Format description of the event cycle on Covid-19 data sharing. The event series is intended to o... more Format description of the event cycle on Covid-19 data sharing. The event series is intended to offer the participants a deep understanding of the motivations behind the sharing of data and other research results (publications, software, etc), and how they can perform it in a simple way. The format can be reused and adapted for a similar event cycle. This record is a work in progress and it will be updated as tutorials and webinars will be carried out.
This poster describes the MR-Bi and outlines how it can be utilized to support instructional and ... more This poster describes the MR-Bi and outlines how it can be utilized to support instructional and curriculum design for biology, genetics, or bioinformatics instruction in higher education and training contexts.
<b>Copyright information:</b>Taken from "Local comparison of protein structures ... more <b>Copyright information:</b>Taken from "Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites"http://www.biomedcentral.com/1471-2105/8/S1/S24BMC Bioinformatics 2007;8(Suppl 1):S24-S24.Published online 8 Mar 2007PMCID:PMC1885854. number and type of aligned amino acids. The arrows describe permutations and inversions in protein sequences; the N to C-term direction is colour-coded (blue is associated to N-term and red to C-term). a) The residues involved in the match bind S-adenosyl-homocysteine (1boo) and S-adenosyl-methionine (1vidA), and share a high structural similarity. b) Matching residues bind ADP, Mg and PHY in the 1iow structure; and ADP, Mg and GSH in the 2hgs structure c) The 1dljA residues involved in the match bind a 1,4-dihydronicotinamide adenine dinucleotide; 1say is 92% identical to 1pjc, which binds nicotinamide-adenine-dinucleotide with the residues involved in the 3D match. d) In 1b0uA, the matching residues bind an ATP molecule; 1kklA is 100% identical to 1jb1A, which binds PO4 with the residues involved in the 3D match (see Results).
ELIXIR [1] is an intergovernmental organization that brings together life science resources acros... more ELIXIR [1] is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are divided into the following five areas Data, Tools, Interoperability, Compute and Training known as "platforms". The ELIXIR Tools Platform works to improve the discovery, quality and sustainability of software resources. Software Best Practices task of the Tools Platform aims to raise the quality and sustainability of research software by producing, adopting, promoting and measuring information standards and best practices applied to the software development life cycle. We have published four (4OSS) simple recommen...
Linear motifs are short, evolutionarily plastic com-ponents of regulatory proteins and provide lo... more Linear motifs are short, evolutionarily plastic com-ponents of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling protein turnover and directing protein localization. Given their importance, our understanding of motifs is surprisingly limited, largely as a result of the difficulty of discovery, both experimentally and computationally. The Eukaryotic Linear Motif (ELM) resource at
Summary: Rapid technological advances have led to an explosion of biomedical data in recent years... more Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training mater-ials and courses, including a catalogue of trainers and course organ-izers, and an announcement service for training events. For course
It is widely agreed that rare disease patient registries should be international and follow the g... more It is widely agreed that rare disease patient registries should be international and follow the guiding principles of Findable, Accessible, Interoperable, Reusable (FAIR) for humans and computers. Furthermore, the procedures to collect and exchange data should be harmonised. Since 2014, the Bring Your Own Data (BYOD) annual workshop has been organised by and held at the National Centre for Rare Diseases Istituto Superiore di Sanitá (CNMR-ISS), Rome, Italy with the aim to promote the establishment of FAIR rare disease registries in compliance with IRDiRC and EU recommendations. The event has been arranged with the support of RD-Connect and ELIXIR, in particular, the Dutch Techcentre for Life Sciences representative of ELIXIR-NL. The general roadmap of the BYOD workshop contains at least a preparatory phase, an execution phase, and a follow-up phase to foster the results of the workshop by surveying and having phone conferences with participants. At the 4th edition of the BYOD this ye...
Curriculum development in higher education should follow a formal process. Although the focus in ... more Curriculum development in higher education should follow a formal process. Although the focus in formal curriculum theory is on long-term programs of study, the theoretical and practical considerations are also applicable to shorter-form learning experiences (single courses, lessons, or training sessions). With these considerations in mind, we discuss here an iterative model of curriculum design, the starting point of which (indeed, in the construction of any learning experience), is the articulation of the target learning outcomes: everything follows from these, including the selection of learning experiences and content, the development of assessments, and evaluation of the resulting curriculum. We discuss how the iterative process can be used in curriculum and instructional development, and provide a set of practical guidelines for curriculum and course preparation.
Biodiversity Information Science and Standards, 2019
ELIXIR (ELIXIR Europe 2019a) is an intergovernmental organization that brings together life scien... more ELIXIR (ELIXIR Europe 2019a) is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are divided into the following five areas: Data, Tools, Interoperability, Compute and Training, each known as “platform”. The ELIXIR Tools Platform works to improve the discovery, quality and sustainability of software resources. The Software Development Best Practices task of the Tools Platform aims to raise the quality and sustainability of research software by producing, adopting, and promoting information standards and best practices relevant to the software development life cycle. We have published four (...
Format description of the event cycle on Covid-19 data sharing. The event series is intended to o... more Format description of the event cycle on Covid-19 data sharing. The event series is intended to offer the participants a deep understanding of the motivations behind the sharing of data and other research results (publications, software, etc), and how they can perform it in a simple way. The format can be reused and adapted for a similar event cycle. This record is a work in progress and it will be updated as tutorials and webinars will be carried out.
This poster describes the MR-Bi and outlines how it can be utilized to support instructional and ... more This poster describes the MR-Bi and outlines how it can be utilized to support instructional and curriculum design for biology, genetics, or bioinformatics instruction in higher education and training contexts.
<b>Copyright information:</b>Taken from "Local comparison of protein structures ... more <b>Copyright information:</b>Taken from "Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites"http://www.biomedcentral.com/1471-2105/8/S1/S24BMC Bioinformatics 2007;8(Suppl 1):S24-S24.Published online 8 Mar 2007PMCID:PMC1885854. number and type of aligned amino acids. The arrows describe permutations and inversions in protein sequences; the N to C-term direction is colour-coded (blue is associated to N-term and red to C-term). a) The residues involved in the match bind S-adenosyl-homocysteine (1boo) and S-adenosyl-methionine (1vidA), and share a high structural similarity. b) Matching residues bind ADP, Mg and PHY in the 1iow structure; and ADP, Mg and GSH in the 2hgs structure c) The 1dljA residues involved in the match bind a 1,4-dihydronicotinamide adenine dinucleotide; 1say is 92% identical to 1pjc, which binds nicotinamide-adenine-dinucleotide with the residues involved in the 3D match. d) In 1b0uA, the matching residues bind an ATP molecule; 1kklA is 100% identical to 1jb1A, which binds PO4 with the residues involved in the 3D match (see Results).
ELIXIR [1] is an intergovernmental organization that brings together life science resources acros... more ELIXIR [1] is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are divided into the following five areas Data, Tools, Interoperability, Compute and Training known as "platforms". The ELIXIR Tools Platform works to improve the discovery, quality and sustainability of software resources. Software Best Practices task of the Tools Platform aims to raise the quality and sustainability of research software by producing, adopting, promoting and measuring information standards and best practices applied to the software development life cycle. We have published four (4OSS) simple recommen...
Linear motifs are short, evolutionarily plastic com-ponents of regulatory proteins and provide lo... more Linear motifs are short, evolutionarily plastic com-ponents of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling protein turnover and directing protein localization. Given their importance, our understanding of motifs is surprisingly limited, largely as a result of the difficulty of discovery, both experimentally and computationally. The Eukaryotic Linear Motif (ELM) resource at
Summary: Rapid technological advances have led to an explosion of biomedical data in recent years... more Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training mater-ials and courses, including a catalogue of trainers and course organ-izers, and an announcement service for training events. For course
It is widely agreed that rare disease patient registries should be international and follow the g... more It is widely agreed that rare disease patient registries should be international and follow the guiding principles of Findable, Accessible, Interoperable, Reusable (FAIR) for humans and computers. Furthermore, the procedures to collect and exchange data should be harmonised. Since 2014, the Bring Your Own Data (BYOD) annual workshop has been organised by and held at the National Centre for Rare Diseases Istituto Superiore di Sanitá (CNMR-ISS), Rome, Italy with the aim to promote the establishment of FAIR rare disease registries in compliance with IRDiRC and EU recommendations. The event has been arranged with the support of RD-Connect and ELIXIR, in particular, the Dutch Techcentre for Life Sciences representative of ELIXIR-NL. The general roadmap of the BYOD workshop contains at least a preparatory phase, an execution phase, and a follow-up phase to foster the results of the workshop by surveying and having phone conferences with participants. At the 4th edition of the BYOD this ye...
Curriculum development in higher education should follow a formal process. Although the focus in ... more Curriculum development in higher education should follow a formal process. Although the focus in formal curriculum theory is on long-term programs of study, the theoretical and practical considerations are also applicable to shorter-form learning experiences (single courses, lessons, or training sessions). With these considerations in mind, we discuss here an iterative model of curriculum design, the starting point of which (indeed, in the construction of any learning experience), is the articulation of the target learning outcomes: everything follows from these, including the selection of learning experiences and content, the development of assessments, and evaluation of the resulting curriculum. We discuss how the iterative process can be used in curriculum and instructional development, and provide a set of practical guidelines for curriculum and course preparation.
Biodiversity Information Science and Standards, 2019
ELIXIR (ELIXIR Europe 2019a) is an intergovernmental organization that brings together life scien... more ELIXIR (ELIXIR Europe 2019a) is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are divided into the following five areas: Data, Tools, Interoperability, Compute and Training, each known as “platform”. The ELIXIR Tools Platform works to improve the discovery, quality and sustainability of software resources. The Software Development Best Practices task of the Tools Platform aims to raise the quality and sustainability of research software by producing, adopting, and promoting information standards and best practices relevant to the software development life cycle. We have published four (...
Abstract for poster and talk combination presented 25 July 2019 at ISMB/ECCB 2019 as part of the ... more Abstract for poster and talk combination presented 25 July 2019 at ISMB/ECCB 2019 as part of the Education COSI:
Background: As the life sciences have become more computational and data intensive, the pressure to incorporate the requisite training into life-science education and training programs has increased. To facilitate curriculum development, various sets of bioinformatics competencies have been articulated; however, these have proved difficult to implement in practice. Addressing this issue, we have created a curriculum design and evaluation tool – the Mastery Rubric for Bioinformatics (MR-Bi) - to support the development of specific Knowledge, Skills and Abilities (KSAs) that promote bioinformatics practice and the achievement of competencies.
Methods: 12 KSAs were extracted, and stages along a developmental trajectory were identified. The KSAs and their performance level descriptors at each stage were formulated, ultimately yielding the MR-Bi.
Results and Conclusions: The MR-Bi prioritizes the development of independence and scientific reasoning. It can be used by practicing scientists at all career stages to direct their (and their team’s) acquisition of new, or to deepen existing, bioinformatics KSAs. It can be used to strengthen teaching and learning and for curriculum building. It can thereby contribute to the cultivation of a next generation of bioinformaticians who can design reproducible and rigorous research, and to critically analyze results from their own, and others’, work.
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Background: As the life sciences have become more computational and data intensive, the pressure to incorporate the requisite training into life-science education and training programs has increased. To facilitate curriculum development, various sets of bioinformatics competencies have been articulated; however, these have proved difficult to implement in practice. Addressing this issue, we have created a curriculum design and evaluation tool – the Mastery Rubric for Bioinformatics (MR-Bi) - to support the development of specific Knowledge, Skills and Abilities (KSAs) that promote bioinformatics practice and the achievement of competencies.
Methods: 12 KSAs were extracted, and stages along a developmental trajectory were identified. The KSAs and their performance level descriptors at each stage were formulated, ultimately yielding the MR-Bi.
Results and Conclusions: The MR-Bi prioritizes the development of independence and scientific reasoning. It can be used by practicing scientists at all career stages to direct their (and their team’s) acquisition of new, or to deepen existing, bioinformatics KSAs. It can be used to strengthen teaching and learning and for curriculum building. It can thereby contribute to the cultivation of a next generation of bioinformaticians who can design reproducible and rigorous research, and to critically analyze results from their own, and others’, work.