Industrial and Academic Demonstrations

  Oberlin Leicester Schumann Boston Bartholdi Rohan Stuttgart
Monday
1:30 - 2:00 IFB Tools (ID01) BMA
(ID03)
Uniprot (ID05) sbvImprover (ID07) PMP/SMW (ID09) Garuda (ID12) Totalinux (ID13)
2:00 - 2:30 Galaxy (ID02) Isilon
(ID04)
Biobase (A) (ID06) KLAST (ID08) BioMercator (ID10) Garuda (ID12) Totalinux (ID13)
Tuesday
1:30 - 2:00 IFB Tools (ID01) BMA
(ID03)
Uniprot (ID05) KLAST (ID08) PMP/SMW (ID09) iPlant
(ID11)
GPB
(ID18)
 
2:00 - 2:30 Galaxy (ID02) Isilon
(ID04)
Biobase (B)
(ID06)
sbvImprover (ID07) BioMercator (ID10) iPlant
(ID11)
GPB
(ID18)
Wednesday
1:30 - 2:00   POPS (ID16)   Sushi  (ID14)      
2:00 - 2:30   Taxator-Tk (ID17)   JAMM (ID15)      

 

Downloads

[Industrial and Academic Demonstrations Programme Book in pdf file]

[All Presentation Fliers in zip archive]

Programme

ID01:¬†Bringing the Tools to the Data ‚Äď Providing Scientists with Personalized and On-Demand Bioinformatics Services on the Cloud of the French Institute of Bioinformatics

Abstract: Life science researchers, thanks to the continuous improvement of experimental technologies, face a deluge of data whose exploitation requires large computing resources and appropriate software tools. To tackle these issues, the French Institute of Bioinformatics (IFB) developed predefined, personalized bioinformatics cloud services and turnkey appliances encapsulating common bioinformatics tools, workflows  and gateways. The size of these appliances, at most a few gigabytes, allows users to move them easily  to the data, rather than moving the data (whose size can be three order of magnitude larger - terabytes) to the computing resources.  IFB is currently running an academic cloud infrastructure with the appropriate biological data and bioinformatics tools to meet the needs of the life science community.

Presentation Flier: [pdf]

Presenters: 

  • Christophe Blanchet [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Jean-Francois Gibrat [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: Institut Français de Bioinformatique, IFB-core, CNRS UMS3601, France

External Link: http://www.france-bioinformatique.fr

 

ID02: A panel of European Public Galaxy Instances

Abstract: Galaxy, a web-based platform for data intensive biomedical research, is available as a web server (http://UseGalaxy.org), and as customisable open source software. The first session will introduce the Galaxy project and then the deepTools webserver. The second session will feature the public Galaxy instances "Nebula" and "IFB's cloud".

Presentation Flier: [pdf]

Presenters: 

  • Hans-Rudolf Hotz1¬†[ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Bj√∂rn Gr√ľning2 [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Alban Lermine3 [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Valentina Boeva3 [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Olivier Inizan4 [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Christophe Blanchet5 [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]¬†

Affiliations: 

1 Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
2 Albert-Ludwig-Universität Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
3 Institut Curie, INSERM U900, Mines ParisTech, 26 rue d'Ulm, 75248 Paris, France
4 INRA, Unité de recherche en genomique info. RD 10 Rte de Saint Cyr, 78026 Versailles, France
5¬†IFB, CNRS UMS 3601, Avenue de la Terrasse - B√Ęt 21, 91190 Gif-sur-Yvette, France

External Link: http://UseGalaxy.org

 

ID03: Building and Testing Executable Biological Models in the BioModelAnalyzer

Abstract: Executable models of biological phenomena offer a new set of techniques to address problems arising from biological complexity. Here we present the BioModelAnalyzer, a web-based tool for building and testing executable models, and showcase how it can be used to identify missing protein-protein interactions and understand complex signalling networks.

Presentation Flier: [pdf]

Presenter: Ben Hall [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: Microsoft Research, Cambridge, CB1 2FB, UK

External Link: http://biomodelanalyzer.research.microsoft.com/

 

ID04:¬†EMC Isilon ‚Äď the Foundation of NGS Data Analysis

Abstract: NGS usually means PBytes of data. But not only that, the workflow involves different steps, different files with different sizes and bandwidth requirements and different algorithms are used to do the data analysis. And to add another angle different algorithms may even use different protocols to access the data. EMC Isilon takes care of all that in one system. It can be flexibly deployed to your data storage needs and handles all possible requirements. So you end up doing your analysis not solving the data storage problem.

Presentation Flier: [pdf]

Presenter: Wolfgang Mertz [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: IIsilon Storage Division, EMC International S.à.r.l., Osterfeldstr. 84, 85737 Ismaning, Germany

 

ID05: UniProt: New Website and Latest Developments

Abstract: The demonstration will cover: 1. A description of UniProt - 2. New UniProt beta site, functionalities and design - 3. Accessing UniProt using simple query syntax - 4. Proteomes querying and retrieval - 5. Sequence similarity searches, alignments and ID mapping tools provided.

Presentation Flier: [pdf]

Presenter: Diego Poggioli [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK

External Link: http://www.uniprot.org/

 

ID06: Enhanced Human NGS Variant and Gene Regulation Analysis

Abstract: BIOBASE is the leading provider of expert-curated biological databases, software and services for the life sciences. Our products and services identify relations critical to drug and biomarker discovery as well as improve biomedical research by transforming data into scientific concepts.

In the first session (A), you will learn more about the TRANSFAC¬ģ database of eukaryotic transcription factors and in¬†the second session (B) more about the NGS analysis tool Genome TraxTM.

Presentation Flier: [pdf]

Presenter: Jasmin Dröge [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation:¬†BIOBASE GmbH, Halchtersche Str. 33, 38304 Wolfenb√ľttel, Germany

External Link: http://www.biobase-international.com/

 

ID07: A Reputation-Based Web Application (sbv IMPROVER Network Verification Challenge) that Facilitates Collaboration and Applications on Biological Network Models

Abstract: Part 1. Collaborative crowd-verification approach allows domain experts from various fields of biology to gather robust peer-reviewed information from which relationships are identified and evaluated. The approach is used to investigate smarter solutions to complement classical peer review and expand biological network models suitable for research in respiratory diseases.

Part 2. Using transcriptomics data, we assess the activation of causal network models from sbv IMPROVER BioNet in a quantitative, statistical and interpretable manner. The Biological Impact Factor (BIF) quantifies the response of a cell system to an insult by aggregating the overall network responses.

Presentation Flier: [pdf]

Presenters: 

  • Jennifer Park [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Florian Martin [ This email address is being protected from spambots. You need JavaScript enabled to view it. ¬†]

Affiliation: Philip Morris International R&D, Quai Jeanrenaud 5, Neuchatel, 2000, Switzerland

External Link: www.pmi.com

 

ID08: KLAST: Fast, Accurate and NGS Scalable Bank-To-Bank Sequence Similarity Search Tool

Abstract: KLAST is a professional sequence similarity search tool for processing high volumes of genomic sequences. The demo will present the use of the KLAST software on the following application domains: genome annotation, genome comparison and analysis of metagenomic data.

Presentation Flier: [pdf]

Presenters: 

  • Dominique Lavenier [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Patrick Durand [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: Inria/IRISA, Campus de Beaulieu, Avenue du General Leclerc, 35042 Rennes, France

External Link: https://koriscale.inria.fr/

 

ID09: Protein Model Portal and SWISS-MODEL Workspace: Giving the Proteome a Third Dimension

Abstract: The three-dimensional structure of a protein provides valuable information for understanding its molecular function and guides the rational design of experiments. In this tutorial, we will illustrate how protein structure homology modelling can be used to study proteins still lacking experimental characterization.

Presentation Flier: [pdf]

Presenter: 

  • Juergen Haas 1,2 [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Torsten Schwede 1,2 [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliations: 

1 Biozentrum Unversitaet Basel, Klingelbergstr 50-70, 4056 Basel, Switzerland
2 SIB - Swiss Institute of Bioinformatics, Klingelbergstr 50-70, 4056 Basel, Switzerland

External Links:  www.proteinmodelportal.org
                         www.swissmodel.expasy.org

 

ID10: BioMercator 4.0: A Complete Framework to Integrate QTL, Meta-QTL and Genome Annotation

Abstract: Compilation of genetic maps combined to QTL meta-analysis has proven to be a powerful approach for identification of candidate genes underlying quantitative traits. BioMercator is the first software covering all steps required to perform QTL meta-analysis and mine genome functional annotation related to QTL and meta-QTL. BioMercator V4 is freely available: http://moulon.inra.fr/biomercator

Presentation Flier: [pdf]

Presenters: 

  • Yannick de Oliveira
  • Olivier Sosnowski
  • Alain Charcosset
  • Johann Joets [ This email address is being protected from spambots. You need JavaScript enabled to view it. ¬†]

Affiliation: INRA, UMR 0320 / UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France

External Link: http://moulon.inra.fr/

 

ID11: : iPlant CollaborativeTM  A Scalable Cyberinfrastructure for Life Science

Abstract: The iPlant Collaborative develops cyberinfrastructure to solve data-intensive problems of biology - those involving genome, phenotype, and environmental data. iPlant provides free access to cyberinfrastructure through web-based platforms and services, many of which are accessible to biologists without extensive computational backgrounds. This demo surveys these tools and their applications.

Presentation Flier: [pdf]

Presenter: Jason Williams [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd. Cold Spring Harbor, NY 11724, USA

External Link: http://www.iplantcollaborative.org

 

ID12: Garuda : Fly to the Future of Biology

Abstract: With the ever-increasing diversity of omics-scale experimental data, a key challenge is the ability to discover the right tools for a specific analysis and navigate through their specific formats. Garuda is an open, community-driven, platform that provides a framework to discover, connect & navigate through different applications in bio-medical research.

Presentation Flier: [pdf]

Presenters: 

  • Samik Ghosh [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Yukiko Matsuoka
  • Hiroaki Kitano

Affiliation: The Systems Biology Institute, Tokyo, Japan

External Link: http://www.garuda-alliance.org

 

ID13: TotaLinux

Abstract: Created in 2004, TotaLinuX is a french compagny providing IT solutions and specialized in HPC and Big Data. Totalinux main skills are focused on designing and building IT infrastructure dedicated to computing (HPC), storage (Scale-out, Big Data) and graphical simulation (VDI).

Presentation Flier: [pdf]

Presenter: Jacques Pasteau

Affiliation: Totalinux, 2/4 rue Jean Baptiste Huet, 78350 Jouy-en-Josas, France

External Link: http://www.totalinux.fr

 

ID14: Sushi: An Exquisite Recipe for Fully Documented, Reproducible and Reusable NGS Data Analysis

Abstract: We present Sushi, an agile framework for web- and commandline-based data analysis that lets users build fully reproducible analysis workflows. All results and associated meta-information are fully defined on the file system in tabular clear text format that is independent of Sushi and ready for sharing and distribution. 

Presentation Flier: [pdf]

Presenters:

  • Masomi Hatakeyama [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Hubert Rehrauer [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: Functional Genomics Center, University of Zurich, Switzerland

External Link:  http://fgcz-sushi.uzh.ch

 

ID15: JAMM: A Peak Finder for Joint Analysis of NGS Replicates

Abstract: We introduce JAMM: a peak finder that can integrate biological replicates and determine enrichment site widths accurately. JAMM is a universal peak finder that is applicable to different types of datasets. It is available for free and can run on Linux machines through the command line: http://code.google.com/p/jammpeak-finder.

Presentation Flier: [pdf]

Presenters: 

  • Mahmoud Ibrahim [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Scott A. Lacadie
  • Uwe Ohhler [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation:¬†Max-Delbr√ľck Center for Molecular Medicine Berlin-Buch, Robert-R√∂ssle-str. 10, Berlin 13125, Germany

External Link: https://www.mdc-berlin.de/

 

ID16: POPS: Predicting and Enhancing Protein Solubility

Abstract: Protein solubility is a prerequisite for many biophysical and biochemical applications. However, it remains challenging to produce soluble proteins by using heterologous expression systems. In this regard, computational approaches to correctly predict the solubility level of a protein and enhancing the solubility level by modifying the protein sequences are highly valuable.

Presentation Flier: [pdf]

Presenters: 

  • Yi-An Tung [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]
  • Chien-Yu Chen¬† [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation: National Taiwan University and Academia Sinica, Taipei 106, Taiwan

External Link: http://c4lab.bime.ntu.edu.tw/pops/service.html

 

ID17: Computational Tools for the Taxonomic Analysis of Shotgun Metagenome Samples

Abstract: Metagenomics characterizes microbial communities by shotgun sequencing of environmental DNA. We present software (taxator-tk, PhyloPythiaS+) to facilitate the taxonomic analysis of large NGS data-sets. The taxonomic assignment of individual (sub)sequences allows estimating the abundances of community members and to reconstruct taxonomic bins with sequence data for the individual taxa.

Presentation Flier: [pdf]

Presenter: Johannes Dröge [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation:¬†Heinrich-Heine-Universit√§t D√ľsseldorf, Germany

External Link: http://algbio.cs.uni-duesseldorf.de/software/

 

ID18: Goes Open: publish with Genomics, Proteomics & Bioinformatics

Abstract: Genomics, Proteomics and Bioinformatics (GPB) is a peer-reviewed and fast-track open access journal that focuses on disseminating the newest discoveries in the -omics and bioinformatics studies. A thorough introduction on the GPB would facilitate your publishing with this fast-processing journal and help increase the impacts of your study.

Presentation Flier: [pdf]

Presenter: Andreas Keller [ This email address is being protected from spambots. You need JavaScript enabled to view it. ]

Affiliation:¬†Chair for Clinical Bioinformatics, Saarland University, Saarbr√ľcken, Germany

External Link: http://www.journals.elsevier.com/genomics-proteomics-and-bioinformatics/

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Awards ECCB'14 awards have been announced during the closing ceremony of ECCB'14 on Wednesday September... Read more
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