D8.3 Interim Report on Training Activities

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HEALTH-F4-2007-200754 www.gen2phen.org
D8.3 Interim Report on Training Activities
WP8 – GEN2PHEN Knowledge Centre
V1.3 Final
Lead beneficiary: ULEIC Date: 12/08/2010 Nature: Report Dissemination level: Public
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
Final
2/10
TABLE OF CONTENTS DOCUMENT INFORMATION............................................................................................. 3 DOCUMENT HISTORY ........................................................................................................ 3 DEFINITIONS......................................................................................................................... 4 INTRODUCTION ................................................................................................................... 5 1. THE NATURE OF TRAINING ACTIVITIES WITHIN GEN2PHEN.......................................... 5 1.1 The training activities.................................................................................................. 5 1.2 The training materials ................................................................................................. 5 1.3 Training materials on the Knowledge Centre ............................................................. 6 1.4 Addressing Internal Training Needs ........................................................................... 6 2. CATALOGUE OF TRAINING ACTIVITIES AND MATERIALS.................................................. 7 2.1 Annex 1: EBI Workshops............................................................................................. 7 2.2 Annex 2: LRG Presentations in Workshops ................................................................ 7 2.3 Annex 3: Miscellaneous Workshops ............................................................................ 7 2.4 Annex 4: Online Resources.......................................................................................... 7 2.5 Annex 5: Materials from Other Deliverables .............................................................. 7 ANNEXES ................................................................................................................................ 8 ANNEX 1 – EBI WORKSHOPS (2010) ...................................................................................... 8 ANNEX 2 – LRG PRESENTATIONS IN WORKSHOPS ................................................................. 9 ANNEX 3 – MISCELLANEOUS WORKSHOPS ............................................................................. 9 ANNEX 4 – ONLINE RESOURCES ........................................................................................... 10 ANNEX 5 – MATERIALS FROM OTHER DELIVERABLES ........................................................... 10
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
Final
3/10
Document Information
Grant Agreement HEALTH-F4-2007-200754 Number Full title Project URL Acronym GEN2PHEN
Genotype-To-Phenotype Databases: A Holistic Solution http://www.gen2phen.org
EU Project officer Dr. Iiro Eerola (Iiro.EEROLA@ec.europa.eu) Deliverable Number 8.3 Title Interim Report on Training Activities Title GEN2PHEN Knowledge Centre Month 30 Actual final Other 12/08/2010
Work package Number 8 Delivery date Status Nature Dissemination Level Report Public Contractual
Version 1.3 Prototype Confidential
Authors (Partner) Raymond Dalgleish (ULEIC) Responsible Author Raymond Dalgleish Partner ULEIC Email raymond.dalgleish@le.ac.uk Phone 00 44 (0)116 252 3425
Document History
Name Date Version Description
Raymond Dalgleish Raymond Dalgleish, Adam Webb, Jacopo Celli Raymond Dalgleish Raymond Dalgleish
22/06/2010 02/07/2010 05/08/2010 12/08/10
1.0 1.1 1.2 1.3
First draft First revision Second revision Final version
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
Final
4/10
Definitions
Partners of the GEN2PHEN Consortium are referred to herein according to the following codes: ULEIC – University of Leicester (UK) – Coordinator EMBL – European Molecular Biology Laboratory (Germany) – Beneficiary FIMIM – Fundació IMIM (Spain) – Beneficiary LUMC – Leiden University Medical Center (Netherlands) – Beneficiary INSERM – Institut National de la Santé et de la Recherche Médicale (France) – Beneficiary KI – Karolinska Institutet (Sweden) – Beneficiary FORTH – Foundation for Research and Tecnology Hellas (Greece) – Beneficiary CEA – Comissariat à l’Energie Atomique (France) – Beneficiary EMC – Erasmus Universitair Medisch Centrum Rotterdam (Netherlands) – Beneficiary UH.FGC – Helsingin Yliopisto (Finland) – Beneficiary UAVR – Universidade de Aveiro (Portugal) – Beneficiary UWC – University of the Western Cape (South Africa) – Beneficiary CSIR – Council of Scientific and Industrial Research (India) – Beneficiary SIB – Swiss Institute of Bioinformatics (Switzerland) – Beneficiary UNIMAN – The University of Manchester (UK) – Beneficiary BIOBASE – BioBase GmbH. (Germany) – Beneficiary deCODE – Islensk Erfoagreining EH (Iceland) – Beneficiary PHENO – Phenosystems S.A. (Belgium) – Beneficiary BCP – Biocomputing Platforms Ltd. Oy (Finland) – Beneficiary UPAT – University of Patras (Greece) – Beneficiary Grant Agreement: The agreement signed between the beneficiaries and the European Commission for the undertaking of the GEN2PHEN project (HEALTH-200754). Project: The sum of all activities carried out in the framework of the Grant Agreement by the Consortium. Work plan: Schedule of tasks, deliverables, efforts, dates and responsibilities corresponding to the work to be carried out for the GEN2PHEN project, as specified in Annex I to the Grant Agreement. Consortium: The GEN2PHEN Consortium, conformed by the above-mentioned legal entities. Consortium agreement: agreement concluded amongst GEN2PHEN participants for the implementation of the Grant Agreement. Such an agreement shall not affect the parties’ obligations to the Community and/or to one another arising from the Grant Agreement.
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
Final
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INTRODUCTION
1. The nature of training activities within GEN2PHEN
The GEN2PHEN project aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality. The project is establishing the technological building-blocks needed for the evolution of today’s diverse G2P databases into a future seamless G2P biomedical knowledge environment. The building blocks that are being developed are varied in nature and their full potential will only be fully realised if they are first brought to the attention of workers in the field and, secondly, are supported by appropriate training activities and materials. The Training Activities component of the GEN2PHEN project aims to address these dual demands by advertising activities through presentations at meetings and conferences and by providing specific training. Training might be delivered in several formats. This report will describe the training actions that have been carried out at this halfway point of the project. It will document the activities’ scope and the audiences reached. More difficult at this stage is any valid assessment of the success of these activities other than by way of anecdotal evidence. Processes will need to be developed during the second half of the project to provide objective assessment of our training activities. Although GEN2PHEN has dissemination activities under WP9, it is important to acknowledge that similar activities are a vital component of WP8. The difference is that WP8 activities aim to “advertise” key technologies in the context of scientific workshops, meetings, training sessions, etc. where the emphasis is on the application of such technologies.
1.1 The training activities
A key aspect of training is the presentation of GEN2PHEN technologies at workshops. Although the majority of these have been open to the public, some have been for partners or for invited participants who could provide expert opinion or guidance. Examples of workshops in which GEN2PHEN partners have participated are listed in Annexes 1, 2 and 3.
1.2 The training materials
Training materials may take various forms. Written materials may be in the form of “manuals” or “tutorials” with the former providing a guide to the basic operation of a piece of software or algorithm. By way of contrast, tutorials take a more “hands-on” approach by leading the user through a particular concept in some depth or by providing guidance on some more esoteric aspect of a particular software package. Examples of both types of written material can be found in Annex 4.
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
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An additional form of training material is the “screencast” which takes the form of an edited and annotated recording of the actions seen on a computer screen when using a particular software package. Screencasts also allow the simultaneous recording of a spoken commentary. As yet, screencasts have not yet been widely exploited as a delivery medium for external training, but have been mainly used internally to discuss aspects of software development. An example of this sort of use is listed in Annex 4 along with a screencast depicting the installation of the LOVD LSDB system.
1.3 Training materials on the Knowledge Centre
The Knowledge Centre already provides the facility to store and categorise information, but no specific section yet exists for Training activities. A new section has been created (http://www.gen2phen.org/training) and will be developed throughout the remaining 30 months of the project to provide a comprehensive source of training materials for partners and for the public. As with most Knowledge Centre content, there are subscriptions (e.g. RSS) and feedback options (e.g. comments, ratings).
1.4 Addressing Internal Training Needs
Deliverable 8.1 (Procedures to Establish Internal Training Needs) identified training needs and opportunities within GEN2PHEN at the end of 2008. The present deliverable is intended to report all training activities that have been undertaken in the first 30 months of the project. However it is useful to review how many of these activities have addressed needs identified in D8.1. For the sake of brevity, the table lists the training needs using the broad categories used in that previous deliverable. Deliverable 8.1 Internal Training Needs Project Management & Related Skills Generic Computing Skills Applied Computing Skills Data Modelling and Ontologies Molecular Genetic Technologies Other Skills including Ethics Training Provided ? ?
?
It is important to recognise that D8.1 demonstrated that most of the perceived training needs were actually addressable by corresponding offers of training by partners in the project. Any perceived failure to actually address the training needs may in fact be due to failure to report the provision of training, especially if it was carried out on a one-toone basis. This is especially true of instances where personnel from one partner centre have spent collaborative time in another centre. This is reported in the monthly record of GEN2PHEN activities, but may not be recorded specifically as a training activity. Additionally, some of the perceived needs in D8.1 might have been addressed by training provided other than by GEN2PHEN. It may be prudent to re-assess the perceived internal training needs before setting training priorities for the second half of the project as such needs have almost certainly changed in the last 18 months. In addition, during the remaining 30 months of the project, more systematic recording of all training activities will be implemented.
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
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2.
Catalogue of training activities and materials
2.1 Annex 1: EBI Workshops
This annex contains a comprehensive list of workshops organised by EBI at which aspects of the GEN2PHEN project standards and software have been included in the context of how these might be usefully adopted by the participants into their own activities. EBI has delivered such workshops through the entire first 30 months of this project. For the sake of brevity, only the workshops presented in 2010 are included.
2.2 Annex 2: LRG Presentations in Workshops
The Locus Reference Genomic (LRG) reference sequence format for LSDB curation has sparked considerable interest form many quarters of the community including one vendor of commercial software. The LRG format has been actively promoted by EBI in its general workshops, but there has also been specific promotion in workshops focused on the specific tasks of variant reporting and database curation.
2.3 Annex 3: Miscellaneous Workshops
There are a number of workshops organised by GEN2PHEN that have taken place during the first 30 months of the project. These have been diverse in nature, reflecting the broad range of activities within the project.
2.4 Annex 4: Online Resources
Several resources have been created to meet explicit training needs. The document on data submission to an LOVD LSDB was originally written for a particular database installation, but the core document is available for modification to suit other similar needs. No material in video format has yet been developed for specific needs. A link is provided to an example video that was created to facilitate discussion of a bug in LOVD. This provides a guide to the type of materials that will be developed during the remaining 30 months of the project. The Knowledge Centre will require some modifications to support the display of video directly within its pages.
2.5 Annex 5: Materials from Other Deliverables
Annex 5 lists training materials produced for other deliverables.
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
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ANNEXES
Annex 1 – EBI Workshops (2010)
Date  19‐20 Jan  25‐27 Jan  26 Jan  3‐4 Feb  11 Feb  11‐12 Feb  16‐18 Feb  22‐26 Feb  1‐2 Mar  3‐5 Mar  4 Mar  8‐12 Mar  9‐12 Mar  13 Apr  15‐16 Apr  15‐16 Apr  19 Apr  20 Apr  21 Apr  20‐21 Apr  21‐22 Apr  23 Apr  22‐23 Apr  26‐27 Apr  27‐28 Apr  29 Apr  29‐30 Apr  28‐30 Apr  29‐30 Apr  5‐6 May  Host Organisation/Institution  EBI / City of Hope  Moroccan Society of Bioinformatics  Institute of Genetics, School of Biology,  University of Nottingham  EBI / University of Aberdeen  NHS, Western General Hospital  University of Cambridge  EBI / Jozef Stefan Institute and University of  Ljubljana  EBI / Programmatic Access to Biological  Databases (Perl)  EBI / ITSEM  EBI / UNAM  EBI / Open Day  EBI / CIBNOR  Wellcome Trust / Instituto de Higiene  Walter and Eliza Hall Institute of Medical  Research  The University of Adelaide  Molecular Medicine Postgraduate School,  Erasmus Medical Center  VIB Flanders Interuniversity Institute of  Biotechnology  VIB Flanders Interuniversity Institute of  Biotechnology  Hubrecht Laboratory  EBI / Dana‐Farber Cancer Institute  The University of New South Wales  The University of New South Wales  EBI / Harvard School of Public Health  EBI / Northwestern University  The University of Queensland / Griffith  University  The University of Queensland / Griffith  University  EBI / University of Pennsylvania  University of Cambridge  The Australian National University  EMBL  Location  Duarte, CA, US  Tangier, MA  Nottingham, UK  Aberdeen, UK  Edinburgh, UK  Cambridge, UK  Ljubljana, SI  Hinxton, UK  Mexico City, MX  Mexico City, MX  Hinxton, UK  La Paz, Baja California, MX  Montevideo, UY  Parkville, AU  Adelaide, AU  Rotterdam, NL  Leuven, BE  Ghent, BE  Utrecht, NL  Boston, MA, US  Sydney, AU  Sydney, AU  Boston, MA, US  Chicago, IL, US  Brisbane, AU  Brisbane, AU  Philadelphia, PA, US  Cambridge, UK  Canberra, AU  Heidelberg, DE 
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
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6 May 
10‐12  May  11 May  27‐28  May  2‐4 Jun  10 Jun 
Bioinformatics for Molecular Geneticists and  Cytogeneticists / National Genetics Reference  Lab  Wellcome Trust  EBI  University of Cambridge  EBI  Gothenburg University 
Manchester, UK 
Hinxton, UK  Edinburgh, UK  Cambridge, UK  Prague, CZ  Gothenburg, SE 
Annex 2 – LRG Presentations in Workshops
Date  24 Apr 2009  13 Jun 2010  28 Jun 2010  Workshop Description  UK Clinical Molecular Genetics Society Training Day  European Society of Human Genetics Conference 2010  European Molecular Genetics Quality Network (EMQN)  Workshop: Best Practice in Diagnostics and Reporting in  Osteogenesis Imperfecta  Location  Birmingham, UK  Gothenburg, SE  Amsterdam, NL 
Annex 3 – Miscellaneous Workshops
Date  Apr 2008  Apr 2008  Jul 2008  Nov 2008  Jan 2009  Mar 2009  Apr 2009  May 2009  May 2009  Jul 2009  Sep 2009  Mar 2010  Workshop Description  UHTS Sequencing Standards Workshop  MIBBI Workshop on Standards for the Biomedical Domain  Wellcome Trust Workshop on Ethics in GWAS  Workshop on Coordinating Activities Related to Bio‐banking  (Samples and Databases at EU Level)  2nd GEN2PHEN Domain Modelling Workshop  Workshop on the Status of Genetic Information in Society  Workshop on Building LSDBs for Genes Involved in Congenital  Muscular Dystrophies  Phenotype modelling workshop.  Identifying Researchers on the Biomedical Web (IRBW2009).  Workshop: “L'information génétique est‐elle particulière?”  RNA splicing and genetic diseases ‐ Prediction Tools Workshop  Modelling Pathogenicity Workshop  Location  Berkeley, US  Cambridge, UK  London, UK  Brussels, BE  Helsinki, FI  Toulouse, FR  Newcastle, UK  Geneva, CH  Toronto, CA  Toulouse, FR  Montpellier, FR  Manchester, UK 
© Copyright 2010 GEN2PHEN Consortium
Interim Report on Training Activities
WP8: GEN2PHEN Knowledge Centre
HEALTH-200754
Author(s): Raymond Dalgleish (ULEIC)
Security: PU Version: v1.1 –
Final
10/10
Annex 4 – Online Resources
Resource Description  HGVbaseG2P help documentation  LOVD LSDB‐in‐a‐box documentation  Data submission guide for LOVD OI and  EDS LSDBs  Guide to adding a custom logo to LOVD  Mutalyzer sequence variation  nomenclature checker demonstration  MOLGENIS 3.3 Training Guide  Screencast (with commentary) to  illustrate the possibilities of screencasts  as a training delivery medium  Screencast (without commentary)  illustrating how to install LOVD  URL  http://www.hgvbaseg2p.org/info/help http://www.lovd.nl/2.0/docs/index.php http://www.gen2phen.org/document/submitting‐ mutation‐data‐oi‐and‐eds‐database‐v13 http://www.gen2phen.org/document/adding‐ custom‐logo‐lovd‐v10 http://www.humgen.nl/mutalyzer_exercise.html http://www.gen2phen.org/document/molgenis‐ training https://oi.gene.le.ac.uk/video/LOVD2.swf
http://www.lovd.nl/2.0/screenshots.php
Annex 5 – Materials from other deliverables
Other relevant training materials have already been presented as appendices to deliverables or as entire deliverables for other work packages. Rather than re-submit these materials, they are available from the Knowledge Centre Deliverables page (http://www.gen2phen.org/deliverables).
Deliverable  D3.1  D3.2  D3.2  D3.5  D3.6  D3.7  Appendix Number or Document Name  Appendix 2  Appendix 2  Appendix 3  Appendix 1  Appendix 1  Derivation and Specification of Exchange Format 
© Copyright 2010 GEN2PHEN Consortium