A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning.

Demand for training life scientists in bioinformatics methods, tools and resources and computational approaches is urgent and growing. To meet this demand, new trainers must be prepared with effective teaching practices for delivering short hands-on training sessions-a specific type of education that is not typically part of professional preparation of life scientists in many countries. A new Train-the-Trainer (TtT) programme was created by adapting existing models, using input from experienced trainers and experts in bioinformatics, and from educational and cognitive sciences. This programme was piloted across Europe from May 2016 to January 2017. Preparation included drafting the training materials, organizing sessions to pilot them and studying this paradigm for its potential to support the development and delivery of future bioinformatics training by participants. Seven pilot TtT sessions were carried out, and this manuscript describes the results of the pilot year. Lessons learned include (i) support is required for logistics, so that new instructors can focus on their teaching; (ii) institutions must provide incentives to include training opportunities for those who want/need to become new or better instructors; (iii) formal evaluation of the TtT materials is now a priority; (iv) a strategy is needed to recruit, train and certify new instructor trainers (faculty); and (v) future evaluations must assess utility. Additionally, defining a flexible but rigorous and reliable process of TtT 'certification' may incentivize participants and will be considered in future.

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

ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR's framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course.

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience.

Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge "Introduction to Bioinformatics" course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery-mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online "question and discussion" forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings.

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

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 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 identifying relevant training events and activities locally and worldwide. AVAILABILITY AND IMPLEMENTATION: http://mygoblet.org/training-portal.

Best practices in bioinformatics training for life scientists.

The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

iAnn: an event sharing platform for the life sciences.

SUMMARY: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. AVAILABILITY: http://iann.pro/iannviewer CONTACT: manuel.corpas@tgac.ac.uk.

Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments.

The synthesis of di-myo-inositol phosphate (DIP), a common compatible solute in hyperthermophiles, involves the consecutive actions of inositol-1-phosphate cytidylyltransferase (IPCT) and di-myo-inositol phosphate phosphate synthase (DIPPS). In most cases, both activities are present in a single gene product, but separate genes are also found in a few organisms. Genes for IPCT and DIPPS were found in the genomes of 33 organisms, all with thermophilic/hyperthermophilic lifestyles. Phylogeny of IPCT/DIPPS revealed an incongruent topology with 16S RNA phylogeny, thus suggesting horizontal gene transfer. The phylogenetic tree of the DIPPS domain was rooted by using phosphatidylinositol phosphate synthase sequences as out-group. The root locates at the separation of genomes with fused and split genes. We propose that the gene encoding DIPPS was recruited from the biosynthesis of phosphatidylinositol. The last DIP-synthesizing ancestor harboured separated genes for IPCT and DIPPS and this architecture was maintained in a crenarchaeal lineage, and transferred by horizontal gene transfer to hyperthermophilic marine Thermotoga species. It is plausible that the driving force for the assembly of those two genes in the early ancestor is related to the acquired advantage of DIP producers to cope with high temperature. This work corroborates the view that Archaea were the first hyperthermophilic organisms.

The GTPB training programme in Portugal.

The Gulbenkian Training Programme in Bioinformatics has been offering hands-on training courses in Oeiras, PT for more than a decade. This article is a review of its functional organization and evolution. We aim to share our experience with people considering setting-up similar training facilities elsewhere. More than 1600 course attendees, so far, have attended our courses. Their experiences have helped us to know how to satisfy their training requirements and what is feasible with very limited resources.

Training bioinformaticians in High Performance Computing.

In the last decade, bioinformatics has become an indispensable branch of modern science research, experiencing an explosion in financial support, developed applications and data collection. The growth of the datasets that are emerging from research laboratories, industry, the health sector, etc., are increasingly raising the levels of demand in computing power and storage. Processing biological data, in the large scales of these datasets, often requires the use of High Performance Computing (HPC) resources, especially when dealing with certain types of omics data, such as genomic and metagenomic data. Such computational resources not only require substantial investments, but they also involve high maintenance costs. More importantly, in order to keep good returns from the investments, specific training needs to be put in place to ensure that wasting is minimized. Furthermore, given that bioinformatics is a highly interdisciplinary field where several other domains intersect (such as biology, chemistry, physics and computer science), researchers from these areas also require bioinformatics-specific training in HPC, in order to fully take advantage of supercomputing centers. In this document, we describe our experience in training researchers from several different disciplines in HPC, as applied to bioinformatics under the framework of the leading European bioinformatics platform ELIXIR, and analyze both the content and outcomes of the course.

The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training.

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 out seven pilot EE-TtT courses (training more than sixty new instructors), collaboratively drafted the training materials, and started establishing a network of trainers and instructors within the ELIXIR community. The EE-TtT pilot represents an essential step towards the development of a sustainable and scalable ELIXIR TtT programme. Indeed, the lessons learned from the pilot, the experience gained, the materials developed, and the analysis of the feedback collected throughout the seven pilot courses have both positioned us to consolidate the programme in the coming years, and contributed to the development of an enthusiastic and expanding ELIXIR community of instructors and trainers.

Clinical pathology differences in laboratory utilization in hospice and nonhospice units.

A significant difference can be observed between hospice and nonhospice philosophy. Nonhospice units direct its effort to cure and sustain patient's life using disease-modifying therapeutic procedures, while hospice units focus on patient's quality of life. However, despite the differences between the 2 basic philosophies in question, both approaches share 1 aspect in common: the correct diagnosis of the patient. In any case above, laboratory analysis is a valuable tool. This work aims to compare the laboratory utilization between nonhospice cancer and hospice cancer units. Laboratory requests from patients within a 1-year period were evaluated and the hospice laboratory profile was presented. We demonstrated that nonhospice unit had a major volume of requested laboratory test than hospice unit, but for inpatients this difference was not so dramatic.

Semente de linhaça e o efeito de seus compostos sobre as células mamárias / Flaxseed and the effect of his compound on human breast cell

O câncer de mama é uma doença que afeta principalmente as mulheres e segundo as estatísticas esta vem aumentando com certa frequência nos países ocidentais, e isto tem preocupado a comunidade científica. Esta doença está associada a diversos fatores de risco, sendo a dieta um fator que tem demonstrado relação com a promoção de câncer de mama. Uma alimentação rica em substância funcional tem sido alvo de atenção, pois os fitoestrógenos têm mostrado através de estudos experimentais, propriedades benéficas à saúde, e parece contribuir para a redução do risco de câncer de mama. Alimentos como a semente de linhaça tem sido objeto de estudo, já que contêm substâncias consideradas como quimioprotetora e sua estrutura química assemelha-se ao estrogênio humano e compete com este pelo seu sítio de ligação. De acordo com os estudos experimentais, realizados com animais e humanos, a semente de linhaça é rica em lignana e outros componentes, que apresentaram ter efeito fracamente estrogênico e antiestrogênico, mostrando exercer influência na diminuição do risco de câncer de mama.

The breast cancer is a disease that affects especially women, and according to statistics, this is increasing with certain frequency in western country and it has been concerning the scientific society. This disease is associated with various factors of risk, and diets have being considered a factor that has promoted breast cancer. Food rich in functional substances has drawn attention, because phytoestrogens have showed, through experimental studies, beneficial properties for health and appeared to contribute for the decrease of breast cancer risk. Food with flaxseed has been object of study, because it contains substances called chemoprotective and its chemistry structure resembles human estrogens and competes with its link site. According to the experimental studies made in animals and humans, flaxseed is rich in lignans and other components, that seem to have weak estrogenic/antiestrogenic effect showing to exert influence in the decreasing of breast cancer risk.