Patricia Palagi

Swiss Institute of Bioinformatics · Training Group

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 SFT’s effectiveness and inclusiveness. Prior work, includi...

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 I...

Single-cell omics (SCO) has revolutionized the way and the level of resolution by which life science research is conducted, not only impacting our understanding of fundamental cell biology but also providing novel solutions in cutting-edge medical research. The rapid development of single-cell technologies has been accompanied by the active develop...

Background: Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, t...

Background: Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, t...

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 bioinf...

Author summary 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...

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 preparatio...

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 t...

Switzerland has been a pioneer in the field of bioinformatics since the early 1980s. As time passed, the need for one entity to gather and represent bioinformatics on a national scale was felt and, in 1998, the SIB Swiss Institute of Bioinformatics was created. Hence, 2018 marks the Institute's 20th anniversary. Today, the Institute federates 65 re...

Quality training in computational skills for life scientists is essential to allow them to deliver robust, reproducible and cutting-edge research. A pan-European bioinformatics programme, ELIXIR, has adopted a well-established and progressive programme of computational lab and data skills training from Software and Data Carpentry, aimed at increasi...

The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials, etc .) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping 'recommendat...

Due to its impact on society, the design of new drugs has the potential to interest a wide audience, and provides a rare opportunity to introduce several concepts in chemistry and biochemistry. Drug design can be seen as a multiobjective cyclic optimization process. Indeed, it is important to develop the understanding not only that a drug is genera...

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...

Abstract The Global Organisation for Bioinformatics Learning, Education and Training [1] (GOBLET: http://mygoblet.org) was established to provide a global, sustainable support structure to foster international communities of bioinformatics trainers and trainees. The activities of GOBLET are carried out via committees, which have independent but ove...

The ‘ Metagenomic Pizza ‘ workshop is a bioinformatics-based activity which allows to identify the species present in a pizza thanks to their DNA by using bioinformatics tools. The workshop includes pen and pencil activities. Since 2013, it has been successfully offered to over 2,000 people from the age of nine up. It is an ideal way for them to un...

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of S...

n 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” bioinfor...

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 pl...

Differential expression of soluble proteins was explored in roots of metallicolous (M) and non-metallicolous (NM) plants of Agrostis capillaris L. exposed to increasing Cu to partially identify molecular mechanisms underlying higher Cu tolerance in M plants.Plants were cultivated 2 months on perlite with a CuSO4 (1–30 μM) spiked-nutrient solution....

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This art...

Background / Purpose: ChromosomeWalk.ch is a virtual exhibition which explains the role of bioinformatics in the life sciences today. Visitors are introduced to the world of DNA, proteins and bioinformatics by going on an interactive and recreational journey into the heart of human chromosomes. Main conclusion: Answers are given to questions s...

Background / Purpose: There is a need to improve the quality of the code and software produced by the scientific community. The idea of 3-5 day course was proposed, consisting of talks and exercises. All exercises were written in Python. Main conclusion: After the first version of a course, people left the feedback, that the prepared examples...

Several observations suggest the expansion of a distinct medial smooth muscle cell (SMC) subset in atherosclerosis and restenosis. We characterized the phenotypic features of SMC subsets in cultures derived from human carotid endarterectomy specimens. Specimens comprised an undiseased portion (thin intimal thickening with the underlying media) and...

Background: Different experimental observations suggest the expansion of a distinct medial smooth muscle cell (SMC) subset during atheromatous plaque establishment and restenosis. Objectives: We investigated the presence and features of such SMC subset in cell cultures derived from human carotid endarterectomy (CEA) specimens; moreover, we aimed at...

IntroductionPTM Discovery with MSDatabase Resources for PTM AnalysisConclusions References

In this chapter, we describe the use of SuperHirn and MSight, two complementary tools developed to the processing of label-free LC/MS data in view of the quantitation of proteomics samples. While MSight is mainly dedicated to the visualisation and navigation into LC/MS data, SuperHirn is specialised in peak detection, normalisation and alignment of...

8. Abstracts & Posters , The following values have no corresponding Zotero field: pub-location: Sydney, Australia

8. Abstracts & Posters , The following values have no corresponding Zotero field: pub-location: Estoril, Portugal

Protein identification is a key aspect in the investigation of proteomes. Typically, in a 2-DE gel-based proteomics analysis, the spots are enzymatically digested and the resulting peptide masses are measured, producing mass spectra. Peptides can also be isolated and fragmented within the mass spectrometer, leading to tandem mass spectra. For prote...

Bioinformatics tools may assist scientists in all steps of a typical 2-DE gel analysis workflow, that is, from the description of the sample preparation protocols, going through the gel image analysis and protein identification, to the publication of Internet-ready 2-DE gel databases. This short communication highlights in a single and summarised v...

Plans for the European Proteomics Association (EuPA) were conceived and established during 2004 and 2005, and culminated in the formal inception of the organisation during the 4th HUPO World Congress held in Munich in 2005. The mission from the outset has been three-tiered and is to: i) strengthen the national Proteomics organizations in their effo...

Indeed, the development of two-dimensional (2-D) electrophoresis technology has provided an important research tool for comparative proteomics. A number of other technologies for protein separation have also been investigated in the last few years, such as protein chips, liquid chromatography, and high-pressure liquid chromatography, to name just a...

The early transition of knowledge from highly specialised and sophisticated proteomics research to a diverse community in need of know-how is a challenge that requires backing from advanced research centres and groups, and a coordinating body for the dissemination of this knowledge. The European Proteomics Association (EuPA) Education Committee sig...

The field of proteomics has benefited enormously from the use of images, in particular those resulting from the analysis of samples by two-dimensional electrophoresis. Proteome imaging has the same function as a microscope: it allows the resolution of features and constituents of an object, in this case a proteome, which are otherwise invisible to...

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This chapter describes the role of image analysis software for carrying out proteomics research involving comparisons of two-dimensional electrophoresis (2-DE) gels to identify protein expression changes between different samples. Currently, at least ten different commercial software packages for the analysis of 2-DE gel images are available commer...

Bioinformatics tools for proteomics, also called proteome informatics tools, span today a large panel of very diverse applications ranging from simple tools to compare protein amino acid compositions to sophisticated software for large-scale protein structure determination. This review considers the available and ready to use tools that can help en...

8. Abstracts & Posters , The following values have no corresponding Zotero field: pub-location: Fortaleza, Brazil

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Despite the consolidation of the specialized proteomics literature around a few established journals, such as Proteomics, Molecular and Cellular Proteomics, and the Journal of Proteome Research, a lot of information is still spread in many different publications from different fields, such as analytical sciences, MS, bioinformatics, etc. The purpos...

Images obtained from high-throughput mass spectrometry (MS) contain information that remains hidden when looking at a single spectrum at a time. Image processing of liquid chromatography-MS datasets can be extremely useful for quality control, experimental monitoring and knowledge extraction. The importance of imaging in differential analysis of pr...

Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges in proteomics. Today’s commonly used high throughput approaches combine two-dimensional electrophoresis (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automation is often possible, a number of limitations stil...

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8. Abstracts & Posters , The following values have no corresponding Zotero field: pub-location: INRIA Rh“ne-Alpes, Montbonnot (Grenoble)

6. Guest Edition