Finnish Center for Science

Espoo, Finland

Finnish Center for Science

Espoo, Finland

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Schneider M.V.,External Services Team | Walter P.,External Services Team | Blatter M.-C.,Swiss Institute of Bioinformatics | Watson J.,External Services Team | And 18 more authors.
Briefings in Bioinformatics | Year: 2012

Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time thatmust be devoted to the design, delivery andmaintenance of high-quality trainingmaterials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections. © The Author(s) 2011. Published by Oxford University Press.


Via A.,University of Rome La Sapienza | Blicher T.,Copenhagen University | Bongcam-Rudloff E.,Swedish University of Agricultural Sciences | Brazas M.D.,Ontario Cancer Institute | And 12 more authors.
Briefings in Bioinformatics | Year: 2013

The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem- solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists. © The Author 2013.


Schneider M.V.,EMBL EBI | Watson J.,EMBL EBI | Attwood T.,University of Manchester | Rother K.,Metropolitan Autonomous University | And 14 more authors.
Briefings in Bioinformatics | Year: 2010

As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009. © The Author 2010. Published by Oxford University Press.


Tallinen T.,University of Jyväskylä | Ojajarvi J.,University of Jyväskylä | Astrom J.A.,Finnish Center for Science | Timonen J.,University of Jyväskylä
Physical Review Letters | Year: 2010

The mechanics and stability of thin-walled structures is a challenging and important branch in structural mechanics. Under vertical compression the deformation of a thin-walled box differs from that of, e.g., a cylindrical shell. It is demonstrated here that compression of a box can be described by a set of generic scaling laws representing three successive regimes: a linear, wrinkled, and collapsed regime. The linear Hookean regime represents the normal behavior before any instability sets in, while the following wrinkled regime is shown to be analogous to compression of thin-film blisters. The compression force reaches its maximum at the onset of the final collapsed regime that has all the characteristics of membrane crumpling. The theoretical scaling laws were confirmed by numerical simulations. © 2010 The American Physical Society.


Sundstrom A.M.,University of Stockholm | Kremp A.,Finnish Environment Institute | Kremp A.,University of Helsinki | Tammilehto A.,University of Oulu | And 3 more authors.
Aquatic Microbial Ecology | Year: 2010

Cold-water dinoflagellates frequently dominate the spring phytoplankton community of the northern Baltic Sea and contribute substantially to the spring primary production. These dinoflagellate communities are largely composed of 3 different species (Biecheleria baltica, Scrippsiella hangoei, Gymnodinium corollarium) that cannot be unambiguously separated by conventional light microscopy. In this study, a fluorescence in situ hybridization (FISH) assay was developed for the detection of B. baltica in field samples. The probe-based method was tested and optimized in vitro, and potential effects of the B. baltica life-cycle transitions were evaluated by examining the labeling quality of the probes on different life-cycle stages before the assay was applied in a field study. The BbRNA4 probe had the highest specificity and was chosen for downstream applications. The lifecycle experiment showed significant differences in labeling efficiency between cultured cells from different growth phases, particularly for the nutrient-limited treatment compared to the control. Tests with spiked field samples revealed that cell recovery in the FISH assay was low (30%), resulting in a considerable underestimation of in situ abundances. However, a strong relationship between FISH and Utermöhl counts of field samples suggests that trends of the bloom dynamics can be followed reliably by this method. By applying the FISH detection method in a field survey, we found that the dynamics of the B. baltica bloom follows that established earlier for the Scrippsiella/Biecheleria/ Gymnodinium complex, with 2 peaks throughout the season. When corrected for processing losses, FISH-based abundance estimates suggest that B. baltica comprised the major fraction of the total dinoflagellate complex during the spring bloom at the southwest coast of Finland. © Inter-Research 2010.


Kaukola T.,University of Oulu | Ojaniemi M.,University of Oulu | Tuimala J.,Finnish Center for Science | Herva R.,University of Oulu | And 3 more authors.
Cytokine | Year: 2011

Background: Signals originating from both maternal and fetal compartments participate in the preterm labor process. Objective: To investigate whether cord blood immunoproteins predict spontaneous preterm labor. Methods: Cord blood from 125 very preterm (gestational age <32 weeks) singleton infants and 33 term infants was collected after birth and analyzed for 107 immunoproteins on microarrays. Immunoproteins from spontaneous preterm births (SPTB) were compared to immunoproteins from preterm births without labor. The placentas were studied for histology and immunohistochemistry. The data was modeled by classification and regression trees (CART) analysis. Results: In preterm births, low CCL16 level predicted SPTB with a sensitivity of 94.7%, and specificity of 46.9%. According to logistic regression analysis, low CCL16 (OR 57.9), histologic chorioamnitis (OR 33.6), and high CCL23 (OR 44.6) were independent risk factors of SPTB. Cord blood CCL16 was higher in preterm births without labor and in term births than in SPTBs. CCL16 and its signaling receptor CCR1 were visualized in syncytiotrophoblast and cytotrophoblast cells of placental villi. Conclusion: Low umbilical cord blood chemokine CCL16 associates with spontaneous preterm birth. Further studies are required to show whether CCL16 is involved in spontaneous preterm labor or in placental disease necessitating elective preterm delivery. © 2011 Elsevier Ltd.


Aspnas M.,Åbo Akademi University | Mattila K.,Finnish Center for Science | Osowski K.,Åbo Akademi University | Westerholm J.,Åbo Akademi University
Journal of Computational Biology | Year: 2010

A central task in protein sequence characterization is the use of a sequence database homology search tool to find similar protein sequences in other individuals or species. PSI-BLAST is a widely used module of the BLAST package that calculates a position-specific score matrix from the best matching sequences and performs iterated searches using a method to avoid many similar sequences for the score. For some queries and parameter settings, PSI-BLAST may find many similar high-scoring matches, and therefore up to 80% of the total run time may be spent in this procedure. In this article, we present code optimizations that improve the cache utilization and the overall performance of this procedure. Measurements show that, for queries where the number of similar matches is high, the optimized PSI-BLAST program may be as much as 2.9 times faster than the original program. Copyright 2010, Mary Ann Liebert, Inc.

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