Browsing by Subject "SYSTEMS"

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  • Gatta, Viviana; Tomašič, Tihomir; Ilaš, Janez; Zidar, Nace; Peterlin Mašič, Lucija; Barančoková, Michaela; Frlan, Rok; Anderluh, Marko; Kikelj, Danijel; Tammela, Päivi (2020)
    Quorum sensing (QS), a bacterial communication strategy, has been recognized as one of the control mechanisms of virulence in bacteria. Thus, targeting QS offers an interesting opportunity to impair bacterial pathogenicity and develop antivirulence agents. Aiming to enhance the discovery of QS inhibitors, we developed a bioreporter Escherichia coli JW5505 pET-Plsrlux and set up a cell-based assay for identifying inhibitors of autoinducer-2 (AI-2)-mediated QS. A comparative study on the performance of target- versus cell-based assays was performed, and 91 compounds selected with the potential to target the ATP binding pocket of LsrK, a key enzyme in AI-2 processing, were tested in an LsrK inhibition assay, providing 36 hits. The same set of compounds was tested by the AI-2-mediated QS interference assay, resulting in 24 active compounds. Among those, six were also found to be active against LsrK, whereas 18 might target other components of the pathway. Thus, this AI-2-mediated QS interference cell-based assay is an effective tool for complementing target-based assays, yet also stands as an independent assay for primary screening.
  • Ottka, Claudia; Vapalahti, Katariina; Puurunen, Jenni; Vahtera, Laura; Lohi, Hannes (2021)
    Background Metabolomics has been proven to be an invaluable research tool by providing comprehensive insight into systemic metabolism. However, the lack of scalable and quantitative methods with known reference intervals (RIs) and documented reproducibility has prevented the use of metabolomics in the clinical setting. Objective The objective of this study was to validate the developed quantitative nuclear magnetic resonance (NMR) spectroscopy-based metabolomics platform for canine serum and plasma samples and determine optimal sample handling conditions for its use. Methods Altogether, 8247 canine samples were analyzed using a Bruker's 500 MHz NMR spectrometer. Using statistical approaches derived from international guidelines, we studied method precision, measurand stability in various long- and short-term storage conditions, as well as the effect of prolonged contact with red blood cells (RBCs), and differences among blood collection tubes. We also screened interferences with lipemia, hemolysis, and bilirubinemia. The results were compared against routine clinical chemistry methods, and RIs were defined for all measurands. Results We determined RIs for 123 measurands, most of which were previously unpublished. The reproducibility of the results of the NMR platform appeared generally outstanding, and the integrity of the results can be ensured by following standard blood drawing and processing guidelines. Conclusions Owing to the advantages of quantitative results, high reproducibility, and scalability, this canine metabolomics platform holds great potential for numerous clinical and research applications to improve canine health and well-being.
  • Kyykallio, Heikki; Faria, Alessandra V. S.; Hartmann, Rosabella; Capra, Janne; Rilla, Kirsi; Siljander, Pia R-M (2022)
    Recent advances in cell biology research regarding extracellular vesicles have highlighted an increasing demand to obtain 3D cell culture-derived EVs, because they are considered to more accurately represent EVs obtained in vivo. However, there is still a grave need for efficient and tunable methodologies to isolate EVs from 3D cell cultures. Using nanofibrillar cellulose (NFC) scaffold as a 3D cell culture matrix, we developed a pipeline of two different approaches for EV isolation from cancer spheroids. A batch method was created for delivering high EV yield at the end of the culture period, and a harvesting method was created to enable time-dependent collection of EVs to combine EV profiling with spheroid development. Both these methods were easy to set up, quick to perform, and they provided a high EV yield. When compared to scaffold-free 3D spheroid cultures on ultra-low affinity plates, the NFC method resulted in similar EV production/cell, but the NFC method was scalable and easier to perform resulting in high EV yields. In summary, we introduce here an NFC-based, innovative pipeline for acquiring EVs from 3D cancer spheroids, which can be tailored to support the needs of variable EV research objectives.
  • Wennlund, Klara Torlen; Kurland, Lisa; Olanders, Knut; Castren, Maaret; Bohm, Katarina (2022)
    Background The requirement concerning formal education for emergency medical dispatcher (EMD) is debated and varies, both nationally and internationally. There are few studies on the outcomes of emergency medical dispatching in relation to professional background. This study aimed to compare calls handled by an EMD with and without support by a registered nurse (RN), with respect to priority level, accuracy, and medical condition. Methods A retrospective observational study, performed on registry data from specific regions during 2015. The ambulance personnel's first assessment of the priority level and medical condition was used as the reference standard. Outcomes were: the proportion of calls dispatched with a priority in concordance with the ambulance personnel's assessment; over- and undertriage; the proportion of most adverse over- and undertriage; sensitivity, specificity and predictive values for each of the ambulance priorities; proportion of calls dispatched with a medical condition in concordance with the ambulance personnel's assessment. Proportions were reported with 95% confidence intervals. chi(2)-test was used for comparisons. P-levels < 0.05 were regarded as significant. Results A total of 25,025 calls were included (EMD n = 23,723, EMD + RN n = 1302). Analyses relating to priority and medical condition were performed on 23,503 and 21,881 calls, respectively. A dispatched priority in concordance with the ambulance personnel's assessment were: EMD n = 11,319 (50.7%) and EMD + RN n = 481 (41.5%) (p < 0.01). The proportion of overtriage was equal for both groups: EMD n = 5904, EMD + RN n = 306, (26.4%) p = 0.25). The proportion of undertriage for each group was: EMD n = 5122 (22.9%) and EMD + RN n = 371 (32.0%) (p < 0.01). Sensitivity for the most urgent priority was 54.6% for EMD, compared to 29.6% for EMD + RN (p < 0.01), and specificity was 67.3% and 84.8% (p < 0.01) respectively. A dispatched medical condition in concordance with the ambulance personnel's assessment were: EMD n = 13,785 (66.4%) and EMD + RN n = 697 (62.2%) (p = 0.01). Conclusions A higher precision of emergency medical dispatching was not observed when the EMD was supported by an RN. How patient safety is affected by the observed divergence in dispatched priorities is an area for future research.
  • Kivimaa, Paula; Brisbois, Marie Claire; Jayaram, Dhanasree; Hakala, Emma; Siddi , Marco (2022)
    A transition to net-zero carbon energy systems, imperative to combat climate change, is unfolding around the world. Other socio-technical systems also face the need to transition to become more environmentally and socially sustainable. We argue that such transitions will have both positive and negative security implications on numerous issues which deserve attention but have been little addressed in transition studies. We take a socio-technical lens and propose that these security implications can be ex-ante analysed via three elements of socio-technical systems: technology, actors, and institutions. We provide an illustration of such analysis in the energy transition context and use this to create a categorisation framework for expectations analysis. Regarding the technology dimension, expectations concerning, e.g., resource and technology dependencies, risk for technical system disruptions, and effects on interconnected systems can be analysed as relevant security issues. For the actor dimension, issues such as geopolitical uncertainties, regional (in)stability, internal tensions, and diffusion of power are identified. For institutions, e.g., influence on democratic institutions, peace building and structural violence can be assessed. We argue there is a need for improved and forward-looking policy coordination across domains and for academic studies that utilise foresight approaches to assess different security expectations more concretely.
  • Baumeister, Dorothea; Järvisalo, Matti; Neugebauer, Daniel; Niskanen, Andreas; Rothe, Jörg (2021)
    A Abstract argumentation frameworks (AFs), originally proposed by Dung, constitute a central formal model for the study of computational aspects of argumentation in AI. Credulous and skeptical acceptance of arguments in a given AF are well-studied problems both in terms of theoretical analysis-especially computational complexity-and the development of practical decision procedures for the problems. However, AFs make the assumption that all attacks between arguments are certain (i.e., present attacks are known to exist, and missing attacks are known to not exist), which can in various settings be a restrictive assumption. A generalization of AFs to incomplete AFs was recently proposed as a formalism that allows the representation of both uncertain attacks and uncertain arguments in AFs. In this article, we explore the impact of allowing for modeling such uncertainties in AFs on the computational complexity of natural generalizations of acceptance problems to incomplete AFs under various central AF semantics. Complementing the complexity-theoretic analysis, we also develop the first practical decision procedures for all of the NP-hard variants of acceptance in incomplete AFs. In terms of complexity analysis, we establish a full complexity landscape, showing that depending on the variant of acceptance and property/semantics, the complexity of acceptance in incomplete AFs ranges from polynomial-time decidable to completeness for Sigma(p)(3). In terms of algorithms, we show through an extensive empirical evaluation that an implementation of the proposed decision procedures, based on boolean satisfiability (SAT) solving, is effective in deciding variants of acceptance under uncertainties. We also establish conditions for what type of atomic changes are guaranteed to be redundant from the perspective of preserving extensions of completions of incomplete AFs, and show that the results allow for considerably improving the empirical efficiency of the proposed SAT-based counterexample-guided abstraction refinement algorithms for acceptance in incomplete AFs for problem variants with complexity beyond NP. (C) 2021 The Authors. Published by Elsevier B.V.
  • Vuorinne, Ilja; Heiskanen, Janne; Maghenda, Marianne; Mwangala, Lucas; Muukkonen, Petteri; Pellikka, Petri K.E. (2021)
    Biomass is a key variable for crop monitoring and for assessing carbon stocks and bioenergy potential. This study aimed to develop an allometric model for predicting the dry leaf biomass of sisal, an agave plant with crassulacean acid metabolism grown for fibre production in the tropics and subtropics and whose biomass can be utilised as a feedstock to produce biogas through anaerobic digestion. The allometric model was used to estimate leaf biomass and productivity across different stand ages in a sisal plantation in semi-arid region in south-east Kenya (annual rainfall 611 mm and temperature 24.9 °C). Based on a sample of 38 leaves, the best predictor for biomass was leaf maximum width and plant height used as a combined variable in a log-log regression model (cross-validated R2 = 0.96 and root-mean-square error = 7.69 g). The mean productivity in nine 26- to 36-month-old plots was 11.1 Mg ha−1 yr−1, which could potentially yield approximately 3000 m3 CH4 ha−1 yr−1. The leaf biomass in 55 field plots (400 m2 in area) ranged from 2.7 to 42.7 Mg ha−1, with mean at 13.5 Mg ha−1, which equals to 6.3 Mg C ha−1. The yielded allometric equations can be utilised for predicting the leaf biomass of sisal in similar agro-ecological zones. The estimates on plantation biomass can be used in assessing the role of sisal plantations as a regional carbon storage. In addition, the results provide reference on the productivity of agave and crassulacean acid metabolism in semi-arid regions of East Africa, where such reports are few.
  • Palojoki, Sari; Makela, Matti; Lehtonen, Lasse; Saranto, Kaija (2017)
    The aim of this study was to analyse electronic health record-related patient safety incidents in the patient safety incident reporting database in fully digital hospitals in Finland. We compare Finnish data to similar international data and discuss their content with regard to the literature. We analysed the types of electronic health record-related patient safety incidents that occurred at 23 hospitals during a 2-year period. A procedure of taxonomy mapping served to allow comparisons. This study represents a rare examination of patient safety risks in a fully digital environment. The proportion of electronic health record-related incidents was markedly higher in our study than in previous studies with similar data. Human-computer interaction problems were the most frequently reported. The results show the possibility of error arising from the complex interaction between clinicians and computers.
  • Polvi, J.; Heinola, K.; Nordlund, K. (2016)
    N-2 gas is routinely used as a seeding species in fusion plasma to control the amount of power emitted from the plasma by radiation to the tungsten walls of an ITER-like divertor. Nitrogen atoms interact with the plasma-facing materials beryllium and tungsten, and form chemical bonds with the wall surfaces, as well as with plasma hydrogen isotopes, thus raising a special interest in W-N and N-H interactions in the fusion community. In this work we describe the development of an analytical interatomic potential for W-N interactions and benchmark the potential against DFT calculation results for N defects in tungsten.
  • Siirtola, Antti; Heljanko, Keijo (2020)
    The verification of contemporary distributed software systems is challenging, because they are heavily parameterised, containing components whose number and connections cannot be a priori fixed. In this work, we consider the multi-parameterised verification of safety properties by refinement checking in the context of labelled transition systems (LTSs). The LTSs are parameterised by using first-order constructs, sorts, variables, and predicates, while preserving compositionality. This allows us to parameterise not only the number of replicated components but also the communication topology of the system. Our approach to solving a verification task in the parameterised LTS formalism is to determine a finite cut-off set of parameter values such that in order to prove a parameterised system implementation correct with respect to its specification, it is sufficient to consider only finitely many instances of the parameterised system generated by the parameter values in the cut-off set. In the conference version of this work, we converted the problem of determining a finite cut-off set into the unsatisfiability of a first-order formula and provided a satisfiability modulo theories (SMT)-based semi-algorithm for dynamically, i.e., iteratively, computing a cut-off set. In this article, we present a new version of the algorithm and prove that the cut-off sets computed by this new algorithm are optimal. Hence, we call the new version the optimal cut-off algorithm. The algorithm will always terminate for system topologies expressible in the there exists*for all* fragment of first-order logic. It also enables us to consider systems with topologies beyond this fragment, but for these systems, the algorithm is not guaranteed to terminate. We have implemented the approach on top of the Z3 SMT solver and successfully applied it to several system models. As a running example, we consider the leader election phase of the generalised (Byzantine) Raft consensus algorithm and prove the optimal cut-off set of six (respectively, thirteen) parameter values corresponding to instances up to three (respectively, four) servers. To the best of our knowledge, this is the first time a Byzantine variant of the parameterised Raft leader election is automatically verified. (C) 2020 Elsevier B.V. All rights reserved.
  • Siirtola, Antti; Heljanko, Keijo (2020)
    The verification of contemporary distributed software systems is challenging, because they are heavily parameterised, containing components whose number and connections cannot be a priori fixed. In this work, we consider the multi-parameterised verification of safety properties by refinement checking in the context of labelled transition systems (LTSs). The LTSs are parameterised by using first-order constructs, sorts, variables, and predicates, while preserving compositionality. This allows us to parameterise not only the number of replicated components but also the communication topology of the system. Our approach to solving a verification task in the parameterised LTS formalism is to determine a finite cut-off set of parameter values such that in order to prove a parameterised system implementation correct with respect to its specification, it is sufficient to consider only finitely many instances of the parameterised system generated by the parameter values in the cut-off set. In the conference version of this work, we converted the problem of determining a finite cut-off set into the unsatisfiability of a first-order formula and provided a satisfiability modulo theories (SMT)-based semi-algorithm for dynamically, i.e., iteratively, computing a cut-off set. In this article, we present a new version of the algorithm and prove that the cut-off sets computed by this new algorithm are optimal. Hence, we call the new version the optimal cut-off algorithm. The algorithm will always terminate for system topologies expressible in the there exists*for all* fragment of first-order logic. It also enables us to consider systems with topologies beyond this fragment, but for these systems, the algorithm is not guaranteed to terminate. We have implemented the approach on top of the Z3 SMT solver and successfully applied it to several system models. As a running example, we consider the leader election phase of the generalised (Byzantine) Raft consensus algorithm and prove the optimal cut-off set of six (respectively, thirteen) parameter values corresponding to instances up to three (respectively, four) servers. To the best of our knowledge, this is the first time a Byzantine variant of the parameterised Raft leader election is automatically verified. (C) 2020 Elsevier B.V. All rights reserved.
  • Haaranen, Mia; Scuppa, Giulia; Tambalo, Stefano; Järvi, Vilja; Bertozzi, Sine M.; Armirotti, Andrea; Sommer, Wolfgang H.; Bifone, Angelo; Hyytiä, Petri (2020)
    The anterior insular cortex plays a key role in the representation of interoceptive effects of drug and natural rewards and their integration with attention, executive function, and emotions, making it a potential target region for intervention to control appetitive behaviors. Here, we investigated the effects of chemogenetic stimulation or inhibition of the anterior insula on alcohol and sucrose consumption. Excitatory or inhibitory designer receptors (DREADDs) were expressed in the anterior insula of alcohol-preferring rats by means of adenovirus-mediated gene transfer. Rats had access to either alcohol or sucrose solution during intermittent sessions. To characterize the brain network recruited by chemogenetic insula stimulation we measured brain-wide activation patterns using pharmacological magnetic resonance imaging (phMRI) and c-Fos immunohistochemistry. Anterior insula stimulation by the excitatory Gq-DREADDs significantly attenuated both alcohol and sucrose consumption, whereas the inhibitory Gi-DREADDs had no effects. In contrast, anterior insula stimulation failed to alter locomotor activity or deprivation-induced water drinking. phMRI and c-Fos immunohistochemistry revealed downstream activation of the posterior insula and medial prefrontal cortex, as well as of the mediodorsal thalamus and amygdala. Our results show the critical role of the anterior insula in regulating reward-directed behavior and delineate an insula-centered functional network associated with the effects of insula stimulation. From a translational perspective, our data demonstrate the therapeutic potential of circuit-based interventions and suggest that potentiation of insula excitability with neuromodulatory methods, such as repetitive transcranial magnetic stimulation (rTMS), could be useful in the treatment of alcohol use disorders.
  • Niemi, Riitta; Vilar, Maria J; Dohoo, I.R.; Hovinen, Mari; Simojoki, Heli; Rajala-Schultz, Päivi Johanna (2020)
    Antibiotic dry cow therapy (DCT) is an important part of most mastitis control programs. Updating DCT recommendations is an ongoing topic due to the global problem of antimicrobial resistance. Finland, along with other Nordic countries, has implemented selective DCT for decades. Our study analyzed Dairy Herd Improvement (DHI) information from 241 Finnish farmers who participated in a survey about their drying-off practices. The aim was to evaluate herd-level associations between milk somatic cell count (SCC), milk production, and various antimicrobial DCT approaches both cross-sectionally in 2016 and longitudinally in 2012 - 2016. The three DCT approaches in the study were selective, blanket, and no DCT use. An additional aim was to evaluate whether dynamic changes occurred in herd-average SCC and annual milk production over five years, and whether these potential changes differed between different DCT approaches. The method for the longitudinal analyses was growth modeling with random coefficient models. Differences in SCC and milk production between farms with different DCT approaches were minor. Regardless of the farm's DCT approach, annual milk production increased over the years, while average SCC was reasonably constant. The variability in SCC and milk production across all DCT groups was low between years, and most of the variability was between farms. Compared to other milking systems, farms with automatic milking system (AMS) had higher SCC, and in 2016 higher milk production. The results of this study suggest that it is possible to maintain low herd-average SCC and good milk production when using selective DCT and following the guidelines for prudent antimicrobial use. Average SCC and milk production varied across the herds, suggesting that advice on DCT practices should be herd-specific. The methodology of growth modeling using random coefficient models was applicable in analyzing longitudinal data, in which the time frame was relatively short and the number of herds was limited.
  • Holopainen, Jani; Mattila, Osmo; Poyry, Essi; Parvinen, Petri (2020)
  • Bogacheva, Mariia; Egorova, Anna; Slita, Anna; Maretina, Marianna; Baranov, Vladislav; Kiselev, Anton (2017)
    The major barriers for intracellular DNA transportation by cationic polymers are their toxicity, poor endosomal escape and inefficient nuclear uptake. Therefore, we designed novel modular peptide-based carriers modified with SV40 nuclear localization signal (NLS). Core peptide consists of arginine, histidine and cysteine residues for DNA condensation, endosomal escape promotion and interpeptide cross-linking, respectively. We investigated three polyplexes with different NLS content (10 mol%, 50 mol% and 90 mol% of SV40 NLS) as vectors for intranuclear DNA delivery. All carriers tested were able to condense DNA, to protect it from DNAase I and were not toxic to the cells. We observed that cell cycle arrest by hydroxyurea did not affect transfection efficacy of NLS-modified carriers which we confirmed using quantitative confocal microscopy analysis. Overall, peptide carrier modified with 90 mol% of SV40 NLS provided efficient transfection and nuclear uptake in non-dividing cells. Thus, incorporation of NLS into arginine-rich cross-linking peptides is an adequate approach to the development of efficient intranuclear gene delivery vehicles. (C) 2017 Elsevier Ltd. All rights reserved.
  • Paatela, Teemu; Vasara, Anna; Nurmi, Heikki; Kautiainen, Hannu; Kiviranta, Ilkka (2020)
    The International Cartilage Repair Society (ICRS) score and the Oswestry Arthroscopic Score (OAS) have been validated to evaluate repair tissue quality. However, the performance of these scores has not been studied in typical patients undergoing cartilage repair and who have lesions of varying sizes. In this study, we compared the performance of the ICRS and the OAS scores and analyzed the effect of lesion characteristics on the performance of these two scores. Cartilage repair quality was assessed in a total of 104 arthroscopic observations of cartilage repair sites of the knee in 62 patients after autologous chondrocyte implantation. Two observers scored the repair areas independently with the ICRS and the OAS scores. The performance of both scores was evaluated according to internal consistency and inter-rater reliability and correlation between the scores. The frequency and proportion of disagreements were analyzed according to the repair site area and the given score. The correlation between the scores was good (r = 0.91, 95% confidence interval [CI]: 0.87-0.94). Both scores showed moderate internal consistency and inter-rater reliability. Cronbach's alpha was 0.88 (95% CI: 0.80-0.92) for the ICRS score and 0.79 (95% CI: 0.70-0.86) for the OAS score. The intraclass correlation coefficient was 0.89 (95% CI: 0.84-0.92) for the ICRS and 0.81 (95% CI: 0.74-0.87) for the OAS scores. The frequency and proportion of disagreements were higher in larger repair sites. In arthroscopic use, both ICRS and OAS scores perform similarly, however, their reliability deteriorates as the lesion size increases. (c) 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
  • Cattaneo, Marco; Giorgi, Gian Luca; Maniscalco, Sabrina; Paraoanu, Gheorghe Sorin; Zambrini, Roberta (2021)
    A common environment acting on a pair of qubits gives rise to a plethora of different phenomena, such as the generation of qubit-qubit entanglement, quantum synchronization, and subradiance. Here, time-independent figures of merit for entanglement generation, quantum synchronization, and subradiance are defined, and an extensive analytical and numerical study of their dependence on model parameters is performed. A recently proposed measure of the collectiveness of the dynamics driven by the bath is also addressed, and it is found that it almost perfectly witnesses the behavior of entanglement generation. The results show that synchronization and subradiance can be employed as reliable local signatures of an entangling common-bath in a general scenario. Finally, an experimental implementation of the model based on two transmon qubits capacitively coupled to a common resistor is proposed, which provides a versatile quantum simulation platform of the open system in any regime.
  • Halliday, Fletcher W.; Rohr, Jason R.; Laine, Anna-Liisa (2020)
    The dilution effect predicts increasing biodiversity to reduce the risk of infection, but the generality of this effect remains unresolved. Because biodiversity loss generates predictable changes in host community competence, we hypothesised that biodiversity loss might drive the dilution effect. We tested this hypothesis by reanalysing four previously published meta-analyses that came to contradictory conclusions regarding generality of the dilution effect. In the context of biodiversity loss, our analyses revealed a unifying pattern: dilution effects were inconsistently observed for natural biodiversity gradients, but were commonly observed for biodiversity gradients generated by disturbances causing losses of biodiversity. Incorporating biodiversity loss into tests of generality of the dilution effect further indicated that scale-dependency may strengthen the dilution effect only when biodiversity gradients are driven by biodiversity loss. Together, these results help to resolve one of the most contentious issues in disease ecology: the generality of the dilution effect.
  • Pale, Ville; Nikkonen, Taru; Vapaavuori, Jaana; Kostiainen, Mauri; Kavakka, Jari; Selin, Jorma; Tittonen, Ilkka; Helaja, Juho (2013)
  • Hardisty, Alex R.; Bacall, Finn; Beard, Niall; Balcazar-Vargas, Maria-Paula; Balech, Bachir; Barcza, Zoltan; Bourlat, Sarah J.; De Giovanni, Renato; de Jong, Yde; De Leo, Francesca; Dobor, Laura; Donvito, Giacinto; Fellows, Donal; Guerra, Antonio Fernandez; Ferreira, Nuno; Fetyukova, Yuliya; Fosso, Bruno; Giddy, Jonathan; Goble, Carole; Guentsch, Anton; Haines, Robert; Ernst, Vera Hernandez; Hettling, Hannes; Hidy, Dora; Horvath, Ferenc; Ittzes, Dora; Ittzes, Peter; Jones, Andrew; Kottmann, Renzo; Kulawik, Robert; Leidenberger, Sonja; Lyytikäinen-Saarenmaa, Paivi; Mathew, Cherian; Morrison, Norman; Nenadic, Aleksandra; de la Hidalga, Abraham Nieva; Obst, Matthias; Oostermeijer, Gerard; Paymal, Elisabeth; Pesole, Graziano; Pinto, Salvatore; Poigne, Axel; Fernandez, Francisco Quevedo; Santamaria, Monica; Saarenmaa, Hannu; Sipos, Gergely; Sylla, Karl-Heinz; Tähtinen, Marko; Vicario, Saverio; Vos, Rutger Aldo; Williams, Alan R.; Yilmaz, Pelin (2016)
    Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on- line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.