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AllBio: Open Science & Reproducibility Best Practice Workshop

Date: Monday 15 to Wednesday 17 September 2014

Scientific Organisers:

  • Vicky Schneider, The Genome Analysis Centre (TGAC), UK
  • Robert Davey, The Genome Analysis Centre (TGAC), UK
  • Richard Smith-Unna, University of Cambridge, UK

Advisory Committee

 

  • Vicky Schneider, The Genome Analysis Centre (TGAC), UK
  • Robert Davey, The Genome Analysis Centre (TGAC), UK
  • Richard Smith-Unna, University of Cambridge, UK
  • Erik Bongcam-Rudloff, Swedish University of Agricultural Sciences , Sweden
  • Terri Attwood, University of Manchester, UK

 

Event Organiser:

  • Matt Drew, The Genome Analysis Centre (TGAC), UK

Venue: The Genome Analysis Centre

Participation: By invitation only

 

About

Under the auspices of AllBio, this workshop will gather together both researchers and non-researchers that have been working within different life science fields but who share one common interest: open science and reproducibility! AllBio coordinates the efforts to transfer and adapt those technologies initially developed to study the human genome to other fields such as microbial, plant, and livestock bioinformatics. Openness not only exists in terms of publications and data, but can be applied to the research process itself. More than ever, given the magnitude of data the ability to adopt best practice in workflows, standards, tools for storing and sharing the actual data, as well as its analysis is key to making progress in science and discovery.

Researchers need to have mechanisms and tools to share methods, data, preliminary results, workflows, annotations protocols etc. in a traceable and identifiable manner. The era of cyber infrastructure brings great opportunities for sharing and enhancing collaboration.

This workshop will concentrate on the creation of 3 case studies, inspired by the projects submitted in AllBio, where participants will work there and then to create a workflow, adopt standards and tools as well as to develop list of skills and outline future training which will address how to ensure that future researchers can also adopt these.

The final agenda will be defined together with participants as will the key outcomes.

PROGRAMME DAY 1 - 15th September 2014
Time Topic Lead
12:00 - 13:00 Lunch and Registration
13:00 - 14:30 Welcome and getting to know each other - Flash presentations V.Schneider
14:30 - 15:00 Coffee Break
15:00 - 17:00

Standards: challenges, defining a common view on why we need standards.

Group discussions in 3 groups: visualisation, software interoperability and formats

R.Davey

L.Lahti

17:00 - 17:30 Coffee Break
17:30 - 18:30 Group presentations and wrap up V.Schneider
PROGRAMME DAY 2 - 16th September 2014
Time Topic Lead
09:00 - 09:30 Morning Coffee
09:30 - 10:00 Recap and any new ideas/thoughts V.Schneider
10:00 - 12:00

Discussion and presentation in 2 groups:

Coders metadata software

Non-coders metadata for storing data and publishing

R.Smith-Unna

D.MacLean

M.Markie

12:00 - 13:30 Lunch and easy to use tooling for linking and referencing research objects
13:30 - 15:00 Open peer review and publishing N.Attar
15:00 - 15:15 Coffee Break
15:15 - 17:15

Applying discussions to case studies

Creating a roadmap (data, datasets, publications, protocols, tools, databases and pipelines

V.Schneider

C.Scott

17:15 - 17:30 Coffee Break
17:30 - 18:30 Group discussions: major challenges, doubts and robust aspects V.Schneider
PROGRAMME DAY 3 - 17th September 2014
Time Topic Lead
09:00 - 09:30 Morning Coffee
09:30 - 12:00 What is the roadmap for Open Science in the standard research workflow based on reproducibility

V.Schneider

R.Davey

R.Smith-Unna

12:00 - 13:00 Lunch
13:00 - 15:00 The Plan: how can we do it? Where and how we collaborate? Who does what and by when?

V.Schneider

R.Davey

R.Smith-Unna

15:00 - 15:30 Wrap up and farewell V.Schneider


Participants

Vicky

Schneider

TGAC

@MVickySchneider

Robert

Davey

TGAC

@froggleston

Richard

Smith-Unna

University of Cambridge

@blahah404

Konrad

Förstner

University of Würzburg

@konradfoerstner

Jean-Karim

Heriche

EMBL

-

Holger

Dinkel

EMBL

-

Neil

Chue Hong

Software Sustainability Institute

@npch

Michael

Markie

F1000

@MMMarksman

Camille

Scott

Michigan State University

@camille_codon

Jenny

Molloy

OKFN

@jenny_malloy

Dan

Bolser

EMBL-EBI

@danbolser

Terri

Attwood

University of Manchester

-

Leo

Lahti

Open Knowledge Foundation, Finland

@antagomir

Ivo

Grigorov

DTU

@OAforClimate

Bruno

Vieira

QMUL

@bmpvieira

Dan

MacLean

The Sainsbury Laboratory

@danmaclean

Milos

Tanurdzic

UQ

Luis

Pedro Coelho

EMBL

@luispedrocoelho

Jelena

Aleksik

University of Cambridge

-

Catherine

Shang

Bioplatforms

-

Martin

Dahlö

Uppsala University

-

Naomi

Attar

BioMed Central

@naomiattar

 

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