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There are emerging concerns in biomedical science regarding the limited success in reproducing research data and translating them into applications. This scenario is a major problem for academic science as well as for the economy and the society at large which benefit from research findings. Excluding fraud, the reasons for this might be found in the lack of identification and application of standards, poor description and sharing of data, protocols and procedures, and underdevelopment of quality control activities. Driven by stakeholders and scientific networks, several attempts to face the reproducibility crisis have been initiated. In this chapter we discuss the actions implemented into the academic research environment, as well as the difficulties encountered due principally to the limitation of resources. Our aim is to highlight how the identification and adoption of best practice for Quality and Data Management are key issues in this battle, and to propose a roadmap for their implementation, based on the involvement of all the interested actors, such as the academic community, research agencies and government programs.

Background Involvement in research activities is complex in pediatric nursing and allied health professionals (AHPs). It is important to understand which individual factors are associated with it to inform policy makers in promoting research. Methods A cross-sectional observational study was conducted to describe the level of participation in research activities over the last ten years of nurses and AHPs working in a tertiary pediatric hospital. A large sample of nurses and AHPs working in an Italian academic tertiary pediatric hospital completed an online self-report questionnaire between June and December 2018. Three multivariate logistic regression analyses were performed to predict participation in research projects, speaking at conferences, and writing scientific articles. Results Overall, data from 921 health professionals were analyzed (response rate = 66%), of which about 21% (n = 196) reported participating in a research project, while 33% (n = 297) had attended a scientific conference as a speaker, and 11% (n = 94) had written at least one scientific paper. Having a Master or a Regional Advanced Course, working as an AHP or a ward manager, as well as regularly reading scientific journals and participation in an internal hospital research group or attendance in a specific course about research in the hospital, significantly predicted participation in research projects, speaking at conferences and writing scientific papers. It is important to foster research interest and competencies among health professionals to improve participation in research projects, speaking at conferences, and writing scientific papers. Conclusions Overall, we found a good level of attendance at conferences as speakers (33%), a moderate level of participation in research (21%), and low levels for writing scientific papers (11%). Our study highlighted the need to support participation in research activities among nurses and AHPs. Policymakers should identify strategies to promote research among nurses and AHPs, such as protected rewarded time for research, specific education, strengthened collaboration with academics, and financial support. Moreover, hospital managers should promote the development of research culture among health professionals, to improve their research competencies and evidence-based practice.

GOBLET presentation at GOBLET Exhibitor Booth at ISMB/ECCB2021, 25-30 July 2021 (https://www.iscb.org/ismbeccb2021) &nbsp

This study was supported by the COST Action CA18131 "Statistical and machine learning techniques in human microbiome studies." IM-I was supported by the "MS type I" program (CP16/00163) from the Instituto de Salud Carlos III and co-funded by Fondo Europeo de Desarrollo Regional-FEDER. MN was grateful for the additional support by the project "Information and Communication Technologies for a Single Digital Market in Science, Education and Security" of the Scientific Research Center, NIS-3317 and National roadmaps for research infrastructures (RIs) grant number NIS-3318. LL was supported by Academy of Finland (decision 295741). IE was supported by H2020-EU.4.b. project "Integration of knowledge and biobank resources in comprehensive translational approach for personalized prevention and treatment of metabolic disorders (INTEGROMED)" (grant agreement ID 857572). MD was supported by the Luxembourg National Research Fund (FNR) CORE grant (C18/BM/12585940). The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 "ML4Microbiome" that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies. European Cooperation in Science and Technology (COST) CA18131 European Commission CP16/00163 project "Information and Communication Technologies for a Single Digital Market in Science, Education and Security" of the Scientific Research Center NIS-3317 National roadmaps for research infrastructures (RIs) NIS-3318 Academy of Finland 295741 H2020-EU.4.b. project "Integration of knowledge and biobank resources in comprehensive translational approach for personalized prevention and treatment of metabolic disorders (INTEGROMED)" 857572 Luxembourg National Research Fund (FNR) CORE grant C18/BM/12585940

The Ketogenic Diet (KD) is a high-fat, low-carbohydrate diet that has been utilized as the first line treatment for contrasting intractable epilepsy. It is responsible for the presence of ketone bodies in blood, whose neuroprotective effect has been widely shown in recent years but remains unclear. Since glutathione (GSH) is implicated in oxidation-reduction reactions, our aim was to monitor the effects of KD on GSH brain levels by means of magnetic resonance spectroscopy (MRS). MRS was acquired from 16 KD patients and seven age-matched Healthy Controls (HC). We estimated metabolite concentrations with linear combination model (LCModel), assessing differences between KD and HC with t-test. Pearson was used to investigate GHS correlations with blood serum 3-B-Hydroxybutyrate (3HB) concentrations and with number of weekly epileptic seizures. The results have shown higher levels of brain GSH for KD patients (2.5 ± 0.5 mM) compared to HC (2.0 ± 0.5 mM). Both blood serum 3HB and number of seizures did not correlate with GSH concentration. The present study showed a significant increase in GSH in the brain of epileptic children treated with KD, reproducing for the first time in humans what was previously observed in animal studies. Our results may suggest a pivotal role of GSH in the antioxidant neuroprotective effect of KD in the human brain.

Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation.

The bacteria living in and on us, over 100 trillion, are essential for human development, immunity and nutrition and ultimately for human health. Researchers awareness of the importance of the microbiome for human wellbeing brought in the latest decade to the flourishing of new and numerous projects focused on the human microbiome, increasing the number of large microbiome datasets available. As a result, statistical and machine learning techniques to solve microbiome data analysis challenges are in high demand. The workshop “Statistical and Machine Learning Techniques for Microbiome Data Analysis” was organised by the COST Action ML4Microbiome to introduce the main concepts of study design and statistical/machine learning techniques used in human microbiome studies to a broad community of researchers and to foster connections between the discovery-oriented microbiome and statistical/machine learning researchers inside and outside the ML4Microbiome COST Action. To this aim, the workshop was organised as part of the training programme of the GOBLET & EMBnet Annual General Meeting 2021. This allowed ML4Microbiome to reach a broad and multidisciplinary community of scientists working in Bioinformatics and Computational Biology research and education from all over the world. The workshop attracted more than 80 participants from 40 different countries. In this paper, we report about the main topics treated and discuss the attendants’ feedback regarding their level of satisfaction and their specific needs/demands for possible improvement of the training offer of ML4Microbiome in the microbiome research field. Under the authors’ permission, presentations were recorded and are available as an ML4Microbiome playlist on YouTube (www.youtube.com/playlist?list=PL2aQNGWO1UUUmK7GJBK29yZr8Hnq6xFSD). The programme and presentations files are available at the ML4Microbiome website (https://www.ml4microbiome.eu/activities-and-events/ml4microbiome-workshop-on-statistical-and-machine-learning-techniques-for-microbiome-data-analysis/).

I present CHARME, an Action funded through COST (European Cooperation in Science and Technology). CHARME aims to identify needs and gaps in standards, teaming up with other initiatives and organisations, and proposing new strategies for successful assimilation of standards into the daily work-flow of researchers. This presentation underlinesthe scenario in which CHARME moves forward and actions that the scientific community is called to support in this field to increase the efficiency and competitiveness of life-science research in Europe and worldwide.

MicroRNAs (miRNAs) are ubiquitous regulators of gene expression, evolutionarily conserved in plants and mammals. In recent years, although a growing number of papers debate the role of plant miRNAs on human gene expression, the molecular mechanisms through which this effect is achieved are still not completely elucidated. Some evidence suggest that this interaction might be sequence specific, and in this work, we investigated this possibility by transcriptomic and bioinformatics approaches. Plant and human miRNA sequences from primary databases were collected and compared for their similarities (global or local alignments). Out of 2,588 human miRNAs, 1,606 showed a perfect match of their seed sequence with the 5' end of 3,172 plant miRNAs. Further selections were applied based on the role of the human target genes or of the miRNA in cell cycle regulation (as an oncogene, tumor suppressor, or a biomarker for prognosis, or diagnosis in cancer). Based on these criteria, 20 human miRNAs were selected as potential functional analogous of 7 plant miRNAs, which were in turn transfected in different cell lines to evaluate their effect on cell proliferation. A significant decrease was observed in colorectal carcinoma HCT116 cell line. RNA-Seq demonstrated that 446 genes were differentially expressed 72 h after transfection. Noteworthy, we demonstrated that the plant mtr-miR-5754 and gma-miR4995 directly target the tumor-associated long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and nuclear paraspeckle assembly transcript 1 (NEAT1) in a sequence-specific manner. In conclusion, according to other recent discoveries, our study strengthens and expands the hypothesis that plant miRNAs can have a regulatory effect in mammals by targeting both protein-coding and non-coding RNA, thus suggesting new biotechnological applications.

Using a transcriptomic approach, we performed a pilot study in healthy subjects to evaluate the changes in gene expression induced by grape consumption. Blood from twenty subjects was collected at baseline (T0), after 21 days of grape-rich diet (T1) and after one-month washout (T2). Gene expression profiling of peripheral blood mononuclear cells from six subjects identified 930 differentially expressed transcripts. Gene functional analysis revealed changes (at T1 and/or T2) suggestive of antithrombotic and anti-inflammatory effects, confirming and extending previous finding on the same subjects. Moreover, we observed several other favourable changes in the transcription of genes involved in crucial processes such as immune response, DNA and protein repair, autophagy and mitochondrial biogenesis. Finally, we detected significant changes in many long non-coding RNAs genes, whose regulatory functions are being increasingly appreciated. Altogether, our data suggest that a grape diet may exert its beneficial effects by targeting different strategic pathways.

In the current era of Big Data production and Artificial Intelligence development, one of the fastest growing scientific and professional areas that is generating petabytes of data is Life Sciences. In this context, many scientific and educational institutions recognize that it is no longer possible to carry out adequate studies and research in this area without well-trained computational biologists and bioinformaticians. GOBLET is an international organization, established in 2012, with the mission to cultivate a global community of bioinformatics trainers who support learning, education and training. GOBLET's mission was defined under the vision that there is a clear worldwide need to harmonize bioinformatics training activities and to unite, inspire and equip bioinformatics trainers. This can only be achieved by developing active linkages and collaborations with many national and international institutions that work in the field of Life Sciences. Relevant activities conducted last year by GOBLET members, together with other international experts, include the initiation of a series of assets, standards and guidelines, to define competencies, promote best practices and provide high-quality resources for learning, education and training in bioinformatics and computational biology, worldwide. GOBLET's new website offers a comprehensive portal, providing many materials and resources for the international bioinformatics community.

In this paper, we first summarise the 2020 International Conference of EMBnet (The Global Bioinformatics Network) on “Bioinformatics Approaches to Precision Research”, held on 23th-24th September 2020, and then briefly introduce the main topics and contributions presented at the Conference and published in this supplement issue. The Conference’s main aim was to share the knowledge and scientific achievements of EMBnet members to prompt the cross-fertilisation of ideas and collaborations. The title reflects the type of contributions presented (20 in total), covering a wide range of cutting-edge research topics for which advanced bioinformatics methods and precision approaches are essential, and training in Bioinformatics. As for many other organisations, 2020 was the first year that the EMBnet Annual General Meeting was not in presence but ran on a virtual meeting platform because of the pandemic’s travel restrictions to moves. If this situation represented a limitation to our social activities, it allowed us to offer the possibility to attend the Conference to a larger number of researchers (i.e., 190 from 38 different countries). Among all registered people, 148 were following the conference presentations on both days. Under the authors’ permission, presentations were recorded and are available at the EMBnet Conference 2020 playlist on YouTube (https://youtube.com/playlist?list=PLVP2771lOozCHAOgVXBdqPW3oclEmzNIA), whereas the programme is available at the EMBnet Conference 2020 Google Drive folder (https://drive.google.com/file/d/1wWqp_I5vf-1GUlKmbCUq45EDQ9LfbrpC/view)

Objectives The aim of this study was to ascertain predictors of survival, liver disease (LD), and enteral autonomy 48 months after resection in neonatal short bowel syndrome (SBS) patients with residual small bowel length (SBL) ≤40 cm. Patients and Methods Medical records of all SBS patients followed up between 1996 and 2016 were retrospectively reviewed. Survival rate, prevalence of LD, and of enteral autonomy were evaluated. Results Forty-seven patients were included, and 43 were still alive at the end of the study period, with cumulative 48-month survival of 91.5%. Twenty-one (45%) patients developed LD, all within the first 6 months. On the final follow-up visit, three (6%) patients were still jaundiced and progressed toward end-stage LD. LD prevalence was higher in patients with recurrent bloodstream infections (odds ratio [OR] 5.4, 95% confidence interval [CI] 1.5–19.3). Of the 43 surviving patients, 22 (51%) had enteral autonomy 48 months after resection. The probability of weaning off parenteral nutrition (PN) was strongly correlated with the remaining SBL. Conclusion Survival of patients who have undergone neonatal massive small bowel resection has improved in recent years. Multidisciplinary strategies can improve the course of LD, but not the probability of weaning off PN, which seems to be strongly dependent on the anatomical profile of residual bowel. Therefore, the primary surgical approach should be as conservative as possible to gain even small amounts of intestinal length, which may be crucial in promoting intestinal adaptation.

CADASIL syndrome is a rare disease that belongs to a group of disorders called leukodystrophies. It is well established that NOTCH3 gene on chromosome 19 is primarily responsible for the development of the CADASIL syndrome. Herein, an attempt is made to shed light on the actual molecular mechanism underlying CADASIL syndrome, through insights extracted from comprehensive evolutionary studies and in silico modelling on Notch 3 protein. In particular, we suggest the use of optical coherence tomography angiography for the detection of early signs of small vessel diseases, which are the major precursors to a repertoire of neurodegenerative conditions, including CADASIL.

Research publications and data nowadays should be publicly available on the internet and, theoretically, usable for everyone to develop further research, products, or services. The long-term accessibility of research data is, therefore, fundamental in the economy of the research production process. However, the availability of data is not sufficient by itself, but also their quality must be verifiable. Measures to ensure reuse and reproducibility need to include the entire research life cycle, from the experimental design to the generation of data, quality control, statistical analysis, interpretation, and validation of the results. Hence, high-quality records, particularly for providing a string of documents for the verifiable origin of data, are essential elements that can act as a certificate for potential users (customers). These records also improve the traceability and transparency of data and processes, therefore, improving the reliability of results. Standards for data acquisition, analysis, and documentation have been fostered in the last decade driven by grassroot initiatives of researchers and organizations such as the Research Data Alliance (RDA). Nevertheless, what is still largely missing in the life science academic research are agreed procedures for complex routine research workflows. Here, well-crafted documentation like standard operating procedures (SOPs) offer clear direction and instructions specifically designed to avoid deviations as an absolute necessity for reproducibility. Therefore, this paper provides a standardized workflow that explains step by step how to write an SOP to be used as a starting point for appropriate research documentation., Zweitver��ffentlichungen der Universit��t Potsdam : Mathematisch-Naturwissenschaftliche Reihe; 1201

Using Human Gene Expression Microarrays (Agilent) technologies, we investigated changes of the level of gene expression in peripheral blood mononuclear cells of healthy subjects after 21 days of fresh table grape-rich diet and after an additional 28-day washout. Several hundreds of genes were differentially expressed after grape intake or after washout. The functional analysis of these genes detected significant changes in key processes such as inflammation and immunity, thrombosis, DNA and protein repair, autophagy and mitochondrial biogenesis. Moreover, fresh grape intake was found to influence the expression of many long non-coding RNA genes. The data can be valuable for researchers interested in nutrigenetics and nutrigenomics studies and are related to the research article “Gene expression signature induced by grape intake in healthy subjects reveals wide-spread beneficial effects on PBMCs” [1]. Keywords: Peripheral blood mononuclear cells, Microarray data, Pathway analyses, Biological processes, Grape intake, Diets, Human health, Health benefits

Background High throughput technologies have provided the scientific community an unprecedented opportunity for large-scale analysis of genomes. Non-coding RNAs (ncRNAs), for a long time believed to be non-functional, are emerging as one of the most important and large family of gene regulators and key elements for genome maintenance. Functional studies have been able to assign to ncRNAs a wide spectrum of functions in primary biological processes, and for this reason they are assuming a growing importance as a potential new family of cancer therapeutic targets. Nevertheless, the number of functionally characterized ncRNAs is still too poor if compared to the number of new discovered ncRNAs. Thus platforms able to merge information from available resources addressing data integration issues are necessary and still insufficient to elucidate ncRNAs biological roles. Results In this paper, we describe a platform called Arena-Idb for the retrieval of comprehensive and non-redundant annotated ncRNAs interactions. Arena-Idb provides a framework for network reconstruction of ncRNA heterogeneous interactions (i.e., with other type of molecules) and relationships with human diseases which guide the integration of data, extracted from different sources, via mapping of entities and minimization of ambiguity. Conclusions Arena-Idb provides a schema and a visualization system to integrate ncRNA interactions that assists in discovering ncRNA functions through the extraction of heterogeneous interaction networks. The Arena-Idb is available at http://arenaidb.ba.itb.cnr.it

Standards and SOP implementation in the life-sciences research: a snapshot from the COST Action CHARME In a world where the biological and clinical research relay almost entirely on new and advanced high-throughput technologies and sophisticated approaches to omics data integration, the quality, reliability and format of data represents the most valuable features to be ensured. To answer to this pressing need, in 2005 the Research Data Management (RDM) initiative introduced a new set of principles for data management services. Following their principles, data should be FAIR – Findable, Accessible, Interoperable and Reusable. However, applying the FAIR data principles mainly addresses the metadata levels and does not necessarily take into account the quality of the source datasets, an essential prerequisite of good research. Generating data according to standards, using Standard Operating Procedures (SOPs) and implementing efficient Data Management Plans (DMP), by also hosting data on sustainable infrastructures are crucial steps forward a safe and reliable way to do research. Harmonising standardisation strategies to increase the efficiency and competitiveness of European life-science research (CHARME), is an 4-year Action founded through COST (European Cooperation in Science and Technology) which addresses two main challenges: the sensibilization of the European scientific community and of different stakeholders around the theme of standards, and the unification of efforts of different initiatives toward the implementation of a common and efficient strategy to promote good practices at all levels of the data production and analysis processes. In her talk, Domenica D’Elia will present CHARME by underlining the scenario in which it moves forward and actions that the scientific community is called to support for a global implementation of standards and SOPs in the life-sciences research.

Modern, high-throughput methods for the analysis of genetic information, gene and metabolic products and their interactions offer new opportunities to gain comprehensive information on life processes. The data and knowledge generated open diverse application possibilities with enormous innovation potential. To unlock that potential skills in generating but also properly annotating the data for further data integration and analysis are needed. The data need to be made computer readable and interoperable to allow integration with existing knowledge leading to actionable biological insights. To achieve this, we need common standards and standard operating procedures as well as workflows that allow the combination of data across standards. Currently, there is a lack of experts who understand the principles and possess knowledge of the principles and relevant tools. This is a major barrier hindering the implementation of FAIR (findable, accessible, interoperable and reusable) data principles and the actual reusability of data. This is mainly due to insufficient and unequal education of the scientists and other stakeholders involved in producing and handling big data in life science that is inherently varied and complex in nature, and large in volume. Due to the interdisciplinary nature of life science research, education within this field faces numerous hurdles including institutional barriers, lack of local availability of all required expertise, as well as lack of appropriate teaching material and appropriate adaptation of curricula.

Objectives: The aim of this study was to evaluate the safety and efficacy of home parenteral nutrition (HPN) service in patients with benign chronic intestinal failure (CIF). Methods: This was a 10-y retrospective, non-interventional, multicenter study conducted with adult and pediatric patients with CIF who received HPN service. We analyzed data prospectively collected from a dedicated register by HPN nurses. Results: From January 2002 to December 2011 a total of 794 patients (49.7% male, median age 1 y for children and 57 y for adults) were included in the analysis. Over the 10-y period, 723 central venous catheter (CVC) complications occurred, of which 394 were infectious (54.5%), 297 were mechanical (41.1%), and 32 (3.3%) were defined as CVC-related thrombosis. The complication rate was higher in children (1.11 per patient) than in adults (0.70 per patient). During the observation period, the rates of both infectious and mechanical complications showed a global declining trend and ∼75% of patients had neither infectious nor mechanical CVC complications. HPN efficacy was evaluated in 301 patients with a minimum follow-up of 36 mo. Body mass index and Karnofsky score showed that the median growth significantly increased (P < 0.001) over baseline for adults and pediatric patients in the 0 to 2 age range. Conclusions: The use of a structured register has proved to be a key strategy for monitoring the outcomes of long-term treatment, improving time efficiency, and preventing potential malpractice. To our knowledge, this is largest survey ever documented; the results were consistent despite the heterogeneity of the centers because of duly applied standard rules and protocols.

Open Science describes the ongoing transitions in the way research is performed, i.e. researchers collaborate, knowledge is shared, and science is organized. It is driven by digital technologies and by the enormous growth of data, globalization, enlargement of the scientific community and the need to address societal challenges [23]. It has now widely been recognized that making research results more accessible to all societal actors contributes to better and more efficient science, as well as to innovation in the public and private sectors [1, 17]. However, the reuse of research results can only be achieved reliably and efficiently, if these data are valorized in a specific manner. Data are to be generated, formatted and stored according to Standard Operating Procedures (SOPs) and according to sophisticated Data Management Plans [23]. Hence, to generate accurate and reproducible data sets, to allow interlaboratory comparisons as well as further and future use of research data it is mandatory to work in line with good laboratory practices and well-defined and validated methodologies. Within this article, members of the Cost Action CHARME [10] will discuss aspects of quality management and standardization in context with Open Access (OA) efforts. We will address the question: Are Standardization and Quality Management measures in life-science research crucially needed or introduce further unwanted means of regulation?.

The COST Action CHARME: a European initiative for the harmonisation of standards for life-science research Open Science (OS) describes the ongoing transitions in the way research is performed, i.e. researchers collaborate, knowledge is shared, and science is organised. OS is driven by digital technologies and by the growth of data, globalisation, enlargement of the scientific community and the need to address societal challenges. It has now widely been recognised that making research results more accessible contributes to more efficient science and innovation in the public and private sectors. To unlock that potential, data needs to be made computer readable and interoperable. Therefore, they must be generated, formatted and stored according to Standard Operating Procedures and Data Management Plans included as an integral part of any projects. Although several initiatives are actives in different life science research fields, they are still too much fragmented. A significant barrier hindering the implementation of FAIR (findable, accessible, interoperable and reusable) data principles is the lack of awareness and insufficient education of scientists and other stakeholders in the process of producing, handling, publishing and transferring knowledge to biotech applications. CHARME: "Harmonising standardisation strategies to increase the efficiency and competitiveness of European life-science research", is an Action funded through COST (European Cooperation in Science and Technology). CHARME aims to identify needs and gaps in standards, teaming up with other initiatives and organisations, and proposing new strategies for successful assimilation of standards into the daily work-flow of researchers. This presentation underlines the scenario in which CHARME moves and actions needed to increase the efficiency and competitiveness of life-science research.

Standardisation and quality management are important drivers in the life sciences and biotechnology, as only data generated with minimum quality assurance can be easily implemented into industrial applications. Standards assure and ensure that data become easily accessible, shareable and comparable along the value chain. Reproducibility, standards and standard operating procedures (SOPs) in data generation and analysis are challenging topics of modern research and bioinformatics. Only by the use of common standards life science research will improve its efficiency and competitiveness. CHARME aims to identify needs and gaps in standards, teaming up with other initiatives and organisations, and proposing new strategies for the successful assimilation of standards into the daily work-flow of researchers. Currently, 30 EU countries are involved in this initiative, which makes it one of the most widely recognised Actions among all COST initiatives.

The 15th International NETTAB workshop and the 11th Integrative Bioinformatics Symposium were held together in Bari, on October 14-16, 2016, as Joint NETTAB/IB 2015 Meeting. A special topic for the meeting was "Bioinformatics for ncRNA", but the traditional topics of both meetings series were also included in the event. About 60 scientific contributions were presented, including six keynote lectures, one special guest lecture, and many oral communications and posters. A " Two-Day Hands-on Tutorial" event was organised before the workshop. Selected full papers from some of the best works presented in Bari were submitted either to the Journal of Integrative Bioinformatics or to a purpose Call for a Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been either accepted for publication in this Supplement or published in the Journal of Integrative Bioinformatics, for a more complete presentation of the outcomes of the meeting.