W13 - sbv IMPROVER Workshop

How Crowd-Sourcing can drive and improve Data Analysis and Data Visualization

About sbv IMPROVER

sbv IMPROVER stands for Systems Biology Verification combined with Industrial Methodology for Process Verification in Research. This approach aims to provide a measure of quality control of industrial research and development by verifying the soundness of the methods used.

sbv IMPROVER is a challenge-based program with a specific focus on the verification of industrial research processes related to systems biology.

Challenges

The first challenge (Diagnostic Signature) was designed to determine to what extent transcriptomic data can be used for phenotype prediction and to identify best-performing computational methods.

The second challenge (Species Translation) was designed to address the extent to which biological effects of stimulus-induced perturbations in one species (rats) translate to those in another species (humans).

In the third challenge (Network Verification) we provided the community with 50 network models of molecular events that can be categorized on the basis of five different biological themes: cell fate, cell proliferation, cell stress, inflammation, and tissue repair and angiogenesis. These models of key biological processes include access to underlying scientific literature citations that have been expertly curated to provide mechanistic substantiation for each molecular relationship present in the network model. The scientific community is encouraged to review the relationships between molecular entities and to make improvements on the represented biology covering fundamental processes involved in respiratory disease. Web-based graphical interfaces and crowdsourcing principles enable participants to annotate these relationships based on literature evidences.

About this workshop

During this workshop participants will be given the opportunity to learn more about using the crowd engagement methods to advance research. In the first part of the workshop we will focus on the design and results of our first two challenges (Case Study 1).

In the second part, we will introduce the ongoing Network Verification Challenge and give the workshop participants the opportunity to experience our network verification platform. This will lead to an open discussion about the platform and how methods to visualize and interact with biological data can be further developed to improve functionality for the user (Case Study 2).

In the third part of the workshop we will look into other analysis and visualization tools and their capability to deal with data sets from different fields of research, e.g. data sets from metabolomics, proteomics, transcriptomics or genomics. The key discussion here will focus on finding optimal ways, both to integrate different datasets into the analysis, and to be able to visualize results in a comprehensive and intuitive manner (Case Study 3 ).

Why you should attend this workshop

The workshop provides participants a platform to:

  • discuss technical challenges that come from working with the broad variety of data, as well as potential solutions to these challenges;
  • exchange ideas on how to combine methods to visualize and interact with biological data, whilst leveraging open source software;
  • share practical experiences and the challenges associated to working with different types of data at the same time;
  • learn about a platform to benchmark your classification algorithms;
  • learn about crowd engagement methods to verify your algorithms and biological models.

Target Audience

The potential target audience contains researchers from a wide range of research fields, e.g.: Computational Biologists/Bioinformaticians, Clinical Researchers, Biologists, and Biocurators to name a few.

Agenda

The agenda will cover keynote presentations about past and future sbv IMPROVER challenges, as well as the challenge of integrative biology and crowd-sourcing approaches.

The following agenda is tentative and subject to change:

09:00 - 09:15 Introduction of Session Chair (Dr. Manuel Peitsch, Philip Morris International, Switzerland)
09:15 - 09:45 Keynote: Diagnostic Signature Benchmarking (Prof. Dr. Heinz Koeppl, TU Darmstadt, Germany)
09:45 - 10:15 Coffee Break
10:15 - 10:45 Keynote: Network Verification Challenge (Dr. Jennifer Park, Selventa, USA)
10:45 - 11:15 Keynote: Quantification of miRNA-mRNA interactions (Dr. Angel Rubio, University of Navarra, Spain)
11:15 - 11:45 Keynote: A semiautomatic extraction process for causal network generation (Dr. Juliane Fluck, Fraunhofer Institute SCAI, Germany)
11:45 - 12:30 Case study: mini network modeling jamboree moderated by Selventa
12:30 - 13:30 Lunch Break
13:30 - 14:00 Keynote: Integrating public -omics data to leverage the analysis of your own experiments: challenges and opportunities (Dr. Philip Zimmermann, NEBION, Switzerland)

14:00 - 14:30

Keynote: Landscape of DNA sequences specifically binding transcription factors  (Dr. Vsevolod Makeev, Vavilov Institute of General Genetics, Russian Academy of Sciences, Russia)
14:30 - 15:00 Coffee Break
15:00 - 15:45 Keynote: Integrative omics analysis and computational approaches (Dr. Joaquin Dopazo, Principe Felipe Research Center, Spain)
15:45 - 16:30 Keynote: GARUDA alliance and gateway (Dr. Samik Ghosh, The Systems Biology Institute, Japan)
16:30 - 17:00 Keynote: Systems pharmacology modeling of disease development and progression (Dr. Oleg Demin, Institute for Systems Biology Moscow, Russia)
17:00 End of Workshop

Important dates

May 5 - August 1 Early registration (Register here)
August 2 - 29 Late registration (Register here)
September 7 sbv IMPROVER workshop
September 7-10 ECCB’14 main conference

Workshop Venue

Palais de la Musique et des Congrès
Place de Bordeaux
67082 Strasbourg, France

Organizing Committee

The organizing committee contains the following persons:

  • Manuel Peitsch, Ph.D. (PMI, Vice President Biological Systems Research R&D)
  • Julia Hoeng, Ph.D. (PMI, Manager Systems Toxicology R&D)
  • William Hayes, Ph.D. (Selventa, Chief Technical Officer)
  • Jennifer Park, Ph.D. (Selventa, Senior Scientist)

For more information please contact the sbv IMPROVER project team ( This email address is being protected from spambots. You need JavaScript enabled to view it. )

References

Selection of articles published in 2013
Magazine Date Title Link
Science View November 2013 sbv IMPROVER Symposium 2013 in Athens Link
Drug Discovery News November 2013 All together now … Link
American Laboratory 7 November 2013 Results are in for the Second sbv IMPROVER Challenge on Species Translation Link

More articles: https://www.sbvimprover.com/sbv-improver/publications/

 

Selection of scientific publications published in 2013
Journal Date Title Link
Bioinformatics 20 August 2013 Strengths and limitations of microarray-based phenotype prediction: Lessons learned from the IMPROVER Diagnostic Signature Challenge Link
Systems Biomedicine Oct-Dec 2013 sbv IMPROVER Special Issue, Volume 1, Issue 4 Link
Bioinformatics and Biology Insights 11 October 2013 On Crowd-verification of Biological Networks. Link

More scientific publications: https://www.sbvimprover.com/sbv-improver/publications/

 

Announcements in Nature for sbv IMPROVER challenge best performers can be found on our website

Diagnostic Signature Challenge (as published in Nature, 24 Jan. 2013, page 565)

Species Translation Challenge (as published in Nature, 21 Nov. 2013, Naturejobs page 12)

Network Verification Challenge (as published in Nature, 8 May 2014, page 127)

 

 

The sbv IMPROVER project, the website and the Symposia are part of a collaborative project designed to enable scientists to learn about and contribute to the development of a new crowd sourcing method for verification of scientific data and results. The current challenges, website and biological network models were developed and are maintained as part of a collaboration among Selventa, OrangeBus and ADS. The project is led and funded by Philip Morris International. For more information on the focus of Philip Morris International’s research, please visit www.pmi.com.

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