Charting microRNA (miRNA) regulation across pathways is key to characterizing their function. Yet, no method currently exists that can quantify how miRNAs regulate multiple interconnected pathways or prioritize them for their ability to regulate coordinate transcriptional programs. Existing methods primarily infer one-to-one relationships between miRNAs and pathways using differentially expressed genes. We introduce PanomiR, an in silico framework for studying the interplay of miRNAs and disease functions. PanomiR integrates gene expression, mRNA-miRNA interactions and known biological pathways to reveal coordinated multi-pathway targeting by miRNAs. PanomiR utilizes pathway-activity profiling approaches, a pathway co-expression network and network clustering algorithms to prioritize miRNAs that target broad-scale transcriptional disease phenotypes. It directly resolves differential regulation of pathways, irrespective of their differential gene expression, and captures co-activity to establish functional pathway groupings and the miRNAs that may regulate them. PanomiR uses a systems biology approach to provide broad but precise insights into miRNA-regulated functional programs. It is available at https://bioconductor.org/packages/PanomiR.

[This corrects the article DOI: 10.1371/journal.pcbi.1010220.].

The emergence of the Coronavirus Disease 2019 (COVID-19) crisis forced training providers worldwide to move their face-to-face (F2F) courses to virtual environments, challenging course organisers to transfer successful F2F concepts into a virtual format.While recording traditional stand-and-deliver lectures was simple enough, facilitating interaction among course participants proved the key challenge, as virtual environments were new to trainees, trainers, and organisers.Interaction in learning always carries an element of risk, whether F2F or virtual.Sometimes, groups do not get along, a strong personality takes over a course discussion, or trainees get lost in activities as they do not feel comfortable asking for help.Interaction in a virtual environment amplifies this problem as disengaging is easier.Trainees can leave their camera and mic off, leave meetings, or simply not attend more easily than in a F2F setting.Trainers too can struggle, as they are unable to walk around the room peering at screens, easily monitoring trainee progress, and initiating casual chats.Trainees can then become lost and feel excluded.Creating a comfortable and efficient interactive learning atmosphere that satisfies a wide variety of learning preferences and home/office-working settings is challenging but crucial for an efficient learning experience in a classroom setting [1].Indeed, well-planned and well-facilitated interactive learning ensures that trainees feel comfortable and included, allowing them to fully engage with each other, the trainers and the training material.In addition to learning, training courses provide networking opportunities-particularly crucial for early career researchers hoping to find collaborators.This networking can happen organically in a F2F setting during poster sessions, over coffee or during dinner.However, this is not without its challenges-more introverted trainees may feel uncomfortable in these networking situations.Entire books are dedicated to networking for those that dislike networking [2].Delivering networking virtually requires extensive restructuring-simply leaving nibbles in a seminar room is no longer feasible-but also provides an opportunity to better capture those who feel alienated in F2F networking events.

[This corrects the article DOI: 10.1371/journal.pcbi.1009218.].

ntroductionBioinformatics training is required at every stage of a scientist's research career.Continual bioinformatics training allows exposure to an ever-changing and growing repertoire of techniques and databases, and so biologists, computational scientists, and healthcare practitioners are all seeking learning opportunities in the use of computational resources and tools designed for data storage, retrieval, and analysis.TAU : PleasecheckwhethertheeditstothesentenceThereareabundantopportunitiesforaccessing:::areco here are abundant opportunities for accessing bioinformatics training for scientists in high-income countries (HICs), with well-equipped facilities and participants and trainers requiring minimal travel and financial costs alongside a range of general advice for developing short bioinformatics training courses [1-3].However, regionally targeted bioinformatics training in low-and middle-income countries (LAU : Pleasenotethatlow À middleincomecountrieshasbeenc MICs) often requires more extensive local and external support, organization, and travel.Due to the limited expertise in bioinformatics in LMICs in general, most bioinformatics training requires a fair amount of collaboration with experts beyond the local community, country, or region.A common model of training, used as the basis of this article, includes a local host collaborating with local, regional, and international experts gathering to train local or regional participants.Recently, there has been a growth of capacity strengthening initiatives in LMICs, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABi-oNet) Initiative [4-6], the Capacity Building for Bioinformatics in Latin America (CABANA) Project [7], the Asia Pacific BioInformatics Network (APBioNet) [8], and the Wellcome Connecting Science Courses and Conferences program [9].One of the important strands of these initiatives is a drive to organize and deliver valuable bioinformatics training, but organizing

Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, it's sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: They're often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.

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.

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.

Demand for training life scientists in bioinformatics skills led to the development of a train-the-trainer collaboration between the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-the-trainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors.

Bioinformatics learning opportunities are now easily available face to face [1] or online [2]. As a rule of thumb, the former can (and will) trump the latter for its level of interactivity and engagement [3]. Most, if not all, students appreciate having the trainer (and classmates) available and close by. Their questions will get answered on the spot, on a case-by-case basis, with a personal touch. If the students happen to be in Europe (e.g., [4,5]) or North America (e.g., [6, 7]), they are in luck: there is no shortage of opportunities for such engaging encounters. Funding is often available for these students to attend face-to-face training. However, other parts of the globe tend to get neglected when it comes to live (and lively) face-to-face scientific training. Although capacity-strengthening initiatives, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABioNet) Initiative [8], CABANA [9], Asia Pacific BioInformatics Network (APBioNet) [10], attempt to address this inequality, especially in low- and middle-income countries, scalability will always be an issue for face-to-face training. Online courses [11–13], however, allow training at scale, regardless of the trainees’ location. Funding for travel is no longer a hurdle: the only requirement is access to a computer (perhaps a smart phone or tablet) and an internet connection. The course is taken in the comfort and convenience of the trainee’s home, office, a library, or perhaps a coffee place with free Wi-Fi. However, on-demand access can be offset by lack of interactivity. Although online training portals often have chat rooms or other means of interacting with fellow learners or the course provider, discussions initiated this way often have a lag time. Web-based seminars (webinars) offer the best of both worlds: they are run online and therefore at no (or little) cost for trainees, they can be scheduled at a convenient time for the target audience, the geographic distance between the trainer and the trainee is no longer an issue, and they allow for interaction between trainer and trainees at the moment of delivery. Webinars are short and straight to the point; the duration is usually no longer than 60 minutes. Questions are encouraged. Quick polls can be launched at any time for further interaction and getting to know the audience. Hands-on exercises can be provided, and follow-up webinars can be arranged for further discussions. How can you achieve a stress-free and successful live streaming of bioinformatics training, which is interactive and available to everyone everywhere? Here are 10 simple rules that we have developed over the past five years of organising and delivering webinars [14]. Although our 10 simple rules are designed to deliver training on bioinformatics resources and projects, they can be easily applied to other domains. Due to the low cost, short duration, and flexible, potentially global access, webinars can be used to train and/or promote a variety of themes in bioinformatics, computational biology, and computer science. Webinars will shorten the cycle time of your training and give you leeway to broaden your arsenal of content. You will be able to cover examples on protists, bacteria, plants—typically of great interest in low- and middle-income countries [15]—and have time to explore new trends in the application of machine learning, artificial intelligence, and blockchain in life sciences. Despite the possibilities of different contents, please be aware this article is not about selecting a training topic but rather on delivering training using webinars.

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

The Curriculum Task Force (CTF) of ISCB’s Education Committee seeks to define curricular guidelines for those who educate or train bioinformatics professionals at all career stages. A recent report of the CTF [1] presented a draft set of bioinformatics core competencies, derived from the results of surveys of (1) core facility directors, (2) career opportunities, and (3) existing curricula. Since the publication of its 2014 report, the CTF has focused on the application of the guidelines in varied contexts to identify areas where refinement is needed. As a first step, the task force held an open meeting at the ISMB conference in July 2014. The ideas discussed at the meeting spawned four working groups (WGs), which focus on (i) defining core competencies for specific types and levels of bioinformatics training, (ii) mapping the curriculum guidelines and competencies to existing materials in order to identify the need for development of new materials, and (iii) identifying where revision of the guidelines may be valuable. The CTF is engaging the ISCB community through open WG meetings at ISCB’s official conferences. Thus far, the WGs have convened at the ISCB Great Lakes Bioinformatics Conference (Purdue University, May 2015) and at the ISMB/ECCB Conference (Dublin, Ireland, July 2015). Additionally, the CTF held a workshop at the Annual General Meeting of the Global Organization of Bioinformatics Learning, Education and Training (Cape Town, South Africa, November 2015). Specifically, the draft competencies have been employed in a wide range of activities and contexts (see Table 1 and [2–11]), including the development of new curricula, the analysis of existing curricula, and the creation of new roles involving bioinformatics. These activities have resulted in the identification of several areas where refinement would be useful: Table 1 Summary of the activities of the ISCB Curriculum Task Force. Identify different levels or phases of competency. It would be helpful to define different phases of competency development, or different levels of competency appropriate for distinct roles. Define competency profiles for disciplines that don’t fit into our current silos. Bioengineering provides an illustrative example of a discipline that requires core competency in bioinformatics but does not fit into our current categories. There are almost certainly others. It would be helpful if we could provide some guidance on how to produce ‘hybrid’ competency profiles, perhaps borrowing some competencies from the TF’s core set and others from different disciplines. The LifeTrain initiative (www.lifetrain.eu) [2, 3] is collecting competency profiles for a range of disciplines of relevance to the biomedical sciences and may provide a useful resource kit for this. Broaden the scope of the competency profiles in response to cutting-edge and emerging research. Current areas requiring improvement include incorporating competencies that capture a fundamental understanding of the biological principles central to analyzing biomolecular data, and broadening the user WG to include applications beyond medicine. Provide guidance on the evidence required to assess whether someone has acquired each competency. For undergraduate, Master’s and PhD programs, learning outcomes for each competency, perhaps with examples of appropriate means of assessment, would be valuable. For established professionals who need to assimilate competencies into their working lives, a different approach may be required (such as keeping a portfolio to capture evidence of competency); the CTF should seek guidance from relevant professional bodies, especially in regulated professions such as healthcare. Provide indicative course content or examples of programs that map to the competency requirements. We do not wish to prescribe what course providers should teach or how they should teach it; however, if a course provider is designing a course to meet a specific competency requirement, it may be helpful to find examples of other programs that do this successfully. One way of achieving this is by mapping existing training content to the TF’s competencies. Another way might be to provide an indication, perhaps based on several courses, of the course content that would meet the competency requirements. This would give course providers the freedom to build their own course syllabi without having to reinvent the wheel. Initiatives to collect examples of Creative Commons (or otherwise reusable) course materials will provide an extremely valuable bank of training materials that could be mapped to the core competencies.