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Your search keyword '"Korpelainen, Eija"' showing total 18 results
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18 results on '"Korpelainen, Eija"'

1. Community-driven ELIXIR activities in single-cell omics

Author

Czarnewski, Paulo, primary, Mahfouz, Ahmed, additional, Calogero, Raffaele A., additional, Palagi, Patricia M., additional, Portell-Silva, Laura, additional, Gonzalez-Uriarte, Asier, additional, Soneson, Charlotte, additional, Burdett, Tony, additional, Szomolay, Barbara, additional, Videm, Pavankumar, additional, Hotz, Hans-Rudolf, additional, Papatheodorou, Irene, additional, Hancock, John M., additional, Grüning, Björn, additional, Haerty, Wilfried, additional, Krause, Roland, additional, Capella-Gutierrez, Salvador, additional, Leskošek, Brane, additional, Alessandri, Luca, additional, Arigoni, Maddalena, additional, Rezen, Tadeja, additional, Botzki, Alexander, additional, Ferk, Polonca, additional, Lindvall, Jessica, additional, Heil, Katharina F, additional, Ishaque, Naveed, additional, and Korpelainen, Eija, additional

Published
2022
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3. Ten Simples Rules on How to Organise a Bioinformatics Hackathon

Author

Hollmann, Susanne, primary, Regierer, Babette, additional, Attwood, Teresa K, additional, Gisel, Andreas, additional, Van Helden, Jacques, additional, Rossier, Gregoire, additional, Kersey, Paul J, additional, Korpelainen, Eija, additional, Vriend, Gert, additional, and Bongcam-Rudloff, Erik, additional

Published
2021
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4. The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers

Author

Corpas, Manuel, Jimenez, Rafael C., Bongcam-Rudloff, Erik, Budd, Aidan, Brazas, Michelle D., Fernandes, Pedro L., Gaeta, Bruno, van Gelder, Celia, Korpelainen, Eija, Lewitter, Fran, McGrath, Annette, MacLean, Daniel, Palagi, Patricia M., Rother, Kristian, Taylor, Jan, Via, Allegra, Watson, Mick, Schneider, Maria Victoria, and Attwood, Teresa K.

Published
2015
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5. A framework to assess the quality and impact of bioinformatics training across ELIXIR

Author

Gurwitz, Kim T., Gaur, Prakash Singh, Bellis, Louisa J., Larcombe, Lee, Alloza, Eva, Balint, Balint Laszlo, Botzki, Alexander, Dimec, Jure, del Angel, Victoria Dominguez, Fernandes, Pedro L., Korpelainen, Eija, Krause, Roland, Kuzak, Mateusz, Le Pera, Loredana, Leskošek, Brane, Lindvall, Jessica M., Marek, Diana, Martinez, Paula A., Muyldermans, Tuur, Nygård, Ståle, Palagi, Patricia M., Peterson, Hedi, Psomopoulos, Fotis, Spiwok, Vojtech, van Gelder, Celia W. G., Via, Allegra, Vidak, Marko, Wibberg, Daniel, Morgan, Sarah L., Rustici, Gabriella, Gurwitz, Kim T., Gaur, Prakash Singh, Bellis, Louisa J., Larcombe, Lee, Alloza, Eva, Balint, Balint Laszlo, Botzki, Alexander, Dimec, Jure, del Angel, Victoria Dominguez, Fernandes, Pedro L., Korpelainen, Eija, Krause, Roland, Kuzak, Mateusz, Le Pera, Loredana, Leskošek, Brane, Lindvall, Jessica M., Marek, Diana, Martinez, Paula A., Muyldermans, Tuur, Nygård, Ståle, Palagi, Patricia M., Peterson, Hedi, Psomopoulos, Fotis, Spiwok, Vojtech, van Gelder, Celia W. G., Via, Allegra, Vidak, Marko, Wibberg, Daniel, Morgan, Sarah L., and Rustici, Gabriella

Abstract

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.

Published
2020
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6. A framework to assess the quality and impact of bioinformatics training across ELIXIR

Author

Barcelona Supercomputing Center, Gurwitz, Kim T., Singh Gaur, Prakash, Bellis, Louisa J., Larcombe, Lee, Alloza, Eva, Laszlo Balint, Balint, Botzki, Alexander, Dimec, Jure, Dominguez del Angel, Victoria, Fernandes, Pedro L., Korpelainen, Eija, Krause, Roland, Kuzak, Mateusz, Le Pera, Loredana, Leskošek, Brane, Lindvall, Jessica M., Marek, Diana, Martinez, Paula A., Muyldermans, Tuur, Nygård, Ståle, Palagi, Patricia M., Peterson, Hedi, Psomopoulos, Fotis, Spiwok, Vojtech, Gelder, Celia W. G. van, Via, Allegra, Vidak, Marko, Wibberg, Daniel, Morgan, Sarah L., Rustici, Gabriella, Barcelona Supercomputing Center, Gurwitz, Kim T., Singh Gaur, Prakash, Bellis, Louisa J., Larcombe, Lee, Alloza, Eva, Laszlo Balint, Balint, Botzki, Alexander, Dimec, Jure, Dominguez del Angel, Victoria, Fernandes, Pedro L., Korpelainen, Eija, Krause, Roland, Kuzak, Mateusz, Le Pera, Loredana, Leskošek, Brane, Lindvall, Jessica M., Marek, Diana, Martinez, Paula A., Muyldermans, Tuur, Nygård, Ståle, Palagi, Patricia M., Peterson, Hedi, Psomopoulos, Fotis, Spiwok, Vojtech, Gelder, Celia W. G. van, Via, Allegra, Vidak, Marko, Wibberg, Daniel, Morgan, Sarah L., and Rustici, Gabriella

Abstract

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., Postprint (published version)

Published
2020

7. A framework to assess the quality and impact of bioinformatics training across ELIXIR

Author

Gurwitz, Kim T., primary, Singh Gaur, Prakash, additional, Bellis, Louisa J., additional, Larcombe, Lee, additional, Alloza, Eva, additional, Balint, Balint Laszlo, additional, Botzki, Alexander, additional, Dimec, Jure, additional, Dominguez del Angel, Victoria, additional, Fernandes, Pedro L., additional, Korpelainen, Eija, additional, Krause, Roland, additional, Kuzak, Mateusz, additional, Le Pera, Loredana, additional, Leskošek, Brane, additional, Lindvall, Jessica M., additional, Marek, Diana, additional, Martinez, Paula A., additional, Muyldermans, Tuur, additional, Nygård, Ståle, additional, Palagi, Patricia M., additional, Peterson, Hedi, additional, Psomopoulos, Fotis, additional, Spiwok, Vojtech, additional, van Gelder, Celia W. G., additional, Via, Allegra, additional, Vidak, Marko, additional, Wibberg, Daniel, additional, Morgan, Sarah L., additional, and Rustici, Gabriella, additional

Published
2020
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8. How to Use Chipster for Bioinformatics Analysis of Nanomaterial-Based Omics Data

Author

Nymark, Penny, Ehrhart, Friederike, Willighagen, Egon, Kohonen, Pekka, Korpelainen, Eija, and Grafström, Roland

Abstract

This tutorial will get you started on the basic use of the bioinformatics tool Chipster, an alternative to ArrayAnalysis.org described in other eNM tutorials. It will guide you through the import of microarray data (Affymetrix .CEL files), quality checks, normalization, pre-processing, basic statistical analyses methods and visualization of your data. Chipster is not specific to the nanosafety field, but this tutorial will be focused on the specific needs of nanotoxicological research. Chipster is an open source user-friendly analysis software for high-throughput data analysis. It offers over 350 bioinformatics tools and it is constantly updated according to the latest state-of-the-art tools and scripts. Users can analyse and visualize data interactively, and share complete analysis sessions and automatic workflows with colleagues. Chipster supports the analysis of over 120 different microarray platforms, including the most common types by Affymetrix, Agilent and Illumina. In addition, Chipster has extensive functions and tools for the analysis of NGS data. For additional and deeper guidance on how to use Chipster, beyond this tutorial, see the website with manuals and tutorials or contact the Chipster team. The website also includes guidance on how to analyze next-generation sequencing (NGS) data in Chipster.

Published
2017
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9. iAnn: an event sharing platform for the life sciences

Author

Jimenez, Rafael C., Albar, Juan P., Bhak, Jong, Blatter, Marie-Claude, Blicher, Thomas, Brazas, Michelle D., Brooksbank, Cath, Budd, Aidan, De Las Rivas, Javier, Dreyer, Jacqueline, van Driel, Marc A., Dunn, Michael J., Fernandes, Pedro L., van Gelder, Celia W. G., Hermjakob, Henning, Ioannidis, Vassilios, Judge, David P., Kahlem, Pascal, Korpelainen, Eija, Kraus, Hans-Joachim, Loveland, Jane, Mayer, Christine, McDowall, Jennifer, Moran, Federico, Mulder, Nicola, Nyronen, Tommi, Rother, Kristian, Salazar, Gustavo A., Schneider, Reinhard, Via, Allegra, Villaveces, Jose M., Yu, Ping, Schneider, Maria V., Attwood, Teresa K., Corpas, Manuel, Jimenez, Rafael C., Albar, Juan P., Bhak, Jong, Blatter, Marie-Claude, Blicher, Thomas, Brazas, Michelle D., Brooksbank, Cath, Budd, Aidan, De Las Rivas, Javier, Dreyer, Jacqueline, van Driel, Marc A., Dunn, Michael J., Fernandes, Pedro L., van Gelder, Celia W. G., Hermjakob, Henning, Ioannidis, Vassilios, Judge, David P., Kahlem, Pascal, Korpelainen, Eija, Kraus, Hans-Joachim, Loveland, Jane, Mayer, Christine, McDowall, Jennifer, Moran, Federico, Mulder, Nicola, Nyronen, Tommi, Rother, Kristian, Salazar, Gustavo A., Schneider, Reinhard, Via, Allegra, Villaveces, Jose M., Yu, Ping, Schneider, Maria V., Attwood, Teresa K., and Corpas, Manuel

Abstract

Summary: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. Availability: http://iann.pro/iannviewer Contact: manuel.corpas@tgac.ac.uk

Published
2017

10. Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action

Author

Pawlik, Aleksandra, primary, van Gelder, Celia W.G., additional, Nenadic, Aleksandra, additional, Palagi, Patricia M., additional, Korpelainen, Eija, additional, Lijnzaad, Philip, additional, Marek, Diana, additional, Sansone, Susanna-Assunta, additional, Hancock, John, additional, and Goble, Carole, additional

Published
2017
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11. A global perspective on bioinformatics training needs

Author

Brazas, Michelle D., primary, Brooksbank, Cath, additional, Jimenez, Rafael C., additional, Blackford, Sarah, additional, Palagi, Patricia M, additional, De Las Rivas, Javier, additional, Ouellette, B.F. Francis, additional, Kumuthini, Judit, additional, Korpelainen, Eija, additional, Lewitter, Fran, additional, van Gelder, Celia W.G., additional, Mulder, Nicola, additional, Corpas, Manuel, additional, Schneider, Maria Victoria, additional, Tan, Tin Wee, additional, Clements, Dave, additional, Davies, Angela, additional, and Attwood, Teresa K., additional

Published
2017
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14. Experiences with workflows for automating data-intensive bioinformatics

Author

Spjuth, Ola, Bongcam-Rudloff, Erik, Carrasco Hernández, Guillermo, Forer, Lukas, Giovacchini, Mario, Guimera, Roman Valls, Kallio, Aleksi, Korpelainen, Eija, Kańduła, Maciej M., Krachunov, Milko, Kreil, David P., Kulev, Ognyan, Łabaj, Paweł P., Lampa, Samuel, Pireddu, Luca, Schönherr, Sebastian, Siretskiy, Alexey, Vassilev, Dimitar, Spjuth, Ola, Bongcam-Rudloff, Erik, Carrasco Hernández, Guillermo, Forer, Lukas, Giovacchini, Mario, Guimera, Roman Valls, Kallio, Aleksi, Korpelainen, Eija, Kańduła, Maciej M., Krachunov, Milko, Kreil, David P., Kulev, Ognyan, Łabaj, Paweł P., Lampa, Samuel, Pireddu, Luca, Schönherr, Sebastian, Siretskiy, Alexey, and Vassilev, Dimitar

Published
2015
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15. BioImg.org : A catalog of virtual machine images for the life sciences

Author

Dahlö, Martin, Haziza, Frédéric, Kallio, Aleksi, Korpelainen, Eija, Bongcam-Rudloff, Erik, Spjuth, Ola, Dahlö, Martin, Haziza, Frédéric, Kallio, Aleksi, Korpelainen, Eija, Bongcam-Rudloff, Erik, and Spjuth, Ola

Abstract

Virtualization is becoming increasingly important in bioscience, enabling assembly and provisioning of complete computer setups, including operating system, data, software, and services packaged as virtual machine images (VMIs). We present an open catalog of VMIs for the life sciences, where scientists can share information about images and optionally upload them to a server equipped with a large file system and fast Internet connection. Other scientists can then search for and download images that can be run on the local computer or in a cloud computing environment, providing easy access to bioinformatics environments. We also describe applications where VMIs aid life science research, including distributing tools and data, supporting reproducible analysis, and facilitating education.

Published
2015
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16. Experiences with workflows for automating data-intensive bioinformatics

Author

Spjuth, Ola, primary, Bongcam-Rudloff, Erik, additional, Hernández, Guillermo Carrasco, additional, Forer, Lukas, additional, Giovacchini, Mario, additional, Guimera, Roman Valls, additional, Kallio, Aleksi, additional, Korpelainen, Eija, additional, Kańduła, Maciej M, additional, Krachunov, Milko, additional, Kreil, David P, additional, Kulev, Ognyan, additional, Łabaj, Paweł P., additional, Lampa, Samuel, additional, Pireddu, Luca, additional, Schönherr, Sebastian, additional, Siretskiy, Alexey, additional, and Vassilev, Dimitar, additional

Published
2015
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