phenomenal project - deliverable d1.3 minutes of kick-off ......phenomenal 3 1. introduction this...

24
PhenoMeNal 1 PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off Meeting Project ID 654241 Project Title A comprehensive and standardised e- infrastructure for analysing medical metabolic phenotype data Project Acronym PhenoMeNal Start Date of the Project 1st September 2015 Duration of the Project 36 Months Work Package Number 1 Work Package Title Management Delivery Date M2 Work package leader EMBL-EBI Contributing Partners EMBL-EBI

Upload: others

Post on 29-May-2020

4 views

Category:

Documents


0 download

TRANSCRIPT

Page 1: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 1

PhenoMeNal

Project - Deliverable D1.3 Minutes of Kick-Off Meeting

Project ID 654241

Project Title A comprehensive and standardised e-infrastructure for analysing medical metabolic phenotype data

Project Acronym PhenoMeNal

Start Date of the Project 1st September 2015

Duration of the Project 36 Months

Work Package Number 1

Work Package Title Management

Delivery Date M2

Work package leader EMBL-EBI

Contributing Partners EMBL-EBI

Page 2: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 2

Contents: 1. Introduction 2. Organization and structure of the meeting and activities 3. Project Objectives, partners introductions and compute services

a. Project objectives and management structure b. Partner presentations c. EGI, ELIXIR and EUDAT presentations

4. Discussion of the project structure

a. Work packages b. Tools and workflows

5. Project Management and Outreach 6. Used-cases aspects 7. Reviewed plan of work for the first 12 months Annexes 1. Agenda 2. List of participants 3. Photos

Page 3: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 3

1. Introduction This report is a deliverable related to the work package 1: Management and deliverable D1.3 - Minutes of kick-off meeting. The report aims to report the main activities carried out in the frame of this work package deliverable, the presentations made for each Work Package (WP), interactions among different WPs in relation to the execution of deliverables and the overall legal, ethical, financial and administrative arrangement of the consortium. The PhenoMeNal kick off meeting was organised at European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK by EMBL-EBI, the coordinator of the consortium, from 8-10 September 2015. Around 40 participants representing 8 European countries attended the kick off meeting. A detailed list of the participants is enclosed in the Annex 2. 2. Organisation and structure of the meeting and activities The meeting was structured as a 3-days event. ● Day 1 was a plenary session with an overview of the whole project structure,

the consortium agreement and legal implications, introduction of different partners of the consortium and special sessions on European Grid Initiative (EGI), EUDAT- European Collaborative Data Infrastructure and ELIXIR.

● Day 2 was focussed on presentations of the WPs and deliverables including the performance metrics followed by workshops and discussions on tools and workflows that will form the basis of the infrastructure. A comprehensive session on project management and outreach for the project was also accomplished.

● Day 3 included presentations on use-cases from practitioners within the consortia and what steps could be taken in context of workflows and data protection. The meeting was concluded with recommendations of experts for constitution of the PhenoMeNal Scientific Advisory Board (SAB) and detailed planning for staffs exchange programs and workshops foreseen for year 1.

A more detailed agenda of the meeting is reported in Annex 1.

Page 4: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 4

3. Project Objectives, partners introductions and compute services

a. Project objectives and management structure

Title and Speaker Highlights

Introduction Christoph Steinbeck

● e-Infrastructure - compute - clinical data ● Integrate, deliver, scale, audit, train, ethics ● Services-Joint Research Activities- networking ● Challenges ● Availability and access to clinical data ● Conditional ethics clearance ● 830 PM in 3 years ● Adoption by the community ● Opportunities with the project ● Work in an ecosystem of relevant e-

infrastructures (Elixir, EGI, EUDAT, OpenMinted etc.)

● Tour de Table (All)

b. Partner presentations

Title and Speaker Highlights

Cheminformatics and Metabolism Christoph Steinbeck (EMBL-EBI)

● Introduction about EMBL and EBI ● Introduction to database like MetaboLights,

MetabolomeXchange

PhenoMeNal Kick-off Imperial College Tim Ebbels (ICL)

● Metabolomics at Imperial ● MRC-NIHR National Phenome Centre

Bioinformatics and Mass Spectrometry Steffen Neumann

● LC/MS ● R based: XCMS, CAMERA ● Metabolite identification: massbank, metfrag,

Page 5: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 5

(IPB)

metfusion ● Interested in data standards and sharing

Partner 4: Universitat de Barcelona, Spain Silvia Marin (UB)

● Computational and experimental expertise ● Fluxomics analysis (Tools: Isodyn, Mitodyn,

MScor) modelling of experimental data ● Part of WPs - 5, 6, 8, 9 ● Plan to integrate the tools into cloud ● Make their tools available for fluxomics

community ● Create link between PhenoNeNal and ISBE

(Infrastructure for system biology)

Metabolic Analysis in Cancer Ulrich Guenther (UoB)

● NMR technology in HWB-NMR, School of Cancer sciences

● Relevant projects: EU metabolomics: ITNs EUROPOL, HaemMetabolome

● Can contribute to clinical data management; have lot of clinical data

● Cancer and non-cancer metabolomics ● S/W: NMRLab (advanced NMR data

processing) ● WPs: 3,5,6,8,9

CERM/CIRMMP Magnetic Resonance Centre Antonio Rosato (CIRMMP)

● Funded by National government and EC ● An INSTRUCT (Integrated Structural Biology)

core centre: www.structuralbiology.eu ● Centre used partially for metabolomics (25%) ● Part of BBMRI biobanks, EGI ● In process of being certified under ISO/IEC

17025 for metabolomics analysis ● Some activities: Cloud Centurion services

Short intro- Leiden University/Netherlands Metabolomics Centre Thomas Hankemeier (UL)

● Key facility: www.bmfl.nl >15k samples/year, clinical, NPs, Chemical biology etc.

● Work with academics, industry and clinical researchers

● Collaborative studies for exploratory biomarkers

Page 6: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 6

● Difficulty in reproducibility unlike GWAS due to differences in platforms

University of Oxford-Oxford e-research centre David Johnson (UOXF)

● Ontologies, semantic web, data collection; curation; representation, software, infrastructure

● WP8: data provenance, compliance and integrity

● Building upon in ISA, biosharing.org, OBI, STATO

● Related projects: bioCaddie, eTriks, Elixir; Excelerate, The NIH BD2K

● Also work with journals, GigaScience, Nature Scientific Data, Research Data Alliance

ISB/SIB: Swiss Institute of Bioinformatics Sven Bergmann (SIB)

● CoLaus Metabolomics Study ● Metabomatching

Uppsala University Ola Spjuth (UU)

● UPPMAX and CARAMBA ● Sci Life Lab ● Systems for sensitive, data translation of

informatics

PhenoMeNal Kick-off meeting Etienne Thevenot (CEA)

● Part of MetaboHub ● Focussed on algorithms and s/w on high

volume multi omics data ● Projects: READNA, BioMargin ● www.workflow4metabolomics.org ● Contribution: connect W4M to other

infrastructures ● Scale-up, automate, develop: VMs, workflows,

machine learning modules, galaxy modules ● Provide use cases (from MetaboHub)

MetaboHub-INRA Partner MetExplore Team Fabien Jourdan (INRA)

● Metabolomics and fluxomics infrastructure in France

● Food toxicology research centre is the main data provider

Page 7: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 7

● www.metexplore.fr ● Relevant projects: Metabolomics data

mapping: available as Web Service, Network analysis and visualisation

● Provide VRE of available tools; visualisation

c. EGI, ELIXIR and EUDAT presentations

Title and Speaker Highlights

EGI & EUDAT & Elixir Steven Newhouse (ELIXIR and EUDAT) Enol Fernández (EGI)

EUDAT ● Goals: collaborative data infrastructure CDI ● www.eudat.eu/services ● EUDAT and EUDAT2020 and participants ● B2Drop: secure and trusted data exchange

service ● B2Share: store, persist, share data ● B2Safe: Ensures data replication, archiving

and preservation ● B2Stage, B2Find ● Use case: replicating data on global scale ● Set of services, more like integrator rather than

service provider ● Free for individual researchers with less data..

(Up to 20GB free) ● Datasets have PID ● Portals have AAI ● Sustainability based on business model?

EGI

● EGI participants ● Enabling global infrastructures ● Distributed, federated storage and compute

facilities ● Open Science Commons project - EGI-

ENGAGE H2020 ● EGI for Phenomenal: as a federator ● Offer expertise on operation, integration,

Page 8: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 8

training, federation ● Can connect to local NGIs ● Provide frameworks to create high level

environments (VRC portals) ● Resource deployment ● Features that could be re-used: single sign-on,

service registry, accounting, service monitoring, information system of available services, VMI catalogue, VMI replication mechanism etc.…

● For ELIXIR EGI provides above and user certificate generation and management service, cloud computing resources; initial tests going on

● EGI provides configured, secure, base VMIs, automatically built using Packer.

● VM image catalogue ● IaaS support is done using OCCI API ● Support and training ● Integration with other e-infrastructures

ELIXIR

● Elixir Compute Platform is WP4 of Excelerate ● Compute platform uses services similar to

what EGI provides ● Defining basic technical use cases: ● AAI, data, storage, compute, infrastructures

etc. ● Goal is to have tools in place, to move around

data with ease and security across network

4. Discussion of the project structure

a. Work packages

Title and Speaker Highlights

WP1-Management ● Discussion of clause in event of financial loss/

Page 9: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 9

Namrata Kale (EMBL-EBI)

bankruptcy of partner

WP2-Sustainability of PhenoMeNal Thomas Hankemeier (UL)

● Sustainability of software/self-sustainable software

WP3-Outreach and Dissemination Ulrich Guenther (UoB)

● Set publication target early- end of 1st year ● Maybe outreach in metabolomics conference

2016

WP4-Interfacing with Biomedical and Electronic European Infrastructures Antonio Rosato (CIRMMP)

● Ensure that major e-infrastructure interact with PhenoMeNal

● Facilitate communication ● Relevant for WP2 and WP3 ● Review existing connections to infrastructures

based on internal survey-1st step ● Gather requirements from other relevant e-

infrastructures

WP5-Operation and Maintenance of PhenoMeNal grid / e-Infrastructure Ola Spjuth (UU)

● Grid/cloud is a bit ambiguous -use “e-infrastructure”. Unclear what middleware stands for

● Testing of components takes time, proof of principle important milestone performance metrics taken seriously

● Interact with Elixir and EGI ● Continuous build system ● Biweekly meeting with WP9 suggested

WP6-PhenoMeNal Virtual Research Community Ken Haug (EMBL-EBI)

● Entry portal for phenomenal ● Early user experience workshop

Page 10: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 10

WP7-Privacy and Ethics Robert Glen (ICL)

● Pick ELSI member from STAB ● Decide stakeholder panel ● Data manager

WP8-Data Provenance, Compliance and Integrity David Johnson (UOXF)

● Conduct hackathons ● Use cases, workflows for data exchange ● Data inter-operation ● ISA as FAIR research object for Elixir

Excelerate ● Close operation with WP9

WP9-Tools, Workflows, Audit and Data Management Steffen Neumann (IPB)

● WP8 & 9 develops the tools, will “chase” down other partners

● Making PhenoMeNal work with other (existing) GWAS infrastructures

● Migrate from proprietary to open-source

b. Tools and workflows

Title and Speaker Highlights

Tools and Workflows Steffen Neumann (IPB)

● DataVMI: interface between users and “the real data”, different privacy requirements

● Looking for keep it simple benchmark ● How easy is to get phenomenal (getting into

EGI will take time) ● HTC/HPC terminology ● Use of amazon cloud (AWS) ● Bioconductor4metabolomics. Bioconductor,

adopt BiocViews? ● Docker images for metabolomics ● Galaxy workflows and licensing ● MATLAB and open source issues ● Docker images in galaxy as standalone

binaries ● Use cases with Galaxy requirements ● Use Galaxy in *our* workflows, but we may

Page 11: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 11

not expose the “designer” view to the users. End users does not need to know what the middleware is

● Early survey to collect building blocks ● Workflows4metabolomics ● Refers VMIs to create ● MetaDB overlap with W4M, get conversation

going ● MassBank VMI (beta now, Steffen) ● Bring data standards ● mzTAB into MetaboAnalyst ● Spectral visualisation VMI ● Find a common workflow we can use as the

first (POC) case. ICL maybe? ● KNIME and licensing ● Use cases for middleware integration useful

in a clinical setting ● Early hands-on meeting with practitioners

early on to map out what workflows are used

Cloud/Grid Workshop Ola Spjuth (UU)

● Need to understand the difference between HPC/HTC

● Virtual machines and Docker containers ● Containers are very suitable for micro

services ● Jenkins for continuous integration ● MOLNS interesting platform to study ● IPhython is very useful ● iRODS for data federation around for some

years and could be used ● HTTP/REST for data transfer ● Docker for tools containment ● How to integrate existing software into the

VRC. We need to form some working groups now. (WP6, WP8 and WP9)

● Handling sensitive data ● Privacy workshop

Software development, ● Jenkins for continuous integration

Page 12: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 12

deployment and test environments Workshop Ken Haug (EMBL-EBI)

● Need for configuration management tools ● Production vs nightly builds ● Use Jenkins to check and build VIM ● Policy document for code migration from

closed source to open environments ● Phenomenal Github organisation ● Downstream dependency libraries restrictive

licenses can pose tricky situation ● Pick good datasets (open) for test cases ● MATLAB could be a separate topic to look

into in detail. Maybe a “MATLAB migration group”. MATLAB precompiled in the short term?

● PhenoMeNal-development mailing lists to discuss technical details of the build processes etc.

● PhenoMeNal-github master repository

Privacy and Ethics Robert Glen (ICL)

● Possible data sets for PhenoMeNal: COMBI-BIO

● Data protection act 1998 ● ELSI - Ethical, Legal and Social Implications

of research ● Get input for ethics from patients ● Ethics workshop ● Keep track of consent on existing datasets ● Purpose of meeting is for us to learn about

ethics and if we need to implement any changes

● Metabolomics data can be anonymised? ● Data provider form made available

5. Project management and outreach

Speaker Highlights

Ken & Namrata (EMBL-EBI)

● Pivotal tracker as suggested tool for project management

Page 13: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 13

● Responsible partner (WP lead), participating partner(s), work packages, delivery month and delivery year are all labelled, and searchable.

● Responsible person name (if not WP lead) has to be tagged with the deliverable, so it is clear who is responsible for that from the start

● Responsible person for the deliverable will be the point of contact for reminders

● Timesheets- daily hours worked against the deliverable to be recorded?

● Meeting and reporting to track the progress ● Record minutes of meeting ● Consortium meetings ● Consortium website: phenomenal-h2020.eu

is the official

6. Used case aspects

Title and Speaker Highlights

NPC Workflow and PhenoMeNal pipelines Jake Pearce Presented by: Tim Ebbels (ICL)

● Introduction to the National Phenome Centre ● Involved in epidemiological scale research

and training of scientists ● NMR & LC-MS ● Datasets produced focussed on human bio

fluids ● 1.5 PB data per year, 60TB per 2000

samples ● NMR and MS data pre-processed ● Primarily untargeted, identify as many as

possible, building database of standards for automatic annotation

● Reannotate data from previous data ● Backwards compatible- phenomenal will

Page 14: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 14

address ● The workflow is not scaled up -PhenoMeNal

will address ● Making statistical analysis reproducible ● ICL LIMS: not easily portable, the sys at

imperial ● Set up international phenome centres ● Process of migrating to medbio system

Metabolomics for Preventive and Precision Medicine Claudio Luchinat (CIRMMP)

● SOPs and NMR metabolomics ● Cancer and other diseases and

metabolomics ● PhenoMeNal will provide informatics ● EXCEMET to setup a proper use case

idea is to integrate metabolomics with genomics

● Multi-omics study - not much correlation can be discovered - because of the nature of the analysis - but the study itself is useful - need to find use cases

Needs of a Metabolomics Lab Thomas Hankemeier (UL)

● Metabolomics facility and platforms in Leiden ● IT requirements ● ISO 17025 requirements ● Different data format from different vendors

are difficult to handle ● Should the PhenoMeNal infrastructure be

ISO 17025 certified? ● Where would we like to be in 3 years time?

Certifiable? PhenoMeNal has to make a choice now as this will influence our methods, processes and technology choices

● Partner with SMEs to satisfy ISO requirements?

Clinical Analysis and Research Applying Mass Spectrometry and Bioinformatics at

● Introduction to CARAMBA ● Exclusive use Thermo Orbitrap High-

Resolution Accurate Mass Spectrometry ● Metabolomics for Alzheimer's and chronic

Page 15: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 15

Akademiska Kim Kultima (UU)

pain ● e-infrastructure challenges ● Clinical needs for CARAMBA and how

PhenoMeNal can be useful ● Building a long term map, compare/ align

samples (over many years)

7. Reviewed plan of work for the first 12 months As a result of the plenary discussion, a list of possible advisors for the Scientific Advisory Board was made. It was proposed that the relevant partners would invite experts to set up the advisory board. A copy of the extended synopsis for the project was also circulated. A rough draft of the future meetings and workshops was also prepared (see Table 1). As a general comment, frequent meetings/hangouts were proposed for effective management of individual work packages and consortium as a whole. It was also agreed to set up a developers’ community or group that would meet early to decide on policies and guidelines. Table 1: Plan for meetings/workshops in year 1

S. No Meeting/Workshop And total cost

When Partner Where Comments

1 Annual stakeholder meetings

Y1 June 2016

EMBL- EBI

Dublin Metabolomics Meeting

2 Privacy workshop

M3 Nov. 2016

ICL ICL Invite experts

3 Staff exchanges & Hackathons

Y1 October / November 2015

EMBL- EBI

EMBL- EBI

Software standards, procedures & Testing

Y1

February / March

UU UU Hands-on continuous integration,

Page 16: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 16

2016 containerization, API design

Y1 Q1 2016 EMBL- EBI + INRA

EBI Integration of Metabolights/ MetExplore visualization

Y1 Q1 2016 CEA with CNRS + INRA + EBI

TBC Galaxy: Workflow management and tool integration

Y1 Q4 Y1 EBI EBI Constructing pipelines with available tools

Y1 Q3/Q4 OXF, IPB, EBI

OXF Data standards

4 Clinical workshop

Y1 May/June 2016

UB+UU Barcelona

Page 17: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 17

Annex 1

PhenoMeNal Kick-Off Meeting Agenda Draft agenda

Time Description

Day 1: 8th September 2015

12:30 - 13:30 Arrival and Lunch (Conference Centre)

13:30 - 14:00 Introduction (Chris) Tour de Table (All)

14:00 - 15:30 Partner presentations. Max 3 slides and 5 minute each!!! ● EMBL-EBI ● ICL ● IPB ● UB ● UL ● CIRMMP ● UoB ● UOXF ● SIB ● UU ● CEA ● INRA

15:15 - 15:45 Coffee & Tea

15:45 - 17:45 EGI & EUDAT & Elixir presentations (20 min each) + 1h discussions

End of day 1

18:30 - late Dinner at the Conference Centre for all

Day 2: 9th September 2015

Page 18: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 18

09:00 - 10:30 Coffee & Tea available outside the room

Work package deliverables and organisation. ● 10 mins max ● Presentation of Deliverables and Milestones,

not Q&A session ● Hiring status

Plan for engaging with other partners committed and otherwise involved in the WP

● WP1 - Management. EMBL-EBI

● WP2 - Sustainability of PhenoMeNal. UL

● WP3 - Outreach and Dissemination. UoB

● WP4 - Interfacing with Biomedical and Electronic European Infrastructures. CIRMMP

● WP5 - Operation and Maintenance of PhenoMeNal grid / e-Infrastructure. UU

● WP6 - PhenoMeNal Virtual Research Community. EMBL-EBI

● WP7 - Privacy and Ethics. ICL

● WP8 - Data Provenance, Compliance and Integrity. UOXF

● WP9 - Tools, Workflows, Audit and Data Management. IPB

10:35 - 11:15 Tools and Workflows Development Workshop & Discussions (ALL) Kicked off by IPB Lightning talk and lead by IPB => What Building Blocks of the workflow will we have, what Platforms are we trying to focus on

11:15 - 12:00 Cloud / Grid Workshop & Discussions (ALL) Kicked off by UU Lightning talk and lead by UU Alignment with other domains

12:15 - 13:30 Photo outside Hinxton Hall

Page 19: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 19

Lunch (Campus Canteen) + Campus walk if weather & time permits

13:30 - 14:15 Software development, deployment and test environments Workshop & Discussions (ALL) Kicked off by Lightning talk and lead by EMBL-EBI

14:15 - 15:00 Privacy & Ethics Workshop & Discussions (ALL) Kicked off by Lightning talk and lead by ICL Note: The Scientific and Technological Advisory Board will appoint one member to act as the PhenoMeNal Ethics Advisor.

15:00 - 15:30 Coffee & Tea

15:30 - 16:30 Project Management and Outreach ● Project Plan Overview (and early deliverables, M1-M12) ● Timesheets, project will be audited!

○ All time recorded against WP (and Deliverable?) ● WP meeting and reporting schedule examples:

○ David, WP8 ○ Ola, WP5 ○ Steffen, WP9

● Consortium Website

○ phenomenal-h2020.eu, phenomenal.bio, phenomenal.clinic

○ The portal to the infrastructure (VRC)

End of day 2

18:00 Bus to Cambridge

19:00 - late Dinner at Queens College Cambridge, in the “Old Hall” - Drinks from 19:00, sit down at 19:30

Day 3: 10th September 2015

Page 20: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 20

09:00 - 10:00 Short talks by practitioners ● Jake Pearce (ICL) ● Claudio Luchinat (CIRMMP) ● Thomas Hankemeier (UL) ● Kim Kultima (UU)

10:00 - 12:30 (10:30 refreshments)

Detailed planning of Year 1 (Goal: Y1 planned and agreed) Plan for future meetings Breakout sessions if required where WPs decide on short term staff exchanges

Other: ● Use cases (clinical, lab-based) for what we hope to

achieve ○ “Favorite” tools used today

● Gathering requirements from Consortium Members as well as External Stakeholder (UX, Personas)

● Assembly of the Scientific Advisory Board

12:30 - 13:30 Lunch (Campus Canteen)

End of meeting

Meal schedule: Refreshments available all day

Tuesday 8th Wednesday 9th Thursday 10th

12:30 - Lunch (Conf. centre) 15:30 - Refreshments 18:00 - Dinner (Conf. centre)

10:30 - Refreshments 12:30 - Lunch (Canteen) 15:00 - Refreshments 19:00 - Dinner (Queens College Cambridge)

10:30 - Refreshments 12:30 - Lunch (Canteen)

Page 21: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 21

Annex 2 List of Participants

No. Name Affiliation

Attendance

8th Sept

9th Sept

10th Sept

1 Sven Bergmann University of Lausanne

✓ ✓ ✓

2 Roger Mallol University of Lausanne

✓ ✓ ✓

3 Rico Rueedi University of Lausanne

✓ ✓ ✓

4 Marta Cascante Universitat de Barcelona

✗ ✓ ✓

5 Silvia Marin Universitat de Barcelona

✓ ✓ ✗

6 Vitaly Selivanov Universitat de Barcelona

✓ ✓ ✓

7 Pedro de Atauri Universitat de Barcelona

✓ ✓ ✓

8 Tim Ebbels Imperial College London

✓ ✓ ✓

9 Robert Glen Imperial College London

✓ ✓ ✓

10 Ibrahim Karaman Imperial College London

✓ ✓ ✗

11 Merlijn van Rijswijk Netherlands Metabolomics Centre

✓ ✓ ✓

12 Thomas Hankemeier Leiden University/NMC

✓ ✓ ✓

13 Michael van Vliet Leiden University ✓ ✓ ✓

14 Steffen Neumann IPB Halle ✓ ✓ RP

15 Daniel Schober IPB Halle ✓ ✓ ✓

Page 22: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 22

16 Pierrick Roger Mele CEA ✓ ✓ ✓

17 Etienne Thevenot CEA ✓ ✓ ✓

18 Maxime Chazalviel INRA ✓ ✓ ✓

19 Fabien Jourdan INRA ✓ ✓ ✓

20 Florence Vinson INRA ✓ ✓ ✓

21 Benjamin Merlet INRA ✓ ✓ ✓

22 Ulrich Guenther University of Birmingham

✓ ✓ ✗

23 Karen Atkins University of Birmingham

✗ ✓ ✓

24 Claudio Luchinat University of Florence and CIRMMP

✓ ✓ ✓

25 Antonio Rosato CIRMMP ✓ ✓ ✓

26 Ola Spjuth Uppsala University ✓ ✓ ✓

27 Payam Emami Khoonsari Uppsala University ✓ ✓ ✓

28 Kim Kultima Uppsala University ✓ ✓ ✓

29 Marco Capuccini Uppsala University ✓ ✓ ✓

30 David Johnson University of Oxford ✓ ✓ ✓

31 Susanna-Assunta Sansone University of Oxford RP

32 Philippe Rocca-Serra

University of Oxford RP

33 Enol Fernández EGI ✓ ✓ ✗

34 Christoph Steinbeck EMBL-EBI ✓ ✓ ✓

35 Namrata Kale EMBL-EBI ✓ ✓ ✓

36 Kenneth Haug EMBL-EBI ✓ ✓ ✓

37 Reza Salek EMBL-EBI ✓ ✓ ✓

38 Kalai Jayaseelan EMBL-EBI ✓ ✓ ✓

39 Pablo Moreno EMBL-EBI ✗ ✓ ✗

40 Steven Newhouse EMBL-EBI ✓ ✗ ✓

Page 23: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 23

41 Gianni Dalla Torre EMBL-EBI ✓ ✓ ✓

42 Dario Vianello EMBL-EBI ✓ ✓ ✓

RP-Remote Participation

Page 24: PhenoMeNal Project - Deliverable D1.3 Minutes of Kick-Off ......PhenoMeNal 3 1. Introduction This report is a deliverable related to the work package 1: Management and deliverable

PhenoMeNal 24

Annex 3 Photos

Photo 1. Photograph of the Consortium