Biology subjects

Palagi, P. M.

Publications and source records attributed to Palagi, P. M..

5 recordsLinked to original sources

bioRxiv2026

Characterization of heterogeneous bioinformatics training needs in the AI era

Bioinformatics training providers serve heterogeneous audiences, a challenge sharpened by fast-evolving technologies such as generative artificial intelligence (AI). Analyzing training-needs surveys in aggregate can mask this heterogeneity. We present a network-based clustering protocol that groups respondents by the similarity of their Likert-type topic ratings: respondents form a Spearman correlation network, and community detection groups them into learner profiles with shared training needs, independent of demographics. We demonstrate the protocol on the 2026 SIB Swiss Institute of Bioinformatics (SIB) training needs survey (n=260), covering topics, barriers, and formats. We identified four interpretable learner profiles: AI and data, infectious disease genomics, functional genomics, and biochemistry, imaging & AI. Each had distinct topic priorities, barriers, and format preferences that an aggregate analysis hides. For example, LLM-based knowledge extraction ranked 2nd overall but only 16th in the infectious disease genomics profile, whereas phylogenetics ranked 17th overall but first there. Across profiles, AI/LLM skills and reproducible data practices were in high demand, whereas AI-assisted learning was, unexpectedly, the least preferred format. Because the protocol requires only a shared Likert scale, it is reusable for other training-needs assessments; the implementation is openly available. Profile-based curricula can target each group's topics, formats, and barriers.

bioinformatics↗

bioRxiv2026

Community needs for FAIR pathogen data

BackgroundDatasets related to infectious diseases are essential for public health decision-making, yet their reuse remains limited by persistent barriers to data sharing and integration. Achieving data that are Findable, Accessible, Interoperable, and Reusable (FAIR) is widely recognized as essential for accelerating scientific discovery and enabling coordinated responses to emerging threats, but the needs of the global pathogen data community have not been systematically characterized. AimThis study, conducted by the Pathogen Data Network (PDN), aims to identify infrastructural and educational priorities among stakeholders working with infectious disease-related data in order to guide community-responsive support for data sharing and interoperability. MethodsA cross-sectional stakeholder survey was disseminated to a well-defined expert population within PDN networks and via open professional channels. A total of 136 responses from researchers, healthcare professionals, bioinformaticians, and educators were analyzed descriptively to identify prioritized barriers, training needs, and preferred support mechanisms. ResultsRespondents consistently identified structural constraints as the primary impediments to effective data use, including limited funding (74%), data-aggregation challenges (68%), and a shortage of skilled personnel (52%). Respondents identified bioinformatics for infectious disease research (68%) as the highest priority for training, followed by guidance on using the integrated pathogen data and tools portal provided by the PDN, the Pathogens Portal (51%). The Pathogens Portal was also ranked as the most essential PDN resource (72%). Preferred training formats included virtual short courses (68%) and webinars (66%). Notably, while researchers emphasized technical subjects like machine learning, educators prioritized foundational case studies. ConclusionThese findings provide an evidence-based diagnostic of community needs and suggest that barriers to FAIR pathogen data are predominantly systemic rather than purely technological. The survey framework and openly available dataset offer a reusable template for assessing needs in other communities and regions. By aligning training, infrastructure development, and outreach with empirically identified priorities, organizations supporting infectious disease research can strengthen the interoperability and reuse of data and establish a benchmark for future community-driven improvements.

scientific communication and education↗

bioRxiv2023

Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and Beyond

Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and reskilling, but unaddressed challenges limit SFTs effectiveness and inclusiveness. Prior work, including the NSF 2026 Reinventing Scientific Talent proposal, called for addressing SFT challenges, and a diverse international group of experts in education, accessibility, and life sciences came together to do so. This paper describes the phenomenography and content analyses that produced a set of 14 actionable recommendations to systematically strengthen SFT. Recommendations were derived from findings in the educational sciences and the experiences of several of the largest life science SFT programs. Recommendations cover the breadth of SFT contexts and stakeholder groups and include actions for instructors (e.g., make equity and inclusion an ethical obligation), programs (e.g., centralize infrastructure for assessment and evaluation), as well as organizations and funders (e.g., professionalize training SFT instructors; deploy SFT to counter inequity). Recommendations are aligned into a purpose-built framework-- "The Bicycle Principles"--that prioritizes evidenced-based teaching, inclusiveness, and equity, as well as the ability to scale, share, and sustain SFT. We also describe how the Bicycle Principles and recommendations are consistent with educational change theories and can overcome systemic barriers to delivering consistently effective, inclusive, and career-spanning SFT. SIGNIFICANCE STATEMENTSTEMM practitioners need sustained and customized professional development to keep up with innovations. Short-format training (SFT) such as workshops and short-courses are relied upon widely but have unaddressed limitations. This project generated principles and recommendations to make SFT consistently effective, inclusive, and career-spanning. Optimizing SFT could broaden participation in STEMM by preparing practitioners more equitably with transformative skills. Better SFT would also serve members of the STEMM workforce who have several decades of productivity ahead, but who may not benefit from education reforms that predominantly focus on undergraduate STEMM. The Bicycle Principles and accompanying recommendations apply to any SFT instruction and may be especially useful in rapidly evolving and multidisciplinary fields such as artificial intelligence, genomics, and precision medicine.

scientific communication and education↗

bioRxiv2022

Bioschemas Training Profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources

Stand-alone life science training events and e-learning solutions are amongst the most sought-after modes of training because they address both point-of-need learning and the limited timeframes available for upskilling. Yet, finding relevant life sciences training courses and materials is challenging because such resources are not marked up for Internet searches in a consistent way. This absence of mark-up standards to facilitate discovery, re-use and aggregation of training resources limits their usefulness and knowledge-translation potential. Through a joint effort between the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), the Bioschemas Training community and the ELIXIR FAIR Training Focus Group, a set of Bioschemas Training profiles has been developed, published and implemented for life sciences training courses and materials. Here, we describe our development approach and methods, which were based on the Bioschemas model, and present the results for the three Bioschemas Training profiles: TrainingMaterial, Course and CourseInstance. Several implementation challenges were encountered, which we discuss alongside potential solutions. Over time, continued implementation of these Bioschemas Training profiles by training providers will obviate the barriers to skill development, facilitating both the discovery of relevant training events to meet individuals learning needs, and the discovery and re-use of training and instructional materials.

scientific communication and education↗

bioRxiv2017

A global perspective on bioinformatics training needs

In the last decade, life-science research has become increasingly data-intensive and computational. Nevertheless, basic bioinformatics and data stewardship are still only rarely taught in life-science degree programmes, creating a widening skills gap that spans educational levels and career roles. To better understand this situation, we ran surveys to determine how the skills dearth is affecting the need for bioinformatics training worldwide. Perhaps unsurprisingly, we found that respondents wanted more short courses to help boost their expertise and confidence in data analysis and interpretation. However, it was evident that most respondents appreciated their need for training only after designing their experiments and collecting their data. This is clearly rather late in the research workflow, and suboptimal from a training perspective, as skills acquired to address a specific need at a particular time are seldom retained, engendering a cycle of low confidence in trainees. To ensure that such skill gaps do not continue to create barriers to the progress of research, we argue that universities should strive to bring their life-science curricula into the digital-data era. Meanwhile, the demand for point-of-need training in bioinformatics and data stewardship will grow. While this situation persists, international groups like GOBLET are increasing their efforts to enlarge the community of trainers and quench the global thirst for bioinformatics training.

scientific communication and education↗