Search

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. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Sharing, reusing and reproducing data, software and other digital objects forms the cornerstone of open science practices. Such practices are guided by the Findable, Accessible, Interoperable and Reusable (FAIR) principles. Implementing FAIR principles is not always straightforward, especially in the context of Bioinformatics training. If we are to meet worldwide demand for such training, adhering to the FAIR principles is vital not only for data and software, but also for training materials (any digital object used in a training context, such as slide presentations, exercises, datasets). To facilitate this process, and break the principles down into practical steps, the ELIXIR Training Platform community has put together ten simple rules for making training materials FAIR. Above all is the need to plan to share your training materials online from the outset. Amongst the remaining rules is the importance of describing materials properly, assigning unique identifiers, registering them online, defining access criteria, and using interoperable formats. The full set of ten rules is presented here.

This publication hasn't any creative commons license associated. This deposit is composed by the main article plus the supplementary materials of the publication. This deposit is composed by a publication in which the IGC's authors have had the role of collaboration (it's a collaboration publication). This type of deposit in ARCA is in restrictedAccess (it can't be in open access to the public), and can only be accessed by two ways: either by requesting a legal copy from the author (the email contact present in this deposit) or by visiting the following link: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005715#sec022 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. National Human Genome Research Institute; Office of the Director; National Institutes of Health grant: (U41HG006941). info:eu-repo/semantics/publishedVersion

A significant proportion of human immunodeficiency virus type 1 (HIV)-positive individuals are affected by the cognitive, motor and behavioral dysfunction that characterizes HIV-associated neurocognitive disorders (HAND). While the molecular etiology of HAND remains largely uncharacterized, HIV transactivator of transcription (HIV-Tat) is thought to be an important etiological cause. Here we have used mass spectrometry (MS)-based discovery proteomics to identify the quantitative, cell-wide changes that occur when non-transformed, differentiated human neurons are treated with HIV-Tat over time. We identified over 4000 protein groups (false discovery rate

A significant proportion of human immunodeficiency virus type 1 (HIV)-positive individuals are affected by the cognitive, motor and behavioral dysfunction that characterizes HIV-associated neurocognitive disorders (HAND). While the molecular etiology of HAND remains largely uncharacterized, HIV transactivator of transcription (HIV-Tat) is thought to be an important etiological cause. Here we have used mass spectrometry (MS)-based discovery proteomics to identify the quantitative, cell-wide changes that occur when non-transformed, differentiated human neurons are treated with HIV-Tat over time. We identified over 4000 protein groups (false discovery rate

The diverse, rapidly developing discipline of bioinformatics has become an integral component of all areas of biomedical research in recent years. The ability to manage, analyse and interpret large complex datasets hinges on having access to skilled researchers who have received adequate training in specialised technical areas. Currently in Africa, individuals with these specialised skills are sparsely scattered across the continent and there is an urgent need to develop sustainable training programs to improve bioinformatics capacity. As part of the Human Heredity and Health in Africa (H3Africa) initiative, a pan-African bioinformatics network for H3Africa (H3ABioNet) was established to develop bioinformatics infrastructure together with a sustainable high quality training program. Here, we discuss the various training events and approaches developed by H3ABioNet to address the lack of bioinformatics capacity in Africa, together with the valuable lessons learnt.