datasets to GenePattern
Date: Tuesday, July 17: 12:15 p.m. - 12:40 p.m.Room: 104A

Presenting author: Alain Coletta, U.L.B, Belgium

Presentation Overview: Show/Hide
This demo is an illustration subset of the entire presentation of InSilico DB. More material including a video presentation can be found at:
https://insilico.ulb.ac.be/blog/

Presentation PDF:Download Abstract
TOP


TT31 - Desktop solution for genome-wide interaction search
Date: Tuesday, July 17: 12:15 p.m. - 12:40 p.m.Room: 104C

Presenting author: Adam Kowalczyk, , Australia

Presentation Overview: Show/Hide
We introduce GWIS, software enabling an exhaustive scan of all pairwise interactions in GWAS with 500K SNPs and 5K samples, in under 30mins/3hours using GPU/CPU, rather than days. Multiple filters are combined with secondary analysis: false-positive control, detection of interacting LD blocks or genes and integration with on-line genome resources.

Presentation PDF:Download Abstract
TOP


TT32 - GeneWeaver.org: a platform for the analysis of gene set associations
Date: Tuesday, July 17: 12:15 p.m. - 12:40 p.m.Room: 201B

Presenting author: Jeremy Jay, The Jackson Laboratory, United States

Presentation Overview: Show/Hide
GeneWeaver is a web-accessible data repository and analysis platform for the comparison of heterogeneous functional genomics data. We will describe our approach to data integration, and highlight available data sets and tools through the analysis of example use cases in drug addiction and alcoholism.

Presentation PDF:Download Abstract
TOP


TT33 - Protein network analysis with CentiScaPe and Interference plug-ins: the case of leukocyte integrin activation network
Date: Tuesday, July 17: 2:30 p.m. - 2:55 p.m.Room: 201A

Presenting author: Giovanni Scardoni, Center for BioMedical Computing, University of Verona, Italy

Presentation Overview: Show/Hide
We show the combined use of CentiScaPe and Interference Cytoscape plugins for topological analysis of biological networks. Our protocol allows identifying the most relevant nodes and their reciprocal influence in a network. This may hamper gaining a deeper knowledge on complex biological processes and help to drive lab experiments.

Presentation PDF:Download Abstract
TOP


TT34 - Data-Mining with InterMine
Date: Tuesday, July 17: 2:30 p.m. - 2:55 p.m.Room: 201B

Presenting author: Alex Kalderimis, InterMine, United Kingdom

Presentation Overview: Show/Hide
InterMine is an open-source intgrated data-warehousing and data-mining project in use at several major MOD projects. We will be demonstratingthe features that make InterMine a compelling tool for data analysis: sophisticated, flexible queries, list management, powerful export functionality, and a programmable web-service API.

Presentation PDF:Download Abstract
TOP


TT35 - Using HDF5 to Work with Large Quantities of Biological Data
Date: Tuesday, July 17: 3:00 p.m. - 3:25 p.m.Room: 201A

Presenting author: Dana Robinson, The HDF Group, United States

Presentation Overview: Show/Hide
The HDF5 technology platform allows users to organize, store, share, and access large and complicated data. In this presentation, we will give a brief introduction to HDF5 and its capabilities, followed by some examples of how biological data can be stored in HDF5.

Presentation PDF:Download Abstract
TOP


TT36 - CAMERA: Metagenomic Resources and Tools
Date: Tuesday, July 17: 3:00 p.m. - 3:25 p.m.Room: 201B

Presenting author: Shulei Sun, University of California, San Diego, United States

Presentation Overview: Show/Hide
CAMERA provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology. Its computational resources include rich and distinctive bioinformatics tools and a flexible collaborative workflow environment that makes it possible for researchers to analyze large and complex sequencing data generated by NGS technology.

Presentation PDF:Download Abstract
TOP


TT37 - Clear and biologist-friendly analysis software for RNA-, miRNA-, ChIP-, methyl- and CNA-seq data
Date: Tuesday, July 17: 3:30 p.m. - 3:55 p.m.Room: 201A

Presenting author: Eija Korpelainen, CSC - IT Center for Science, Finland

Presentation Overview: Show/Hide
The open source Chipster software (http://chipster.csc.fi) provides a clear and biologist-friendly interface to analysis tools for RNA-, miRNA-, ChIP-, methyl- and CNA-seq data. Users can easily save and share analysis workflows, and built-in genome browser allows seamless viewing of reads and results.

Presentation PDF:Download Abstract
TOP


TT38 - Collaborative Innovation, Open Platforms and Personalized Workflow Solutions
Date: Tuesday, July 17: 3:30 p.m. - 3:55 p.m.Room: 201B

Presenting author: Nishit Bhuva, Elsevier, United States

Presentation Overview: Show/Hide


Presentation PDF:Download Abstract
TOP


TT39 - BioGPS: a community-driven customizable gene annotation portal
Date: Tuesday, July 17: 4:00 p.m. - 4:25 p.m.Room: 201A

Presenting author: Chunlei Wu, The Scripps Research Institute, United States

Presentation Overview: Show/Hide
BioGPS, http://biogps.org, is a centralized gene portal for aggregating distributed online gene annotation resources. Users are allowed to select the resources they need and organize them into a customizable gene-report page. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily contribute to the BioGPS platform by submitting new resources as "plugins".

Presentation PDF:Download Abstract
TOP