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#ISMB2016

Sponsors

Silver:
Bronze:
F1000
Recursion Pharmaceuticals

Copper:
Iowa State University

General and Travel Fellowship Sponsors:
Seven Bridges GBP GigaScience OverLeaf PLOS Computational Biology BioMed Central 3DS Biovia GenenTech HiTSeq IRB-Group Schrodinger TOMA Biosciences

Technology Track Presentations

Attention Conference Presenters - please review the Speaker Information Page available here.

TT01: Transparent toxicology via enhanced peer review platform
Room: America's Seminar
Date: Sunday, July 10: 6:00 pm - 7:00 pm

Presenting Author: Stephanie Boue, Philip Morris International R&D, Philip Morris Products S.A., Switzerland

Chair: Rodrigo Lopez

Presentation Overview: Show/Hide

A case study is presented for transparency in pre-clinical toxicology data sharing and review. The sbv IMPROVER Challenge (sbvimprover.com) has built and hosts a platform for the expert peer review of toxicology-related pre-clinical data. The platform will be presented and illustrated with a large pre-clinical study use case.

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TT02: Chemical Exposure Response Markers Identification in Blood and Genomic-based Diagnostics - Lessons Learned from the sbv IMPROVER Systems Toxicology Computational Challenge
Room: America's Seminar
Date: Monday, July 11: 10:10 am - 12:40 pm

Presenting Author: Carine Poussin, Philip Morris International R&D, Switzerland

Chair: Rodrigo Lopez or Des Higgins

Presentation Overview: Show/Hide

The sbv IMPROVER computational challenge aimed to address questions on (i) the identification of exposure response markers in human blood enabling to discriminate between exposed and non-exposed subjects as well as (ii) the translatability of those markers between species. Challenge results will be shared and genomics applications in everyday care presented.

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TT03: Repeatable Science at Scale: Using Common Workflow Language and Docker for science on AWS
Room: America's Seminar
Date: Monday, July 11: 2:00 pm - 3:00 pm

Presenting Author: Angel Pizarro, Amazon Web Services, United States

Chair: Rodrigo Lopez or Des Higgins

Presentation Overview: Show/Hide

Researchers have started to adopt Docker to package tools, and the Common Workflow Language (CWL) to document, share, and execute best-practice data analysis pipelines. Come learn how to run these tools and pipelines on the Amazon Web Services cloud.

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TT04: Biological interpretation of ‘omics data: The power of causal analysis
Room: America's Seminar
Date: Monday, July 11: 3:30 pm - 4:30 pm

Presenting Author: Andreas Kraemer, QIAGEN Bioinformatics, United States

Chair: Rodrigo Lopez or Des Higgins

Presentation Overview: Show/Hide

Prior biological knowledge greatly facilitates the interpretation of ‘omics data. Causal networks constructed from literature findings are particularly suited for this task, since they allow the creation of mechanistic hypotheses. We discuss existing and upcoming features of Ingenuity Pathway Analysis that implement causal analysis algorithms involving gene expression and phospho-proteomics data.

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TT05: Bisulfite sequence analysis on CyVerse Discovery Environment
Room: Northern Hemisphere A1/A2
Date: Monday, July 11: 6:00 pm - 6:20 pm

Presenting Author: Jawon Song, Texas Advanced Computing Center, United States

Chair: Rodrigo Lopez

Presentation Overview: Show/Hide

DNA methylation is one of the most widely studied epigenetic phenomenon. Advances in sequencing technology have enabled base-resolution study of methylation through bisulfite sequencing. We present how to both run two widely used bisulfite sequence analysis pipelines on CyVerse’s Discovery Environment.

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TT06: GenePattern Notebook: An integrated analytical environment for genomic research
Room: Northern Hemisphere A3/A4
Date: Monday, July 11: 6:00 pm - 6:20 pm

Presenting Author: Michael Reich, UC San Diego, United States

Chair: Des Higgins

Presentation Overview: Show/Hide

The GenePattern Notebook environment allows researchers to embed the hundreds of bioinformatics methods available in GenePattern – including analysis of gene expression, sequence variation, genomic networks, and proteomics, as well as general machine learning tools – into a Jupyter notebook, without the need to write code.

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TT07: BioSchemas: schema.org development for the Life Sciences
Room: America's Seminar
Date: Monday, July 11: 6:00 pm - 6:20 pm

Presenting Author: Niall Beard, University of Manchester, United Kingdom

Chair: Dominic Clark

Presentation Overview: Show/Hide

BioSchemas is a collaborative effort to formally describe online resources in the life sciences domain (e.g. events, training materials, biological database records) by extending existing schemas found on Schema.org. Adoption of these schemas improves discoverability through search engines; and facilitates interoperability with other systems.

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TT08: The bioBakery: a platform for comprehensive analysis of microbial community shotgun sequencing data
Room: Northern Hemisphere A1/A2
Date: Monday, July 11: 6:20 pm - 6:40 pm

Presenting Author: Eric Franzosa, Harvard T. H. Chan School of Public Health, United States

Chair: Rodrigo Lopez

Presentation Overview: Show/Hide

Following a brief overview of meta’omic concepts, we will walk through an example workflow using the bioBakery virtual machine: starting from a raw (downsampled) human gut metagenome, we will generate taxonomic and functional profiles, perform a statistical comparison with other preprocessed samples, and finally visualize the results.

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TT09: Introducing N-of-1-pathways transcriptome analytic tools: Enabling precision medicine through single-subject studies
Room: Northern Hemisphere A3/A4
Date: Monday, July 11: 6:20 pm - 6:40 pm

Presenting Author: Yves Lussier, Lussier Group, United States

Chair: Des Higgins

Presentation Overview: Show/Hide

In this talk, N-of-1-pathways software is introduced. The software transforms a pair of transcriptomes from a single subject to a personal profile of pathway dysregulation. Software quantifies dysregulation (effect size) within a gene set along with statistical significance (p-value) in high throughput. Personal dysregulation profiles are visualized for pattern recognition.

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TT10: FAIRDOM: Publishing FAIR Data and Models in Interdisciplinary Life Sciences
Room: America's Seminar
Date: Monday, July 11: 6:20 pm - 6:40 pm

Presenting Author: Natalie Stanford, University of Manchester, United Kingdom

Chair: Dominic Clark

Presentation Overview: Show/Hide

Showing how the data management platform FAIRDOMHub can be used to publish research assets. This includes taking snapshots of data structures, and assigning DOIs so they can be referenced in publications. Other researchers can download the snapshots as packages containing all data and descriptive information required for understanding and reuse.

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TT11: PISKa: a HPC tool for stochastic agent and rule-based modeling of spatially explicit complex biological systems
Room: Northern Hemisphere A1/A2
Date: Monday, July 11: 6:40 pm - 7:00 pm

Presenting Author: Tomas Perez-Acle, Computational Biology Lab - Fundacion Ciencia & Vida, Chile

Chair: Rodrigo Lopez

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PISKa can be used to produce stochastic multi-scale and spatially explicit models of biological systems. By relying on the Kappa language and built on a HPC architecture, it efficiently deals with millions of agents and thousands of rules by running on distributed and shared memory computer clusters.

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TT12: Big data technology for designing high-quality oligonucleotides via exhaustive homology tests
Room: America's Seminar
Date: Tuesday, July 12: 10:10 am - 10:30 am

Presenting Author: Min-Soo Kim, DGIST, Korea, Rep

Chair: Des Higgins

Presentation Overview: Show/Hide

MRPrimer and MRPrimerW can rapidly design high-quality primers/probes for qPCR experiments by performing homology tests in an exhaustive way and a whole genome scale, even for multiple targets under the same stringent filtering constraints. They could do it through a fairly complicated but parsimonious computation based on the MapReduce framework.

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TT13: MyGene.info and MyVariant.info: high-performance web services for querying gene and variant annotation
Room: America's Seminar
Date: Tuesday, July 12: 10:30 am - 10:50 am

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

Chair: Des Higgins

Presentation Overview: Show/Hide

Will demonstrate the usage of MyGene.info and MyVariant.info web services, including the direct API calls and their Python/R clients.

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TT14: Exploring Open-­Access Genetic Variants & Clinical Associations: The European Variation Archive at EMBL­-EBI
Room: America's Seminar
Date: Tuesday, July 12: 10:50 am - 11:10 am

Presenting Author: Cristina Gonzalez Garcia, EMBL-EBI, United Kingdom

Chair: Des Higgins

Presentation Overview: Show/Hide

The European Variation Archive is an open-access genetic variation resource which integrates SNVs, short INDELs and structural variants from approximately 30 species. The EVA provides a comprehensive view of these data through its website, and coordinates its efforts with other initiatives such as dbSNP/dbVar, ClinVar, Ensembl and OpenTargets.

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TT15: GenomeSpace: An environment for frictionless bioinformatics
Room: America's Seminar
Date: Tuesday, July 12: 11:40 am - 12:00 pm

Presenting Author: Sara Garamszegi, The Broad Institute of MIT and Harvard, United States

Chair: Des Higgins

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GenomeSpace is a platform that supports an open community of genomics analysis tools. Using GenomeSpace, researchers can construct analyses requiring communication and data transfer between diverse tools such as Web applications and client-side tools. GenomeSpace supports cloud-based storage, handles file format compatibility issues automatically, and enables reproducibility of multi-tool analyses.

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TT16: Recent Developments in the Pathway Tools Software and BioCyc Databases
Room: America's Seminar
Date: Tuesday, July 12: 12:00 pm - 12:20 pm

Presenting Author: Peter Karp, SRI International, United States

Chair: Des Higgins

Presentation Overview: Show/Hide

Pathway Tools enables development of organism-specific Pathway/Genome
Databases that integrate genomic, metabolic, and regulatory
information. It supports querying, analysis, and visualization of
those DBs. It infers metabolic pathways from annotated genomes, and
supports construction of metabolic models. It supports analysis of
omics datasets, and comparative analysis.

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TT17: Open PHACTS now offers patent information and interactions from pathways
Room: America's Seminar
Date: Tuesday, July 12: 12:20 pm - 12:40 pm

Presenting Author: Chris Evelo, Maastricht University, Netherlands

Chair: Des Higgins

Presentation Overview: Show/Hide

Open PHACTS is a long term project for integration of multiple open source linked data resources. The API offers an organized and uniform infrastructure to researchers. It allows users to build applications directly relevant to their research. New API v2.1 methods take advantage of old and new data.

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TT18: Integrating 3D Structure with Protein, Gene, and Validation Information at the RCSB PDB
Room: America's Seminar
Date: Tuesday, July 12: 2:00 pm - 2:20 pm

Presenting Author: Peter Rose, UC San Diego, San Diego Supercomputer Center, United States

Chair: Dominic Clark

Presentation Overview: Show/Hide

We describe the integration of genomic data, single nucleotide variations, and protein annotations with 3D structural data in the RCSB Protein Data Bank. In additions, we will demo the latest features for 3D structure validation.

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TT19: Accelerated NGS Interpretation via the GeneCards Suite
Room: Northern Hemisphere E3/E4
Date: Tuesday, July 12: 2:00 pm - 2:20 pm

Presenting Author: Marilyn Safran, Weizmann Institute of Science, Israel

Chair: Rodrigo Lopez

Presentation Overview: Show/Hide

The GeneCards suite knowledgebase integrates ~150 biomedical sources, providing extensive relationships/annotations leveraged in NGS analyses. We will demonstrate how its VarElect tool solved a clinical case by submitting a list of genes from whole exome sequencing with relevant phenotypes, accentuate VarElect’s unique strengths, and the synergistic GeneCards/MalaCards relevant sections’ contributions.

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TT20: Phyre2: Protein modeling and analysis made easy
Room: America's Seminar
Date: Tuesday, July 12: 2:20 pm - 2:40 pm

Presenting Author: Mark Wass , University of Kent, United Kingdom

Chair: Dominic Clark

Presentation Overview: Show/Hide

We present a tour of the facilities available in the Phyre2 web server for protein modelling. This will include result interpretation, advanced analysis with Phyre Investigator, and expert tools such as BackPhyre for searching structures against entire genomes and batch processing for hundreds or thousands of user sequences.

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TT21: Read-Based Phasing Using WhatsHap
Room: Northern Hemisphere E3/E4
Date: Tuesday, July 12: 2:20 pm - 2:40 pm

Presenting Author: Marcel Martin, SciLifeLab, Sweden

Chair: Rodrigo Lopez

Presentation Overview: Show/Hide

WhatsHap is the first production-quality software for read-based phasing that is fast, finds theoretically optimal solutions and is independent of sequencing technology. The user-friendly Open Source tool requires only standard VCF and BAM input. If available, even pedigree information is used to improve phasings significantly.

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TT22: Using CATH-Gene3D to predict the structure and function of novel protein sequences
Room: America's Seminar
Date: Tuesday, July 12: 2:40 pm - 3:00 pm

Presenting Author: Christine Orengo, UCL, United Kingdom

Chair: Dominic Clark

Presentation Overview: Show/Hide

This talk will be demonstrating recent developments in the CATH-Gene3D protein domain classification resource: remote homology detection through machine learning, functional site prediction from analysis of sequence alignments and the tools that make this freely available to the communnity.

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TT23: Large Scale Analyses with Galaxy
Room: Northern Hemisphere E3/E4
Date: Tuesday, July 12: 2:40 pm - 3:00 pm

Presenting Author: John Chilton, Galaxy Project, United States

Chair: Rodrigo Lopez

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This talk will discuss facilities for performing very large scale analyses in an accessible manner with the popular data analysis platform Galaxy - with a particular emphasis on recent developments and workflows.

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TT24: Images for Massively Parallel Drug Discovery
Room: Northern Hemisphere E1/E2
Date: Tuesday, July 12: 3:30 pm - 4:30 pm

Presenting Author: Blake Borgeson, Recursion Pharmaceuticals, United States

Chair: Des Higgins

Presentation Overview: Show/Hide

Recursion is 15 people and 2 years old, but in that short time we’ve generated millions of rich images of billions of cells. We combine high-throughput imaging experiments with intelligent computational methods, testing thousands of drugs against hundreds of diseases in the time typically spent on a single disease.

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TT25: bio.tools - life science software registry
Room: America's Seminar
Date: Tuesday, July 12: 3:30 pm - 3:50 pm

Presenting Author: Jon Ison, ELIXIR Denmark, Denmark

Chair: Dominic Clark

Presentation Overview: Show/Hide

ELIXIR the infrastructure for biological information, is building a discovery portal (https://bio.tools) for bioinformatics software, built upon a distributed, community curation of a wide range of key resources, including analytical tools and data services. Here we introduce and demonstrate bio.tools.

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TT26: IOBIO: interactive, visually-drive, real-time analysis of genomic big data
Room: Northern Hemisphere E3/E4
Date: Tuesday, July 12: 3:30 pm - 3:50 pm

Presenting Author: Alistair Ward, University of Utah, Center for Genetic Discovery, United States

Chair: Rodrigo Lopez or Des Higgins

Presentation Overview: Show/Hide

IOBIO is a web-based analysis platform facilitating real-time analysis and visualization of genomic datasets. We have several web apps including genomic QC, interrogation of potential disease-causing variants, and species classification from sequencing data (http://iobio.io). I will demonstrate how real-time analysis promotes understanding and exploration of complex and opaque genomic data.

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TT27: Visualizing and analyzing protein data with UniProt
Room: America's Seminar
Date: Tuesday, July 12: 3:50 pm - 4:10 pm

Presenting Author: Sangya Pundir, EMBL-EBI, United Kingdom

Chair: Dominic Clark

Presentation Overview: Show/Hide

We will demonstrate an innovative way of visualizing proteins by integrating protein and genomic information for big data discovery. We will show how to programmatically access this data through our REST services and how to integrate UniProt protein features with genome viewers using BED files that UniProt provides.

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TT28: BACNET: An interactive platform for analysis and publication of multi-omics study
Room: Northern Hemisphere E3/E4
Date: Tuesday, July 12: 3:50 pm - 4:10 pm

Presenting Author: Christophe Bécavin, Institut Pasteur, France

Chair: Rodrigo Lopez or Des Higgins

Presentation Overview: Show/Hide

To face up to the exponential growth of heterogeneous omics datasets of various organisms and the lack of personalised user interface dedicated to biologists. We developed BACNET, a Java based platform for rapid development of multi-omics website and desktop application with genome viewer, heatmap viewer and many other tools.

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TT29: Linking literature and data through text mining in Europe PMC: SciLite - An annotation platform for biocuration
Room: America's Seminar
Date: Tuesday, July 12: 4:10 pm - 4:30 pm

Presenting Author: Senay Kafkas, EMBL-EBI, United Kingdom

Chair: Dominic Clark

Presentation Overview: Show/Hide

We present SciLite – an annotation system which overlays text-mined annotations on scientific articles from Europe PMC, aiming to aid biocuration by bridging the gap between literature and data.

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TT30: GeneWeaver.org: A system for cross-species heterogeneous functional genomic data integration
Room: Northern Hemisphere E3/E4
Date: Tuesday, July 12: 4:10 pm - 4:30 pm

Presenting Author: Elissa Chesler, The Jackson Laboratory, United States

Chair: Rodrigo Lopez or Des Higgins

Presentation Overview: Show/Hide

We will present an overview and description of advances in GeneWeaver, a web based system for cross-species integration of heterogeneous functional genomics data. This system supports applications in ontology inference, gene prioritization, cross-species functional matching, characterization and organization of publicly available and user submitted gene sets and gene network data.

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