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1. Systems Biology in ELIXIR: modelling in the spotlight [version 2; peer review: 1 approved, 2 approved with reservations]

Author

Katharina F. Heil, Anze Zupanic, Chris T. Evelo, Carole Goble, Kristel Van Steen, Tadeja Rezen, Hans V Westerhoff, Rahuman S. Malik Sheriff, Maria Suarez Diez, Henning Hermjakob, Marco Pagni, Damjana Rozman, Barbara Szomolay, Miguel Rocha, Jasper Koehorst, Alexey Kolodkin, Victoria Dominguez Del Angel, David Šafránek, Dirk Fey, Ilja Arts, Rui Benfeitas, Vitor Martins dos Santos, Mihail Anton, Marek Ostaszewski, Ulrike Wittig, John M. Hancock, Brane Leskošek, Katherine Wolstencroft, Martin Golebiewski, Wolfgang Müller, Polonca Ferk, Kristina Gruden, William T. Scott, Elena Domínguez-Romero, Martina Kutmon, Maria I. Klapa, Sébastien Moretti, and Pascal Kahlem

Subjects
Systems Biology, Systems Medicine, ELIXIR Communities, Biomolecular Models, Network Biology, FAIR, eng, Medicine, Science
Abstract

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR’s future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.

Published
2024
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2. Systems Biology in ELIXIR: modelling in the spotlight [version 1; peer review: 1 approved, 2 approved with reservations]

Author

Katharina F. Heil, Anze Zupanic, Chris T. Evelo, Carole Goble, Kristel Van Steen, Tadeja Rezen, Hans V Westerhoff, Rahuman S. Malik Sheriff, Maria Suarez Diez, Henning Hermjakob, Marco Pagni, Damjana Rozman, Barbara Szomolay, Miguel Rocha, Jasper Koehorst, Alexey Kolodkin, Victoria Dominguez Del Angel, David Šafránek, Dirk Fey, Ilja Arts, Rui Benfeitas, Vitor Martins dos Santos, Mihail Anton, Marek Ostaszewski, Ulrike Wittig, John M. Hancock, Brane Leskošek, Katherine Wolstencroft, Martin Golebiewski, Wolfgang Müller, Polonca Ferk, Kristina Gruden, Martina Kutmon, Maria I. Klapa, Sébastien Moretti, and Pascal Kahlem

Subjects
Systems Biology, Systems Medicine, ELIXIR Communities, Biomolecular Models, Network Biology, FAIR, eng, Medicine, Science
Abstract

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR’s future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.

Published
2022
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4. Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.

Author

Benjamin Moore, Patricia Carvajal-López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L Morgan, Guilherme Oliveira, Verena Ras, Alejandro Reyes, Javier De Las Rivas, and Nicola Mulder

Subjects
Biology (General), QH301-705.5
Published
2021
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5. Challenges and Considerations for Delivering Bioinformatics Training in LMICs: Perspectives From Pan-African and Latin American Bioinformatics Networks

Author

Verena Ras, Patricia Carvajal-López, Piraveen Gopalasingam, Alice Matimba, Paballo Abel Chauke, Nicola Mulder, Fatma Guerfali, Victoria Dominguez Del Angel, Alejandro Reyes, Guilherme Oliveira, Javier De Las Rivas, and Marco Cristancho

Subjects
training, low to middle income countries, best practices, Africa, Latin America, Education (General), L7-991
Published
2021
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6. The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved]

Author

David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltran, Salvador Capella-Gutierrez, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Joaquin Dopazo, Laura I. Furlong, Bo Gao, Leyla Garcia, Dietlind Gerloff, Ivo Gut, Attila Gyenesei, Nina Habermann, John M. Hancock, Marc Hanauer, Eivind Hovig, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer, Steve Laurie, Brane Leskošek, David Lloyd, Tomas Marques-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz, Ana Rath, Pubudu Samarakoon, Ferran Sanz, Gary Saunders, Daoud Sie, Morris A. Swertz, Kirill Tsukanov, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra, and Christophe Béroud

Subjects
Medicine, Science
Abstract

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

Published
2020
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7. A framework to assess the quality and impact of bioinformatics training across ELIXIR.

Author

Kim T Gurwitz, Prakash Singh Gaur, Louisa J Bellis, Lee Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez Del Angel, Pedro L Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera, Brane Leskošek, Jessica M Lindvall, Diana Marek, Paula A Martinez, Tuur Muyldermans, Ståle Nygård, Patricia M Palagi, Hedi Peterson, Fotis Psomopoulos, Vojtech Spiwok, Celia W G van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L Morgan, and Gabriella Rustici

Subjects
Biology (General), QH301-705.5
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.

Published
2020
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8. Ten simple rules for making training materials FAIR.

Author

Leyla Garcia, Bérénice Batut, Melissa L Burke, Mateusz Kuzak, Fotis Psomopoulos, Ricardo Arcila, Teresa K Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C Dimopoulos, Victoria Dominguez Del Angel, Michel Dumontier, Kim T Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W G van Gelder, and Patricia M Palagi

Subjects
Biology (General), QH301-705.5
Abstract

Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, it's sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: They're often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.

Published
2020
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9. Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations]

Author

Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, and Yasset Perez-Riverol

Subjects
Medicine, Science
Abstract

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent. They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Published
2019
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10. Ten steps to get started in Genome Assembly and Annotation [version 1; referees: 2 approved]

Author

Victoria Dominguez Del Angel, Erik Hjerde, Lieven Sterck, Salvadors Capella-Gutierrez, Cederic Notredame, Olga Vinnere Pettersson, Joelle Amselem, Laurent Bouri, Stephanie Bocs, Christophe Klopp, Jean-Francois Gibrat, Anna Vlasova, Brane L. Leskosek, Lucile Soler, Mahesh Binzer-Panchal, and Henrik Lantz

Subjects
Medicine, Science
Abstract

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).

Published
2018
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11. Systems Biology in ELIXIR: modelling in the spotlight [version 2; peer review: 2 approved, 1 approved with reservations]

Author

Vitor Martins dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja Arts, Rui Benfeitas, Victoria Dominguez Del Angel, Elena Domínguez-Romero, Polonca Ferk, Dirk Fey, Carole Goble, Martin Golebiewski, Kristina Gruden, Katharina F. Heil, Henning Hermjakob, Pascal Kahlem, Maria I. Klapa, Jasper Koehorst, Alexey Kolodkin, Martina Kutmon, Brane Leskošek, Sébastien Moretti, Wolfgang Müller, Marco Pagni, Tadeja Rezen, Miguel Rocha, Damjana Rozman, David Šafránek, William T. Scott, Rahuman S. Malik Sheriff, Maria Suarez Diez, Kristel Van Steen, Hans V Westerhoff, Ulrike Wittig, Katherine Wolstencroft, Anze Zupanic, Chris T. Evelo, and John M. Hancock

Subjects
Opinion Article, Articles, Systems Biology, Systems Medicine, ELIXIR Communities, Biomolecular Models, Network Biology, FAIR, Biological data, Biotechnology
Abstract

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR’s future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.

Published
2024
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12. Systems Biology in ELIXIR: modelling in the spotlight [version 1; peer review: 1 approved, 2 approved with reservations]

Author

Vitor Martins dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja Arts, Rui Benfeitas, Victoria Dominguez Del Angel, Polonca Ferk, Dirk Fey, Carole Goble, Martin Golebiewski, Kristina Gruden, Katharina F. Heil, Henning Hermjakob, Pascal Kahlem, Maria I. Klapa, Jasper Koehorst, Alexey Kolodkin, Martina Kutmon, Brane Leskošek, Sébastien Moretti, Wolfgang Müller, Marco Pagni, Tadeja Rezen, Miguel Rocha, Damjana Rozman, David Šafránek, Rahuman S. Malik Sheriff, Maria Suarez Diez, Kristel Van Steen, Hans V Westerhoff, Ulrike Wittig, Katherine Wolstencroft, Anze Zupanic, Chris T. Evelo, and John M. Hancock

Subjects
Opinion Article, Articles, Systems Biology, Systems Medicine, ELIXIR Communities, Biomolecular Models, Network Biology, FAIR, Biological data, Biotechnology
Abstract

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR’s future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.

Published
2022
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13. Towards FAIR principles for research software.

Author

Anna-Lena Lamprecht, Leyla J. García, Mateusz Kuzak, Carlos Martinez-Ortiz, Ricardo Arcila, Eva Martin Del Pico, Victoria Dominguez Del Angel, Stephanie van de Sandt, Jon C. Ison, Paula Andrea Martínez, Peter McQuilton, Alfonso Valencia, Jennifer L. Harrow, Fotis E. Psomopoulos, Josep Lluis Gelpí, Neil P. Chue Hong, Carole A. Goble, and Salvador Capella-Gutiérrez

Published
2020
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14. Recommendations for the packaging and containerizing of bioinformatics software [version 1; referees: 2 approved with reservations]

Author

Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, and Yasset Perez-Riverol

Subjects
Opinion Article, Articles, containers and packages, best practices bioinformatics, reproducibility
Abstract

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent. They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Published
2018
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15. MetaBase - the wiki-database of biological databases.

Author

Dan M. Bolser, Pierre-Yves Chibon, Nicolas Palopoli, Sungsam Gong, Daniel Jacob, Victoria Dominguez Del Angel, Daniel Swan, Sebastian Bassi, Virginia González, Prashanth Suravajhala, Seungwoo Hwang, Paolo Romano 0001, Rob Edwards, Bryan Bishop, John Eargle, Timur Shtatland, Nicholas J. Provart, Dave Clements, Daniel P. Renfro, Daeui Park, and Jong Bhak

Published
2012
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16. Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Author

Patricia Carvajal-López, Piraveen Gopalasingam, Amel Ghouila, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Paballo Abel Chauke, Alice Matimba, Alejandro Reyes, Selene L. Fernandez-Valverde, Nicola Mulder, Marco Cristancho, Javier De Las Rivas, Fatma Z. Guerfali, Victoria Dominguez Del Angel, Benjamin Moore, Wellcome Trust, National Institutes of Health (US), Biotechnology and Biological Sciences Research Council (UK), Global Challenges Research Fund, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Universidad de Salamanca, and Instituto Nacional de Bioinformática (España)

Subjects
Budgets, Financial Management, Economics, Computer science, Social Sciences, Economic Geography, Database and Informatics Methods, Learning and Memory, 0302 clinical medicine, Sociology, Simple (abstract algebra), Psychology, Biology (General), 0303 health sciences, Geography, Ecology, 4. Education, Software Engineering, ComputingMilieux_GENERAL, Professions, Interdisciplinary Placement, Editorial, Computational Theory and Mathematics, Modeling and Simulation, Low and Middle Income Countries, Educational Status, Engineering and Technology, Workshops, Curriculum, Human learning, Computer and Information Sciences, Coronavirus disease 2019 (COVID-19), Bioinformatics, QH301-705.5, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Training course, MEDLINE, Research and Analysis Methods, Education, Computer Software, Human Learning, 03 medical and health sciences, Cellular and Molecular Neuroscience, Genetics, Learning, Animals, Humans, Molecular Biology, Developing Countries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Cognitive Psychology, Sustainability science, Biology and Life Sciences, Computational Biology, Data science, Trainees, Low and middle income countries, Instructors, People and Places, Earth Sciences, Cognitive Science, Population Groupings, Finance, 030217 neurology & neurosurgery, Neuroscience
Abstract

© 2021 Moore et al., Bioinformatics training is required at every stage of a scientist’s research career. Continual bioinformatics training allows exposure to an ever-changing and growing repertoire of techniques and databases, and so biologists, computational scientists, and healthcare practitioners are all seeking learning opportunities in the use of computational resources and tools designed for data storage, retrieval, and analysis. There are abundant opportunities for accessing bioinformatics training for scientists in high-income countries (HICs), with well-equipped facilities and participants and trainers requiring minimal travel and financial costs alongside a range of general advice for developing short bioinformatics training courses [1–3]. However, regionally targeted bioinformatics training in low- and middle-income countries (LMICs) often requires more extensive local and external support, organization, and travel. Due to the limited expertise in bioinformatics in LMICs in general, most bioinformatics training requires a fair amount of collaboration with experts beyond the local community, country, or region. A common model of training, used as the basis of this article, includes a local host collaborating with local, regional, and international experts gathering to train local or regional participants. Recently, there has been a growth of capacity strengthening initiatives in LMICs, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABioNet) Initiative [4–6], the Capacity Building for Bioinformatics in Latin America (CABANA) Project [7], the Asia Pacific BioInformatics Network (APBioNet) [8], and the Wellcome Connecting Science Courses and Conferences program [9]. One of the important strands of these initiatives is a drive to organize and deliver valuable bioinformatics training, but organizing and delivering short bioinformatics training workshops in an LMIC present a unique set of challenges. This paper attempts to build upon the sage advice for organizing bioinformatics workshops with specific guidance for organizing and delivering them in LMICs. It describes the processes to follow in organizing courses taking into consideration the low-resource setting. We should also note that LMICs are not a monolithic group and that setting, context, temporality, and specific location matters. LMICs are a complex regional grouping [10] and should be treated as such; however, we will present some common lessons that we hope will help organizers and trainers of bioinformatics training events in LMICs to navigate the often different, challenging, and rewarding experience., The authors who contributed to this manuscript are funded as follows: BM receives salary support from Wellcome Trust grants [WT108749/Z/15/Z, WT108749/Z/15/A], PC, VR, NM, AG’s salaries are funded in whole, or in part, by the NIH Common Fund H3ABioNet grant [U24HG006941], MC, SLFV, AR, PG, PCL’s salaries were partly funded by the UKRI-BBSRC ‘Capacity building for bioinformatics in Latin America’ (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1], JDLR is funded by ISCiii AES [ref. PI18/00591] at the CSIC/USAL (Spain) and by CYTED, RIABIO (Red Iberoamericana 521RT0118), AM’s salary is funded by [WT206194/Z/17/Z], GO is funded by the CABANA grant and SM is funded by the EMBL-EBI.

Published
2021

17. Challenges and Considerations for Delivering Bioinformatics Training in lmics: Perspectives From Pan-African and Latin American Bioinformatics Networks

Author

Nicola Mulder, Piraveen Gopalasingam, Paballo Abel Chauke, Javier De Las Rivas, Fatma Z. Guerfali, Guilherme Oliveira, Victoria Dominguez Del Angel, Verena Ras, Patricia Carvajal-López, Alice Matimba, Alejandro Reyes, Marco Cristancho, Wellcome Trust, National Institutes of Health (US), Consejo Superior de Investigaciones Científicas (España), Universidad de Salamanca, and Biotechnology and Biological Sciences Research Council (UK)

Subjects
Best practices, Latin Americans, Pan african, Best practice, Library science, Education (General), Training (civil), Education, Low to middle income countries, Latin America, Political science, Africa, Training, L7-991
Abstract

© 2021 Ras, Carvajal-López, Gopalasingam, Matimba, Chauke, Mulder, Guerfali, Del Angel, Reyes, Oliveira, De Las Rivas and Cristancho., In general, institutions and research groups based in Low to Middle Income Countries (LMICs) battle a number of challenges ranging from a shortage of infrastructure, lack of training facilities, and poor internet, to a lack of local expertise (Karikari et al., 2015; Tastan Bishop et al., 2015; Shaffer et al., 2019). A shortage of local experts, particularly within more specialised topics, still remains a key obstacle in developing bioinformatics research capacity within LMICs (Tastan Bishop et al., 2015; Mulder et al., 2018)., The authors who contributed to this manuscript are funded in whole, or in part, by the Wellcome Trust (WT108749/Z/15/Z), (WT108749/Z/15/A), H3ABioNet NIH grant U24HG006941, H3ABioNet NIH grant U24HG006942, CABANA—Capacity building for bioinformatics in Latin America’ (CABANA), funded by UKRI-BBSRC on behalf of the Global Challenges Research Fund (BB/P027849/1), CSIC/ USAL and EMBL-EBI.

Published
2021

18. The future of metabolomics in ELIXIR.

Author

Merlijn N. van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-García, Rafael C. Jiménez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata P. Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, and Christoph Steinbeck

Published
2017
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19. A framework to assess the quality and impact of bioinformatics training across ELIXIR

Author

Eija Korpelainen, Allegra Via, Marko Vidak, Brane Leskošek, Lee Larcombe, Louisa J. Bellis, Mateusz Kuzak, Loredana Le Pera, Patricia M. Palagi, Paula Martinez, Celia W.G. van Gelder, Sarah L. Morgan, Tuur Muyldermans, Jessica M. Lindvall, Gabriella Rustici, Kim T. Gurwitz, Hedi Peterson, Alexander Botzki, Roland Krause, Fotis Psomopoulos, Victoria Dominguez Del Angel, Balint L. Balint, Ståle Nygård, Diana Marek, Eva Alloza, Daniel Wibberg, Pedro Fernandes, Prakash Singh Gaur, Jure Dimec, Vojtech Spiwok, Barcelona Supercomputing Center, Department of Genetics [Cambridge], University of Cambridge [UK] (CAM), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, MRC Human Genetics Unit, University of Edinburgh-Western General Hospital, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Department of Biochemistry and Molecular Biology, University of Debrecen, Flanders Interuniversity Institute for Biotechnology (VIB), Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana -University of Ljubljana, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian, CSC - IT Center for Science Ltd, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], Dutch Techcentre for Life Sciences [Utrecht], Bioenergetics and Molecular Biotechnologies ( IBIOM), Institute of Biomembranes, National Research Council of Italy (CNR)-National Research Council of Italy (CNR), National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University-Stockholm University-Department of Biochemistry and Biophysics, Stockholm University-Stockholm University, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Department of Informatics [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Institute of Computer Science [University of Tartu, Estonie], University of Tartu, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague (UCT Prague), Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), Genome Research of Industrial Microorganisms, Universität Bielefeld = Bielefeld University, European Commission within the Research Infrastructures programme of Horizon 2020 676559, Gurwitz, Kim T [0000-0003-1992-5073], Singh Gaur, Prakash [0000-0003-3272-628X], Bellis, Louisa J [0000-0001-9581-870X], Larcombe, Lee [0000-0003-3150-6445], Alloza, Eva [0000-0001-8385-9336], Botzki, Alexander [0000-0001-6691-4233], Dimec, Jure [0000-0002-9525-9028], Dominguez Del Angel, Victoria [0000-0002-5514-6651], Fernandes, Pedro L [0000-0003-2124-0241], Krause, Roland [0000-0001-9938-7126], Kuzak, Mateusz [0000-0003-0087-6021], Le Pera, Loredana [0000-0002-0076-9878], Leskošek, Brane [0000-0001-5202-2349], Lindvall, Jessica M [0000-0002-5042-8481], Marek, Diana [0000-0002-9812-6351], Martinez, Paula A [0000-0002-8990-1985], Muyldermans, Tuur [0000-0002-3926-7293], Palagi, Patricia M [0000-0001-9062-6303], Peterson, Hedi [0000-0001-9951-5116], Psomopoulos, Fotis [0000-0002-0222-4273], Spiwok, Vojtech [0000-0001-8108-2033], van Gelder, Celia WG [0000-0002-0223-2329], Vidak, Marko [0000-0001-7901-3936], Wibberg, Daniel [0000-0002-1331-4311], Morgan, Sarah L [0000-0001-9528-8323], Rustici, Gabriella [0000-0003-3085-1271], and Apollo - University of Cambridge Repository

Subjects
FOS: Computer and information sciences, 0301 basic medicine, Program evaluation, Biomedical Research, Databases, Factual, Economics, Computer science, Social Sciences, Surveys, Bioinformatics, Geographical Locations, Computational biology, Database and Informatics Methods, Software Pipelines, Multidisciplinaire, généralités & autres [F99] [Sciences du vivant], User-Computer Interface, Software, 0302 clinical medicine, Information processing, Biology (General), computer.programming_language, media_common, training, Careers, Ecology, ELIXIR Training Platform, Member states, Data Collection, FOS: Social sciences, bioinformatics, Research Assessment, Elixir, Research Personnel, Europe, Computational Theory and Mathematics, Research Design, Modeling and Simulation, impact, Elixir (programming language), Curriculum, Algorithms, Employment, Quality Control, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], Information storage and retrieval systems, Computer and Information Sciences, Education, Continuing, quality assessment, QH301-705.5, media_common.quotation_subject, Multidisciplinary, general & others [F99] [Life sciences], Research and Analysis Methods, Education, Instruction Pipelines, 03 medical and health sciences, Cellular and Molecular Neuroscience, Data visualization, Modelling and Simulation, Computational Techniques, Bioinformatica, Genetics, Relevance (information retrieval), Quality (business), [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Survey Research, Data collection, Impact assessment, Data Visualization, Sustainability science, Computational Pipelines, Computational Biology, Reproducibility of Results, ELIXIR, 030104 developmental biology, Labor Economics, People and Places, Portfolio, computer, 030217 neurology & neurosurgery, Program Evaluation
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. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Published
2020
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20. Making training materials FAIR in 10 steps

Author

Melissa Burke1, Leyla Garcia, Bérénice Batut, Mateusz Kuzak, Fotis Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, and Patricia M. Palagi2

Subjects
training, FAIR principles, training materials
Abstract

Sharing, reusing and reproducing data, software and other digital objects forms the cornerstone of open science practices. Such practices are guided by the Findable, Accessible, Interoperable and Reusable (FAIR) principles. Implementing FAIR principles is not always straightforward, especially in the context of Bioinformatics training. If we are to meet worldwide demand for such training, adhering to the FAIR principles is vital not only for data and software, but also for training materials (any digital object used in a training context, such as slide presentations, exercises, datasets). To facilitate this process, and break the principles down into practical steps, the ELIXIR Training Platform community has put together ten simple rules for making training materials FAIR. Above all is the need to plan to share your training materials online from the outset. Amongst the remaining rules is the importance of describing materials properly, assigning unique identifiers, registering them online, defining access criteria, and using interoperable formats. The full set of ten rules is presented here.

Published
2020

21. 2017-2018 Activity Report, FRENCH INSTITUTE OF BIOINFORMATICS

Author

Victoria, DOMINGUEZ DEL ANGEL, SAND Olivier, MEDIGUE Claudine, and Jacques, VAN HELDEN

Subjects
FOS: Computer and information sciences, Docker, Bioinformatics, HPC, Training, Cloud Computing, Ansible
Abstract

The Institut Français de Bioinformatique (IFB) is one of the 22 French national research infrastructures that have been created to address these challenges in the context of the Programme Investissement d’Avenir (PIA) launched by the Research Ministry in 2010. IFB began to operate in summer 2013. Following the midterm evaluation report (autumn 2016), a new work plan was prepared under the co-leadership of Claudine Médigue (Research Director at the Centre National de la Recherche Scientifique) and Jacques van Helden (Professor at Aix-Marseille University). The plan was submitted for external evaluation, and the revised version was definitively validated in May 2018. The current report describes the results achieved by IFB in the context of this restructuration.

Published
2019
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22. Recommendations for the packaging and containerizing of bioinformatics software

Author

Fábio Madeira, Dan Søndergaard, Victoria Dominguez Del Angel, Daniel Blankenberg, Susheel Varma, Hannes L. Röst, Yasset Perez-Riverol, BioContainers Community, Olivier Sallou, Hervé Ménager, Bjorn Gruening, Michael R. Crusoe, Rafael C. Jimenez, Brian O'Connor, Timo Sachsenberg, Felipe da Veiga Leprevost, Pablo Moreno, Department of Computer Science [Freiburg], University of Freiburg [Freiburg], Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Department of Pathology [Ann Arbor, USA], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics Research Centre, Aarhus University [Aarhus], Donnelly Centre [Toronto, ON, Canada], University of Toronto, Wilhelm-Schickard-Institut für Informatik [Tübingen], Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Santa Cruz Genomics Institute, University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Université Paris-Saclay, Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Microbiology and Molecular Genetics, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Genomic Medicine Institute [Cleveland], Cleveland Clinic, ELIXIR Hub [Cambridge], This work was partially supported by ELIXIR-EXCELERATE. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement numbers 676559. The BioContainers workshop (Paris 2017) and the BioContainers community that developed these recommendations are supported by the ELIXIR Tools platform. FVL is supported by NIH grants R01GM94231 and U24CA210967., BioContainers Community, European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Ménager, Hervé, ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. - ELIXIR-EXCELERATE - - H20202015-09-01 - 2019-08-31 - 676559 - VALID, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of California [Santa Cruz] (UCSC), University of California-University of California, and Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, best practices bioinformatics, Computer science, media_common.quotation_subject, General Biochemistry, Genetics and Molecular Biology, Scientific software, Workflow, Set (abstract data type), 03 medical and health sciences, Software, 0302 clinical medicine, Bioinformatics software, 11. Sustainability, Humans, Quality (business), General Pharmacology, Toxicology and Pharmaceutics, reproducibility, media_common, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], General Immunology and Microbiology, containers and packages, business.industry, Computational Biology, Articles, General Medicine, Opinion Article, Research Personnel, 030104 developmental biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software engineering, business, 030217 neurology & neurosurgery, Research software
Abstract

International audience; Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent. They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Published
2018
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23. Ten steps to get started in Genome Assembly and Annotation

Author

Lieven Sterck, Brane Leskošek, Lucile Soler, Cederic Notredame, Erik Hjerde, Stéphanie Bocs, Mahesh Binzer-Panchal, Laurent Bouri, Henrik Lantz, Joelle Amselem, Christophe Klopp, Jean-François Gibrat, Olga Vinnere Pettersson, Salvadors Capella-Gutierrez, Anna Vlasova, Victoria Dominguez Del Angel, Institut Français de Bioinformatique, Université Paris-Saclay, Department of Chemistry, RIDER UNIVERSITY, Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Department of Plant Systems Biology, VIB, Spanish National Bioinformatics Institute (INB), Centro Nacional de Supercomputación, BSC Electronics, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Uppsala Genome Center, NGI/SciLifeLab - Department of Immunology, Genetics and Pathology, Uppsala University, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Université de Tunis [Tunis], Laboratory of Technologies of Information and Communication and Electrical Engineering, National Superior School of Engineers of Tunis, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), South Green Bioinformatics Platform, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Faculty of Medicine, Institute for Biostatistics and Medical Informatics, University of Ljubljana, IMBIM/NBIS/SciLifeLab, Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Universitat Pompeu Fabra [Barcelona] (UPF), Université de Tunis, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Barcelona Supercomputing Center, Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), South Green Bioinformatics Platform [Montpellier], and Hjerde, Erik

Subjects
0301 basic medicine, Computer science, General assembly, Data management, [SDV]Life Sciences [q-bio], Annotation, Interoperability, Assembly, Sequence assembly, Bioinformatik och systembiologi, Genome, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, Workflows, World Wide Web, 03 medical and health sciences, DNA--Analysis, Genomes, General Pharmacology, Toxicology and Pharmaceutics, ADN--Anàlisi, FAIR, Genome assembly, Bioinformatics and Systems Biology, General Immunology and Microbiology, business.industry, Biology and Life Sciences, General Medicine, Genome project, Articles, DNA, Opinion Article, L10 - Génétique et amélioration des animaux, ELIXIR-EXCELERATE, 030104 developmental biology, Workflow, NGS, business, Ciències de la salut [Àrees temàtiques de la UPC], Genome annotation
Abstract

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR). ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures Programme of Horizon 2020 [676559].

Published
2018
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24. MetaBase-the wiki-database of biological databases

Author

Nicholas J. Provart, Prashanth Suravajhala, Daniel Swan, Daeui Bhak, Dan Bolser, John Eargle, Nicolas Palopoli, Virginia González, Victoria Dominguez Del Angel, Daniel J. Jacob, Dave Clements, Jong Bhak, Daniel P. Renfro, Seungwoo Hwang, Pierre-Yves Chibon, Sebastian Bassi, Paolo Romano, Sungsam Gong, Timur Shtatland, Bryan Bishop, Robert Edwards, Genome Research Foundation, Wageningen University and Research Centre (WUR), Universidad Nacional de Quilmes (UNQ), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Oxford Gene Technology, Partenaires INRAE, Genes Digitales, Bioinformatics Organization Inc., Korea Research Institute of Bioscience & Biotechnology (KRIBB), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Diego State University (SDSU), University of Illinois at Urbana Champaign (UIUC), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Emory University [Atlanta, GA], Texas A&M University System, Pusan National University, Theragen BiO Institute, Ministry of Knowledge Economy (MKE, Korea) 10040231, Genome Research Foundation, Bolser, Dan M., Gong, Sung [0000-0001-5796-4423], and Apollo - University of Cambridge Repository

Subjects
Botanics, catalog, metabase, Databases, Factual, Biological database, Biology, computer.software_genre, information, 03 medical and health sciences, 0302 clinical medicine, Resource (project management), Laboratorium voor Plantenveredeling, collection, Genetics, biologie de la plante, 030304 developmental biology, 0303 health sciences, Internet, base de données en ligne, life sciences, Database, business.industry, Articles, persistence, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Botanique, Systems Integration, Plant Breeding, web services, 030220 oncology & carcinogenesis, System integration, The Internet, Web service, business, computer
Abstract

International audience; Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.

Published
2012
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