Leading Professional Society for Computational Biology and Bioinformatics
Connecting, Training, Empowering, Worldwide

banner

Technology Track Presentations

Attention Presenters - please review the Speaker Information Page available here



Schedule subject to change
Monday, July 9th
10:40 AM-11:00 AM
PubMed Labs: An experimental platform for improving biomedical literature search
Room: Columbus KL
  • Zhiyong Lu, NCBI, NLM, NIH, United States

Presentation Overview: Show

PubMed Labs is a newly developed experimental website for biomedical literature search. It differs from PubMed in several notable ways such as relevance search by default and optimized UI for small screen devices. We encourage users to test PubMed Labs and share their experience with us for its further improvement.

Download Abstract

11:00 AM-11:20 AM
NetworkAssessor: An interactive visualization tool for ranking the significance of canonical cancer pathways in gene networks
Room: Columbus KL
  • Anna Calinawan, Icahn School of Medicine at Mount Sinai, United States

Presentation Overview: Show

We introduce NetworkAssessor, a full-stack web application with a novel approach to pathway-gene-interaction network enrichment analysis and visualization, integrating major disease and cancer pathways to derive meaningful networks from gene sets. We discuss the cancer-focused biological applications, and the algorithms that enable fast construction and retrieval of large-scale interaction networks.

Download Abstract

11:20 AM-11:40 AM
Tibanna: a cloud-based stand-alone workflow automation system for data processing at the 4D Nucleome Data Coordination and Integration Center
Room: Columbus KL
  • Soohyun Lee, Harvard Medical School, United States

Presentation Overview: Show

We introduce Tibanna, a tool to execute standardized genomic workflows on the AWS cloud. The tool features automated management of cloud resources, metadata tracking, and real-time monitoring. Tibanna executes reproducible Dockerized workflows described in Common Workflow Language. Tibanna has been used in production for processing data at the 4DNucleome Portal.

Download Abstract

11:40 AM-12:00 PM
Deciphering genetic diseases using WGS regulatory elements and ncRNAs
Room: Columbus KL
  • Marilyn Safran, Weizmann Institute of Science, Israel

Presentation Overview: Show

Interpretation of variants stemming from WGS analyses within the GeneCards Suite including promoters, enhancers, and ncRNAs, provides an extensive route to clinical significance of coding and non-coding single nucleotide and structural genomic variations, often elucidating unsolved clinical cases enabling accurate clinical diagnosis and comprehensive genetic counseling.

Download Abstract

12:00 PM-12:20 PM
EBI Search as a Service
Room: Columbus KL
  • Young mi Park, EMBL-EBI, United Kingdom

Presentation Overview: Show

I’d like to talk about EBI Search, which is a powerful text search engine providing access to the biological data resources hosted at the EMBL-EBI, and its ‘Search as a Service’ capabilities.

Download Abstract

12:20 PM-12:40 PM
Bioinformatics Web Services at the EMBL-EBI
Room: Columbus KL
  • Fábio Madeira, EMBL-EBI, United Kingdom

Presentation Overview: Show

The EMBL-EBI Job Dispatcher framework (https://www.ebi.ac.uk/services) provides free access to several Bioinformatics tools and related data, via the web browser or programmatically via Web Services APIs. I would like to present our recent work on the framework, particularly focusing on the latest enhancements to the RESTful APIs user interface.

12:40 PM-2:00 PM
Lunch Break
4:00 PM-4:40 PM
Coffee Break
4:40 PM-5:40 PM
Jetstream - A national research and education cloud
Room: Columbus GH
  • Sanjana Sudarshan, Jetstream - Indiana University, United States

Presentation Overview: Show

Jetstream: First of its kind production cloud resource intended to support science and engineering research. Our goal is to aid traditional and non-traditional researchers that need modest amounts of interactive computing power. Part of the goal in implementing Jetstream is to increase the disciplinary diversity of the XD ecosystem.

Download Abstract

5:40 PM-6:00 PM
KnowEnG: Knowledge Engine for Genomics
Room: Columbus GH
  • Colleen Bushell, University of Illinois, NCSA, United States

Presentation Overview: Show

The KnowEnG cloud-based platform transforms how biologists analyze spreadsheets of genomic data by incorporating prior domain knowledge within the algorithmic and visualization process. It aggregates curated data, creating a network of genes, proteins and their complex relationships. This network augments machine-learning approaches, resulting in powerful knowledge-guided methods that improve analysis.

Download Abstract

Tuesday, July 10th
8:40 AM-9:40 AM
Streaming big genomic data with MPEG-G, the emerging ISO standard for genomic information representation
Room: Columbus GH
  • Claudio Alberti, GenomSys, Switzerland

Presentation Overview: Show

This demonstration shows how MPEG-G enables seamless streaming of compressed genomic data among processing centers without latency introduced by compression or processing. MPEG-G provides higher data compression ratios than existing file formats together with enhanced random access and data classification.

Download Abstract

9:40 AM-10:15 AM
Coffee Break
10:20 AM-11:20 AM
D-SPACE: Deep Semantic Protein Annotation Classification and Exploration
Room: Columbus GH
  • Matthew LaFave, Synthetic Genomics, Inc., United States

Presentation Overview: Show

D-SPACE uses deep learning to rapidly search and annotate proteins based on function, rather than sequence. Participants will learn how to annotate, predict uncharacterized protein function, identify functional homologs too remote for sequence identity-based detection, and mutagenize in silico to locate residues critical for specific functions.

Download Abstract

11:20 AM-11:40 AM
DART – a fast and accurate RNA-seq mapper with a partitioning strategy
Room: Columbus GH
  • Wen-Lian Hsu, Academia Sinica, Taiwan

Presentation Overview: Show

DART is a novel RNA-seq mapping algorithm, which adopts a partitioning strategy. The experiment results showed that DART is a highly efficient aligner that yields the highest or comparable sensitivity and accuracy compared to most state-of-the-art aligners, and it spends the least amount of time among the selected aligners.

Download Abstract

11:40 AM-12:00 PM
The New PSIPRED Protein Analysis Workbench
Room: Columbus GH
  • Daniel Buchan, University College London, United Kingdom

Presentation Overview: Show

We will demonstrate the new PSIPRED Workbench, discussing changes we've made to speed up analyses by more than 5 times and introduce the audience to the new user interface. We will also demonstrate the new RESTful API framework and software downloads we are making available for developers and bioinformaticians.

12:40 PM-2:00 PM
Lunch Break
2:00 PM-2:20 PM
Phyre2, PhyreRisk and EzMol: Protein structure prediction, variant analysis and visualization made easy
Room: Columbus GH
  • Michael J.E. Sternberg, Imperial College London, United Kingdom

Presentation Overview: Show

The Phyre2 web portal provides rapid, accurate prediction and analysis of protein structure (www.imperial.ac.uk/phyre2). Annual there are c. 80,000 distinct users of Phyre2. PhyreRisk, which is being developed, provides a mapping of missense variants onto experimental and predicted structures. EzMol (www.ezmol.org ) is a simple-to-use graphics viewer

Download Abstract

2:20 PM-2:40 PM
The SUPERFAMILY 2.0: HMM library and genome assignments server
Room: Columbus GH
  • Arun Prasad Pandurangan, MRC Laboratory of Molecular Biology, United Kingdom

Presentation Overview: Show

The SUPERFAMILY database provides structural and functional annotation to protein sequences using hidden Markov models. The models are calculated using sequences obtained from structural classification databases at the superfamily level. We introduce key features and functionalities of the new website serving the rapidly growing proteome data from completely sequenced genomes.

Download Abstract

2:40 PM-3:00 PM
The Proteins API, Tool Suites for Interpreting the Molecular Mechanisms of Diseases
Room: Columbus GH
  • Benoit Bely, EMBL-EBI, United Kingdom

Presentation Overview: Show

Combining biological information, like, protein and genomic sequences, and functional data is critical to understanding the role of individual proteins or genes in complex biological processing. We will demonstrate how UniProt provides a range of tools and services to easily integrate this information into workflows for that purpose.

Download Abstract

4:40 PM-5:00 PM
Coffee Break (on the go) to Closing Keynote