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ELIXIR-Training-2018-ELIXIR-CZ-Conference

Celia Van Gelder, Patricia M. Palagi, Gabriella Rustici, Pascal Kahlem
2018 Figshare  
The ELIXIR Training Platform activities build on the training expertise of the 22 ELIXIR member states (Nodes) and are implemented in collaboration with the Training Coordinators Group (TrCG). Together we have established a high-quality and impactful training programme for researchers (TtR), developers and infrastructure operators (TtD), and trainers (TtT) as well as a training infrastructure, including the ELIXIR Training Portal TeSS, an e-learning platform and the Virtual Coffee Room (VCR).
more » ... assess and monitor the quality and impact of ELIXIR courses, the Training Platform has defined a core set of KPIs, which is now gradually being adopted throughout the Nodes. The Training Platform has ongoing collaborations with partners such as BD2K-TCC, EDISON, GOBLET and CODATA-RDA. Currently the Training Platform activities focus on sustaining the training infrastructure and extending the portfolio with courses related to newly identified gaps (e.g. Data Management and Stewardship) and on combining courses into learning paths tailored to end-users' individual needs and competencies. Our ambition is to achieve adoption by all ELIXIR Nodes of the community-defined best-practices, standards, training descriptors and feedback systems (the ELIXIR Training Toolkit), thereby supporting capacity building within the Nodes. National training coordinators play a key role in ensuring the synergy and alignment of the ELIXIR Training Platform activities with their own national training programs. In this way the ELIXIR Training Platform facilitates provision and delivery of high quality training in Europe, which helps to further advance research in the life sciences
doi:10.6084/m9.figshare.7378283.v1 fatcat:mpohwwuozjg27jfgqvjbxulgvy

Cellular phenotype database: a repository for systems microscopy data

Catherine Kirsanova, Alvis Brazma, Gabriella Rustici, Ugis Sarkans
2015 Bioinformatics  
Motivation: The Cellular Phenotype Database (CPD) is a repository for data derived from highthroughput systems microscopy studies. The aims of this resource are: (i) to provide easy access to cellular phenotype and molecular localization data for the broader research community; (ii) to facilitate integration of independent phenotypic studies by means of data aggregation techniques, including use of an ontology and (iii) to facilitate development of analytical methods in this field. Results: In
more » ... his article we present CPD, its data structure and user interface, propose a minimal set of information describing RNA interference experiments, and suggest a generic schema for management and aggregation of outputs from phenotypic or molecular localization experiments. The database has a flexible structure for management of data from heterogeneous sources of systems microscopy experimental outputs generated by a variety of protocols and technologies and can be queried by gene, reagent, gene attribute, study keywords, phenotype or ontology terms. Availability and implementation: CPD
doi:10.1093/bioinformatics/btv199 pmid:25861964 pmcid:PMC4528631 fatcat:r6b2cfe5wve7finlcj7uyaotni

The cellular microscopy phenotype ontology

Simon Jupp, James Malone, Tony Burdett, Jean-Karim Heriche, Eleanor Williams, Jan Ellenberg, Helen Parkinson, Gabriella Rustici
2016 Journal of Biomedical Semantics  
Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues. Description: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is
more » ... le with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. Conclusion: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability.
doi:10.1186/s13326-016-0074-0 pmid:27195102 pmcid:PMC4870745 fatcat:3su4umevqnedhdq6yn2d5p4xza

Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability

Bastian Schiffthaler, Myrto Kostadima, Nicolas Delhomme, Gabriella Rustici, Francis Ouellette
2016 PLoS Computational Biology  
The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for training scientists in HTS data analysis. Embarking on developing new training materials is challenging for many reasons. Trainers often do not have prior experience in preparing or delivering such materials and struggle to keep them up to date. A repository of curated HTS training materials
more » ... support trainers in materials preparation, reduce the duplication of effort by increasing the usage of existing materials, and allow for the sharing of teaching experience among the HTS trainers' community. To achieve this, we have developed a strategy for materials' curation and dissemination. Standards for describing training materials have been proposed and applied to the curation of existing materials. A Git repository has been set up for sharing annotated materials that can now be reused, modified, or incorporated into new courses. This repository uses Git; hence, it is decentralized and self-managed by the community and can be forked/built-upon by all users. The repository is accessible at http://bioinformatics.upsc.se/htmr. Author Summary In recent years, the advancement of high-throughput sequencing (HTS) and the rapid development of numerous analysis algorithms and pipelines in this field have resulted in an unprecedentedly high demand for training scientists in HTS data analysis. Generating effective training materials is time-consuming, and a large body of training materials on HTS data analysis has already been generated but is rarely shared among trainers. In this PLOS Computational Biology |
doi:10.1371/journal.pcbi.1004937 pmid:27309738 pmcid:PMC4910983 fatcat:tqu3o5qzizddxgezlvq7glbksu

Gene Expression Atlas at the European Bioinformatics Institute

Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen Parkinson, Alvis Brazma
2009 Nucleic Acids Research  
The Gene Expression Atlas (http://www.ebi.ac .uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/ experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential
more » ... e expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types. The gene queries return the conditions where expression has been reported, while condition queries return which genes are reported to be expressed in these conditions. A combination of both query types is possible. The query results are ranked using various statistical measures and by how many independent studies in the database show the particular gene-condition association. Currently, the database contains information about more than 200 000 genes from nine species and almost 4500 biological conditions studied in over 30 000 assays from over 1000 independent studies.
doi:10.1093/nar/gkp936 pmid:19906730 pmcid:PMC2808905 fatcat:ruisihx4frgvbkwhmun2b6dyoy

Periodic gene expression program of the fission yeast cell cycle

Gabriella Rustici, Juan Mata, Katja Kivinen, Pietro Lió, Christopher J Penkett, Gavin Burns, Jacqueline Hayles, Alvis Brazma, Paul Nurse, Jürg Bähler
2004 Nature Genetics  
Cell-cycle control of transcription seems to be universal, but little is known about its global conservation and biological significance. We report on the genome-wide transcriptional program of the Schizosaccharomyces pombe cell cycle, identifying 407 periodically expressed genes of which 136 show high-amplitude changes. These genes cluster in four major waves of expression. The forkhead protein Sep1p regulates mitotic genes in the first cluster, including Ace2p, which activates transcription
more » ... the second cluster during the M-G1 transition and cytokinesis. Other genes in the second cluster, which are required for G1-S progression, are regulated by the MBF complex independently of Sep1p and Ace2p. The third cluster coincides with S phase and a fourth cluster contains genes weakly regulated during G2 phase. Despite conserved cell-cycle transcription factors, differences in regulatory circuits between fission and budding yeasts are evident, revealing evolutionary plasticity of transcriptional control. Periodic transcription of most genes is not conserved between the two yeasts, except for a core set of ∼40 genes that seem to be universally regulated during the eukaryotic cell cycle and may have key roles in cell-cycle progression.
doi:10.1038/ng1377 pmid:15195092 fatcat:x45rc2l7ejdzvpjyazvbep4dfi

11.1 Deliver The Identified Evaluation Systems And Good Practice Guidelines For Training. Deliver A Tess Platform And Identify E-Learning Solutions

Gabriella Rustici, Kim Gurwitz, Bellis Louisa, ELIXIR Training Community
2018 Zenodo  
This document (D11.1 - Deliver the identified evaluation systems and good practice guidelines for training. Deliver a TeSS platform and identify e-learning solutions) reports the efforts undertaken in the last 2 years by the ELIXIR Training Platform, subtask leaders, ELIXIR Training Coordinators and ELIXIR training colleagues to build the underlying structure of the ELIXIR Training Platform and bring it up to speed. It describes the achievements within the Task 11.1 of the WP11, Building the
more » ... XIR infrastructure. The deliverable in fact touches upon 3 subtasks (11.1.1, 11.1.2 and 11.1.3). "Deliver the identified evaluation systems and good practice guidelines for training" belongs to Subtask 11.1 of the WP11 Assessing training quality¨ good practice and impact . In order to ensure that ELIXIR Training needs are met (see training activities reported in the MTR report) and the training delivered is impactful, of high quality and at scale, we have worked together with multiple stakeholders to define specifications, standards, metrics and key performance indicators for ELIXIR training. It resulted in a harmonized mechanism, and its companion good practice guidelines, that allow to capture and report on ELIXIR training efforts and their impact, across Nodes. This mechanism has been so far adopted by approximately 12 Nodes, and over 2254 short-term feedback surveys have been collected to date. We are currently in the process of introducing long-term feedback surveys, which will allow to collect complementary and invaluable information of ELIXIR training impact in the long term.
doi:10.5281/zenodo.1453020 fatcat:cqcpoyz26ngcdh646mc2nwewyi

FAIR Training in ELIXIR Europe

Mateusz Kuzak, Leyla García Castro, Bérénice Batut, Ricardo Arcila, Niall Beard, Melissa Burke, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Kim Gurwitz, Pascal Kahlem, Paula Martinez, Sarah Morgan (+5 others)
2019 Zenodo  
Rustici 9,12 1 Findable Accessi Use descriptive/relevant keywords, use controlled vocabularies if they exist Use unique identifier, include version and release via a public repository Make  ...  Biosciences ( 18 ELIXIR GreeceInclude references to other data, materials, software, any other digital objects → try to use those that are FAIR as well McQuilton 9,14 , Patricia Palagi 15,16 , Fotis Psom Gabriella  ... 
doi:10.5281/zenodo.3349846 fatcat:z67seyd445crteupitx6h275ry

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology

Robert Hoehndorf, Midori A. Harris, Heinrich Herre, Gabriella Rustici, Georgios V. Gkoutos
2012 Computer applications in the biosciences : CABIOS  
Motivation: The systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed. Applying ontologies to unify phenotype descriptions in the domain of physiology has been a particular challenge due to the high
more » ... omplexity of the underlying domain. Results: In this study, we present the outline of a theory and its implementation for an ontology of physiology-related phenotypes. We provide a formal description of process attributes and relate them to the attributes of their temporal parts and participants. We apply our theory to create the Cellular Phenotype Ontology (CPO). The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created. Availability and implementation: The CPO and the source code we generated to create the CPO are freely available on
doi:10.1093/bioinformatics/bts250 pmid:22539675 pmcid:PMC3381966 fatcat:j5rixqrb4nas7hqmnp7mbkqyva

ArrayExpress update—simplifying data submissions

Nikolay Kolesnikov, Emma Hastings, Maria Keays, Olga Melnichuk, Y. Amy Tang, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova, Marco Brandizi, Tony Burdett, Karyn Megy, Ekaterina Pilicheva (+6 others)
2014 Nucleic Acids Research  
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public sequencing and 42 000 array-based studies comprising over 1.5 million assays in total. The proportion of sequencing-based submissions has grown significantly over the last few
more » ... ars and has doubled in the last 18 months, whilst the rate of microarray submissions is growing slightly. All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold. In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource. Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multiomics data.
doi:10.1093/nar/gku1057 pmid:25361974 pmcid:PMC4383899 fatcat:c4fvlffcnfcpde7agoxjir4beu

Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data

Rachel Lyne, Gavin Burns, Juan Mata, Chris J Penkett, Gabriella Rustici, Dongrong Chen, Cordelia Langford, David Vetrie, Jürg Bähler
2003 BMC Genomics  
The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarrays, optimised protocols to improve array performance, and carried out experiments to assess various characteristics of microarrays. We designed PCR primers to amplify specific probes (180-500 bp) for all known and predicted fission yeast genes, which are printed in duplicate onto
more » ... e regions of glass slides together with control elements (approximately 13,000 spots/slide). Fluorescence signal intensities depended on the size and intragenic position of the array elements, whereas the signal ratios were largely independent of element properties. Only the coding strand is covalently linked to the slides, and our array elements can discriminate transcriptional direction. The microarrays can distinguish sequences with up to 70% identity, above which cross-hybridisation contributes to the signal intensity. We tested the accuracy of signal ratios and measured the reproducibility of array data caused by biological and technical factors. Because the technical variability is lower, it is best to use samples prepared from independent biological experiments to obtain repeated measurements with swapping of fluorochromes to prevent dye bias. We also developed a script that discards unreliable data and performs a normalization to correct spatial artefacts. This paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website.
doi:10.1186/1471-2164-4-27 pmid:12854975 pmcid:PMC179895 fatcat:vluwfrkhhrd2pbwlkjj3zocbeu

Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study

Gabriella Rustici, Harm van Bakel, Daniel H Lackner, Frank Holstege, Cisca Wijmenga, Jurg Bahler, Alvis Brazma
2007 Genome Biology  
8, Issue 5, Article R73 Rustici et al. http://genomebiology.com/2007/8/5/R73 Genome Biology 2007, 8:R73 R73. 14 Genome Biology 2007, Volume 8, Issue 5, Article R73 Rustici et al. http://genomebiology.com  ...  Click here for file R73.4 Genome Biology 2007, Volume 8, Issue 5, Article R73 Rustici et al. http://genomebiology.com/2007/8/5/R73 Genome Biology 2007, 8:R73 R73.12 Genome Biology 2007, Volume  ... 
doi:10.1186/gb-2007-8-5-r73 pmid:17477863 pmcid:PMC1929147 fatcat:p4scycddi5a2biolim6auaw2ja

The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training

Sarah L Morgan, Patricia M Palagi, Pedro L Fernandes, Eija Koperlainen, Jure Dimec, Diana Marek, Lee Larcombe, Gabriella Rustici, Teresa K Attwood, Allegra Via
2017 F1000Research  
: Investigation, Resources, Writing -Review & Editing; : Marek D Larcombe L Conceptualization, Investigation; : Conceptualization, Resources; : Conceptualization, Data Curation, Investigation, Rustici  ... 
doi:10.12688/f1000research.12332.1 pmid:28928938 pmcid:PMC5596339 fatcat:pyiibcvy7fbunpdkdryzzqihfu

Report on training provided across the ELIXIR community [article]

Terri Attwood, Daniel Ben-Avraham, Niall Beard, Victoria Dominguez del Angel, Pedro Fernandes, Kim Gurwitz, Pascal Kahlem, Eija Korpelainen, Brane Leskošek, Jessica Lindvall, Sarah Morgan, Stale Nygard (+7 others)
2019 Zenodo  
Chris Ponting (up to 1/3/2017), Gabriella Rustici (since 1/3/2017) (UK), Celia Van Gelder (since 1/3/2017) (NL) and Patricia Palagi (CH) Description of work and role of partners WP11 -ELIXIR-EXCELERATE  ... 
doi:10.5281/zenodo.3375427 fatcat:46wcktdh55e45mbxqpzu2lqihi

The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination [article]

Eleanor Williams, Josh Moore, Simon W Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Balint Antal, Richard K Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E Carazo-Salas (+1 others)
2016 bioRxiv   pre-print
Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links high-content screening, super-resolution microscopy, time-lapse and digital pathology imaging experiments to public genetic or chemical databases, and to cell and tissue phenotypes expressed using controlled
more » ... ies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on IPython notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.
doi:10.1101/089359 fatcat:isxrnplq3nclndpzy6mhrdqt6y
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