Integrative Bioinformatics Symposium 2018

IB2018 Programme

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In the post-genomics era, we are drowning in data but are starved for knowledge. Integrative Bioinformatics provides the key science and technology platforms to integrate, align and model heterogenous data types to generate meaningful insights from big data and from complex biological systems.

The 14th Integrative Bioinformatics symposium (#IB18) takes place 13-15 June 2018 at Rothamsted Research – the longest running agricultural research institute in the world. The meeting will bring together experts in the field of bioinformatics, computer science, statistics, computational and systems biology. This year, in addition to scientific presentations, it will include workshops, flash talks, software demos, poster presentations and networking opportunities.

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Topics of Interest

This years topics of interest include, but are not limited to:

Big Data: Large-scale systems for text and graph analysis, biomedical knowledge discovery and data mining, tool integration and workflow systems, algorithmic and statistical techniques for big data.
Data Science: Methods for analysing biological data, networks, time series; mining sequences, omics data, protein structures and functions, gene regulatory networks, genotype to phenotype data.
Foundations: Databases and data warehouses, biological ontologies, linked data; models and algorithms; machine learning, classification, clustering, regression; visualization.

Key Dates

2 March 2018	—	Full paper submission for oral presentation & special issue
6 April 2018	—	Notification of acceptance
20 April 2018	—	Final paper submission deadline
7 May 2018	—	Short Talk abstract submission deadline
7 May 2018	—	Early Bird Deadline
29 May 2018	—	Poster abstract submission deadline
13 June 2018	—	IB2018 Workshops
14-15 June 2018	—	IB2018 Symposium

Conference History

June 22^nd – 23^rd, 2017: Odense, Denmark
September 21^st – 23^rd, 2016: Bielefeld, Germany
October 14^th – 16^th, 2015: Bari, Italy
March 12^th – 24^th, 2014: Newcastle, UK
March 18^th – 20^th, 2013: Gatersleben, Germany
March 2^nd – 4^th, 2012: Hangzhou, China
March 21^st – 23^rd, 2011: Wageningen, Netherlands
March 22^nd – 24^th, 2010: Cambridge, UK
August 20^th– 22^nd, 2008: Leucorea, Lutherstadt Wittenberg, Germany
September 10^th – 12^th, 2007: University of Ghent, Belgium
September 4^th– 6^th, 2006: Rothamsted Research, Harpenden, UK
July 4^th– 5^th, 2005: Bielefeld, Germany
July 4^th – 9^th, 2004: Dagstuhl, Germany

To register visit: ib2018.eventzilla.net

IB2018 DRAFT Programme

IB2018 Workshops

June 13, 2018

FAIR Data Management for Plant Genomics & Phenomics: Standards, Tools and Infrastructures

Matthias Lange, Daniel Arend (IPK, Germany) and Cyril Pommier (INRA URGI, France)

Description: This workshop focuses on the implementation of FAIR data management principles for plant phenotyping and genotyping projects. The workshop will give an overview of FAIR principles, infrastructures, repositories and meta data standards. During hands-on training, participants will gain insights into the use of plant genome and phenomic web portals as well as plant phenotypic data standards. Furthermore, tools for managing and publishing phenotypic data and the embedding of such tools into your own systems will be presented. The need for managing plant phenotypic data will be a central topic of discussion. Read more…

13 June 2018, 10:00 – 13:00

Connecting the dots in life science data: data integration, knowledge graphs and the KnetMiner use case

Organizers: Keywan Hassani-Pak and Marco Brandizi (Rothamsted, UK)

Description: This workshop will focus on approaches for knowledge discovery and data mining in biological databases. We will look into important aspects of data modelling and explore differences between RDF and linked property graphs for biological knowledge representation. The workshop will include a hands-on session to compare two increasingly popular query languages SPARQL and Cypher. We will illustrate real examples of biological knowledge discovery in plants using the KnetMiner (Knowledge Network Miner) software developed at Rothamsted Research. Our guest speakers will be Mark Needham (Neo4j) and Kevin Dialdestoro (Genestack).

13 June 2018, 14:00 – 17:30

Protein Structure Prediction, Molecular Visualisation and Variant Analysis using Phyre, EzMol and PhyreRisk

Lawrence Kelley, Charles Ofoegbu and Michael Sternberg (Imperial College London)

Description: Phyre2 (1) (pronounced FIRE2) (www.imperial.ac.uk/phyre) provides a web-based resource for the community to obtain predicted 3D structures based on the known structure of a template. Predicted models typically are returned via an e-mail link within a few hours and the user can examine alternate models with their multiple sequence alignments. There are facilities for users to examine the accuracy of the model along the sequence (Phyre Investigator), to request weekly re-runs of their query against updates databases (PhyreAlarm), and to see if a 3D structure occurs in other genomes (BackPhyre). Users can also submit batch files with numerous sequences to process. Phyre2 is now a resource with the UK node of ELIXIR, a European distributed infrastructure for life-science information. There are over 80,000 distinct users of Phyre2 per yearPhyre2 (1) (pronounced FIRE2) (www.imperial.ac.uk/phyre) provides a web-based resource for the community to obtain predicted 3D structures based on the known structure of a template. Predicted models typically are returned via an e-mail link within a few hours and the user can examine alternate models with their multiple sequence alignments. There are facilities for users to examine the accuracy of the model along the sequence (Phyre Investigator), to request weekly re-runs of their query against updates databases (PhyreAlarm), and to see if a 3D structure occurs in other genomes (BackPhyre). Users can also submit batch files with numerous sequences to process. Phyre2 is now a resource with the UK node of ELIXIR, a European distributed infrastructure for life-science information. There are over 80,000 distinct users of Phyre2 per year.

EzMol (2) (www.ezmol.org) is a web-based wizard-driven resource to visualise protein structures catering for the occasional user. In EzMol, after the user has uploaded the coordinate file, no command lines are required until the final image is saved. Residue selection, colouring and labelling is via a mouse driven paint box. Ribbon, lines and space filling are available.

PhyreRisk, phyrerisk.bc.ic.ac.uk (which is available and soon to be released) provides a resource for a user with human variant data, either at the genomic or the protein level, to map any missense, nonsense or stop gain variant onto the structure of an individual protein and its complex. PhyreRisk has an interactive sequence/structure viewer to provide user-driven mapping.

(1) Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nature protocols. 2015 Jun;10(6):845.
(2) Reynolds CR, Islam SA, Sternberg MJ. EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures. Journal of molecular biology. 2018 Jan 31.

13 June 2018, 10:00 – 13:00

COPO – A portal for plant scientists to describe, store and retrieve data more easily

Toni Etuk, Simon Tyrrell and Rob Davey (Earlham Institute)

Description: Collaborative Open Plant Omics (COPO) is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of data.

COPO user interface wizards allow metadata to be added to research objects (e.g., samples, datafiles) with guided help and natural workflows. Metadata can be suggested, that might be appropriate for data based on past submissions and similar workflows.

The Grassroots Infrastructure project aims to create an easily- deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected.

With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can federate both services and data.

The workshop will highlight key features of COPO and Grassroots. A demonstration of the work done so far will be given, with discussions on future directions. Also, participants will have the opportunity at a hands-on experience of the systems.