1
|
Soltwedel JR, Haase R. Challenges and opportunities for bioimage analysis core-facilities. J Microsc 2024; 294:338-349. [PMID: 37199456 DOI: 10.1111/jmi.13192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 05/19/2023]
Abstract
Recent advances in microscopy imaging and image analysis motivate more and more institutes worldwide to establish dedicated core-facilities for bioimage analysis. To maximise the benefits research groups at these institutes gain from their core-facilities, they should be established to fit well into their respective environment. In this article, we introduce common collaborator requests and corresponding potential services core-facilities can offer. We also discuss potential competing interests between the targeted missions and implementations of services to guide decision makers and core-facility founders to circumvent common pitfalls.
Collapse
Affiliation(s)
| | - Robert Haase
- DFG Cluster of Excellence 'Physics of Life', TU Dresden, Germany
| |
Collapse
|
2
|
Abstract
There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.
Collapse
|
3
|
Woda A, Hansen J, Thomas Dreifuerst K, Johnson BK, Loomis A, Nolan C, Bradley CS. Debriefing for Meaningful Learning: Implementing a Train-the-Trainer Program for Debriefers. J Contin Educ Nurs 2022; 53:321-327. [PMID: 35858149 DOI: 10.3928/00220124-20220603-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Debriefing for Meaningful Learning (DML) is a method of debriefing grounded in the theory of reflection used following a simulation or clinical learning experience to engage participants in an interactive dialogue aimed at examining and evaluating their thinking and decision-making processes. With increasing adoption of DML worldwide, a sustainable training program for nurse educators is needed. Attending conferences and workshops that provide training is challenging for many nurse educators because of time and cost constraints. One promising solution is the train-the-trainer (TTT) model. In this article, the development and implementation of a TTT model of DML debriefer training, adaptable to both academic and clinical nursing professional development, is described. [J Contin Educ Nurs. 2022;53(7):321-327.].
Collapse
|
4
|
Hollmann S, Kremer A, Baebler Š, Trefois C, Gruden K, Rudnicki WR, Tong W, Gruca A, Bongcam-Rudloff E, Evelo CT, Nechyporenko A, Frohme M, Šafránek D, Regierer B, D'Elia D. The need for standardisation in life science research - an approach to excellence and trust. F1000Res 2020; 9:1398. [PMID: 33604028 PMCID: PMC7863991 DOI: 10.12688/f1000research.27500.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
Abstract
Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation.
Collapse
Affiliation(s)
- Susanne Hollmann
- Faculty of Science, University of Potsdam, Potsdam, Brandenburg, 14476, Germany.,SB Science Management UG (Haftungsbeschränkt), Berlin, Berlin, 12163, Germany
| | - Andreas Kremer
- Information Technology for Translational Medicine S.A. ITTM S.A., Esch-sur-Alzette, Esch, 4354, Luxembourg
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Christophe Trefois
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, 4367, Luxembourg
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Witold R Rudnicki
- Institute of Computer Science, University of Białystok, Białystok, 15-328, Poland
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, Jefferson, USA
| | - Aleksandra Gruca
- Department of Computer Networks and Systems, Silesian University of Technology, Gliwice, 44-100, Poland
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics section, University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands.,Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Alina Nechyporenko
- Department of Systems Engineering, Kharkiv National University of Radio Electronics, Kharkiv Oblast, 61000, Ukraine
| | - Marcus Frohme
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Brandenburg, 15745, Germany
| | | | - Babette Regierer
- SB Science Management UG (Haftungsbeschränkt), Berlin, Berlin, 12163, Germany.,Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Brandenburg, 14979, Germany
| | - Domenica D'Elia
- Institute for Biomedical Technologies, National Research Council, Italy, Bari, 70126, Italy
| |
Collapse
|
5
|
Gurwitz KT, Singh Gaur P, Bellis LJ, Larcombe L, Alloza E, Balint BL, Botzki A, Dimec J, Dominguez del Angel V, Fernandes PL, Korpelainen E, Krause R, Kuzak M, Le Pera L, Leskošek B, Lindvall JM, Marek D, Martinez PA, Muyldermans T, Nygård S, Palagi PM, Peterson H, Psomopoulos F, Spiwok V, van Gelder CWG, Via A, Vidak M, Wibberg D, Morgan SL, Rustici G. A framework to assess the quality and impact of bioinformatics training across ELIXIR. PLoS Comput Biol 2020; 16:e1007976. [PMID: 32702016 PMCID: PMC7377377 DOI: 10.1371/journal.pcbi.1007976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course.
Collapse
Affiliation(s)
- Kim T. Gurwitz
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Louisa J. Bellis
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lee Larcombe
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Eva Alloza
- Barcelona Supercomputing Center (BSC), INB Coordination node, Life Sciences Department, Barcelona, Spain
| | - Balint Laszlo Balint
- University of Debrecen, Medical Faculty, Department of Biochemistry and Molecular Biology, Debrecen, Hungary
| | - Alexander Botzki
- VIB Flanders Institute for Biotechnology, VIB Bioinformatics Core, Ghent, Belgium
| | - Jure Dimec
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics (IBMI), University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mateusz Kuzak
- DTL Dutch Techcentre for Life Sciences, Utrecht, the Netherlands
| | - Loredana Le Pera
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), Bari, Italy
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics (IBMI), University of Ljubljana, Ljubljana, Slovenia
| | - Jessica M. Lindvall
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Diana Marek
- SIB Training, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paula A. Martinez
- VIB Flanders Institute for Biotechnology, VIB Bioinformatics Core, Ghent, Belgium
| | - Tuur Muyldermans
- VIB Flanders Institute for Biotechnology, VIB Bioinformatics Core, Ghent, Belgium
| | - Ståle Nygård
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Patricia M. Palagi
- SIB Training, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Fotis Psomopoulos
- Institute of Applied Biosciences (INAB), Center for Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Vojtech Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | | | - Allegra Via
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), Rome, Italy
| | - Marko Vidak
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics (IBMI), University of Ljubljana, Ljubljana, Slovenia
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Sarah L. Morgan
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
6
|
Carretero-Puche C, García-Martín S, García-Carbonero R, Gómez-López G, Al-Shahrour F. How can bioinformatics contribute to the routine application of personalized precision medicine? EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1758062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Carlos Carretero-Puche
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Laboratorio de Oncología Clínico-Traslacional, Unidad de Investigación en Tumores Digestivos, Instituto de Investigación I+12, Hospital 12 de Octubre, Madrid, Spain
| | | | - Rocío García-Carbonero
- Laboratorio de Oncología Clínico-Traslacional, Unidad de Investigación en Tumores Digestivos, Instituto de Investigación I+12, Hospital 12 de Octubre, Madrid, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| |
Collapse
|
7
|
Tangaro MA, Donvito G, Antonacci M, Chiara M, Mandreoli P, Pesole G, Zambelli F. Laniakea: an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures. Gigascience 2020; 9:giaa033. [PMID: 32252069 PMCID: PMC7136032 DOI: 10.1093/gigascience/giaa033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios where users can be better served by full administrative control over a private Galaxy instance, including, but not limited to, concerns about data privacy, customisation needs, prioritisation of particular job types, tools development, and training activities. In such cases, a cloud-based Galaxy virtual instance represents an alternative that equips the user with complete control over the Galaxy instance itself without the burden of the hardware and software infrastructure involved in running and maintaining a Galaxy server. RESULTS We present Laniakea, a complete software solution to set up a "Galaxy on-demand" platform as a service. Building on the INDIGO-DataCloud software stack, Laniakea can be deployed over common cloud architectures usually supported both by public and private e-infrastructures. The user interacts with a Laniakea-based service through a simple front-end that allows a general setup of a Galaxy instance, and then Laniakea takes care of the automatic deployment of the virtual hardware and the software components. At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance and to the underlying virtual machine (VM). Laniakea features deployment of single-server or cluster-backed Galaxy instances, sharing of reference data across multiple instances, data volume encryption, and support for VM image-based, Docker-based, and Ansible recipe-based Galaxy deployments. A Laniakea-based Galaxy on-demand service, named Laniakea@ReCaS, is currently hosted at the ELIXIR-IT ReCaS cloud facility. CONCLUSIONS Laniakea offers to scientific e-infrastructures a complete and easy-to-use software solution to provide a Galaxy on-demand service to their users. Laniakea-based cloud services will help in making Galaxy more accessible to a broader user base by removing most of the burdens involved in deploying and running a Galaxy service. In turn, this will facilitate the adoption of Galaxy in scenarios where classic public instances do not represent an optimal solution. Finally, the implementation of Laniakea can be easily adapted and expanded to support different services and platforms beyond Galaxy.
Collapse
Affiliation(s)
- Marco Antonio Tangaro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
| | - Giacinto Donvito
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Marica Antonacci
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, Italy
| | - Pietro Mandreoli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Federico Zambelli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, Italy
| |
Collapse
|
8
|
McGrath A, Champ K, Shang CA, van Dam E, Brooksbank C, Morgan SL. From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training. PLoS Comput Biol 2019; 15:e1006923. [PMID: 31246949 PMCID: PMC6597034 DOI: 10.1371/journal.pcbi.1006923] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Demand for training life scientists in bioinformatics skills led to the development of a train-the-trainer collaboration between the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-the-trainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors.
Collapse
Affiliation(s)
| | | | | | - Ellen van Dam
- Bioplatforms Australia, Sydney, New South Wales, Australia
| | - Cath Brooksbank
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah L. Morgan
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| |
Collapse
|
9
|
Zhan YA, Wray CG, Namburi S, Glantz ST, Laubenbacher R, Chuang JH. Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors. PLoS Comput Biol 2019; 15:e1007026. [PMID: 31194735 PMCID: PMC6563947 DOI: 10.1371/journal.pcbi.1007026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bioinformatics has become an indispensable part of life science over the past 2 decades. However, bioinformatics education is not well integrated at the undergraduate level, especially in liberal arts colleges and regional universities in the United States. One significant obstacle pointed out by the Network for Integrating Bioinformatics into Life Sciences Education is the lack of faculty in the bioinformatics area. Most current life science professors did not acquire bioinformatics analysis skills during their own training. Consequently, a great number of undergraduate and graduate students do not get the chance to learn bioinformatics or computational biology skills within a structured curriculum during their education. To address this gap, we developed a module-based, week-long short course to train small college and regional university professors with essential bioinformatics skills. The bioinformatics modules were built to be adapted by the professor-trainees afterward and used in their own classes. All the course materials can be accessed at https://github.com/TheJacksonLaboratory/JAXBD2K-ShortCourse.
Collapse
Affiliation(s)
- Yingqian Ada Zhan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Charles Gregory Wray
- Genomic Education, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Spencer T. Glantz
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Reinhard Laubenbacher
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Center for Quantitative Medicine, UConn Health, Farmington, Connecticut, United States of America
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, United States of America
| |
Collapse
|
10
|
Guien C, Blandin G, Lahaut P, Sanson B, Nehal K, Rabarimeriarijaona S, Bernard R, Lévy N, Sacconi S, Béroud C. The French National Registry of patients with Facioscapulohumeral muscular dystrophy. Orphanet J Rare Dis 2018; 13:218. [PMID: 30514324 PMCID: PMC6280451 DOI: 10.1186/s13023-018-0960-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/22/2018] [Indexed: 12/19/2022] Open
Abstract
Background Facioscapulohumeral muscular dystrophy is a rare inherited neuromuscular disease with an estimated prevalence of 1/20,000 and France therefore harbors about 3000 FSHD patients. With research progress and the development of targeted therapies, patients’ identification through registries can facilitate and improve recruitment in clinical trials and studies. Results The French National Registry of FSHD patients was designed as a mixed model registry involving both patients and physicians, through self-report and clinical evaluation questionnaires respectively, to collect molecular and clinical data. Because of the limited number of patients, data quality is a major goal of the registry and various automatic data control features have been implemented in the bioinformatics system. In parallel, data are manually validated by molecular and clinical curators. Since its creation in 2013, data from 638 FSHD patients have been collected, representing about 21% of the French FSHD population. The mixed model strategy allowed to collect 59.1% of data from both patients and clinicians; 26 and 14.9% from respectively patients and clinicians only. With the identification of the FSHD1 and FSHD2 forms, specific questionnaires have been designed. Though FSHD2 patients are progressively included, FSHD1 patients still account for the majority (94.9%). The registry is compatible with the FAIR principles as data are Findable, Accessible and Interoperable. We thus used molecular standards and standardized clinical terms used by the FILNEMUS French network of reference centers for the diagnosis and follow-up of patients suffering from a rare neuromuscular disease. The implemented clinical terms mostly map to dictionaries and terminology systems such as SNOMED-CT (75% of terms), CTV3 (61.7%) and NCIt (53.3%). Because of the sensitive nature of data, they are not directly reusable and can only be accessed as aggregated data after evaluation and approval by the registry oversight committee. Conclusions The French National Registry of FSHD patients belongs to a national effort to develop databases, which should now interact with other initiatives to build a European and/or an international FSHD virtual registry for the benefits of patients. It is accessible at www.fshd.fr and various useful information, links, and documents, including a video, are available for patients and professionals. Electronic supplementary material The online version of this article (10.1186/s13023-018-0960-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Céline Guien
- Aix Marseille Univ, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | - Gaëlle Blandin
- Aix Marseille Univ, INSERM, MMG, Bioinformatics & Genetics, Marseille, France
| | - Pauline Lahaut
- Université Côte d'Azur, Service Système Nerveux Périphérique, Muscle et SLA, Centre Hospitalier Universitaire de Nice, Nice, France
| | - Benoît Sanson
- Université Côte d'Azur, Service Système Nerveux Périphérique, Muscle et SLA, Centre Hospitalier Universitaire de Nice, Nice, France
| | - Katia Nehal
- APHM, Hôpital Timone Enfants, Laboratoire de Génétique Moléculaire, Marseille, France
| | | | - Rafaëlle Bernard
- APHM, Hôpital Timone Enfants, Laboratoire de Génétique Moléculaire, Marseille, France
| | - Nicolas Lévy
- Aix Marseille Univ, INSERM, MMG, Bioinformatics & Genetics, Marseille, France.,APHM, Hôpital Timone Enfants, Laboratoire de Génétique Moléculaire, Marseille, France
| | - Sabrina Sacconi
- Université Côte d'Azur, Service Système Nerveux Périphérique, Muscle et SLA, Centre Hospitalier Universitaire de Nice, Nice, France.,Institute for Research on Cancer and Aging of Nice (IRCAN), INSERM U1081, CNRS UMR 7284, Université Côte d'Azur (UCA), Faculté de Médecine, Nice, France
| | - Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Bioinformatics & Genetics, Marseille, France. .,APHM, Hôpital Timone Enfants, Laboratoire de Génétique Moléculaire, Marseille, France.
| |
Collapse
|
11
|
Morgan SL, Palagi PM, Fernandes PL, Koperlainen E, Dimec J, Marek D, Larcombe L, Rustici G, Attwood TK, Via A. The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training. F1000Res 2017; 6:ELIXIR-1557. [PMID: 28928938 PMCID: PMC5596339 DOI: 10.12688/f1000research.12332.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
One of the main goals of the ELIXIR-EXCELERATE project from the European Union's Horizon 2020 programme is to support a pan-European training programme to increase bioinformatics capacity and competency across ELIXIR Nodes. To this end, a Train-the-Trainer (TtT) programme has been developed by the TtT subtask of EXCELERATE's Training Platform, to try to expose bioinformatics instructors to aspects of pedagogy and evidence-based learning principles, to help them better design, develop and deliver high-quality training in future. As a first step towards such a programme, an ELIXIR-EXCELERATE TtT (EE-TtT) pilot was developed, drawing on existing 'instructor training' models, using input both from experienced instructors and from experts in bioinformatics, the cognitive sciences and educational psychology. This manuscript describes the process of defining the pilot programme, illustrates its goals, structure and contents, and discusses its outcomes. From Jan 2016 to Jan 2017, we carried out seven pilot EE-TtT courses (training more than sixty new instructors), collaboratively drafted the training materials, and started establishing a network of trainers and instructors within the ELIXIR community. The EE-TtT pilot represents an essential step towards the development of a sustainable and scalable ELIXIR TtT programme. Indeed, the lessons learned from the pilot, the experience gained, the materials developed, and the analysis of the feedback collected throughout the seven pilot courses have both positioned us to consolidate the programme in the coming years, and contributed to the development of an enthusiastic and expanding ELIXIR community of instructors and trainers.
Collapse
Affiliation(s)
- Sarah L Morgan
- EMBL-European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD , UK
| | - Patricia M Palagi
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Genopode, 1015 Lausanne, Switzerland
| | - Pedro L Fernandes
- Instituto Gulbenkian de Ciência, R. Q.ta Grande 6, 2780-156 Oeiras, Portugal
| | - Eija Koperlainen
- CSC - IT Center for Science, Keilaranta 14, 02150 Espoo, Finland
| | - Jure Dimec
- Faculty of Medicine , Institute for Biostatistics and Medical Informatics, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Diana Marek
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Genopode, 1015 Lausanne, Switzerland
| | - Lee Larcombe
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Gabriella Rustici
- Department of Genetics , University of Cambridge, Downing Street, Cambridge , CB2 3EH, UK
| | - Teresa K Attwood
- School of Computer Science, The University of Manchester, Oxford Road, Manchester , M13 9PL, UK
| | - Allegra Via
- National Research Council of Italy (CNR), Institute of Molecular Biology and Pathology (IBPM) c/o Department of Biochemical Sciences , Sapienza University, 00185 Rome, Italy
| |
Collapse
|