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ISMB/ECCB 2017 – Tutorial Program – Friday, July 21

ISMB/ECCB 2017 features half-day tutorial sessions on Friday, July 21, 2017 one day prior to the start of conference scientific program.

Tutorial attendees should register using the on-line registration system. Tutorial participants must be registered for the ISMB/ECCB conference to attend a tutorial. Attendees will receive a Tutorial Entry Pass (ticket) at the time they register on site. Lunch is included in the registration fee for attendees registering for two tutorials. Those attending one tutorial only have the option to purchase a lunch ticket during on-line registration.

Tutorial A1: Single cell transcriptomics

Friday, July 21, 10:00 am - 1:30 pm

Presenters:
Anagha Joshi, Division of Developmental Biology, Roslin Institute, University of Edinburgh, United Kingdom Jeanette Baran-Gale, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, United Kingdom

After nearly a decade in existence, short-read bulk RNA-sequencing has decidedly gone mainstream, but new technologies keep evolving to reveal ever more intricate aspects of the transcriptional landscape of a cell. Single cell sequencing makes it possible to trace cellular differentiation in minute detail, to study cell-to-cell heterogeneity or to identify rare cell types. Being a recent and currently evolving technique, the data processing and analysis protocols are currently far from standardized. This half a day tutorial session will present recent advances in the development and application of new computational tools, resources and methods to analyze single cell RNA sequencing data highlighting the strengths and weaknesses of these techniques. We will particularly provide a hands-on activity to analyze single cell data generated by smart-seq2 and 10x platforms.

Schedule Overview
TimingPresenterTopic Area/Activity Description
10:00 am – 10:30 am Introduction to single cell technologies
10:30 am – 11:30 am Hands-on session – Smart-seq2 data analysis
11:30 am – 11:45 am Break
11: 45 am – 1:00 pmHands-on session – 10x data analysis
1:00 pm – 1:30 pmDiscussion and conclusion

Participant Overview:
Beginner or Intermediate

The target audience are researchers who have recently started working on or plan to work in near future with single cell data (Beginner or Intermediate), as well as anyone who is working with large scale genome-wide data and wants to know more about the opportunities and challenges presented by these new data (Broad Interest).

Class Size: 30

Presenter Bios:
Anagha Joshi, Roslin Institute, University of Edinburgh. Anagha Joshi Group Leader in the Division of Developmental Biology at the Roslin Institute, University of Edinburgh. The research in her group includes the development of innovative mathematical and computational approaches for integrating large-scale data, building predictive models and learning new biology, using blood as a model system. Her expertise in next generation sequencing data analysis (RNA and ChIP sequencing) has led to many collaborative projects including FANTOM5 consortium resulting into over 40 peer reviewed publications. She has worked on data generated using single cell technologies from diverse platforms. http://www.roslin.ed.ac.uk/anagha-joshi/

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Jeanette Baran-Gale, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh Jeanette Baran-Gale is a postdoctoral research fellow in the lab of Chris Ponting at the MRC Institute of Genetics & Molecular Medicine, University of Edinburgh. Her current research focuses on investigating the mechanisms underlying promiscuous gene expression in thymic epithelial cells using single cell RNAseq. Her past research includes high-throughput analysis of both coding and non-coding RNAs in several disease models including the estrogen response in breast cancer.

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Tutorial A2: Ontologies in computational biology

Friday, July 21, 10:00 am - 1:30 pm

Presenters:
Dr. Michel Dumontier, Maastricht University, Netherlands
Dr. Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia

Tutorial Overview:

Ontologies have long provided a core foundation in the organization of biomedical entities, their attributes, and their relationships. With over 500 biomedical ontologies currently available there are a number of new and exciting new opportunities emerging in using ontologies for large scale data sharing and data analysis. This tutorial will help you understand what ontologies are and how they are being used in computational biology and bioinformatics.

Schedule Overview
TimingPresenterTopic Area/Activity Description
10:00-10:45Introduction to ontologies
10:45-11:30Ontologies and biological data: annotation and text mining
11:30 am – 11:45 am Break
11:45 am - 12:30 pmOntology-based data analysis: gene set enrichment and semantic similarity
12:30 pm - 1:00 pmUnderstanding ontologies and axioms through automated reasoning
1:00 pm - 1:30 pmOntologies and big data

Participant Overview
The tutorial will be of interest to any researcher who will use or produce large structured datasets in computational biology. The tutorial will be at an introductory level, but will also describe current research directions and challenges that will be of broad interest to researchers in computational biology.

Presenter Bios:
Dr. Michel Dumontier, Maastricht University, Netherlands . Dr. Michel Dumontier is a Distinguished Professor of Data Science at Maastricht University. His research focuses on the development of computational methods for scalable integration and reproducible analysis of FAIR (Findable, Accessible, Interoperable and Reusable) data across scales - from molecules, tissues, organs, individuals, populations to the environment. His group combines semantic web technologies with effective indexing, machine learning and network analysis for drug discovery and personalized medicine. Dr. Dumontier leads a new inter-faculty Institute for Data Science at Maastricht University with a focus on accelerating discovery science, empowering communities, and improving health and well being. He is the editor-in-chief for the IOS press journal Data Science and an associate editor for the IOS press journal Semantic Web. He is the scientific director for Bio2RDF, an open source project to generate Linked Data for the Life Sciences and is a technical lead for the FAIR (Findable, Accessible, Interoperable, Re-usable) data initiative. He has published over 125 articles in top rated journals and international conferences. He is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies as evidenced by awards, keynote talks at international conferences, and collaborations on international projects.
Dr. Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia . Dr. Robert Hoehndorf is an Assistant Professor in Computer Science at the King Abdullah University of Science and Technology in Thuwal. His research focuses on the applications of ontologies in biology and biomedicine, with a particular emphasis on integrating and analyzing heterogeneous, multimodal data. Dr. Hoehndorf has developed the PhenomeNET system for ontology-based prioritization of disease genes using model organism phenotypes, and contributed to the development of the AberOWL ontology repository. He is an associate editor for the Journal of Biomedical Semantics and editorial board member of the IOS press journal Data Science. He published over 80 papers in journals and international conferences, and presented previous tutorials on ontologies and their applications at ISMB, OWL-ED, and ECCB.


Tutorial PM4: Network Analysis in Cytoscape: Advanced Topics

Friday, July 21, 2:30 pm - 6:00 pm

Presenters:
Alexander Pico, Gladstone Institutes, San Francisco, United States
John “Scooter” Morris, University of California, San Francisco, United States
Barry Demchak, University of California, San Diego, United States

Tutorial Overview:

By the end of tutorial, you should be able to:
•  Know when and how to use Cytoscape in your research area
•  Identify and discriminate relevant source of interactions, networks and datasets
•  Command programmatic control over Cytoscape
•  Integrate Cytoscape into your bioinformatics pipelines
•  Publish, share and export networks online
•  Generalize network analysis methods to multiple problem domains

Schedule Overview
TimingPresenterTopic Area/Activity Description
2:30 pm - 2:45 pmIntroductory (15 min)
  • General network biology overview
  • Cytoscape intro (consortium/history)
    • Roadmap: theme of integration/protocol
    • 3.5/3.6 features
  • Introduce tutorial protocol
    • Functional enrichment of RNA-seq data
    • Use this protocol as the context and examples for subsequent sections...
2:45 pm - 3:30 pm – Intermediate (45 min)
  • Getting data
    • Types of data (networks, datasets), sources, and relevant apps
    • How to choose a network source: String, GeneMANIA, NDEx, WikiPathways
  • Network visualization overview
    • Style mappers & layouts
    • Apps: enhancedGraphics, etc
  • Network analysis overview
    • clusterMaker, BiNGO/ClueGO, etc
3:30 pm - 4:00 pm – Advanced (30 min)
  • R integration via CyREST
    • Hands-on with code examples: setup and intro
4:00 pm - 4:15 pm - Coffee break
4:15 pm - 6:00 pm – Advanced (105 min)
  • R integration via CyREST (continued)
    • Start with dataset of calculated expression values
    • Step one: perform standard diff expression
    • Inject tabular data into Cytoscape and set styles, etc.
    • Other scripting options
    • Interactive options in Cytoscape
  • Cytoscape scripting: advanced (now with loops and args!)
  • Additional advanced topics, per time and interest:
    • cyAnimator
    • Groups and sets
    • Custom linkouts on nodes/edges
    • CyBrowser (new!)
    • Shared sessions
    • NDex
    • Export to web and publishing

Participant Overview:
The Advanced Topics tutorial is intended for an audience that has prior experience with at least one of the following:
•  Cytoscape software
•  Data integration and analytical methods
•  Network biology concepts
•  Bioinformatics analysis pipelines
•  Please bring your laptop to this session

Presenter Bios:
Alexander Pico, Gladstone Institutes, San Francisco, United States Alexander Pico is the Executive Director of the National Resource for Network Biology, the Vice President of the Cytoscape Consortium, and Associate Director of Bioinformatics at Gladstone Institutes. He has been a contributing member to Cytoscape since 2006 and has led numerous Cytoscape and Network Biology workshops and mentoring programs over the past 10 years.
John “Scooter” Morris, University of California, San Francisco, United States John “Scooter” Morris is the Executive Director of the Resource for Biocomputing, Visualization, and Informatics at UCSF, the “Roving Engineer” for Cytoscape, and an Adjunct Assistant Professor of Pharmaceutical Chemistry at UCSF. He has given numerous presentations on using and extending Cytoscape and is a Cytoscape core developer as well as the developer of over a dozen Cytoscape apps, including chemViz, structureViz, clusterMaker, and cddApp.
Barry Demchak, University of California, San Diego, United States Barry Demchak is the Chief Architect of Cytoscape, Secretary/Treasurer of the Cytoscape Consortium and Project Manager in the Ideker lab at UCSD. He has been a contributing member to Cytoscape development since 2012 and has led numerous Cytoscape and Network Biology workshops and mentored projects over the past 5 years.


Tutorial PM5: Prediction of Regulatory Networks from Expression and Chromatin Data

Friday, July 21, 2:30 pm – 6:00 pm

Presenters
Ivan G. Costa, RWTH Aachen University, Germany
Marcel Schulz, Saarland University & Max Planck Institute for Informatics, Germany
Matthias Heinig, Helmholtz Center Munich, Germany

One of the main molecular mechanisms controlling the temporal and spatial expression of genes is transcriptional regulation. In this process, transcription factors (TFs) bind to the promoter and enhancers in the vicinity of a gene to recruit (or block) the transcriptional machinery and start gene expression. Inference of gene regulatory networks, i.e. factors controlling the expression of a particular gene, is a key challenge when studying development and disease progression. The availability of different experimental assays (Histone ChIP-seq, Dnase1-seq, ATAC-seq, NOME-seq etc.) that allow to map in-vivo chromatin dynamics and gene expression (RNA-seq), has triggered the development of novel computational modelling approaches for accurate prediction of TF binding and activity by integrating these diverse epigenomic datasets. However, in practice researchers are faced with the problems that come with handling diverse assays, understanding the tools involved and building specific workflows that are tailored to the data they have.

This tutorial is targeted to an audience of bioinformaticians with previous experience in gene expression and next generation sequencing analysis. This Intermediary level tutorial will provide you knowledge on the use of state-of-art tools for inference of gene regulatory networks from chromatin and expression data. First, we will review tools to conduct the following analyses: 1) predict regulatory regions from different epigenetic datasets, e.g., using differential peak callers (histoneHMM - Heinig et al., 2015) or footprint methods (HINT - Gusmao et al., 2014) and 2) show how to determine cell-specific TF binding in these regions (e.g. TEPIC - Schmidt et al. 2016) and 3) build regulatory networks to study a cell type of interest (e.g. Schmidt et al. 2016, Durek et al. 2016). After introductory presentation we will guide participants through a hands on practical. Therefore, we require that all participants bring their own laptop. Software that needs to be installed before the tutorial as well as data used in the tutorial will be made available on the course website, where also more details are announced.

Course Website https://github.com/SchulzLab/EpigenomicsTutorial-ISMB2017

Schedule Overview
TimingPresenterTopic Area/Activity Description
2:30 pm - 2:45 pmIvan G. CostaIntroduction / gene regulation / transcription / chromatin
2:45 pm - 3:00 pmMatthias HeinigIntroduction ChIP-seq peak calling
3:00 pm - 3:50 pmMatthias HeinigPractical peak calling
4:00 pm - 4:15 pm Break
4:15 pm - 4:30 pmIvan G. CostaIntroduction Footprints
4:30 pm - 4:45 pmMarcel SchulzIntroduction Regulatory networks
4:45 pm - 6:00 pmIvan G. Costa and Marcel SchulzPractical Regulatory Networks

Participant Overview:
Intermediate level

Presenter Bios: TBA