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3. 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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4. Employees' Choices in Learning How to Use Information and Communication Technology Systems at Work: Strategies and Approaches

Author

Korpelainen, Eija and Kira, Mari

Abstract

The purpose of this paper is to promote the understanding of how employees learn to use information and communication technology (ICT) systems at work. The elements of a learning activity in the context of ICT use are identified from the literature. In particular, approaches to learning, learning strategies and problem-solving strategies are reviewed. The empirical part of the study examines how employees choose to start learning how to use ICT systems, and how they choose to learn while solving problems related to system use. The data were collected using qualitative semi-structured interviews with 39 employees in three organizations. The interviewees usually preferred to learn how to use ICT quickly and without investing too much effort. The interviewees preferred informal learning and problem-solving strategies. The most commonly used strategies were to try things out alone or together with peers, or to ask for help from peers. The main conclusions of the study are that the users' learning intentions affect the kind of learning support they need and that ICT learning is best approached as a learning activity strongly rooted in collaboration and the social context.

Published
2010
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6. 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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7. 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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9. RNA-seq Data Analysis

Author

Korpelainen, Eija, primary, Tuimala, Jarno, additional, Somervuo, Panu, additional, Huss, Mikael, additional, and Wong, Garry, additional

Published
2014
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11. 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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12. 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

14. 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., and Corpas, Manuel

Published
2013
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18. 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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19. Self-determined adoption of an ICT system in a work organization

Author

Korpelainen, Eija, Vartiainen, Matti, and Kira, Mari

Subjects
Information systems -- Research, Motivation (Psychology) -- Research, Satisfaction -- Research, Information technology -- Research, Organizational structure -- Research, Information technology, Computers and office automation industries
Abstract

This interpretive single case study examines the process and implications of the self-determined adoption of an internet-based meeting system in a global company. Self-determination theory and structuration theory are used as theoretical lenses to understand the adoption and use of an ICT system. The data were collected using qualitative semi-structured interviews with eleven system users and analyzed using a content analysis approach. The research shows that the self-determined adoption of ICT systems has benefits like user motivation and satisfaction. Problems in such adoption relate to users' experiencing uncertainty regarding the organizational legitimization of the system and support for its use. Employees and organizations are likely to benefit from self-determined adoption because it promotes employees' motivation and initiative-taking. However, a shared understanding of self-determination and organizational support for it are required. Keywords: Implementation of ICT Systems, Institutional Change, Interpretive Single Case Study, Self-Determination, Structuration Theory, User Adoption, INTRODUCTION The implementation of Information and Communication Technology (ICT) systems is often described as a predetermined and controlled process. This paper documents an ICT system implementation process of a very [...]

Published
2010
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20. Experience using web services for biological sequence analysis

Author

Stockinger, Heinz, Attwood, Teresa, Chohan, Shahid Nadeem, Côté, Richard, Cudré-Mauroux, Philippe, Falquet, Laurent, Fernandes, Pedro, Finn, Robert D., Hupponen, Taavi, Korpelainen, Eija, Labarga, Alberto, Laugraud, Aurelie, Lima, Tania, Pafilis, Evangelos, Pagni, Marco, Pettifer, Steve, Phan, Isabelle, and Rahman, Nazim

Published
2008

22. The receptor for interleukin 3 is selectively induced in human endothelial cells by tumor necrosis factor alpha potentiates interleukin 8 secretion and neutrophil transmigration

Author

Korpelainen, Eija I., Gamble, Jennifer R., Smith, William B., Goodall, Gregory J., Sun Qiyu, Woodcock, Joanna M., Dottore, Mara, Vadas, Mathew A., and Lopez, Angel F.

Subjects
Leukocytes -- Research, Cytokines -- Analysis, Tumor necrosis factor -- Analysis, Endothelium -- Cytology, Science and technology
Abstract

An analysis to establish a probable in vivo function of interleukin (IL)-3 involved a study of cells outside the hemopoiesis lineage. IL-3R expression in human endothelial cells was analyzed. Human umbilical vein endothelial cells express functional high-affinity receptors for IL-3, following activation with liposaccharides, IL-1 beta or tumor necrosis factor alpha. Chronic inflammation and allergic disorders may be linked to IL-3.

Published
1993

23. Chipster: user-friendly analysis software for microarray and other high-throughput data

Author

Scheinin Ilari, Gentile Massimiliano, Klemelä Petri, Hupponen Taavi, Tuimala Jarno T, Kallio M Aleksi, Koski Mikko, Käki Janne, and Korpelainen Eija I

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Results Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Conclusions Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

Published
2011
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25. Cytokines and allergy

Author

Vadas, Mathew, Lopez, Angel, Gamble, Jennifer, Khew-Goodall, Yeesim, Smith, William, Bernard, Christophe, Cockerill, Gillian, Cockerill, Peter, Shannon, Frances, Sun, Qiyu, Korpelainen, Eija, van den Heuvel, Cameron, and Hercus, Timothy

Published
1994
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26. 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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27. 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

28. 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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29. 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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32. 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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33. 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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35. 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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38. The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers

Author

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

Published
2014
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39. IAnn: An event sharing platform for the life sciences

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Jimenez, Rafael, Albar, Juan, Bhak, Jong, Blatter, Marie-Claude, Blicher, Thomas, Brazas, Michelle, Brooksbank, Cath, Budd, Aidan, Rivas, Javier De Las, 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, Schneider, Reinhard, Via, Allegra, Villaveces, Jose M., Yu, Ping, Schneider, Maria V., Attwood, Teresa, Corpas, Manuel, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Jimenez, Rafael, Albar, Juan, Bhak, Jong, Blatter, Marie-Claude, Blicher, Thomas, Brazas, Michelle, Brooksbank, Cath, Budd, Aidan, Rivas, Javier De Las, 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, Schneider, Reinhard, Via, Allegra, Villaveces, Jose M., Yu, Ping, Schneider, Maria V., Attwood, Teresa, 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.

Published
2013

40. 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

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.

Published
2013

41. Chipster

Author

University of Helsinki, Dep. of Virology (Haartman Institute) (-2009), University of Helsinki, Haartman Institute, Kallio, M. Aleksi, Tuimala, Jarno T., Hupponen, Taavi, Klemela, Petri, Gentile, Massimiliano, Scheinin, Ilari, Koski, Mikko, Kaki, Janne, Korpelainen, Eija I., University of Helsinki, Dep. of Virology (Haartman Institute) (-2009), University of Helsinki, Haartman Institute, Kallio, M. Aleksi, Tuimala, Jarno T., Hupponen, Taavi, Klemela, Petri, Gentile, Massimiliano, Scheinin, Ilari, Koski, Mikko, Kaki, Janne, and Korpelainen, Eija I.

Published
2011

42. MicroRNA Expression Profiling Reveals MiRNA Families Regulating Specific Biological Pathways in Mouse Frontal Cortex and Hippocampus

Author

University of Helsinki, Research Programs Unit, University of Helsinki, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Department of Biosciences, Juhila, Juuso, Sipila, Tessa, Icay, Katherine, Nicorici, Daniel, Ellonen, Pekka, Kallio, Aleksi, Korpelainen, Eija, Greco, Dario, Hovatta, Iiris, University of Helsinki, Research Programs Unit, University of Helsinki, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Department of Biosciences, Juhila, Juuso, Sipila, Tessa, Icay, Katherine, Nicorici, Daniel, Ellonen, Pekka, Kallio, Aleksi, Korpelainen, Eija, Greco, Dario, and Hovatta, Iiris

Published
2011

43. PDB_REDO : automated re-refinement of X-ray structure models in the PDB

Author

Joosten, Robbie P., Salzemann, Jean, Bloch, Vincent, Stockinger, Heinz, Berglund, Ann-Charlott, Blanchet, Christophe, Bongcam-Rudloff, Erik, Combet, Christophe, Da Costa, L, Deleage, Gilbert, Diarena, Matteo, Fabbretti, Roberto, Fettahi, Geraldine, Flegel, Volker, Gisel, Andreas, Kasam, Vinod, Kervinen, Timo, Korpelainen, Eija, Mattila, Kimmo, Pagni, Marco, Reichstadt, Matthieu, Breton, Vincent, Tickle, J, Vriend, Gert, Joosten, Robbie P., Salzemann, Jean, Bloch, Vincent, Stockinger, Heinz, Berglund, Ann-Charlott, Blanchet, Christophe, Bongcam-Rudloff, Erik, Combet, Christophe, Da Costa, L, Deleage, Gilbert, Diarena, Matteo, Fabbretti, Roberto, Fettahi, Geraldine, Flegel, Volker, Gisel, Andreas, Kasam, Vinod, Kervinen, Timo, Korpelainen, Eija, Mattila, Kimmo, Pagni, Marco, Reichstadt, Matthieu, Breton, Vincent, Tickle, J, and Vriend, Gert

Abstract

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Published
2009
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45. Biologist-friendly analysis software for NGS data

Author

Kallio, Aleksi, primary, Hupponen, Taavi, additional, Gentile, Massimiliano, additional, Tuimala, Jarno, additional, Mattila, Kimmo, additional, Saren, Ari-Matti, additional, Klemelä, Petri, additional, Scheinin, Ilari, additional, and Korpelainen, Eija, additional

Published
2013
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48. COST Action BM 1006 (SeqAhead): MC BUSINESS MEETING AND SCIENTIFIC MEETING

Author

Gisel, Andreas, primary, Attwood, Teresa, additional, Van Helden, Jacques, additional, Valverde, Jose R, additional, Conesa, Ana, additional, Herwig, Ralf, additional, Korpelainen, Eija, additional, Mäkinen, Veli, additional, Pettifer, Steve, additional, Policriti, Alberto, additional, Svensson, Thomas, additional, Vriend, Gert, additional, and Bongcam-Rudloff, Erik, additional

Published
2012
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