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Data Management Plans (DMPs) describe the data management lifecycle for the data corresponding to a research project, including activities from collection to preservation Machine-actionable DMPs improve text-based DMPs by adding a semantic layer representing the most common elements relevant to DMPs, from datasets to funders. Similar to DMPs, Software Management Plans (SMPs) follow the software management lifecycle. The ELIXIR SMP was developed to support life science researchers and make it easier to follow research software good practices aligned to the findable, accessible, interoperable and reusable principles for research software. Currently, the ELIXIR SMP is a questionnaire-based document that would benefit from a machine-actionable approach. Here, we present a preliminary metadata analysis including possible types and properties from Schema.org that could be used to model machine-actionable SMPs.

Data-driven research requires handling data together with the software that is used to collect, transform, and create such data. Data Management Plans have emerged as a systematic way to record the data management lifecycle for data corresponding to a research project. Similar to DMPs, Software Management Plans (SMPs) follow the research software management lifecycle, becoming a complement of DMPs. Initially, both DMPs and SMPs were conceived as text-based documents, sometimes guided by a set of questions targeting key points related to the corresponding lifecycle. Machine-actionable DMPs improve text-based DMPs by adding a semantic layer representing the most common elements relevant to DMPs, from datasets to funders. Here, we use the ELIXIR SMP as a use-case and present a preliminary metadata schema including possible types and properties useful to represent machine-actionable SMPs.

Similar to Data Management Plans, Software Management Plans help formalize a set of structures and goals that ensure the software is accessible and reusable in the short, medium and long term. The ELIXIR SMP (DOI:10.37044/osf.io/k8znb) has been developed by the ELIXIR Software Development Best Practices Group in the ELIXIR Tools Platform to support researchers in life sciences. Although targeting the life sciences community, most of the elements of the ELIXIR SMPs are domain agnostic and could be used by other communities as well. DMPs and SMPs can be presented as text-based documents, sometimes guided by a set of questions corresponding to key points related to the lifecycle of either data or software. The FAIRification road for ELIXIR SMPs include two main components: turning them into machine-actionable SMPs (maSMPs) and aligning them to FAIR Digital Objects (FDOs). Our maSMP version will be based on the machine-actionable DMPs proposed by the Research Data Alliance DMP Common Standards Working Group, which corresponds to a structured representation of the most common elements present in a DMP (DOI:10.15497/rda00039) while the alignment with FDOs will be supported by Research Object Crates (RO-Crates). An RO-Crate (DOI:10.3233/DS-210053) is an open, community-driven, and lightweight approach based on schema.org annotations. This poster corresponds to the FDO2022 conference publication https://riojournal.com/article/94608/element/4/8000890, {"references":["Alves R, Bampalikis D, Castro LJ, González JMF, Harrow J, Kuzak M, Martin E, Psomopoulos F, Via A (2021) ELIXIR Software Management Plan for Life Sciences. BioHackrXiv. https://doi.org/10.37044/osf.io/k8znb","Miksa T, Walk P, Neish P (2020b) RDA DMP Common Standard for Machine-actionable Data Management Plans. https://doi.org/10.15497/rda00039","Soiland-Reyes S, Sefton P, Crosas M, Castro LJ, Coppens F, Fernández J, Garijo D, Grüning B, La Rosa M, Leo S, Ó Carragáin E, Portier M, Trisovic A, RO-Crate Community, Groth P, Goble C (2022) Packaging research artefacts with RO-Crate. Data Science1‑42. https://doi.org/10.3233/DS-210053"]}

ELIXIR-IIB ha partecipato allaFiera Didacta Italia, che ha avutoluogo dal 20 al 22 maggio 2022 a Firenze (Fortezza da Basso) con un seminario interamente dedicato alla bioinformatica, non come disciplina a sé, ma come strumento innovativo per l’apprendimento della biologia. Il seminario, dal titolo “La bioinformatica per apprendere la biologia: uno strumento didattico innovativo”, è statoerogato mediante tecniche di apprendimento attivo, interattivo e collaborativo, venerdì 20 maggio dalle 16:30 alle 18 nella Palazzina Lorenese (sala S6). Attraverso un approccio pratico ed efficace, proposto dalla piattaforma del training di ELIXIR-IIB, si è mostratoai docenti della scuola superiore come utilizzare risorse della bioinformatica per studiare alcuni selezionati argomenti di biologia, come la struttura del DNA e delle proteine o le funzioni e l’evoluzione del genoma. In questo modo è stato possibile comprendere come la bioinformatica possa essere un valido strumento di supporto didattico per esplorare e comprendere la biologia. In altre parole, non si tratterebbe di inserire la bioinformatica nel curriculum come disciplina a sé stante, ma di utilizzarne le risorse e gli strumenti per imparare la biologia in modo efficace e innovativo. Nella prima parte del seminario, si sono propostealcune risorse bioinformatiche da utilizzare per lo studio di selezionati argomenti di biologia molecolare e cellulare. La restante parte del seminario, è stata dedicata a discutere con i docenti presenti le sfide e difficoltà dell’approccio proposto. ELIXIR-IIB offre inoltre ai docenti interessati, un successivo percorso formativo per l’apprendimento di risorse e strumenti bioinformatici utili a insegnare la biologia in modo efficace e innovativo. Allegra Via (Cnr-Ibpm)allegra.via@cnr.it Francesca De Leo (Cnr-Ibiom)francesca.deleo@cnr.it Luana Licata (Università di Roma "Tor Vergata" e Fondazione Human Technopole, Milano)luana.licata@uniroma2.it Anna Marabotti (Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno)amarabotti@unisa.it

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.

Presentation given during the webinar "Covid-19 e condivisione dei dati: perché in Italia si fa troppo poco?" belonging to the event series "Open Science e Covid-19. Collaborare per contrastare la pandemia", on July 21st 2020. Presentation outline: Introduction and programme Rationale ELIXIR, OpenAIRE, RDA ELIXIR support to COVID-19 research European Covid-19 data portal EOSC

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.

Presentation given during the second edition of the webinar "Covid-19 e condivisione dei dati: perché in Italia si fa troppo poco?" belonging to the event series "Open Science e Covid-19. Collaborare per contrastare la pandemia", on November 16th2020. Presentation outline: Introduction Rationale ICDI, ELIXIR, OpenAIRE, RDA ELIXIR support to COVID-19 research European Covid-19 data portal EOSC Programme

ELIXIR 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 recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. The next step is to adopt, promote, and recognise these information standards and best practices, by developing comprehensive guidelines for software curation, and through workshops for training researchers and developers towards the adoption of software best practices.

ELIXIR 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 recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. The next step is to adopt, promote, and recognise these information standards and best practices, by developing comprehensive guidelines for software curation, and through workshops for training researchers and developers towards the adoption of software best practices.

The “ELIXIR Training Platform” is partnering with The Carpentries (Software and Data Carpentry) to train life science researchers in computing and data management skills. The “ELIXIR Software development best practices” group, which is part of the ELIXIR Tools Platform, has proposed “Four simple recommendations to encourage best practices in research software” aiming to help researchers and developers to adopt Open Source Software (OSS) practices and thus improve the quality and sustainability of research software. In order to encourage researchers and developers to adopt the four recommendations (4OSS) and build FAIR software, we are developing specific and practical training materials, taking advantage of the Carpentries approach and experience in training material development and maintenance., published at WSSSPE6.1, October 29, 2018, Amsterdam

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.

Protein phosphorylation is one of the most abundant reversible post-translational modifications in eukaryotes. It is involved in virtually all cellular processes by regulating protein function, localization and stability and by mediating protein-protein interactions. Furthermore, aberrant protein phosphorylation is implicated in the onset and progression of human diseases such as cancer and neurodegenerative disorders. In the last years, tens of thousands of in vivo phosphorylation events have been identified by large-scale quantitative phospho-proteomics experiment suggesting that a large fraction of the proteome might be regulated by phosphorylation. This data explosion is increasingly enabling the development of computational approaches, often combined with experimental validation, aiming at prioritizing phosphosites and assessing their functional relevance. Some computational approaches also address the inference of specificity determinants of protein kinases/phosphatases and the identification of phosphoresidue recognition domains. In this context, several challenging issues are still open regarding phosphorylation, including a better understanding of the interplay between phosphorylation and allosteric regulation, agents and mechanisms disrupting or promoting abnormal phosphorylation in diseases, the identification and modulation of novel phosphorylation inhibitors, and so forth. Furthermore, the determinants of kinase and phosphatase recognition and binding specificity are still unknown in several cases, as well as the impact of disease mutations on phosphorylation-mediated signaling. The articles included in this Research Topic illustrate the very diverse aspects of phosphorylation, ranging from structural changes induced by phosphorylation to the peculiarities of phosphosite evolution. Some also provide a glimpse into the huge complexity of phosphorylation networks and pathways in health and disease, and underscore that a deeper knowledge of such processes is essential to identify disease biomarkers, on one hand, and design more effective therapeutic strategies, on the other.

Background Genes involved in post-mating processes of multiple mating organisms are known to evolve rapidly due to coevolution driven by sexual conflict among male-female interacting proteins. In the malaria mosquito Anopheles gambiae - a monandrous species in which sexual conflict is expected to be absent or minimal - recent data strongly suggest that proteolytic enzymes specifically expressed in the female lower reproductive tissues are involved in the processing of male products transferred to females during mating. In order to better understand the role of selective forces underlying the evolution of proteins involved in post-mating responses, we analysed a cluster of genes encoding for three serine proteases that are down-regulated after mating, two of which specifically expressed in the atrium and one in the spermatheca of A. gambiae females. Results The analysis of polymorphisms and divergence of these female-expressed proteases in closely related species of the A. gambiae complex revealed a high level of replacement polymorphisms consistent with relaxed evolutionary constraints of duplicated genes, allowing to rapidly fix novel replacements to perform new or more specific functions. Adaptive evolution was detected in several codons of the 3 genes and hints of episodic selection were also found. In addition, the structural modelling of these proteases highlighted some important differences in their substrate specificity, and provided evidence that a number of sites evolving under selective pressures lie relatively close to the catalytic triad and/or on the edge of the specificity pocket, known to be involved in substrate recognition or binding. The observed patterns suggest that these proteases may interact with factors transferred by males during mating (e.g. substrates, inhibitors or pathogens) and that they may have differently evolved in independent A. gambiae lineages. Conclusions Our results - also examined in light of constraints in the application of selection-inference methods to the closely related species of the A. gambiae complex - reveal an unexpectedly intricate evolutionary scenario. Further experimental analyses are needed to investigate the biological functions of these genes in order to better interpret their molecular evolution and to assess whether they represent possible targets for limiting the fertility of Anopheles mosquitoes in malaria vector control strategies.

Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time thatmust be devoted to the design, delivery andmaintenance of high-quality trainingmaterials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections. © The Author(s) 2011. Published by Oxford University Press.

Background 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. Results 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 falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases), the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion Our method can be applied to any type of functional motif or pattern (not only PROSITE ones) which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available.

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. Description Phospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins. Conclusion Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.

Questions and answers collected during the Ask Me Anything webinar "Fai una domanda su Covid-19. Gli esperti rispondono", held on 27 November 2020. Besides this document reports on the main aspects of organizing an Ask Me Anything webinar, which was intended to be an online informative event addressing young people on the Covid-19 pandemic. Several months after the start of the pandemic, there were still many doubts and uncertainties among people. On the occasion of the 2020 edition of the European Researchers' Night, an effort was made to open up and discuss with experts and scientists studying and dealing with Sars-Cov-2 virus and Covid-19 disease. &nbsp

This Bachelor's thesis is based on a study of point mutations in the topoisomerase IV ParC subunit of Streptococcus pneumoniae leading to resistance to fluoroquinolones. This bacterium is a well-known pathogen causing many diseases like pneumonia, meningitis, otitis or sepsis. Due to immoderate use of antibiotics in medicine, agriculture and farming, S. pneumoniae, as many other bacteria, has gained resistance to various antimicrobial agents. This can happen through several molecular mechanisms. A typical mechanism of resitance is the appearing of point mutations in one or more proteins of the pathogen interfering with the binding to the drug. This mechanism was not comprehensively studied so far in S. pneumoniae, thus making it difficult to understand the molecular reasons of non-susceptibility to antibiotics. Fluoroquinolones are a class of broad-spectrum antibiotics, used for Gram-positive as well as Gram-negative bacteria. With the help of bioinformatics tools and resources, 49 genomes from different strains of S.pneumoniae were aligned and analysed for possible mutations. This thesis focuses on the structural and functional analysis of three point mutations found in the topoisomerase ParC subunit: changes from serine to phenylalanine at position 79, lysine to asparagine at position 137 as well as change from glutamic acid to lysine at position 379. The first two mutations were previously reported in the literature to cause resistance to fluoroquinolones. They are known to entail important structural changes in the interaction of ParC with DNA and the fluoroquinolone, respectively. The third dramatic alteration at position 379 was identified in this study from the multiple sequence alignment of ParC genes from different strains. Therefore, it was analysed for potential structural changes leading to non-susceptibility to the drug. The structural and functional analysis did not highlight important disruption of bonds or interactions were found. This thesis also covers an overview of all the 20 mutations identified during this study, and a description of the biochemical properties of each mutation.

Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in the PDB with respect to the great amount of interaction data coming from high-throughput experiments (two-hybrid or affinity purification of protein complexes and mass spectrometry). Nevertheless, we can rely on computational techniques for the extraction of high-quality and information-rich data from the known structures and for their spreading in the protein sequence space. We describe here the ongoing research projects in our group: we analyse the protein complexes stored in the PDB and, for each complex involving one domain belonging to a family of interaction domains for which some interaction data are available, we can calculate its probability of interaction with any protein sequence. We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low selectivity and specificity, and build extended patterns. To this aim, we consider residues that are well-conserved in the structure, even if their conservation cannot easily be recognized in the sequence alignment of the proteins holding the function. We also analyse protein surface regions and, through the annotation of the solvent-exposed residues, we annotate protein surface patches via a structural comparison performed with stringent parameters and independently of the residue order in the sequence. Local surface comparison may also help in identifying new sequence patterns, which could not be highlighted with other sequence-based methods. © 2003 John Wiley & Sons, Ltd.

Contains fulltext : 171819.pdf (Publisher’s version ) (Open Access) 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 network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.