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.
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.
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.
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.
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
4:00 PM-4:40 PM
4:40 PM-5:40 PM
Jetstream - A national research and education cloud
Room: Columbus GH
Sanjana Sudarshan, Jetstream - Indiana University, United States
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.
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.
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.
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.
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.
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
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
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
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.
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.