# Workflow4Metabolomics: Towards an international computing infrastructure and a tools showcase for Metabolomics

Gildas Le Corguillé, Franck Giacomoni, Christophe Caron

► To cite this version:

Gildas Le Corguillé, Franck Giacomoni, Christophe Caron. Workflow4Metabolomics: Towards an international computing infrastructure and a tools showcase for Metabolomics. GCC2017 Galaxy Community Conferences, Jun 2017, Montpellier, France. 2017. [hal-01604843](https://hal.science/hal-01604843)

HAL Id: hal-01604843

https://hal.science/hal-01604843

Submitted on 2 Jun 2020

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution - ShareAlike 4.0 International License
Towards an international
computing infrastructure and a tools
showcase for Metabolomics

GCC2017

29/06/2017

Gildas Le Corguillé, Franck Giacomoni

Christophe Caron

<figure><img src="image_1.png" /></figure>

UPMC
SORBONNE UNIVERSITÉS

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>
<figure><img src="image_2.png" /></figure>

26 - 30 June France

# GCC 2017
# Montpellier

2017 Galaxy Community Conference

Le Corum

Montpellier, France

26-30 June 2017

Hack the Galaxy: 26-27 June

Training: 27-28 June

Conference: 29-30 June

https://gcc2017.scienceconf.org/

https://gcc2017.sched.com/

<figure><img src="image_3.png" /></figure>

#usegalaxy @galaxyproject
# Biological context

* Identification and quantification of small molecules from the metabolism (metabolites)

* the most recent -omics research domain

<figure><img src="image_5.png" /></figure>
Sponsors

<figure><img src="image_4.png" /></figure>

ifb
INSTITUT FRANÇAIS
DE BIOINFORMATIQUE

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

INDIANA UNIVERSITY

<figure><img src="image_15.png" /></figure>

Institut de Recherche
pour le Développement
FRANCE
# Metabolomics: a data driven approach

<table><thead><tr><th>name</th><th>namecustom</th><th>mz</th><th>mzmin</th><th>mzmax</th></tr></thead><tbody><tr><td>M100T183</td><td>M100.07529T183</td><td>100.075290217332</td><td>100.073962458109</td><td>100.075856347639</td></tr><tr><td>M101T64</td><td>M101.017412T64</td><td>101.017411813327</td><td>101.016363119337</td><td>101.025598611889</td></tr><tr><td>M101T1090</td><td>M101.094497T1090</td><td>101.094497373251</td><td>101.093825596321</td><td>101.094931330369</td></tr><tr><td>M102T67</td><td>M102.121467T67</td><td>102.121466917005</td><td>102.118620434328</td><td>102.128045805211</td></tr><tr><td>M103T60</td><td>M103.032369T60</td><td>103.032369394794</td><td>103.031358949596</td><td>103.040632681061</td></tr><tr><td>M103T61</td><td>M103.120075T61</td><td>103.120074855461</td><td>103.118630961785</td><td>103.129325340649</td></tr><tr><td>M104T1162</td><td>M103.950053T1162</td><td>103.950052934034</td><td>103.948946676433</td><td>103.95133690961</td></tr><tr><td>M104T60</td><td>M104.037434T60</td><td>104.037433793914</td><td>104.036015958492</td><td>104.046229685927</td></tr><tr><td>M104T47</td><td>M104.100665T47</td><td>104.100665065741</td><td>104.099665732044</td><td>104.108679356773</td></tr><tr><td>M104T88</td><td>M104.095422T88</td><td>104.095422407145</td><td>104.093036006622</td><td>104.100116358936</td></tr><tr><td>M104T42</td><td>M104.195599T42</td><td>104.195598628802</td><td>104.187807623186</td><td>104.197644370905</td></tr><tr><td>M105T61</td><td>M105.045229T61</td><td>105.045228536653</td><td>105.036480671616</td><td>105.046334818564</td></tr><tr><td>M105T242</td><td>M105.069935T242</td><td>105.069934637469</td><td>105.06894296829</td><td>105.071143736243</td></tr><tr><td>M105T48</td><td>M105.103611T48</td><td>105.103611067744</td><td>105.102427529644</td><td>105.111698113321</td></tr></tbody></table>

Data extraction

Analytical methods

<figure><img src="image_6.png" /></figure>

m/z

t

<figure><img src="image_7.png" /></figure>

Identification

Interpretation

<figure><img src="image_8.png" /></figure>

Statistical analysis

M585T579

RF

<figure><img src="image_9.png" /></figure>

ara

can
# Bienvenue !

Welcome to the 2017 Galaxy Community Conference (GCC2017), the eighth annual gathering of the Galaxy Community. GCC2017 features two days of training, two days of Hack the Galaxy, and a two day meeting with accepted and keynote talks, posters, vendor exhibits, birds-of-a-feather (BoF) gatherings, demos, and lightning talks - all about high-throughput biological research and its supporting compute infrastructure. This event also features plenty of time for networking and impromptu gatherings.

<figure><img src="image_16.png" /></figure>

We would like to give an enormous thank you to our sponsors and hosts, our instructors, the Scientific Committee, BoF organisers, speakers, demo and poster presenters, and to everyone who contributed to making this event a success.

Merci beaucoup,

The GCC2017 Organising Committee

## Hosts

<figure><img src="image_17.png" /></figure>

ifb
INSTITUT FRANÇAIS
DE BIOINFORMATIQUE

Inserm

<figure><img src="image_18.png" /></figure>

INVENTORS FOR THE DIGITAL WORLD

<figure><img src="image_19.png" /></figure>

cirad

<figure><img src="image_20.png" /></figure>

INRA
SCIENCE & IMPACT

UPMC
SORBONNE

<figure><img src="image_21.png" /></figure>

Institut de Recherche
pour le Développement
FRANCE

<figure><img src="image_22.png" /></figure>

DE LA RECHERCHE À L'INDUSTRIE
cea

MONTPELLIER
EVENTS

<figure><img src="image_23.png" /></figure>
# Galaxy, the perfect coach.

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>
Institut Français de
Bioinformatique

<figure><img src="image_24.png" /></figure>

IFB consolidates French National centres, services and bioinformatic resources into one Federation

IFB is accelerating life sciences research by delivering tools, data collection, training and **Cloud** Infrastructure for collaborative and reproducible science

IFB is the French node of the **European research Infrastructure ELIXIR**

IFB contributes to the vibrancy of Galaxy community by coordinating the French Galaxy Working Group
# Once upon a time... W4M

2012 - First tools

2013 - First talk at JOBIM - Toulouse

2013 - First [lightning] talk at GCC2013 - Olso

2017 - We're back!

Galaxy
Community
Conference

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

UIO | University of Oslo

<figure><img src="image_15.png" /></figure>

The W4M Community
# Network

Wifi is available throughout all conference facilities.

Wifi-name: GCC2017

Password: galaxy2017

# Social Media

Unless requested by the speaker, Tweeting and other social media activity are actively encouraged. Post early, post often.

<figure><img src="image_25.png" /></figure>

<figure><img src="image_26.png" /></figure>

<figure><img src="image_27.png" /></figure>

<figure><img src="image_28.png" /></figure>

@usegalaxy

@galaxyproject

# Meals

The official conference dinner is Thursday evening. It will be held at Le Château du Pouget. Buses will make the journey from Le Corum.

Coffee, other beverages, and light snacks will be available during breaks. Lunch is provided on the first day of Hack the Galaxy, and during the conference. On Tuesday and Wednesday participants can grab lunch in the city center.

<figure><img src="image_29.png" /></figure>
The W4M environment

<figure><img src="image_16.png" /></figure>
## Getting Around

<figure><img src="image_30.png" /></figure>

GCC2017 takes place at Le Corum Conference Centre. Le Corum is located in the center of Montpellier, and is easily reached on foot or via public transportation.

TaM
Montpellier 3M

See the Conference Centre floor plan on the last page for a map of where events are.

Suggested lodging and several social events are elsewhere around the city centre. A custom Google Map with all conference venues and suggested lodging is also available.

If you are staying in the CROUS student lodging La Colombière, you will want to take the TaM Blue line (#1) from the Hôpital Lapeyronie station to the Corum station.

See http://www.tam-voyages.com/ for information about all TaM lines.

See the map on the second to last page, and http://bit.ly/gcc2017map.

<figure><img src="image_31.png" /></figure>

<figure><img src="image_32.png" /></figure>

INRA
SCIENCE & IMPACT

Galaxy: advancing the digital agricultural revolution.

www.inra.fr
http:// workflow4metabolomics.org

800 accounts
25 000 jobs/year

19 related papers

<figure><img src="image_17.png" /></figure>
# GCC2017 Events Overview

Mon 26 June

Tue 27 June

Wed 28 June

Thu 29 June

Fri 30 June

### Hack the Galaxy
Dev & User Hacks
2 intense days of Galaxy development & data analysis

Training
Full day, single track, using Galaxy

### Training
5 tracks, 15 sessions: covering the full spectrum of Galaxy usage, admin & development

Gala Dinner

### GCC2017 Meeting
2 days of accepted talks, poster sessions, birds-of-a-feather, lightning talks, exhibits, keynotes, and networking.

## ELIXIR: A DISTRIBUTED INFRASTRUCTURE FOR LIFE-SCIENCE DATA

ELIXIR unites Europe's leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. It coordinates and sustains bioinformatics resources across 20 European countries.

<figure><img src="image_33.png" /></figure>

@ELIXIREurope

www.elixir-europe.org

## ELIXIR support to Galaxy users and developers

* ELIXIR Galaxy Working Group: a network of Galaxy administrators, developers and users

* Developing training materials as part of the Galaxy Training network

* Collecting training materials through the ELIXIR Training Portal (TeSS)

* Building a Galaxy ecosystem with integrated and interconnected resources for Tools, Workflows and Services

* Establishing system-agnostic, reproducible and executable environments for bioinformatics software with BioConda and BioContainers

Organising training courses and community events for Galaxy users:

* 21 July 2017, Prague, Czech Republic
  Making Galaxy Work for You
  (ISMB/ECCB tutorial)

* 8-12 January 2018, Oslo, Norway
  Galaxy Admin Workshop
  (Registration opens in Autumn 2017)

Visit ELIXIR Galaxy Working Group page to find out more:
www.elixir-europe.org/galaxy-wg

<figure><img src="image_34.png" /></figure>

elixir
<figure><img src="image_18.png" /></figure>

36 tools

<figure><img src="image_19.png" /></figure>
# Hack the Galaxy

There are two parallel and co-located *Hack the Galaxy* events at GCC2017. The *Dev Hack* focuses on extending *Galaxy* code and capabilities, while the *User/Data Hack* focuses on addressing challenging data integration and analysis problems.

*Hack the Galaxy* runs for two days. Preregistration is required to attend.

## Monday 26 June: Hack the Galaxy

<table><thead><tr><th>Time</th><th></th></tr></thead><tbody><tr><td></td><td>Sully 1 & Sully 2 (Level 1)</td></tr><tr><td>08:00</td><td>Conference Desk Open (until 22:00)</td></tr><tr><td>09:00</td><td>Introductions, Project Ideas, Brownian Motion, Coalescing</td></tr><tr><td>10:00</td><td>Hack the Galaxy (Dev or Data)</td></tr><tr><td>12:30</td><td>Catered lunch</td></tr><tr><td>13:30</td><td>Hack the Galaxy</td></tr><tr><td>17:30</td><td>Dinner on your own</td></tr><tr><td></td><td>Continued hacking at Le Corum or the venue of your choice</td></tr><tr><td>22:00</td><td>Le Corum Closes</td></tr></tbody></table>

## Tuesday 27 June: Hack the Galaxy

<table><thead><tr><th>Time</th><th></th></tr></thead><tbody><tr><td></td><td>Sully 1 & Sully 2 (Level 1)</td></tr><tr><td>08:00</td><td>Conference Desk Open (until 18:00)</td></tr><tr><td>09:00</td><td>Group Reports</td></tr><tr><td>09:40</td><td>Hack the Galaxy (Dev or Data)</td></tr><tr><td>12:30</td><td>Lunch on your own</td></tr><tr><td>13:30</td><td>Hack the Galaxy</td></tr><tr><td>18:00</td><td>Le Corum Closes</td></tr><tr><td>18:30</td><td>Dinner on your own<br>Continued hacking at venue of your choice</td></tr></tbody></table>
Trainings

Workflow4Experimenters

* 3 sessions since 2014

* 10 Trainers for 20 Trainees

* “Bring your own data” tutoring sessions

<figure><img src="image_20.png" /></figure>
# Training

Two full days of training are offered. The first day offers a single track focusing on how to use Galaxy to address biological questions. The second day offers five tracks and 15 topics covering Galaxy usage, development, administration and tool packaging.

Training is hands-on. Please bring an Ethernet-capable laptop. Ethernet cables and power are provided at each desk. (Wi-fi will be available, but discouraged.)

## Tuesday 27 June: Using Galaxy Training

<table><thead><tr><th></th><th></th></tr></thead><tbody><tr><td>Time</td><td>Barthez (Level 2)</td></tr><tr><td>08:00</td><td>Conference Desk Open (until 18:00)</td></tr><tr><td>09:00</td><td><strong>Galaxy 101: A Gentle Introduction to Galaxy</strong><br>Mallory Freeberg, Mo Heydarian</td></tr><tr><td>11:30</td><td>Lunch on your own</td></tr><tr><td>12:30</td><td><strong>RNA-Seq Analysis in Galaxy</strong><br>Mo Heydarian, Mallory Freeberg</td></tr><tr><td>15:00</td><td>Break</td></tr><tr><td>15:30</td><td><strong>Visualisation of BIG DATA in Galaxy</strong><br>Aysam Guerler, Saskia Hiltermann, Jeremy Goecks</td></tr><tr><td>18:00</td><td>Done</td></tr><tr><td>18:30</td><td>Dinner on your own</td></tr></tbody></table>

<figure><img src="image_35.png" /></figure>

amazon
web services™
<figure><img src="image_21.png" /></figure>

DOI

<figure><img src="image_22.png" /></figure>

<figure><img src="image_23.png" /></figure>

<figure><img src="image_24.png" /></figure>

<figure><img src="image_25.png" /></figure>

W4M provides DOI to reference histories and
workflow usable in papers

<figure><img src="image_26.png" /></figure>

DataCite
FIND, ACCESS, AND REUSE DATA

http://workflow4metabolomics.org/referenced_W4M_histories

Paper submitted in *IJBC*
<table><caption>Wednesday 28 June: Galaxy Training</caption><thead><tr><th>Time</th><th>Barthez<br>(Level 2)</th><th>Rondolet<br>(Level 2)</th><th>Sully 1<br>(Level 1)</th><th>Sully 2<br>(Level 1)</th><th>Sully 3<br>(Level 1)</th></tr></thead><tbody><tr><td>08:00</td><td colspan="5">Conference Desk Open (until 18:00)</td></tr><tr><td>09:00</td><td>Galaxy<br>Architecture<br>John Chilton, Nate<br>Coraor</td><td>Writing & Publishing<br>Galaxy Tools<br>M van den Beek, D<br>Blankenberg, D<br>Bouvier, M Čech, G<br>Le Corguillé, N<br>Soranzo, N Stoler</td><td>RNA-Seq Analysis in<br>Galaxy<br>Mo Heydarian, Mallory<br>Freeberg</td><td>Small Genome de<br>novo Assembly Using<br>Galaxy<br>Simon Gladman</td><td>Introduction to<br>Galaxy Admin:<br>Setting up Galaxy as a<br>Service<br>Jochen Bich, Trond<br>Thorbjørnsen, Nikolay<br>Aleksandrov Vzov</td></tr><tr><td>11:30</td><td colspan="5">Lunch on your own</td></tr><tr><td>12:30</td><td>Advanced<br>Customisation of a<br>Galaxy Instance<br>Björn Grüning, Erick<br>Rasche, Martin<br>Čech</td><td>Conda & Containers<br>for Tool<br>Dependencies - a<br>Developer's<br>Perspective<br>Abdulrahman Azab,<br>Marius van den Beek,<br>John Chilton, Nicola<br>Soranzo</td><td>Visualisation of BIG<br>DATA in Galaxy<br>Aysam Guerler,<br>Jeremy Goecks</td><td>How to Analyze<br>Metagenomics &amp;<br>Amplicon in Galaxy<br>Bérénice Batut, Saskia<br>Hiltemann</td><td>Galaxy for<br>Proteomics<br>Clemens Blank,<br>Timothy Griffin, Pratik<br>Jagtap, James Johnson</td></tr><tr><td>15:00</td><td colspan="5">Break</td></tr><tr><td>15:30</td><td>Advanced<br>Accelerated<br>Galaxy Admin<br>Enis Afgan, Dan<br>Blankenberg, Martin<br>Čech, John Chilton,<br>Nate Coraor, Simon<br>Gladman</td><td>Galaxy for Training<br>&amp; Education<br>Bérénice Batut, Björn<br>Grüning</td><td>ChIPseq Analysis<br>Using DeepTools &amp;<br>Macs<br>Devon Ryan</td><td>Visualization<br>Development in<br>Galaxy<br>Jeremy Goecks, Aysam<br>Guerler, Saskia<br>Hiltemann</td><td>SNP Analysis &amp; GWAS<br>Using SNIPlay<br>Alexis Dereeper, Yann<br>Hueber</td></tr></tbody></table>
4
Wm

Workflow4metabolomics

BACK OFFICE

<figure><img src="image_27.png" /></figure>
IBC

Institut de biologie
computationnelle

IBC is a multidisciplinary research institute focused on Computational Biology, gathers circa 100 researchers from several disciplines: life sciences, computer science and math. It was launched in 2012 for promoting interdisciplinary thinking to address critical biological questions.

One industrial member and 8 national trustees

**Scientific domains:** bioinformatics, molecular biology, medecine, agronomy, evolutionary biology, plant & animal biology, math & computer science.

**Overarching aim:** Designing computational methods for analysing and modelling massive data in biology, health, agronomy and environment.

**Biological applications**

• genomics (eg. vertebrate, rice, cancer)

• transcriptomics

• virus and pathogens (HIV, malaria, etc.)

• embryonic development and stem cells

• population genetics

• Next Generation Sequecing analysis tools

• ontologies for agronomy & medecine

• phylogenetic inference

• protein structure

<figure><img src="image_36.png" /></figure>

Education

<figure><img src="image_37.png" /></figure>

**Computational techniques**

• algorithms on sequences & graphs

• statistical inference

• machine learning

• modelling for biology & evolution

• image processing

• heterogeneous databases

• information retrieval

• big data

Animation

<figure><img src="image_38.png" /></figure>

Research

**Contacts:** Eric Rivals
ibc-contact@lirmm.fr
04 67 41 86 64

<figure><img src="image_39.png" /></figure>

ACOBIOM

<figure><img src="image_40.png" /></figure>

cirad

<figure><img src="image_41.png" /></figure>

<figure><img src="image_42.png" /></figure>

INRA

SCIENCE & IMPACT

<figure><img src="image_43.png" /></figure>

<figure><img src="image_44.png" /></figure>

Inserm

Supé

Agro

<figure><img src="image_45.png" /></figure>

<figure><img src="image_46.png" /></figure>

<figure><img src="image_47.png" /></figure>
# Tools

## Developments

- 15 developers from 7 laboratories

- Stick to IUC standards

- A GitHub: github.com/workflow4metabolomics

- Conda / Planemo / TravisCI

<figure><img src="image_28.png" /></figure>

<figure><img src="image_29.png" /></figure>

<figure><img src="image_30.png" /></figure>

<figure><img src="image_31.png" /></figure>
Conference: Thursday 29 June

<table><thead><tr><th>Time</th><th></th></tr></thead><tbody><tr><td></td><td><strong>Einstein Auditorium (Level 0)</strong></td></tr><tr><td>08:00</td><td>Conference Desk Open (until 19:00)</td></tr><tr><td>09:00</td><td><strong>Opening and Welcome</strong><br>Olivier Inizan, INRA; Marilyne Summo, CIRAD</td></tr><tr><td>09:15</td><td><strong>Session 1: Galaxy Framework</strong><br>Moderator: Jeremy Goecks, OHSU</td></tr><tr><td>09:15</td><td><strong>Keynote: The Galaxy Project: from the Planck Epoch to Montpellier</strong><br>Anton Nekrutenko, Penn State University; James Taylor, Johns Hopkins University</td></tr><tr><td>10:00</td><td><strong>Bioconda and BioContainers - Enabling Universal Reproducibility in Galaxy</strong><br>John Chilton, Penn State University</td></tr><tr><td>10:20</td><td><strong>Building an open, collaborative, online infrastructure for bioinformatics training</strong><br>Bérénice Batut, University of Freiburg</td></tr><tr><td>10:40</td><td>Break</td></tr><tr><td>11:10</td><td><strong>Session 2: Galaxy Framework (continued)</strong><br>Moderator: Dave Clements, Johns Hopkins University</td></tr><tr><td>11:10</td><td><strong>An Educational Framework for Galaxy Administration</strong><br>Nate Coraor, Penn State University; Simon Gladman, Melbourne Bioinformatics / University of Melbourne</td></tr><tr><td>11:30</td><td><strong>Integrative analysis of hundreds of datasets in Galaxy</strong><br>Geir Kjetil Sandve, University of Oslo</td></tr><tr><td>11:50</td><td><strong>Galaxy Genome Annotation Project: Galaxy and GMOD for Annotation, Teaching, and Genomic Databases</strong><br>Eric Rasche, Texas A&M University</td></tr><tr><td>12:10</td><td><strong>Apollo in Galaxy: Increasing Opportunities for Collaborative Genome Annotation</strong><br>Nathan Dunn, Lawrence Berkeley National Lab (LBNL)</td></tr><tr><td>12:30</td><td><strong>Galaxy at the IFB: From computing to training</strong><br>Victoria Dominguez del Angel, Institut Français de Bioinformatique; Christophe Caron, INRA</td></tr></tbody></table>
<figure><img src="image_32.png" /></figure>

# GET: An Open Project

All public W4M tools are distributed:

<figure><img src="image_33.png" /></figure>

**Dev:** github.com/workflow4metabolomics

<figure><img src="image_34.png" /></figure>

**Wrappers:** on main Galaxy ToolShed toolshed.g2.bx.psu.edu/groups#/175812cd7caaf439

<figure><img src="image_35.png" /></figure>

**VM:** with the most common W4M tools workflow4metabolomics.org/virtual-environments

<figure><img src="image_36.png" /></figure>

**Docker/Docker:** A Galaxy Flavor

docker run -d -p 8080:80 workflow4metabolomics/galaxy-workflow4metabolomics
Conference: Thursday 29 June (continued)

<table><thead><tr><th>Time</th><th></th></tr></thead><tbody><tr><td></td><td>Einstein Auditorium (Level 0)</td></tr><tr><td>12:45</td><td>Lunch (and Birds-of-a-Feather)</td></tr><tr><td>13:45</td><td><strong>Session 3: Tools & Workflows</strong><br>Moderator: Nicola Soranzo, Earlham Institute</td></tr><tr><td>13:45</td><td><strong>Galaxy Community Update</strong><br>Jeremy Goecks, Oregon Health & Science University; Dan Blankenberg, Penn State University</td></tr><tr><td>14:25</td><td><strong>The Year of IUC</strong><br>Björn Grüning, University of Freiburg</td></tr><tr><td>14:40</td><td><strong>Workflow4Metabolomics: Towards an international computing infrastructure and a tools showcase for Metabolomics</strong><br>Gildas Le Corguillé, ABiMS; Franck Giacomoni, PFEM</td></tr><tr><td>15:00</td><td><strong>South Green Galaxy: a suite of tools for plant genomics</strong><br>Jean-François Dufayard, CIRAD UMR AGAP</td></tr><tr><td>15:20</td><td><strong>Performing Next Generation Phylogenetic Analyses with NGPhylogeny.fr</strong><br>Damien Correia, Institut Français de Bioinformatique</td></tr><tr><td>15:40</td><td><strong>Sponsor, Poster and Demo Session</strong></td></tr></tbody></table>

Ifremer
# PUSH: Contribution

## The main W4M instance as a Showcase

* Hosting on W4M main instance

* Quality standards (IUC Standard)

<figure><img src="image_37.png" /></figure>

<figure><img src="image_38.png" /></figure>

Travis CI®

BIOCONDA®

PLAN ME

## Advanced mode

* Integration in our reference workflows

* Follow your exchange formats between tools

* Collaboration mode if help is needed

However, the support must be done by the developers themselves

<figure><img src="image_39.png" /></figure>
Conference: Thursday 29 June (continued)

<table><thead><tr><th>Time</th><th></th></tr></thead><tbody><tr><td></td><td><strong>Einstein Auditorium (Level 0)</strong></td></tr><tr><td>17:00</td><td><strong>Session 4</strong><br>Moderator: Bérénice Batut, University of Freiburg</td></tr><tr><td>17:00</td><td><strong>The Institute of Computational Biology: an overview</strong><br>Eric Rivals, The Institute of Computational Biology</td></tr><tr><td>17:30</td><td><strong>Lightning Talks</strong></td></tr><tr><td></td><td><strong>Improving Your Text Life</strong><br>James Johnson, University of Minnesota Supercomputing Institute (MSI)</td></tr><tr><td></td><td><strong>Galaxy-E: Towards an accessible, reproducible and transparent data analysis and management universe dedicated to Ecology</strong><br>Valentin Chambon, Thimothée Virgoulay, MNHN CESCO & Staiton de Biologie Marine de Concarneau</td></tr><tr><td></td><td><strong>The Galaxy Gateway on F1000Research</strong><br>Holly Murray, F1000, Science Navigation Group</td></tr><tr><td></td><td><strong>GalaxyCat - The online catalog of Galaxy tools across instances</strong><br>Julien Seiler, Stéphanie Le Gras, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS</td></tr><tr><td></td><td><strong>Galaxy at scale: Analyzing thousands of single cell transcriptomes</strong><br>Mo Heydarian, Johns Hopkins University</td></tr><tr><td>18:00</td><td><strong>Done (and Birds-of-a-Feather)</strong></td></tr><tr><td>19:00</td><td><strong>Gala Dinner @ Chateau du Pouget</strong></td></tr></tbody></table>
# Contribution in progress

UCL

<figure><img src="image_40.png" /></figure>

Université
catholique
de Louvain

BELGIUM

<figure><img src="image_41.png" /></figure>

PhenoMeNal

Large-Scale Computing for Medical Metabolomics

MetaboFlow

<figure><img src="image_42.png" /></figure>

UNIVERSITY OF
BIRMINGHAM

4 Wm

Workflow4metabolomics

<figure><img src="image_43.png" /></figure>

<figure><img src="image_44.png" /></figure>

UNIVERSITY OF MINNESOTA

<figure><img src="image_45.png" /></figure>

Met::rag

<figure><img src="image_46.png" /></figure>

מכה ויצמן למדע

WEIZMANN INSTITUTE OF SCIENCE

<figure><img src="image_47.png" /></figure>

CEU

Universidad
San Pablo
Conference: Friday 30 June

<table><thead><tr><th>Time</th><th></th></tr></thead><tbody><tr><td></td><td><b>Einstein Auditorium (Level 0)</b></td></tr><tr><td>08:00</td><td>Conference Desk Open (until 18:00)</td></tr><tr><td>09:00</td><td><b>Session 5: Galaxy for Life Science and Medicine</b><br>Moderator: Christophe Antoniewski, Institut de Biologie Paris-Seine</td></tr><tr><td>09:10</td><td><b>Keynote: Personalized Analysis of Cancer Data: From Genes to Pathways (and Back)</b><br>Eytan Domany, Weizmann Institute of Science</td></tr><tr><td>10:00</td><td><b>Comparing hundreds of RNA-seq libraries using Galaxy and SeqResults</b><br>Brad Langhorst, New England Biolabs</td></tr><tr><td>10:20</td><td><b>Approaches for small RNA-seq analysis in Galaxy</b><br>Mallory Freeberg, Johns Hopkins University</td></tr><tr><td>10:40</td><td>Break</td></tr><tr><td>11:10</td><td><b>Session 6: Galaxy for Life Science and Medicine</b><br>Moderator: Thérèse Commes, INSERM</td></tr><tr><td>11:10</td><td><b>COMBAT TB: an integrated environment for Tuberculosis data analysis and surveillance</b><br>Peter Van Heusden, South African National Bioinformatics Institute (SANBI)</td></tr><tr><td>11:30</td><td><b>The RNA Workbench - reproducible, transparent, and accessible RNA research</b><br>Florian Eggenhofer, University of Freiburg</td></tr><tr><td>11:50</td><td><b>Interaction Hub: a comprehensive Galaxy-based chromatin folding database, browser, and analysis platform</b><br>Michael Sauria, Johns Hopkins University</td></tr><tr><td>12:10</td><td><b>Mechanizing our biologists with Galaxy and IRIDA platforms</b><br>Philip Mabon, Public Health Agency of Canada</td></tr><tr><td>12:40</td><td><b>Lunch (and Birds-of-a-Feather)</b></td></tr></tbody></table>
<figure><img src="image_48.png" /></figure>

Galaxy Training
Network

<figure><img src="image_49.png" /></figure>

<figure><img src="image_50.png" /></figure>

<figure><img src="image_51.png" /></figure>

Metabolomics lcms preprocess ✗

work-in-progress

\#355 opened 12 days ago by lecorguille

<figure><img src="image_52.png" /></figure>
Conference: Friday 30 June (continued)

Time Einstein Auditorium (Level 0)

13:45 Session 7: Galaxy in today's infrastructures
Moderator: Björn Grüning, University of Freiburg

13:45 ELIXIR supports Galaxy users and developers
Frederik Coppens, ELIXIR Belgium & VIB

14:00 Advancing metaproteomics research via community-based informatics development and dissemination
Pratik Jagtap, University of Minnesota

14:20 Making Galaxy User Interface Pluggable with Webhooks
Martin Čech, Penn State University; Björn Grüning, University of Freiburg

14:40 A reproducible data analysis environment for next-generation sequencing on public cloud computer
Manabu Ishii, RIKEN ACCC Bioinformatics Research Unit

15:00 Developing analytical workflows for plant genomics through the integration of Galaxy and Tripal
Sean Buehler, University of Connecticut

15:20 Sponsor, Poster and Demo Session

Looking for something?

https://galaxyproject.org/search

Galaxy
COMMUNITY HUB

Use -

Community -

Education -

Deploy & Develop -

Support -

Search Galaxy

Q

Searching the Galaxy

Welcome to the comprehensive Galaxy search interface. This is a Google Custom Search Engine that will search all things Galaxy. This includes all the pages on the Hub, the codebase (Galaxy and related projects), the mailing lists, biostars, and more.

If you haven't already, enter your query into the box in the masthead, and results will appear below.

All results

Use

Hub

Corpus

Code

Admin/Dev

Discussion

Shared

Tools

Requests

About 8,910 results (0.42 seconds)

Did you mean: gcc 2017

<figure><img src="image_48.png" /></figure>

Galaxy Community Conference 2017 - Sciencesconf.org

GCC2017 will include keynote talks and exhibits, and plenty of networking opportunities. There are also three days of pre-conference activities, including

https://gcc2017.ac Sciencesconf.org/

Labeled Admin/Dev Use

<figure><img src="image_49.png" /></figure>

GCC2017 Call for Host Proposals

Sep 14, 2015 ... Galaxy's informal policy of rotating between North America and elsewhere every other year is now a formal policy. Hosts for GCC2017 need to

https://galaxyproject.org/news/gcc2017-call-for-host/

Labeled Admin/Dev Hub Use

<figure><img src="image_50.png" /></figure>

2017 Galaxy Community Conference (GCC2017)

GCC2017 is the 8th annual gathering of the Galaxy community. The conference will include keynotes and accepted talks, poster sessions, demos, ...

https://galaxyproject.org/events/2017-gcc/

Labeled Admin/Dev Hub Use
PERSPECTIVE

<figure><img src="image_53.png" /></figure>
Conference: Friday 30 June (continued)

<table><thead><tr><th>Time</th><th>Event</th></tr></thead><tbody><tr><td></td><td><strong>Session 8</strong><br>Moderator: Virginie Rossard, INRA</td></tr><tr><td>16:35</td><td><strong>Lightning Talks</strong><br>Using visual programming in Cervical cancer data of The Cancer Genome Atlas<br>Thais Hosokawa, Barretos Cancer Hospital</td></tr><tr><td></td><td><strong>Analyzing Relationships among Clinical Factors of Cancer Patients by Regression Analysis</strong><br>Sugandima Vidanagamachchi, Thamara Waidyarathna, University of Ruhuna</td></tr><tr><td></td><td><strong>ToolDog - generating tool descriptors from the ELIXIR tool registry</strong><br>Kenzo-Hugo Hillion, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur de Paris</td></tr><tr><td></td><td><strong>Pushing the limits of job flexibility on HPC</strong><br>Carrie Ganote, Indiana University</td></tr><tr><td></td><td><strong>Pulling the Galaxy's Strings</strong><br>Jeffrey Miller, University of Iowa</td></tr><tr><td></td><td><strong>Using Galaxy as a platform for continuous software development</strong><br>Geir Kjetil Sandve, Boris Simovski, University of Oslo</td></tr><tr><td></td><td><strong>Automated Generation of Complex Toolkits for Galaxy</strong><br>Daniel Blankenberg, Penn State / Galaxy Team</td></tr><tr><td></td><td><strong>Hack the Galaxy: Data Report</strong><br>Organizers</td></tr><tr><td></td><td><strong>Hack the Galaxy: Dev Report</strong><br>Organizers</td></tr><tr><td></td><td><strong>JBrowse & Circos Tool Updates</strong><br>Eric Rasche, Texas A&M University</td></tr><tr><td></td><td><strong>Parsec: Intergalactic DevOps and Analysis Automation</strong><br>Eric Rasche, Texas A&M University</td></tr><tr><td>17:42</td><td><strong>GCC2018 Launch</strong><br>Dave Clements, Johns Hopkins University</td></tr><tr><td>17:50</td><td><strong>GCC2017 Closing</strong><br>GCC2017 Organisers</td></tr><tr><td>18:00</td><td><strong>Fini</strong></td></tr></tbody></table>
# Next steps

* Visualization

<figure><img src="image_54.png" /></figure>

* Interoperability

<figure><img src="image_55.png" /></figure>

MetaboLights

* Trainings - e-Learning (2018)

- MOOC4Metabolomics

- Open Course 'e-Bioinformatics4Metabo'

<figure><img src="image_56.png" /></figure>

<figure><img src="image_57.png" /></figure>

<figure><img src="image_58.png" /></figure>

<figure><img src="image_59.png" /></figure>
# Lightning Talks

Topics for lightning talks were solicited before the meeting. They will be presented during Session 4, on Thursday and Session 8 on Friday. There may also be last minute openings, and if you wish to give a lightning talk, please send a proposal to the GCC2017-Scientific Program Committee <gcc_2017_scientific@groupes.france-bioinformatique.fr> before the start of Session 2 (Thursday) or the start of Session 6 (Friday). The slides for all lightning talks will be made available on the conference web site, and the talks may be videotaped and also posted on the conference web site.

## Goals

This is your opportunity to give an impassioned and enthralling talk about something that you care about - but you only have 300 seconds. Make every one count, because your audience may include people suffering from limited attention spans this late in the proceedings.

## Timing

Lightning talks are short.

* We will tell you when there are 2 minutes left.

* At 1 minute left we will take over the presentation laptop and start switching to the next set of slides.

* At 0 minutes left the next talk will start, no matter what.

## Slides

* Your slides (as PDF or PowerPoint or ...) should be on the presentation computer before the session starts (talk to Dave Clements)

## INTEGRATING WORKFLOWS WITH PAPERS

Publish in the GigaScience Special Galaxy Series and benefit from:

- 15% off submissions to the Galaxy Series

- Quick publication—average time to first decision less than 4 weeks

- Free deposition and curation of your data in GigaDB database with no size limit

- All data is hosted and can be integrated into the journal's GigaGalaxy server

- A home & citeable DOI for data & workflows

(GIGA)ⁿGalaxy

(GIGA)ⁿSCIENCE

(GIGA)ⁿDB

OXFORD
UNIVERSITY PRESS

bit.ly/galaxy_series

华大基因
BGI

See http://bit.ly/gcc2017lightning for the current list of lightning talks.
4
Wm

Workflow4metabolomics

<figure><img src="image_60.png" /></figure>

MERCI !

<figure><img src="image_61.png" /></figure>

...
# Birds of a Feather
Meetups

There is no better place than a Galaxy Community Conference to meet and learn from others doing high-throughput biology. GCC2017 includes *Birds of a Feather* (BoF) meetups that are informal gatherings based on participants' shared interests. BoFs are encouraged throughout GCC2017, particularly during the *flocking sessions* each day. These sessions are time set aside specifically for Birds of a Feather gatherings.

If you are interested in a BoF then *just show up*. If you want to organize a BoF, see http://bit.ly/gcc2017createbof for how to get one going. It's never too late to start a BoF, and once one is proposed the organizers will get the word out about it.

The BoFs below were planned when this program was printed. See http://bit.ly/gcc2017_bofs for the current list.

<figure><img src="image_51.png" /></figure>

STAY

Informed
with

genome web

**DID YOU KNOW** THAT

ACADEMIC AND NON-PROFIT
RESEARCHERS HAVE FREE
ACCESS TO GENOME WEB'S
PREMIUM NEWS CONTENT?

Just register with your work
email address and you'll have
access to the entire site!

REGISTER HERE
bit.ly/gcc17gw

## Thursday BoFs

### Arts & Crafts

Thursday & Friday, 29-30 June, Lunch

Organizers: Saskia Hiltemann, Erasmus MC; Eric Rasche Texas A&M

GCC sure can be overwhelming sometimes! This BoF is a quiet place to do some stress free, science related, arts and crafts. A&C was a big hit at GCC2016.

http://sched.co/BABe

## Reproducibility best practices for computational analyses
involving large numbers of datasets

Thursday, 29 June, Lunch

Organizer: Geir Kjetil Sandve, University of Oslo

The aim for this BoF is a very concrete one: to initiate a collaborative project towards a manuscript on best practices for reproducibility and transparency when doing computational analysis involving large numbers of datasets. Anyone curious or potentially interested in contributing to such a manuscript is encouraged to join!
Ensuring that omics analyses are truly transparent and reproducible is always a
challenge, and even more so when analyses involve large numbers of datasets. The
exact scope of a manuscript on this topic and organization of the work is open for
discussion at the BoF session. How to make transparent analyses using Galaxy and
dataset collections will clearly be central. How much focus to put on comparison
with alternative interfaces is open for discussion. As for organization of the work,
collaborative editing on an open document might serve as a main pillar, but this
would also be a point of discussion at the BoF.

http://sched.co/BGzq

Supporting the non-coder Galaxy community *Thurs, 29 June, Lunch*

Organizer: Peter Van Heusden, SANBI

How can we support Galaxy community members whose (main) contribution is not
coding? I.e. they might be doing training (although GTN is generally covering these
people), being "ambassadors" for Galaxy, doing user support. Some questions:

1. How can these people be recognised and

2. what communication channels can enhance this part of the community and

3. how can this community and the coder / developer community link?

http://sched.co/BJ0D

GalaxyAdmins

Thursday, 29 June, 18:05 - 18:45

Organizer: Dave Clements, Johns Hopkins University

GalaxyAdmins is a group of people that are responsible for administering Galaxy
instances. We meet online and at events like GCC2017, where a lot of us happen to
be. GCC2017 will be the 5th in-person GalaxyAdmins meetup. Past meetups have
resulted in action items for the coming year. This meetup will discuss plans for the
coming year, GalaxyAdmins leadership, and whatever else you want to talk about.

http://sched.co/B4DP

Genome Annotation in Galaxy

Thursday, 29 June, 18:05 - 18:45

Organizers: Anthony Bretaudieu, INRA, BIPAA and GenOuest platforms; Nathan Dunn, Lawrence Berkeley Lab; Björn Grüning, University of Freiburg; Eric Rasche, Texas A&M

Discuss genome annotation pipelines in Galaxy. Integration of tools, current / future offerings, needs of biologists. (https://galaxy-genome-annotation.github.io/).

http://sched.co/B78V
## Friday BoFs

## Arts & Crafts

Lunch

Organizers: Saskia Hiltemann, Erasmus MC; Eric Rasche, Texas A&M

GCC sure can be overwhelming sometimes! This BoF is a quiet place to do some stress free, science related, arts and crafts. A&C was a big hit at GCC2016.

http://sched.co/BCVY

## Come Together: Exploring Proteomic Analysis within Galaxy

Organizers: Tim Griffin, Pratik Jagtap, James Johnson; University of Minnesota

Lunch

Mass spectrometry-based proteomic analysis is evolving along with new and emerging research disciplines. For example, advances in genomics and transcriptomics have offered opportunities in multi-omics exploration of biological systems. In particular, conversion of RNASeq data into protein FASTA format greatly aids the field of proteogenomics. Moreover, functional microbiome research is being greatly helped by newer developments in metaproteomics research. There is a need for improved Galaxy workflows for these multi-omics research areas and emerging methods such as data-independent analysis. The GCC offers a great forum for community to come together and discuss challenges, opportunities and possibilities.

http://sched.co/BJ5t

## Containerized Galaxy Deployments and Advanced Testing

Organizers: Johns Chilton, Penn State University; Björn Grüning, University of Freiburg

Lunch

During this buzzword heavy BoF, we hope to gather deployers interested in a broad range of topics from big picture choices (such as DevOps, Containers, and Clouds) to specific technologies (for instance Ansible, Condor, and Kubernetes) and specific Galaxy communities (including docker-galaxy-stable, CloudMan, and GalaxyKickStart). This last year has seen significant sharing and splintering of resources for containerized deployments - we hope this BoF can serve as a venue to coordinate plans for the next year to maximize reuse we can accomplish going forward.

**Possible Topics Include:**

* Discuss plans for major Galaxy virtualization projects for the next year - including at least docker-galaxy-stable but hopefully more such CloudMan and GalaxyKickStart.

* Discuss different options for deploying Galaxy to Kubernetes / Swarm / OpenShift and potentially coordinate reuse across methods.
* Discuss multi-container deployment options being developed as part of the docker-galaxy-stable project including planned development and testing of complete deployment recipes for Kubernetes, Swarm, and OpenShift.

* Discuss plans for major Galaxy-related Ansible efforts this year and develop plans to reduce duplication across projects.

* Discuss our efforts to automate testing of Galaxy deployment artifacts over the last year and how they can be leveraged. Discuss plans for future testing.

http://sched.co/BCVj

## Galaxy for Core Facilities

Lunch

Organizer: Brad Langhorst, New England BioLabs

Do you work with a sequencing core facility? How are you using galaxy (QC, sample tracking, etc)? What missing things do you need?

http://sched.co/BJby

## Trackster support group

Lunch

Organiziers: Frederik Coppens, ELIXIR Belgium & VIB; Mo Heydarian, Johns Hopkins University; Michael Sauria, Johns Hopkins University

We will gather to discuss Trackster, Galaxy's very own genome browser. We'll discuss the benefits of Trackster and start an ongoing discussion on what features could be added to further increase the utility of this valuable feature.

http://sched.co/BHI3
## Social Events

We have numerous scheduled social events at GCC2017. However, GCC is one large social event for our community. When you're free, skip checking your email and introduce yourself to the person next to you. You have at least one thing in common - you both have excellent taste in choosing conferences! If you dig deeper, you'll likely find that you have much more in common and maybe shared interests. Many fruitful collaborations have been initiated at GCC. Strike up a conversation!

## Conference Dinner

The official conference dinner is Thursday evening. It will be held at Le Château du Pouget. Buses will make the journey from, and return to Le Corum. Don't miss it.

## Capture the Flag: Hack the Universe

Saskia Hiltemann and Eric Rasche have put together a *Capture the Flag (CTF)* event for GCC2017. Hack the Universe is a competition where you try to hack into a Galaxy instance and learn about Galaxy, Galaxy Administration, vulnerabilities, and good security practices. CTF will start on the first night of GCC2017, and run until a week after the conference.

Anyone can participate! We strongly recommend you form teams involving at least one bioinformatician or biologist, and one computer person. Get out there, make new friends!

Interested? See https://ctf.galaxians.org/ for more and visit Saskia and Eric at the Arts & Crafts BoF.

## BoFs

BoFs aren't focused on social interactions, but they are an excellent way to meet other participants that are eager to discuss a common interest. The Arts & Crafts BoF, however, is all about relaxing with your fellow participants.

<figure><img src="image_52.png" /></figure>

INDIANA UNIVERSITY

Travel Fellowships / Galaxy Community Fund
# Keynotes & Accepted Talks

The full abstracts are available online.

## Session 1, Thursday, 29 June, morning

**The Evolution of Galaxy: A rough Timeline**

http://sched.co/B4z8

Anton Nekrutenko 1, James Taylor 2

1. Penn State University

2. Johns Hopkins University

**Bioconda and BioContainers - Enabling Universal Reproducibility in Galaxy**

http://sched.co/B4zG

John Chilton 1*, Marius Van Den Beek 2, Björn Grüning 3, Galaxy Team

1. Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16801 - United States

2. Institut Curie, Institut Curie, 26 rue d'Ülm 75248 PARIS CEDEX 05 - France

3. Uni-Freiburg (ALU), Bioinformatics Group Department of Computer Science, Albert-Ludwigs-University Freiburg Georges-Köhler-Allee 106 79110 Freiburg Germany - Germany

*: Corresponding author

**Building an open, collaborative, online infrastructure for bioinformatics training**

http://sched.co/B55d

Bérénice Batut 1*, Galaxy Training Network 2, Dave Clements 3*, Björn Grüning 4*

http://sched.co/B55d

1. University of Freiburg, Bioinformatics Group, Department of Computer Science

2. Galaxy Training Network

3. Johns Hopkins University

4. University of Freiburg, Bioinformatics Group, Department of Computer Science

*: Corresponding author

## Session 2, Thursday, 29 June, late morning

**An Educational Framework for Galaxy Administration**

http://sched.co/B56f

Martin Cech 1*, Enis Afghan 1, Nate Coraor 1, Simon Gladman 2, Daniel Blankenberg 1,

Björn Grüning 3, Ross Lazarus, Dave Clements 4

1. Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA

2. University of Melbourne

3. Department of Computer Science, Albert-Ludwigs-University, Freiburg

4. Department of Biology, Johns Hopkins University, Baltimore, MD

*: Corresponding author

**Integrative analysis of hundreds of datasets in Galaxy**

http://sched.co/B56o

Geir Kjetil Sandve 1, Boris Simovski 1, Sveinung Gundersen, Diana Domanska, Christin

Lund-Andersen

1. Department of Informatics [Oslo], Informatikkbygget Gaustadalléen 23 N-0371 Oslo Norway - Norway
# Galaxy Genome Annotation Project: Galaxy and GMOD for Annotation, Teaching, and Genomic Databases

http://sched.co/B59G

Eric Rasche 1, Björn Grüning 2, Nathan Dunn 3, Anthony Bretaudieu 4

1. Center for Phage Technology, Texas A&M University (CPT)

2. Department of Computer Science [Freiburg], Georges-Kohler-Allee 79, 79108 Freiburg, Germany - Germany

3. Lawrence Berkeley National Laboratory (LBNL)

4. BIPAA/GenOuest, Institut National de la Recherche Agronomique – INRA

# Apollo in Galaxy: Increasing Opportunities for Collaborative Genome Annotation

http://sched.co/B57M

Nathan Dunn 1*, Monica Munoz-Torres 1, Deepak Unni 2, Eric Rasche 3, Eric Yao 4, Ian Holmes 4, Christine Elsik 2, Suzanna Lewis 1

1. Lawrence Berkeley National Lab (LBNL), Lawrence Berkeley National Lab 717 Potter Street Berkeley, CA 94710 - United States

2. Division of Plant Sciences, University of Missouri, 52 Agriculture Lab, Columbia, MO 65211 - United States

3. Center for Phage Technology, Texas A&M University (CPT), 2128 TAMU College Station, TX 77843-2128 - United States

4. Department of Bioengineering, University of California, Berkeley (UC Berkeley), 119 California Hall Berkeley, CA 94720-1500 - United States

# Galaxy at the IFB: From Compute to Training

http://sched.co/B8XT

Victoria Dominguez del Angel 1, Cristophe Caron 2

1. Institut Français de Bioinformatique

2. INRA

## Session 3, Thursday, 29 June, early afternoon

### Galaxy Community Update

http://sched.co/B57W

Jeremy Goecks 1, Dan Blankenberg 2

1. Oregon Health & Science University

2. Penn State University

### The Year of IUC

http://sched.co/B57a

Björn Grüning 1*, Bérénice Batut 1, Marius Van Den Beek 2, Daniel Blankenberg 3, Dave Bouvier 3, Anthony Bretaudieu 4, Nate Coraor 3, John Chilton 3, Peter Cock 5, Saskia Hiltemann 6, Youri Hoogstrate 6, James Johnson 7, Greg Von Kuster 8, Lance Parsons 9, Eric Rasche 10, Nicola Soranzo 11

1. Uni-Freiburg (ALU), Bioinformatics Group Department of Computer Science Albert-Ludwigs-University Freiburg Georges-Köhler-Allee 106 79110 Freiburg Germany

2. Institut Curie, 26 rue d'Ulm 75248 PARIS CEDEX 05 - France

3. Penn State / Galaxy Team

4. Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut national de la recherche agronomique (INRA) : UMR1349, AGROCAMPUS OUEST, UMR1349 IGEPP, F-35042 Rennes, - France

5. James Hutton Institute

6. ErasumusMC

7. University of Minnesota

<footnote>*: Corresponding author</footnote>
8. Penn State University, University Park, PA

9. Princeton University

10. Center for Phage Technology, Texas A&M University (CPT), 2128 TAMU College Station, TX 77843-2128 - United States

11. Earlham Institute

*: Corresponding author

## Workflow4Metabolomics: Towards an international computing infrastructure and a tools showcase for Metabolomics

http://sched.co/B58O

Gildas Le Corguillé 1, Franck Giacomoni 2, Pierrick Roger-Mele 3, Christophe Duperier 2, Mélanie Pétéra 2, Yann Guitton 4, Marie Tremblay-Franco 5, Jean-François Martin 5, Cécile Canlet 5, Alexis Delabrière 3, Etienne Thévenot 3, Christophe Caron 6

1. ABiMS, CNRS : FR2424, Université Pierre et Marie Curie [UPMC] - Paris VI, Station Biologique de Roscoff - France

2. PFEM, Institut national de la recherche agronomique (INRA) : UMR1019, Saint Genes Champanelle - France

3. Laboratory for Data Analysis and Systems Intelligence (CEA-LIST/LADIS), CEA-LIST, Gif-sur-Yvette - France

4. Laboratoire d'Etude des Résidus et Contaminants dans les Aliments - Oniris (LABERCA), LUNAM Université, Nantes - France

5. Toxalim, Institut national de la recherche agronomique (INRA), Université Paul Sabatier - Toulouse 3, Toulouse - France

6. Ingenium, Institut national de la recherche agronomique (INRA), Toulouse - France

## South Green Galaxy: a suite of tools for plant genomics

http://sched.co/B595

Jean-François Dufayard 1, Marilyne Summo 2, Gaëtan Droc 2, Mathieu Rouard 1, Bertrand Pitollat 1, Paul Pastor 1, Delphine Larivière 2, Frédéric De Lamotte 3, Stéphanie Bocs 1, Manuel Ruiz 1, Felix Homa 1, Guillaume Martin 1, Gautier SARAH 4, Sébastien RAVEL 5, Vincent Maillol 1, Jonathan Lorenzo 6, Alexis Dereeper 1

1. CIRAD UMR AGAP (AGAP)

2. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)

3. INRA UMR AGAP (AGAP)

4. Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP)

5. Biologie et génétique des interactions plantes-parasites pour la protection intégrée (BGPI)

6. Institut Français de Bioinformatique (IFB)

## Performing Next Generation Phylogenetic Analyses with NGPhylogeny.fr

http://sched.co/B598

Damien Correia 1, 2, 3*, Vincent Lefort 4, Olivia Doppelt-Azeroual 2, Fabien Mareuil 2, Sarah Cohen-Boulakia 3*, Olivier Gascuel 2, 4

1. Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Centre National de la Recherche Scientifique : UMS3601, IFB-core, Bâtiment 21, 2 av. de la Terrasse, 91190, Gif-sur-Yvette - France

2. Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris], CNRS : USR3756, 25-28 rue du docteur Roux, 75724 Paris cedex 15 - France

3. Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11, Centre National de la Recherche Scientifique : UMR8623, LRI - Bâtiments 650-660 Université Paris-Sud 91405 Orsay Cedex - France

4. Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier : UMR5506, Centre National de la Recherche Scientifique : UMR5506, CC 477, 161 rue Ada, 34095 Montpellier Cedex 5 - France

<footnote>*: Corresponding author</footnote>
## Session 4, Thursday, 29 June, late afternoon

**The Institute of Computational Biology: an overview**

http://sched.co/B59E

Eric Rivals I

I. The Institute of Computational Biology

**Lightning Talks**

**Improving Your Text Life**

http://sched.co/B9jV

James Johnson I

I. University of Minnesota Supercomputing Institute (MSI)

**Galaxy-E: Towards an accessible, reproducible and transparent data analysis and management universe dedicated to Ecology**

http://sched.co/B5xf

Valentin Chambon, Thimothée Virgoulay, Eloïse Trigodet, Marie Delannoy, Marianne

Linares, Grégoire Loïs, Romain Julliard, Yvan Le Bras I, *

I. MNHN CESCO & Staiton de Biologie Marine de Concarneau, Muséum National d'Histoire Naturelle (MNHN)

*: Corresponding author

**The Galaxy Gateway on F1000Research**

http://sched.co/B9id

Holly Murray I

I. Science Navigation Group, Middlesex House, 34-42 Cleveland St - United Kingdom

**GalaxyCat - The online catalog of Galaxy tools across instances**

http://sched.co/BCAV

Julien Seiler I*, Stéphanie Le Gras I

I. Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS : UMR7104, Inserm : U964, université de StrasbourgParc D'Innovation I Rue Laurent Fries - BP 10142 67404 ILLKIRCH CEDEX - France

*: Corresponding author

**Analyzing Relationships among Clinical Factors of Cancer Patients by Regression Analysis**

http://sched.co/B5yY

Sugandima Vidanagamachchi I, Thamara Waidyarathna I*

I. Department of Computer Science (University of Ruhuna)

*: Corresponding author

## Session 5, Friday, 30 June, morning

**Personalized Analysis of Cancer Data: From Genes to Pathways (and Back)**

http://sched.co/B59d

Eytan Domany I

I. Weizmann Institute of Science

**Comparing hundreds of RNA-seq libraries using Galaxy and SeqResults**

http://sched.co/B59n

Brad Langhorst I

I. New England Biolabs (NEB)
## Approaches for small RNA-seq analysis in Galaxy

http://sched.co/B5GD

Mallory Freeberg 1, James Taylor 1

1. Biology Department, Johns Hopkins University (JHU), 3400 N Charles St - United States

## Session 6, Friday, 30 June, late morning

### COMBAT TB: an integrated environment for Tuberculosis data analysis and surveillance

http://sched.co/B5GG

Peter Van Heusden 1*, Thoba Lose 1, Ziphozakhe Mashologu 1, Alan Christoffels 1*

1. South African National Bioinformatics Institute (SANBI)

*: Corresponding author

### The RNA Workbench - reproducible, transparent, and accessible RNA research

http://sched.co/B5Ld

Florian Eggenhofer 1, Jörg Fallmann 2, Björn Grüning 1, 3, Bérénice Batut 1, Peter Stadler 2, 4, 5, Rolf Backofen 1, 3, 6

1. University of Freiburg (ALU), Bioinformatics Group Department of Computer Science Albert-Ludwigs-University Freiburg Georges-Köhler-Allee 106 79110 Freiburg Germany - Germany

2. University of Leipzig, Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany - Germany

3. Center for Biological Systems Analysis (ZBSA), Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany - Germany

4. Institute for Theoretical Chemistry (TBI), Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria - Austria

5. Max Planck Institute for Mathematics in the Sciences (MPI), Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany - Germany

6. Centre for Biological Signaling Studies [Freiburg] (BIOSS), Schänzlestr. 1879104 Freiburg - Germany

## Interaction Hub: a comprehensive Galaxy-based chromatin folding database, browser, and analysis platform

http://sched.co/B5Le

Michael Sauria 1, James Taylor 1

1. Department of Biology [Johns Hopkins University], 3400 N. Charles Street, Mudd 144 Baltimore, MD 21218 - United States

## Mechanizing our biologists with Galaxy and IRIDA platforms

http://sched.co/B5Lf

Philip Mabon 1

1. Public Health Agency of Canada (PHAC), 1015 Arlington Street, Winnipeg, Manitoba R3E3R2 - Canada

## Session 7, Friday, 30 June, early afternoon

### ELIXIR supports Galaxy users and developers

http://sched.co/B5Lh

Frederik Coppens 1, 2

1. ELIXIR-Belgium

2. VIB
Advancing metaproteomics research via community-based informatics development and dissemination

http://sched.co/B5Li

Pratik Jagtap 1*, Björn Grüning, James Johnson, Alessandro Tanca, Bart Mesuere, Judson Hervey, Carolin Kolmeder, Jeremy Fischer, Thomas Doak, Thilo Muth, Dave Clements 2, Praveen Kumar, Subina Mehta, Thomas Mcgoan, Clemens Blank, Bernhard Renard, Josh Elias, Joel Rudney, Timothy Griffin

1. University of Minnesota (Galaxy-P), 7-166 MCB, 420 Washington Ave SE, Minneapolis, MN 55455 - United States

2. Johns Hopkins University

*: Corresponding author

Making Galaxy User Interface Pluggable with Webhooks

http://sched.co/B5Lk

Evgeny Anatskiy 1, Anup Kumar 1, Joachim Wolff 1, Clemens Blank 1, Eric Rasche 2, Martin Cech 3, Björn Grüning 1

1. Bioinformatics Group at Albert-Ludwigs-Universität, Freiburg

2. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX

3. Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA

A reproducible data analysis environment for next-generation sequencing on public cloud computer

http://sched.co/B5Lo

Manabu Ishii 1, Matsushima Akihiro 1, Mika Yoshimura 1, Hiroki Danno 1, Itoshi Nikaido 1

4. RIKEN ACCC Bioinformatics Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198 - Japan

Developing analytical workflows for plant genomics through the integration of Galaxy and Tripal

http://sched.co/B5x9

Sean Buehler 1, Nic Herndon 1, Emily Grau 1, Ming Chen 2, Abdullah Almsaeed 2, Connor Wytko 3, Brian Soto 3, Sook Jung 3, Shawna Spoor 3, Kuangching Wang 4, Chun-Huai Cheng 3, Nick Watts 4, Lacey Sandserson 5, Jill Wegrzyn 6, Doreen Main 3, Alex Feltus 4, Margaret Staton 7, Stephen Ficklin 3, Nathan Henry 7

1. University of Connecticut

2. University of Tennessee Institute of Agriculture

3. Washington State University

4. Clemson University

5. University of Saskatchewan

6. University of Connecticut

7. University of Tennessee

Session 8, Friday, 30 June, late afternoon

Lightning Talks

Using visual programming in Cervical cancer data of The Cancer Genome Atlas

http://sched.co/B5yV

Thais Hosokawa 1, José Fregnani 1, Rui Reis 1, Adriane Evangelista 1

1. Barretos Cancer Hospital (BCH), Barretos, São Paulo, Brazil Galaxy at scale: Analyzing thousands of single cell transcriptomes
Galaxy at scale: Analyzing thousands of single cell transcriptomes

http://sched.co/BH73

Mo Heydarian 1, Enis Afgan 1, James Taylor 1*

I. Johns Hopkins University

*: Corresponding author

ToolDog - generating tool descriptors from the ELIXIR tool registry

http://sched.co/B5yu

Kenzo-Hugo Hillion 1*, Ivan Kuzmin 2, Hedi Peterson 2, Jon Ison 3, Hervé Ménager 1*

1. Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur de Paris

2. Center of Bioinformatics, Biostatistics and Integrative Biology

3. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark

*: Corresponding author

Pushing the limits of job flexibility on HPC

http://sched.co/B5z0

Carrie Ganote 1

I. Indiana University (IU), 107 S. Indiana Avenue Bloomington, IN 47405-7000 - United States

Pulling the Galaxy's Strings

http://sched.co/B5z4

Jeffrey Miller 1*, Brenna Miller 1

I. The University of Iowa

*: Corresponding author

Using Galaxy as a platform for continuous software development

http://sched.co/B5z9

Boris Simovski 1, Geir Kjetil Sandve 1*, Sveinung Gundersen 1

I. Department of Informatics, University of Oslo [Oslo] (UiO), Informatikkbygget Gaustadalléen 23 N-0371 Oslo Norway - Norway

*: Corresponding author

Automated Generation of Complex Toolkits for Galaxy

http://sched.co/B5y5

Daniel Blankenberg 1

I. Penn State / Galaxy Team

Hack the Galaxy: Data Report

http://sched.co/BFR9

Hack the Galaxy: Data Organizers

Hack the Galaxy: Dev Report

http://sched.co/BFRA

Hack the Galaxy: Dev Organizers

JBrowse and Circos Tool Updates

http://sched.co/BH74

Eric Rasche 1, Saskia Hiltemann 2,

1. Center for Phage Technology, Texas A&M University (CPT)

2. Bioinformatics Dept., Erasmus University Medical Center (Erasmus MC)

Parsec: Intergalactic DevOps and Analysis Automation

http://sched.co/BH78

Eric Rasche 1

I. Center for Phage Technology, Texas A&M University (CPT)
# Posters

Odd numbered posters will be presented Thursday at 15:40, and even-numbered posters on Friday at 15:20.

Poster titles and authors are listed here. The full abstracts of posters can be found online at https://gcc2017.sched.com/overview/type/Posters.

## P01: Galaxy-docker-ansible

http://sched.co/B8RO

Ruben Vorderman 1

1. Leiden University Medical Center (LUMC)

## P02: Pulling Galaxy's Strings

http://sched.co/B8WC

Jeffrey Miller 1

1. The University of Iowa (UI), 230 S. Madison St. Iowa City, IA 52242 - United States

## P03: Automated customized deployment Galaxy portal instance in IFB Cloud Computing

http://sched.co/B8RR

Sandrine Perrin 1*, Björn Grüning 2, Bryan Brancotte 1, Christophe Blanchet 1*

1. Institut Français de Bioinformatique (IFB), Institut Français de BioinformatiqueIFB

2. Biological Systems Analysis (ZBSA), Department of Computer Science, Albert-Ludwigs- University, Center for Biological Systems, University of Freiburg, Freiburg, - Germany

*: Corresponding author

## P04: Integration of openBIS - improving metadata management in Galaxy

http://sched.co/B8XW

Aarif Mohamed Nazeer Batcha 1*, Guokun Zhang 1*, Ulrich Mansmann 1

1. Department of Medical Informatics, Biometry and Epidemiology, University of Munich (IBE, LMU), Marchioninistrasse 15, 81377 Munich - Germany

*: Corresponding author

## P05: The EDAM ontology and its integration into Galaxy

http://sched.co/B8RV

Hervé Ménager 1, Jon Ison 2, Matúš Kalaš 3, Veit Schwaemmler 4, Edam Contributors

1. Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur, Institut Pasteur de Paris, 25 rue du Dr Roux. 75015 Paris - France

2. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark

3. Computational Biology Unit (CBU), University of Bergen

4. Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark

## P06: A Public Galaxy platform @Pasteur used as an execution engine for web services

http://sched.co/B8Xm

Fabien Mareuil 1, Olivia Doppelt-Azeroual 1, Hervé Ménager 1

1. Hub Bioinformatique et Biostatistique, Institut Pasteur [Paris], C3BI 25-28, rue du Docteur Roux, 75724 Paris cedex 15 - France
P07: myFAIR Analysis: Personal FAIR Data Management and Analysis

http://sched.co/B8Rc

Saskia Hiltemann 1, Rick Jansen 1, David Van Zessen 1, John Hays 2, Andrew Stubbs 1*

1. Bioinformatics Dept., Erasmus University Medical Center (Erasmus MC)

2. MMIZ, Erasmus University Medical Center (Erasmus MC)

P08: GEGA: An application for secure access and analysis of EGA data with Galaxy

http://sched.co/B9ip

David Van Zessen 1, Alexander Snef 2, Youri Hoogstrate 1, Dylan Spalding 2, Andrew

Stubbs 1*

1. Bioinformatics Dept., Erasmus University Medical Center (Erasmus MC)

2. European Bioinformatics Institute [Hinxton]. EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK - United Kingdom

P09: Wrapping tools: on the shoulders of the GCC community

http://sched.co/B8TT

Valentin Marcon 1, Nathalie Choisne 2, Veronique Jamilloux 2, Gwendoline Andres, Isabelle

Luyten 2, Joelle Amselem 2, Mikael Loaec 2, Françoise Alfama-Depauw 2, Sarah Maman-

Haddad 3, Melanie Petera 4, Luc Jouneau 5, Sandrine Laguerre 6, Olivier Inizan 1

1. MalAGE (MalAGE), Institut National de la Recherche Agronomique - INRA (FRANCE), Centre de Jouy-en-Josas Domaine de Vilvert F78352 JOUY-EN-JOSAS Cedex - France

2. Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique : UR1164, INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles - France

3. Génétique Physiologie et Systèmes d'Elevage (GenPhySE), Institut national de la recherche agronomique [Toulouse], Chemin de Borde Rouge CS 52627 31326 Castanet Tolosan - France

4. Unité de Nutrition Humaine (UNH), Institut national de la recherche agronomique (INRA)

5. Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique : UR0892, UR0892 INRA Centre de Recherche de Jouy-en-Josas F-78352 Jouy-en-Josas cedex - France

6. l'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National des Sciences Appliquées de Toulouse, 135 Avenue de Rangueil, 31400 Toulouse - France

P10: ToolDog - generating tool descriptors from the ELIXIR tool registry

http://sched.co/B8Xp

Kenzo-Hugo Hillion 1*, Ivan Kuzmin 2, Hedi Peterson 2, Jon Ison 3, Hervé Ménager 1*

1. Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur de Paris

2. Institute of Computer Science, University of Tartu

3. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark

P11: Utility scripts for data manipulation in Galaxy

http://sched.co/B8Tc

Simon Gladman 1*, Madison Flannery 1

1. Melbourne Bioinformatics, The University of Melbourne (MelBioinfo), 187 Grattan St, Carlton, Victoria, 3053 - Australia

<footnote>*: Corresponding author</footnote>

<footnote>*: Corresponding author</footnote>

<footnote>*: Corresponding author</footnote>

<footnote>*: Corresponding author</footnote>
P12: Integration of Alvis within the OpenMinTeD platform as Galaxy utilities

http://sched.co/B8Xs

Jean-Baptiste Bohuon *, Mouhamadou Ba, Robert Bossy 1, Claire Nédellec 1

1. Mathématique et Informatique Appliquées du Génome à l'Environnement (MalAGE), Institut national de la recherche agronomique (INRA), MalAGE, INRA, F78350 Jouy-en-Josas - France - France

*: Corresponding author

P13: Prioritizing SNPs using the Neo4j Galaxy Interactive Environment

http://sched.co/B8Ti

Lose Thoba 1, Ziphozakhe Mashologu 1*, Peter Van Heusden 1*, Alan Christoffels 1*

1. South African National Bioinformatics Institute (SANBI)

*: Corresponding author

P14: Du Novo: a simple, reference-free tool for turning duplex sequencing data into extremely accurate reads

http://sched.co/B8Y4

Nicholas Stoler 1*, Barbara Arbeithuber 2, Wilfried Guiblet 1, Marcia Su 3, Kateryna Makova 2, Anton Nekrutenko 1*

1. Department of Biochemistry and Molecular Biology, Penn State University (BMB), University Park, PA 16802 - United States

2. Department of Biology, Penn State University, University Park, PA 16802 - United States

3. The Jackson Laboratory For Genomic Medicine (JAX), Farmington, CT 06032 - United States

*: Corresponding author

P15: The MiModD suite of tools for genetic variant mapping and identification

http://sched.co/B8TI

Wolfgang Maier 1*, Mark Seifert 1, Katharina Moos, Gregory Minevich, Oliver Hobert 2, Ralf Baumeister 1

1. University of Freiburg

2. Department of Biological Sciences, Columbia University

*: Corresponding author

P16: Galaxy-P rides the Jetstream: Cloud-based multi-omic informatics

http://sched.co/B8YY

Timothy Griffin 1*, Matthew Chambers 2, James Johnson 1, Mcgowan Thomas 1, Thomas Doak 3, Jeremy Fischer 3, Praveen Kumar 1, Pratik Jagtap 1

1. University of Minnesota

2. Vanderbilt University

3. Indiana University

*: Corresponding author

P17: ProteoRE, a Galaxy-based infrastructure for interpreting and exploring mass spectrometry-based proteomics data

http://sched.co/B8U9

Lien Nguyen 1, Maud Lacombe 1, Sandra Dérozier 2, Lisa Perus 1, Olivier Rué 2, Florence Combes 1, Christophe Caron 2, Virginie Brun 1, Valentin Loux 2, Yves Vandenbrouck 1

1. Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université de Grenoble, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) - Grenoble, Centre National de la Recherche Scientifique : FR3425, 17, rue des Martyrs 38054 Grenoble cedex 9 - France

2. Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement (MAIAGE), Institut National de la Recherche Agronomique, Université Paris-Saclay, Domaine de Vilvert 78350 Jouy en Josas Cedex - France
P18: Implementation of an interface for exploring molecular diversity by proteogenomics

http://sched.co/B8Yy

Yannick Cogne 1, Christine Almunia 1, Olivier Pible 1, Duarte Gouveia 2, Arnaud Chaumot 2, Olivier Geffard 2, Jean Armengaud 1*

1. Innovative technologies for Detection and Diagnostics (Li2D), CEA Marcoule, BP17171, F-30207 BAGNOLS-SUR-CEZE - France

2. Milieux aquatiques, écologie et pollutions (UR MALY), CEMAGREF, 5 rue de la Doua, CS70077, 69626 Villeurbanne Cedex, France - France

*: Corresponding author

P19: A reproducible data analysis environment for next-generation sequencing on public cloud computer

http://sched.co/B8UA

Manabu Ishii 1, Akihiro Matsushima 1, Mika Yoshimura 1, Hiroki Danno 1, Itoshi Nikaido 1

1. RIKEN ACCC Bioinformatics Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198 - Japan

P20: Development and implementation of a transversal NGS & bioinformatics platform at the Belgian Institute of Public Health: Deployment of a Galaxy instance for routine use in a public health setting

http://sched.co/B8Z6

Julien Van Braekel 1, Bert Bogaerts 1, Raf Winand 1, Quiang Fu 1, Sigrid De Keersmaecker 1, Nancy Roosens 1, Kevin Vanneste 1*

1. Belgian Institute of Public Health (WIV-ISP), Rue Juliette Wytsman 14 1050Ixelles - Belgium

*: Corresponding author

P21: Deployment of genome databases for insects using Galaxy Genome Annotation

http://sched.co/B8VM

Anthony Bretaudieu 1*

1. Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique: UMR1349, Université de Rennes 1: UMR1349, Agrocampus Ouest: UMR1349, Domaine de la Motte au Vicomte BP 3532735653 Le Rheu - France

*: Corresponding author

P22: Enhancing the Multi-omics Visualization Platform (MVP) Plug-in for Galaxy-based Applications

http://sched.co/B5xC

Thomas McGowan 1*, James Johnson 1, Pratik Jagtap 2*

1. University of Minnesota Supercomputing Institute (MSI), 599 Walter Library, 117 Pleasant St. SE Minneapolis, MN 55455 - United States

2. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota (BMBB), - 155 Jackson Hall,321 Church Street SE, Minneapolis, MN 55455 - United States

*: Corresponding author

P23: Detecting somatic de-novo Transposable Element insertions with Galaxy

http://sched.co/B8VS

Marius Van Den Beek 1, Nick Riddiford, Katarzyna Siudeja, Allison Bardin

1. Institut Curie, 26 rue d'Ulm 75248 PARIS CEDEX 05 - France

P24: Annotating microRNA isoforms (isomiRs) of non-model organisms to analyze expression levels using a Galaxy workflow

http://sched.co/B8Z7

Jochen Bick 1, Susanne Ulbrich 1, Stefan Bauersachs 1

1. ETH Zurich Animal Physiology
P25: Galaxy and the full spectrum of needs in a small-scale cancer study

http://sched.co/B8VU

Christin Lund-Andersen 1, Ståle Nygård 2, 3, Stein Larsen 4, Eivind Hovig 1, 3, Kjersti Flatmark 1, 3, 4

1. Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway

2. Bioinformatics Core Facility, Institute for Medical Informatics, Oslo University Hospital.

3. University of Oslo, Oslo, Norway

4. Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway

P26: The Burden of Occupational Cancer in Korea

http://sched.co/B8Z8

Mia Son 1

1. Kangwon National University (KNU)

P27: ASaiM: a Galaxy-based framework to analyze raw sequencing data from microbiota

http://sched.co/B8Vj

Bérénice Batut 1*, Clémence Defois 2, Kévin Gravouil 2, 3, 4, Jean-François Brugère 2, Eric Peyretaillade 2, Pierre Peyret 2

1. Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany

2. Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-
Ferrand-Theix : UMR0454, Université Clermont Auvergne : UMR0454, INRA, Centre de Recherches
de Clermont-Ferrand - Theix / 63122 Saint-Genès Champanelle - France

3. Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne : UMR6023, Centre National de la Recherche Scientifique : UMR6023, Campus des Cézeaux / 24, avenue des Landais BP 80026 / 63170 Aubière - France

4. Laboratoire d'informatique, de Modélisation et d'Optimisation des Systèmes - Clermont Auvergne (LIMOS), SIGMA Clermont, Université Clermont Auvergne : UMR6158, Centre National de la Recherche Scientifique : UMR6158, ISIMA / Campus des Cézeaux BP 10025 / 63173 AUBIERE cedex - France

*: Corresponding author

P28: ChemFlow, chemometrics for everybody

http://sched.co/B8Z9

Virginie Rossard 1, Eric Latrille 1, Fabien Gogé 2, Jean-Michel Roger 3, Martin Ecarnot 1, Jean-Claude Boulet 1

1. INRA

2. IRSTEA

P29: Developing a bioinformatics pipeline for optimization of sperm epigenome analysis in mice and men to be used for the identification of epigenetic signatures in sperm associated with environmental perturbation

http://sched.co/B8Vl

Deepak Tanwar 1, Romain Lambrot 1, Keith Siklenka 2, Mahmoud Aarabi 3, Donovan Chan 3, Clifford Librach 4, Sergey Moskovtsev 4, Jacquetta Trasler 3, Sarah Kimmins 1, 2

1. Department of Animal Science, McGill University, Ste Anne-de-Bellevue, QC - Canada

2. Department of Pharmacology and Therapeutics, McGill University, Montreal, QC - Canada

3. Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC - Canada

4. Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON - Canada
P30: Pushing the limits of job flexibility on HPC

http://sched.co/B9jp

Carrie Ganote I, Sheri Sanders, Phil Blood, Thomas Doak, Bhavya Nalagampalli Papudeshi, Asma Bankapur *, Brian Haas, Tim Tickle, Cicada Brokaw

I. Indiana University (IU), 107 S. Indiana Avenue Bloomington, IN 47405-7000 - United States

*: Corresponding author

P31: In silico toxicity assessment in cultured rat intestinal cells deduced from cellular impedance measurements and transcriptomics data

http://sched.co/BIAZ

Pooja Gupta I

I. Institute for Mathematics, Freie Universität Berlin (FU Berlin)

P32: An odyssey into Galaxy: Quality control and quality assurance of NGS-based laboratory diagnostic tests offered by Newborn Screening Ontario

http://sched.co/BKkj

Lemuel J. Racacho I, *

I. Newborn Screening Ontario (NSO)

*: Corresponding author
Accepted Demos

Odd numbered demos will be presented Thursday at 15:40, and even-numbered demos on Friday at 15:20. Demos with corresponding posters will be presented concurrently with and adjacent to the poster. Full demo abstracts are online.

D01: Integration of Linked Data into Galaxy using AskOmics

http://sched.co/B8ZC

Xavier Garnier 1, 2, Olivier Dameron 2, Olivier Filangi 1, 3, Fabrice Legeai 1, 4, Anthony Bretaudeau 1, 3

1. Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique : UMR1349, Universite de Rennes 1 : UMR1349, Agrocampus Ouest : UMR1349, Domaine de la Motte au Vicomte BP 3532735653 Le Rheu - France

2. DYLISS (INRIA - IRISA), INRIA, Université de Rennes 1, CNRS : UMR6074, Campus de Beaulieu 35042 Rennes cedex - France

3. Plateforme bio-informatique Genouest (Genouest), IRISA/INRIA Plateforme GenOuest Campus de Beaulieu 35042 Rennes cedex, France - France

4. GenScale, IRISA/INRIA équipe Genscale Campus de Beaulieu 35042 Rennes cedex, France - France

D02: Improve Genome Annotation Accuracy through Manual Annotation in Apollo

http://sched.co/B8aC

Nathan Dunn 1*, Monica Munoz-Torres 1, Deepak Unni 2, Eric Rasche 3, Eric Yao 4, Ian Holmes 4, Christine Elsik 2, Suzanna Lewis 1

1. Lawrence Berkeley National Lab (LBNL), Lawrence Berkeley National Lab 717 Potter Street Berkeley, CA 94710 - United States

2. Division of Plant Sciences, University of Missouri, 52 Agriculture Lab, Columbia, MO 65211 Columbia, MO 65211 - United States

3. Center for Phage Technology, Texas A&M University (CPT), 2128 TAMU College Station, TX USA 77843-2128 - United States

4. Department of Bioengineering, University of California, Berkeley (UC Berkeley), 119 California Hall Berkeley, CA 94720-1500 - United States

*: Corresponding author

D03: De novo transcriptome annotation visualization and filtering

http://sched.co/B8ZY

Eduardo De Paiva Alves 1

1. Centre for Genome-Enabled Biology and Medicine, University of Aberdeen (CGEBM), 23 St Machar Dr, Aberdeen, UK AB24 3UU - United Kingdom

D04: KnetMiner: an application suite to integrate, search, and interactively explore large knowledge networks

http://sched.co/BJ5F

Ajit Singh 1, Monika Mistry 1, Marco Brandizi 1, Chris Rawlings 1, Keywan Hassani-Pak 1

1. Rothamsted Research, Harpenden, AL5 2JQ - United Kingdom
## Organising Committee

Christophe Caron
INRA

Dave Clements
Johns Hopkins University

Gildas Le Corguillé
Station Biologique Roscoff

Jean-François Dufayard
CIRAD

Olivier Inizan
INRA

Patricia Laplagne
IFB

Marilyne Summo
CIRAD

Nicole Vasilevsky
OHSU

## Hack the Galaxy: User

Frederic Coppens
VIB

Mallory Freeberg
Johns Hopkins University

Jennifer Hillman-Jackson
Penn State University

Yvan Le Bras
MNHM

Stephanie Le Gras
INSERM

Christian Schudoma
Earlham Institute

## Scientific Committee

Christophe Antioniewski, Chair
UPMC

Sarah Cohen-Boulakia
IRI

Alexis Dereeper
IRD

Thérèse Commes
Université de Montpellier

Anton Nekrutenko
Penn State University

Björn Grüning
University of Freiburg

Jeremy Goecks
OHSU

Jean-François Gibrat
IFB

Vincent Lefort
LIRMM

Nicola Soranzo
Earlham Institute

James Taylor
Johns Hopkins University

## Hack the Galaxy: Dev

Anthony Bretaudieu
INRA

Björn Grüning
University of Freiburg

Marius van den Beek
Institut de Biologie Paris Seine

Julien Seiler
IGBMC
<figure><img src="image_53.png" /></figure>

LE CORUM
BY MONTPELLIER EVENTS

<figure><img src="image_54.png" /><figcaption>Einstein Auditorium
Meeting Venue</figcaption></figure>
<figure><img src="image_55.png" /></figure>

LE CORUM
BY MONTPELLIER EVENTS

Sully 1, 2, and 3
Hack the Galaxy
Training

Level 1

<figure><img src="image_56.png" /></figure>
<figure><img src="image_57.png" /></figure>

LE CORUM
BY MONTPELLIER EVENTS

<figure><img src="image_58.png" /><figcaption>Barthez & Rondelet
Training</figcaption></figure>
<figure><img src="image_59.png" /></figure>

<figure><img src="image_60.png" /></figure>

GCC

BOSC

Portland 2018

GCC2018 & BOSC 2018
are joining up

June 25-30, Reed College, Portland, Oregon

gccbosc2018.sched.com

See you next year!