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,... 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 curriculum design for biology, genetics, or bioinformatics instruction in higher education and training contexts.
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<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... 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 across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of... 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...
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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... 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. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the... 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
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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... 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...
Copyright information: Taken from "pdbFun: mass selection and fast comparison of annotated PDB residues"Nucleic Acids Research 2005;33(Web Server issue):W133-W137.Published online 27 Jun 2005PMCID:PMC1160259.© The Author 2005.... more
Copyright information: Taken from "pdbFun: mass selection and fast comparison of annotated PDB residues"Nucleic Acids Research 2005;33(Web Server issue):W133-W137.Published online 27 Jun 2005PMCID:PMC1160259.© The Author 2005. Published by Oxford University Press. All rights reserved A manual selection of 5p21 (ras protein) residues involved in GTP binding was compared with the ∼5500 chains of a non-redundant PDB (50%). The output is shown in tabular and also graphic format. In the first column of the table, the matching residues of the query PDB chain are reported; in the adjacent columns, the other PDB chains follow, and the residues aligned in three dimensions appear in the same rows. The matched PDB chains are reported in the first row; the number of matched residues in the second one. Matching residues are also displayed upon selection (pressing on the ‘draw’ button) with a Java applet.
Research Interests: Bioinformatics, Computer Science, Education, Social Sciences, Computational Biology, and 10 moreMedicine, Information Processing, Biological Sciences, Europe, Mathematical Sciences, Bioinformatica, Elixir, Qualitative research methods and analysis, People and Places, and Information storage and retrieval systems
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... 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.
Research Interests: Psychology, Computer Science, Curriculum Design, Higher Education, Training and Development, and 11 moreCurriculum Theory, Emergent Curriculum, Learning And Teaching In Higher Education, Curriculum Development, F Mri Research, Curriculum and Instruction, Curriculum, Curriculum mapping, Curriculum and Pedagogy, Teaching and Learning In Adult and Higher Education, and SocArXiv
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... 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 (...
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As the life sciences have become more 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... more
As the life sciences have become more 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 (bio)informatics 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 to support the development of specific Knowledge, Skills and Abilities (KSAs) that reflect the scientific method and promote both bioinformatics practice and the achievement of competencies. Twelve KSAs were extracted via formal analysis, and stages along a developmental trajectory, from uninitiated student to independent practitioner, were identified. Demonstration of each KSA by a performer at each stage was initially described (Performance Level Descriptors, PLDs), evaluated, and revised at an international workshop. This work was subsequently extended and further ref...
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Research Interests: Bioinformatics, Computer Science, Research Design, Biology, Medicine, and 15 moreBiological Sciences, Software, Humans, Mathematical Sciences, Mice, Animals, BMC Bioinformatics, Phosphorylation, Proteins, Rats, Protein Phosphorylation, Protein Kinase, Molecular Interactions, binding sites, and Signaling pathway
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Research Interests: Bioinformatics, Computer Science, Natural Language Processing, Machine Learning, Data Mining, and 12 moreSignal Processing, Network Security, Computational Biology, Text Mining, Training, Computer Security, Mobile Computing, Humans, End Users, Syntactic and Semantic Knowledge, Community Networks, and Biochemistry and cell biology
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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... more
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...
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Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but... more
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.
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Research Interests: Molecular Biology, Humans, Sequence alignment, Animals, Protein structure, and 15 moreActive site, Guanosine Triphosphate, Convergent Evolution, Arginine, Alanine, G protein, Amino Acid Sequence, Asparagine, Gtp Binding Proteins, Static Electricity, Biochemistry and cell biology, Adenosine Triphosphate, Ribonucleases, Molecular Sequence Data, and binding sites
Research Interests: Algorithms, Molecular Biology, Computational Biology, Information Extraction, Probability, and 15 moreHumans, Sequence alignment, Animals, Proteins, Protein Complex Detection, Protein Domains, Substrate Specificity, Amino Acid Sequence, Gene Family, Protein Binding, Complex Structure, Ligands, Biochemistry and cell biology, Molecular Sequence Data, and binding sites
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed,... more
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a n...
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Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer... more
Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and fu...
Background: Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of... more
Background: Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.
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Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the... more
Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.
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A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that--at least in some cases--the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more,... more
A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that--at least in some cases--the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues fal...
Research Interests: Computational Biology, Biological Sciences, Mathematical Sciences, BMC Bioinformatics, Proteins, and 11 moreStructure Analysis, Protein Sequence Analysis, Multiple Sequence Alignment, S100 protein family, Amino Acid Sequence, Sensitivity and Specificity, Visual Inspection, False Positive, Computational Techniques, conserved sequence , and True Positive
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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... more
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 materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and ident...
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ABSTRACT Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals... more
ABSTRACT Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein–protein interaction. Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive over-prediction. The Eukaryotic Linear Motif resource (ELM - &quot;http://elm.eu.org&quot;:http://elm.eu.org) is a bioinformatics facility for investigating candidate short functional motifs in eukaryotic proteins. The ELM database to date has collected more than 140 motifs and their regular expressions patterns as well as information about their instances of occurrence, distribution, crystal structure, publications, etc. In order to reduce the over-prediction inherent to pattern matching against protein sequences and to discriminate true from false positive motif matches, context-based rules and logical filters are applied. The current version includes cell compartment, phylogeny, globular domain clash filters and the more recent structural filter based on known three-dimensional information that relies on structural information, such as residue solvent accessibility and secondary structure features. This implies that a candidate motif can be excluded from further consideration if the protein resides in the wrong cellular compartment or the motif is buried in the core of a globular domain. By considering additional types of context information, we expect that prediction of functional sites by ELM can be considerably improved. In cases where the user cannot provide relevant context information, we consider providing predictions of contextual information in order to improve the ELM performance. For example, since the ELM motif database has been annotated with biological process GO terms, the system could be prepared for addition of a new context filter using biological process.
Trypsins and chymotrypsins are well-studied serine peptidases that cleave peptide bonds at the carboxyl side of basic and hydrophobic l-amino acids, respectively. These enzymes are largely responsible for the digestion of proteins. Three... more
Trypsins and chymotrypsins are well-studied serine peptidases that cleave peptide bonds at the carboxyl side of basic and hydrophobic l-amino acids, respectively. These enzymes are largely responsible for the digestion of proteins. Three primary processes regulate the activity of these peptidases: secretion, precursor (zymogen) activation and substrate-binding site recognition. Here, we present a detailed phylogenetic analysis of trypsins and chymotrypsins in three orders of holometabolous insects and reveal divergent characteristics of Lepidoptera enzymes in comparison with those of Coleoptera and Diptera. In particular, trypsin subsite S1 was more hydrophilic in Lepidoptera than in Coleoptera and Diptera, whereas subsites S2-S4 were more hydrophobic, suggesting different substrate preferences. Furthermore, Lepidoptera displayed a lineage-specific trypsin group belonging only to the Noctuidae family. Evidence for facilitated trypsin auto-activation events were also observed in all the insect orders studied, with the characteristic zymogen activation motif complementary to the trypsin active site. In contrast, insect chymotrypsins did not seem to have a peculiar evolutionary history with respect to their mammal counterparts. Overall, our findings suggest that the need for fast digestion allowed holometabolous insects to evolve divergent groups of peptidases with high auto-activation rates, and highlight that the evolution of trypsins led to a most diverse group of enzymes in Lepidoptera.
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Research Interests: Engineering, Physics, Chemistry, Molecular Dynamics Simulation, Biology, and 13 moreMedicine, Multidisciplinary, Macromolecular X-Ray Crystallography, Sequence alignment, Phosphorylation, Proteins, PLoS one, Protein Conformation, Amino Acid Sequence, Amino Acid Substitution Rates, Protein Binding, Molecular Sequence Data, and binding sites
Research Interests: Algorithms, Malaria, Structural Bioinformatics, Multidisciplinary, Humans, and 15 moreMutation, Animals, Drug Resistance, Structure Analysis, Membrane transport proteins, PLoS one, Plasmodium falciparum, Protein Conformation, Protozoan Proteins, Amino Acid Sequence, Chloroquine, Experimental Data, Protons, Molecular Sequence Data, and Malaria Falciparum
Research Interests: Algorithms, Cell Signaling, Signal Transduction, Biological Sciences, Software, and 13 moreEnvironmental Sciences, World Wide Web, Phosphorylation, Nucleic Acids, Proteins, Protein Sequence Analysis, Substrate Specificity, Molecular weight, In Silico, Two dimensional Gel Electrophoresis, Proteome, Internet, and binding sites
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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... 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.
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.