This is the programme of the workshop only.
In the Agenda page you will find times of all events. For detailed information on the other events, see related pages:
In the Agenda page you will find times of all events. For detailed information on the other events, see related pages:
- ELIXIR Hackathon (October 24, 2016)
- GOBLET / ELIXIR-ITA “Train-the-trainer” Tutorial (October 24, 2016)
- EMBnet Annual General Meeting on the EMBnet web site (October 27-28, 2016)
Slides ae being collected and will be linked from here, previous agreement by the presenters, in PDF. See the 
icon.
| Tuesday October 25, 2016 Workshop day 1 @ CNR Main site, Piazzale Aldo Moro 7, Rome |
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| 08.30-09.15 | Registration and poster hang-up |
| 09.15-09.40 | Welcome and Introduction
Paolo Romano, IRCCS AOU San Martino IST, Italy
 Domenica D’Elia, Biomedical Technology Institute – CNR, Italy Erik Bongcam-Rudloff, Swedish University of Agricultural Sciences, Sweden |
| 09.40-10.20 | Opening Lecture Introduced by Paolo Romano, IRCCS AOU San Martino IST, Italy |
| The future: partly FAIR, partly Cloudy Barend Mons, Leiden University Medical Center (LUMC), Leiden, The Netherlands |
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| 10.20-11.00 | Scientific Session 1 Chair: Paolo Romano, IRCCS AOU San Martino IST, Italy |
| FAIRDOM: Reproducible Systems Biology through FAIR Asset Management Natalie Stanford, Finn Bacall, Martin Golebiewski, et al. |
|
| BioShaDock: a Docker-based tools registry towards a bioinformatics reproducibility usage Olivier Sallou and Francois Moreews |
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| 11.00-12.00 | Poster session with coffee break service |
| 12.00-12.30 | Guest Lecture Introduced by Domenica D’Elia, Biomedical Technology Institute – CNR, Italy |
| Data sharing, standards and workflows in metabolomics; towards reproducibility in Metabolomics Reza Salek, European Bioinformatics Institute, Hinxton, United Kingdom |
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| 12.30-13.10 | Scientific Session 2 Chair: Domenica D’Elia, Biomedical Technology Institute – CNR, Italy |
| Pharmacophore modeling, virtual computational screening and biological evaluation studies Serena Dotolo and Angelo Facchiano |
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| Common Workflow Language Michael Crusoe |
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| 13.10-14.20 | Lunch break |
| 14.20-15.00 | Keynote Lecture Introduced by Erik Bongcam-Rudloff, Swedish University of Agricultural Sciences, Sweden |
| And then magic happens… (about linking different types of data and what is needed to make that work) Chris Evelo, University of Maastricht, The Netherlands |
|
| 15.00-15.40 | Scientific Session 3 Chair: Erik Bongcam-Rudloff, Swedish University of Agricultural Sciences, Sweden |
| Standardization in next-generation sequencing – Issues and approaches of establishing standards in a highly dynamic environment Christoph Endrullat |
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| A standard-based HPC platform for genome annotation, analysis and visualization Andrea Manconi, Marco Moscatelli, Matteo Gnocchi and Luciano Milanesi |
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| 15.40-15.50 | Flash Poster presentations 1 Chair: Erik Bongcam-Rudloff, Swedish University of Agricultural Sciences, Sweden |
| Modelling and Simulation of BioSystems inspired by Electronic Design Automation Rosario Distefano, Nickolas Goncharenko, Rosalba Giugno et al. |
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| Multi-type clustering for the identification of lncRNA-disease relationships Gianvito Pio, Francesco Serafino, Emanuele Barracchia et al. |
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| Good Laboratory Practices and L.I.M.S. system: the Challenge for a Next Generation Sequencing and Bioinformatic Research Laboratory Marinella Marzano, Caterina Manzari, Daniela Filannino et al. |
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| Using the Nextflow framework for reproducible in-silico omics Paolo Di Tommaso, Maria Chatzou, Evan Floden and Cedric Notredame |
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| 15.50-16.20 | Coffee break |
| 16.20-17.00 | Keynote Lecture Introduced by Barend Mons, LUMC, Leiden, The Netherlands |
| Ensuring reproducibility and portability of NGS analysis workflows Jacques van Helden, University of Aix-Marseille, Marseille, France |
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| 17.00-18.10 | Scientific Session 4 Chair: Barend Mons, LUMC, Leiden, The Netherlands |
| The Galaxy tool lifecycle supporting reproducibility in scientific research Björn Grüning and Dannon Baker |
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| A Shiny based tool for NGS data Integration in Reproducible Spirit Dario Righelli, Monica Franzese and Claudia Angelini |
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| Comprehensive approach to use Gene Ontology combinations for automated, semi-automated and expert-driven functional interpretation of high-throughput experimental results Aleksandra Gruca and Marek Sikora |
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| Human non-coding RNAs interactions through network-based relation Giorgio De Caro, Vincenzo Bonnici, Sabino Liuni et al. |
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| 18.10-18.30 | Flash Poster presentations 2 Chair: Barend Mons, LUMC, Leiden, The Netherlands |
| Sustainability and robustness of mined biological knowledge: solutions using network-based pathway analysis Andrey Alexeyenko |
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| PISA-Tree: Standard Directory Tree as a Support for Reproducible Research Andrej Blejec and Kristina Gruden |
|
| 18.30 | Day Closure |
| 20.30-23.00 | Social Dinner (registration required, accompanying persons welcome) |
| Wednesday October 26, 2016 Workshop day 2 @ CNR Main site, Piazzale Aldo Moro 7, Rome |
|
| 08.00-09.00 | Registration and poster hang-up |
| 09.00-09.40 | BITS Lecture
Chair: Luciano Milanesi, Biomedical Technology Institute, CNR, Milan, Italy
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| How to create awareness, inform and educate Susanna Assunta Sansone, Oxford eResearch Center, Oxford, United Kingdom |
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| 09.40-10.20 | Scientific Session 5
Chair: Luciano Milanesi, Biomedical Technology Institute, CNR, Milan, Italy
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| Impact of Software Environment on Replicability of Biomedical Workflows Tomasz Miksa |
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| A Pipeline for the Reconstruction of Cancer Progression Models Based on Probabilistic Causation Marco Antoniotti, Giulio Caravagna, Luca De Sano et al. |
|
| 10.20-11.20 | Poster session with coffee break service |
| 11.20-12.10 | Scientific Session 6
Chair: Chris Evelo, University of Maastricht, The Netherlands
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| Bioschemas: structured data markup for life sciences with Schema.org Rafael C Jimenez and Carole Goble (presented by Roberto Preste) |
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| A Robust Estimate of Performance of Reproducible Analytical Models for DREAM Challenges Wojciech Lesiński, Radosław Piliszek and Witold Rudnicki |
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| Wasabi: a web-based platform for evolutionary sequence analysis supporting reproducible research and sharing (see also slides with audio) Andres Veidenberg, Ari Löytynoja and Alan Medlar |
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| 12.10-12.25 | Flash Poster presentations 3
Chair: Chris Evelo, University of Maastricht, The Netherlands
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| Correlated mutations distinguish misfolded and properly folded proteins Pawel P. Woźniak, Malgorzata Kotulska and Gert Vriend |
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| RNA Structures Description Standards Jacek Śmietański |
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| PyRosetta energy terms as indicators for protein mirror models Monika Kurczynska, Bogumil Konopka and Malgorzata Kotulska |
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| An assessment of reporting quality of data analysis in metabolomics and a recommended tool for encouraging reporting guideline uptake Elizabeth Considine, Greigoire Thomas, Louise Kenny and Ali Khashan |
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| Parallel Prediction of Protein Binding Sites Maria Mirto and Giovanni Aloisio |
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| 12.25-13.00 | Guest Lecture
Introduced by Chris Evelo, University of Maastricht, The Netherlands
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| BioSharing – mapping the landscape of Standards, Databases and Data policies in the life, biomedical and environmental sciences Peter McQuilton, Oxford eResearch Center, Oxford, United Kingdom |
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| 13.00-13.10 | First announcement of NETTAB 2017 Maurizio Urso, HPC & Networking Institute – CNR, Palermo, Italy |
| 13.10-14.10 | Lunch break |
| 14.10-14.40 | Special Session "Education and Training"
Terri Attwood (University of Manchester, UK) – Introduction to the Session
Allegra Via (IBBE-CNR) – The ELIXIR-IIB Training Programme |
| 14.40-15.40 | Invited talks |
| GOBLET: Working towards FAIR bioinformatics training Celia van Gelder, DTL/ELIXIR-NL, The Netherlands |
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| Reproducibility and standards: the ELIXIR Training Platform perspective Patricia Palagi, Swiss Bioinformatics Institute, Switzerland |
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| CHARME, a new initiative for standards training Kristina Gruden, National Institute of Biology, Slovenia |
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| 15.40-16.10 | Tea break |
| 16.10-17.10 | Oral communications |
| Standards in education of bioinformatics – the ideals and practice exemplified by educational programs in Polish universities Malgorzata Kotulska, Wroclaw University of Science and Technology, Poland |
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| Software and Data Carpentry: Building Skills and Perspectives to Enable Data-Driven Research Tracy Teal and Jonah Duckles |
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| Critical Assessment of Student Programming in Italy Lisanna Paladin, Marco Necci, Giulia Babbi et al. |
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| 17.10-17.50 | Invited talks |
| Data Science Skills for Life Science Research and Industry Andrea Manieri, Engineering Ingegneria Informatica Spa, Italy |
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| Using virtual machine (VM) images in training to increase reproducibility: ideas from the VM&Cloud EXCELERATE workshop Eija Korpelainen, CSC, Finland |
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| 17.50-18.30 | Panel discussion |
| Challenges in the training arena in the context of reproducibility and standards in bioinformatics Chairs: Erik Bongcam-Rudloff, SLU, Sweden & Sarah Morgan, EBI, United Kingdom All session speakers attending, comments and questions may follow. |
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[…] Training Coordinators came together. The NETTAB conference also featured a special session about Training and Education, chaired by Terri Attwood (EMBNET, ELIXIR, GOBLET) and Allegra Via (NETTAB, ELIXIR, GOBLET). […]