The first version of this article gave Maria Victoria Schneider's position at the University of Melbourne as Deputy Director, rather than Honorary Assistant Professor. This has now been corrected.

Bioinformatics is now intrinsic to life science research, but the past decade has witnessed a continuing deficiency in this essential expertise. Basic data stewardship is still taught relatively rarely in life science education programmes, creating a chasm between theory and practice, and fuelling demand for bioinformatics training across all educational levels and career roles. Concerned by this, surveys have been conducted in recent years to monitor bioinformatics and computational training needs worldwide. This article briefly reviews the principal findings of a number of these studies. We see that there is still a strong appetite for short courses to improve expertise and confidence in data analysis and interpretation; strikingly, however, the most urgent appeal is for bioinformatics to be woven into the fabric of life science degree programmes. Satisfying the relentless training needs of current and future generations of life scientists will require a concerted response from stakeholders across the globe, who need to deliver sustainable solutions capable of both transforming education curricula and cultivating a new cadre of trainer scientists.

Not too long ago, in 2013, we worked on a special issue for Briefings in Bioinformatics Internationalization, its interdisciplinary nature and the various emerging efforts in multi-level bioinformatics training and education. The benefits of these efforts are becoming evident, with the community of experts delivering training and services becoming better organized and increasingly interconnected. Training plays a fundamental role to overcome the skills gap amongst life scientists, especially in a fast-changing data-driven and multidisciplinary research landscape. Thus, training is becoming a key pillar within organizations aiming to support researchers. Though many of these organizations have their own training strategy we can already see how concrete agreements and collaborations between them are being established to face common problems. The increasing cooperation among bioinformatics organizations and the training community is leading to a better structured effort to scale and increase capabilities to better understand and cater for the training needs of both the life science researchers and their trainers. The research infrastructures and bioinformatics societies highlighted in the articles of this issue are an example of this ecosystem of interconnected organizations. The SIB Swiss Institute of Bioinformatics (SIB), the German Network for Bioinformatics Infrastructure (de.NBI), the Dutch Techcentre for Life Sciences (DTL) and the EMBL Australia Bioinformatics Resource (EMBL-ABR) in Australia described in this issue are national research infrastructures of bioinformatics service providers with the aim of supporting life science researchers. They are federated infrastructures engaging several national partners with a defined programme and an agreed set of priorities. SIB, de.NBI and DTL are also organized at a European level, sharing common objectives as part of a broader effort named ELIXIR. ELIXIR is a European intergovernmental organization encompassing more than 20 countries including 180 organizations. It coordinates and develops life science resources across Europe so that researchers can more easily find, analyse and share data, exchange expertise and implement best practices. Training is one of the five core ELIXIR’s platforms. The ELIXIR Training Platform is focused on the development and implementation of a common training strategy. In this, the ELIXIR training platform relies on the expertise of its members, collaborates with other national research infrastructures such as EMBL-ABR and establishes key partnerships with training organizations including GOBLET and Data Carpentry. Bioinformatics societies also play an important role in education, usually having training and its promotion as part of the remit of their activities. Similar to research infrastructures, bioinformatics societies have links with other societies and training organizations. Despite these efforts, and their broad scope, the training needs of life scientists will require an even more concerted and global response from stakeholders involving not just research infrastructures and bioinformatics societies but policy makers, funding agencies and educational organizations. In this issue of Briefings in Bioinformatics we have brought together the experience of training initiatives across this range of settings: Baillie-Gerritsen et al. provide an overview of Bioinformatics in Switzerland the role of SIB to support bioinformatics and research. SIB is a well-established distributed research infrastructure with more than 19 years of expertise in the field of Bioinformatics. It is comprised of 19 national partners organized in 12 competency centers and 65 research and service groups. Their services, technical activities and training are grouped into thematic areas including gene and genomes, proteins and proteomes, medicine and health, evolution and phylogeny, structural biology, systems biology and bioinformatics infrastructure. Tauch et al. present the de.NBI. de.NBI is a distributed infrastructure formed in 2015 to provide bioinformatics services and training as well as foster national and international cooperation. It has 30 project partners and is organized in 8 service centers: the Center for Microbial Bioinformatics (BiGi), Bioinformatics for Proteomics (BioInfra.Prot), the Center for Biological Data (BioData), the Center for Integrative Bioinformatics (CIBI), the de.NBI Systems Biology Service Center (de.NBI-SysBio), the German Crop BioGreenformatics Network (GCBN), the Heidelberg Center for Human Bioinformatics (HD-HuB) and the RNA Bioinformatics Center (RBC). van Gelder et al. provide a historical overview of bioinformatics in the Netherlands emphasizing the rich legacy of expertise in the field Bioinformatics harnessed and promoted by the DTL. DTL was formed in 2013 with a strong focus on organizing expert data stewardship training in the Dutch life sciences. It includes 50 life science institutions organized in more than 120 expert groups focus on scientific domains such as health and technology areas like genomics. Schneider et al. introduce EMBL-ABR, a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. EMBL-ABR was established in 2016 and comprises 10 geographically distributed national nodes with 1 coordinating hub. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas are Tools, Data, Standards, Platforms, Compute and Training. De Las Rivas et al. give an overview of the history and current state of the research in bioinformatics and computational biology in Latin America. It also introduces the role of SoIBio as a scientific and professional society to promote research and development of bioinformatics and computational biology in the international region of Ibero-America. SoIBio was formed in 2009 and includes representatives from 22 Ibero-American countries. Attwood et al. summarize the work of several surveys evaluating bioinformatics skills gaps. It concludes there is still a considerable training deficit in the life science community that needs to be overcome. It also draws special attention to the need to embed earlier bioinformatics in educational programmes and the need to train future trainers. Organizations like ELIXIR and GOBLET have been instrumental to improve training in life sciences, yet the main challenges in bioinformatics training require the support and collaboration of lecturers, teachers, trainers, policy makers and funding agencies across the world. Via et al. present the results of a pilot for a pan-European Train-the-Trainer bioinformatics programme. If focuses on how to increase bioinformatics capacity and competency across the life science community helping bioinformatics instructors to better design, develop and deliver high-quality training. It emphasizes the need to establish a network of trainers and instructors, and it links with the efforts of organizations like GOBLET and ELIXIR. In any system it is desirable to know the number of process variables that can be regulated. The Degrees of Freedom Analysis is a method that can be used for this purpose and that can be applied to make decisions for bioinformatics training and educations as demonstrated in the article from Tractenberg et al. Ragan et al. present a review of specific phylogenetic inference methods. Research infrastructures rely on the expertise of their partners and their national strengths to provide services and support. This review done by one of the EMBL-ABR partners presents an evaluation of conceptual foundations of alignment-free phylogenetics approaches contributing to research in phylogenomics and gene transfer. Maria Victoria Schneider Honorary Associate Professor University of Melbourne, Australia E-mail: [email protected] Rafael C Jimenez Chief Technical Officer ELIXIR E-mail: [email protected]

EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distributed national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia's capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas-Tools, Data, Standards, Platforms, Compute and Training-are described in this article.

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.

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.

In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences

Rapid advances in the life sciences and in related information technologies necessitate the ongoing refinement of bioinformatics educational programs in order to maintain their relevance. As the discipline of bioinformatics and computational biology expands and matures, it is important to characterize the elements that contribute to the success of professionals in this field. These individuals work in a wide variety of settings, including bioinformatics core facilities, biological and medical research laboratories, software development organizations, pharmaceutical and instrument development companies, and institutions that provide education, service, and training. In response to this need, the Curriculum Task Force of the International Society for Computational Biology (ISCB) Education Committee seeks to define curricular guidelines for those who train and educate bioinformaticians. The previous report of the task force summarized a survey that was conducted to gather input regarding the skill set needed by bioinformaticians [1]. The current article details a subsequent effort, wherein the task force broadened its perspectives by examining bioinformatics career opportunities, surveying directors of bioinformatics core facilities, and reviewing bioinformatics education programs.

Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

Bioinformatics is central to biology in the 21st century. The generation of terabytes to petabytes of data per day has increased the complexity and challenges of contemporary biological research. The use of computer-based analytical tools on electronically stored and distributed data is fundamentally changing not only core life science research but also its application to problems in medicine, agriculture, conservation and forensics. In light of this ‘information revolution’, school, college and university curricula as well as various forms of postgraduate training and informal education must be redesigned to prepare the next generation of life scientists. In this special issue of Briefings in Bioinformatics, we continue to report on various initiatives in bioinformatics education and training begun in a previous special issue published here in 2010 [11 (6)]. To address the needs of diverse learners and citizenries from multiple cultures, there is a tremendous need for heterogeneous approaches. The articles included herein are drawn from (i) multiple countries: Australia, Costa Rica, Israel, the Netherlands, New Zealand, UK, United States; (ii) multiple curricular levels: public citizenry, secondary level, college and university level, graduate students, postgraduate level (PhD and postdoctoral fellows), faculty development, scientific research community; (iii) multiple pedagogies that range from informal education to training and transmission to engagement in open-ended, collaborative and problem-based learning environments; and (iv) software use that range from Wikis and spreadsheets to high-end research suites. All authors desire to enhance, expand and empower an international community of bioinformatics educators, trainers and researchers. Most operate in the copyleft paradigm of sharing software, databases and analytical tools in an open access environment. The authors report that the current revolution in biological research is a wonderful opportunity to reform the way we teach life sciences. Three factors in particular make this a unique time to explore new ways to enhance learning: The research data and analytical tools are now easily accessible in the public domain; Faculty recognize that they need to seek professional development to stay abreast of the changes in biological knowledge and techniques; and Students are aware of the changes in biology and related disciplines, understand that solving biological problems is relevant to their lives and realize that bioinformatics skills hold possibilities for future employment. Taken together, the convergence of these factors affords us the opportunity to move curriculum reform beyond the relatively small group of ‘early adopters’ to engage the much larger ‘early majority’ of biology faculty. Bioinformatics is a subject in transition subject to being defined differently by life scientists, computer scientists, engineers, experimentalists, mathematicians and so forth. However, despite these differences, when it comes to education and training, there is widespread agreement that to use the databases, software, primary literature, theoretical lenses and applications, users need to develop more quantitative reasoning skills to conceptually understand the bioinformatics challenges faced today. Techniques may change such as recently occurred in the shift away from microarrays to analyze gene expression to RNA-seq analyses of transcriptomes or from a reliance on strictly bifurcating phylogenetic trees based on sequences to network models based on complete genomes that accommodate horizontal gene transfer and endosymbiosis. So the challenge is how do we educate for such a rapidly changing, ill-formed discipline? The authors inside describe exciting possibilities that are adoptable, adaptable and implementable in a wide variety of contexts.

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.

The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show-style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.

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: [email protected].

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 that must be devoted to the design, delivery and maintenance of high-quality training materials. 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.

This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers) will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems) as a method for data integration.

[No abstract available]

As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009.

Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.