The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond.

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. To streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo's implementation and describe its broad range of functionality for designing, testing, and executing Galaxy tools, workflows, and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers.

Fluctuations in pelagic fish density linked to ambient conditions.

Animal behaviour has been broadly studied for its social or functional aspects but less often for understanding the interactions between organisms and their ambient conditions. A pilot observational study was performed by means of underwater camera to investigate the correlation between environmental factors and the density of fish in the epipelagic habitat of a European temperate reservoir. Explored factors confirmed a positive correlation between water temperature and all observed categories: nonpredatory, predatory, single nonpredatory and schooling fish, as well as freshwater bream and roach. On the other hand, de-trended solar irradiance was found to be negatively correlated with density of nonpredatory fish, freshwater bream and European perch. Sunshine duration was negatively correlated with the density of predatory fish. Precipitation a showed positive relationship with single nonpredatory fish and European perch, whereas wind strength had a negative relationship with density of schooling fish. Furthermore, density of predatory fish was positively correlated with density of single nonpredatory fish and counts of observed clusters. Altogether, findings indicate that fish density is correlated with abiotic factors and the occurrence of predators. This suggests that more ecologically complex studies should be encouraged for better understanding of ecological interactions that drive the structure of aquatic ecosystems.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

Species-specific schooling behaviour of fish in the freshwater pelagic habitat: an observational study.

Social living of animals is a broadly occurring phenomenon, although poorly studied in freshwater systems, fish schooling behaviour is an excellent example. The composition of fish schools, species-specific schooling tendencies and preferences of adult fish were studied in the pelagic habitat of the Rímov Reservoir, Czech Republic. Video recordings captured over a total of 34 days (16 h per day) in the clear water period of three seasons were analysed. From four species identified as school-forming species - bream, bleak, roach and perch, 40% of the individuals observed formed schools of 3-36 individuals. Although conspecific schools prevailed, 20% of individuals formed heterospecific schools, except bleak that schooled strictly with conspecifics. Schools were composed of individuals of similar body size and life strategy. Heterospecific schools were significantly larger than conspecific schools and showed uneven proportion among species, that is, one species being more abundant when the school dimension increased. Probability of encounter in bleak was lowest and proved highest inclination for schooling. Gregarianism levels depended on species morphology and body size, with larger and morphologically advanced fish tending less to sociability. This indicates that the antipredator function of schooling behaviour is intensified with increasing vulnerability of the species.

The pros and cons of the invasive freshwater apex predator, European catfish Silurus glanis, and powerful angling technique for its population control.

Catfish have spread across Europe and several countries out of this region within the last decades. Basic knowledge of this apex predator has revealed concerns of invasive behaviour and questions regarding its utilization as a biomanipulation species. However, a method enabling its regulation to a required level has not yet been developed. We simulated the impact of angling on the catfish population by method of hook-lines in two post-mining lakes with a monitored population consisting of tagged individuals and in two reservoirs as reference sites. Further, the efficiency of hook-lines as a reducing device was examined and the economic aspects were determined. Catfish population in localities where the species is unwanted or invasive may be efficiently reduced to a harmless level by hook-lines and angling (depending on the approach of anglers). The most efficient time of the year seems to be spring to early summer with catch efficiency of 5.4 individuals per 10 baits in one day. The catch efficiency markedly decreased during the second part of the year and did not exceed 2.8 individuals per 10 baits in one day. Mean size of catfish had negative impact whereas catfish biomass had positive impact on the catch efficiency. Trophic status and number of catfish in the locality had no impact on the catch efficiency. According to model, 11-18 bait-days per 1 ha per season is efficient to decrease catfish population to 10% of the original size. Both angling and hook-lines are very simple, they are financially and time bearable mechanisms of catfish regulation in any condition. However, catfish play an important role as a biomanipulative species in many localities. In this case where catfish is beneficial, angling presents a real threat of population collapse and loss of the biomanipulative effect.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.

High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.

Galaxy Portal: interacting with the galaxy platform through mobile devices.

UNLABELLED: : We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general. AVAILABILITY AND IMPLEMENTATION: The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer. CONTACT: geirksa@ifi.uio.no.

Pyrolysis of Specific Non-Recyclable Waste Materials: Energy Recovery and Detailed Product Characteristics.

This study explores the pyrolysis process applied to various non-utilized waste materials, specifically focusing on separated plastics from municipal waste, wood waste (including pallets and window frames), paper rejects, and automotive carpets. Different combinations of these waste materials were subjected to pyrolysis, a process involving high-temperature treatment (600 °C) in a nitrogen atmosphere. The resulting products, including biochar, gas, and liquid fractions, as well as the residual waste materials, underwent comprehensive analysis. The evaluation of pyrolysis products emphasizes their quality, energy content, and potential applications. Notably, the pyrolysis gas derived from the combination of separated municipal plastics and waste wood exhibited the highest calorific value at 49.45 MJ/m3. Additionally, Mixture 2, consisting of plastic and wood waste, demonstrated the highest calorific value for the pyrolysis condensate, reaching 30.62 MJ/kg. Moreover, Mixture 3, benefiting from biochar utilization as a sorbent, displayed the highest iodine value at 90.01 mg/g.

A non-lethal stable isotope analysis of valued freshwater predatory fish using blood and fin tissues as alternatives to muscle tissue.

Stable isotope analysis (SIA) is widely used to study trophic ecology and food webs in aquatic ecosystems. In the case of fish, muscle tissue is generally preferred for SIA, and the method is lethal in most cases. We tested whether blood and fin clips can be used as non-lethal alternatives to muscle tissue for examining the isotopic composition of two freshwater predatory fish, European catfish (Silurus glanis) and Northern pike (Esox lucius), species of high value for many freshwater systems as well as invasive species in many others. Blood samples from the caudal vein, anal fin clips, and dorsal muscle obtained by biopsy punch were collected from four catfish and pike populations (14-18 individuals per population). Subsequently, these samples were analyzed for δ13C and δ15N. The effects of alternative tissues, study site, and fish body mass on the isotopic offset were investigated. Both species showed a correlation between the isotopic offset and the tissue type, as well as the study site, but no significant relationship with the body mass. The isotopic offsets between tissues were used to calculate the conversion equations. The results demonstrated that both blood and fin clips are suitable and less invasive alternative to muscle in SIA studies focused on European catfish and Northern pike. Blood provided better correspondence to muscle isotope values. However, our results clearly demonstrated that isotopic offsets between tissues vary significantly among populations of the same species. Therefore, obtaining a muscle biopsy from several individuals in any population is advisable to gain initial insights and establish a possible population-specific inter-tissue conversion.

Trophic Position of the Species and Site Trophic State Affect Diet Niche and Individual Specialization: From Apex Predator to Herbivore.

Intra-species variability in isotopic niches, specifically isotopic total niche width (ITNW), isotopic individual niche width (IINW), and isotopic individual specialization (IIS), was studied using an innovative approach without sacrificing the vertebrates. Stable isotopes (δ13C, δ15N) in four body tissues differing in isotopic half-life were analyzed from four freshwater fish species representing different trophic positions. ITNW was widest for the apex predator (European catfish) and narrowest for the obligate predator (Northern pike). IINW exhibited a polynomial trend for the European catfish, Northern pike, and Eurasian perch (mesopredator), decreasing with body mass and increasing again after exceeding a certain species-dependent body mass threshold. Thus, for ectotherms, apex predator status is linked rather to its size than to the species. In herbivores (rudd), IINW increased with body mass. The IIS of predators negatively correlated with site trophic state. Therefore, eutrophication can significantly change the foraging behavior of certain species. We assume that the observed trends will occur in other species at similar trophic positions in either aquatic or terrestrial systems. For confirmation, we recommend conducting a similar study on other species in different habitats.

Fish scale stable isotopes as potential indicators of nutrient pollution: Exploring the response of roach (Rutilus rutilus) scale δ15N and δ13C to a gradient of land use disturbance.

To examine the suitability of fish scales as potential tracers of nutrient pollution, we analysed the nitrogen and carbon stable isotope values (δ15N and δ13C) in scales of a generalist fish species, roach Rutilus rutilus, collected from 22 Czech reservoirs covering wide gradients of catchment land use and nutrient enrichment. Using generalised additive mixed models in the first step and generalised linear mixed models in the second step, we evaluated the response of roach scale stable isotope values to catchment land use variables (percentage of agricultural land and human population density) and in-reservoir water quality variables. Roach scale δ15N values varied by 15 ‰ among the reservoirs and were strongly, linearly, and positively associated with the percentage of agricultural land in the reservoir catchments, pointing to agriculture as the dominant source of nitrogen pollution in the investigated systems. Roach scale δ13C values differed by 8 ‰ among the studied reservoirs and were not related to catchment land use variables or in-reservoir primary production (chlorophyll-a levels). Possible variation in roach foraging strategies (littoral versus pelagic) between reservoirs or the contrasting effects of eutrophication-related autotrophic and heterotrophic processes on baseline δ13C values may explain the lack of relationships between roach scale δ13C values and the explanatory variables. In summary, our findings show that fish scale δ15N values are sensitive bioindicators of catchment-derived anthropogenic nitrogen inputs to freshwater ecosystems. Because scales can be sampled in a nonlethal way and δ15N analysis is relatively inexpensive, we suggest that measuring the δ15N values of fish scales could be an effective method for monitoring nitrogen pollution in aquatic environments.

Different hosts in different lakes: prevalence and population genetic structure of plerocercoids of Ligula intestinalis (Cestoda) in Czech water bodies.

Ligula intestinalis (Linnaeus, 1758) is a tapeworm parasite with a worldwide distribution that uses a wide variety of fish species as its second intermediate host. In the present study, we investigated the prevalence and population genetic structure of plerocercoids of L. intestinalis in five common cyprinoid species, roach Rutilus rutilus (Linnaeus), freshwater bream Abramis brama (Linnaeus), white bream Blicca bjoerkna (Linnaeus), bleak Alburnus alburnus (Linnaeus), and rudd Scardinius erythrophthalmus (Linnaeus), collected in six water bodies of the Czech Republic (Milada, Most, Medard, Jordán, Rímov and Lipno). Of the six study sites, the highest frequency of parasitism was recorded in Lake Medard (15%). The overall prevalence rate among the species was as follows: roach > rudd ≥ freshwater bream > bleak > white bream. Two mitochondrial genes (cytb and COI) were used to compare the population genetic structure of parasite populations using selected samples from the five fish species. The results of the phylogenetic analysis indicated that all populations of L. intestinalis were placed in Clade A, previously identified as the most common in Europe. At a finer scale, haplotype network and PCoA analyses indicated the possible emergence of host specificity of several mtDNA haplotypes to the freshwater bream. Moreover, pairwise Fixation indices (FST) revealed a significant genetic structure between the parasite population in freshwater bream and other host species. Parasite populations in roach not only showed the highest rate of prevalence but also depicted a maximum number of shared haplotypes with populations from bleak and rudd. Our results suggest that recent ecological differentiation might have influenced tapeworm populations at a fine evolutionary scale. Thus, the differences in prevalence between fish host species in different lakes might be influenced not only by the parasite's ecology, but also by its genetic diversity.

Diel changes in vertical and horizontal distribution of cladocerans in two deep lakes during early and late summer.

Temporal and spatial heterogeneity in the distribution of cladocerans in lakes could be caused by abiotic (wind, water currents) and biotic factors (reproduction, food resources, predation). Diel horizontal and vertical distribution of cladoceran assemblages was studied in two deep lakes (Milada and Most Lakes, Czech Republic) in early (June) and late (September) summer. The objective was to study diel vertical migration (DVM) and diel horizontal migration (DHM) of cladocerans under conditions of different macrophyte cover in littoral areas (rich in Milada Lake, poor in Most Lake) and fish assemblages (non-specialised planktivorous species in Milada Lake, and abundant planktivorous fish - maraena whitefish, Coregonus maraena - in open water habitats in Most Lake). Temporal variations in cladoceran assemblages were reported in both lakes in the two sampling periods. DVM was observed in the two lakes, performed by the most vulnerable species to fish predation (the larger Daphnia spp.), but with different patterns (direct and reverse) probably linked with the local fish community and other biotic and abiotic factors in each lake. Horizontal movements were only observed in Most Lake: D. longispina increase its abundance in open waters at night compared to the littoral points; while Ceriodaphnia spp. showed the inverse pattern. In both lakes, higher densities were often found at night in surface layers, producing a great "diurnal deficit": cladocerans remain undetected in some zones during the day (especially in the littoral areas) moving to surface layers at night.

Endoparasites of European perch Perca fluviatilis fry: role of spatial segregation.

A total of 246 perch Perca fluviatilis L. fry, 20 to 106 d old from 3 different reservoir subpopulations (epipelagic perch fry, EPF; bathypelagic perch fry, BPF; littoral perch fry, LPF), were examined for parasites. Six species of endoparasites were found: the nematode Camallanus lacustris was the most common, followed by the cestodes Proteocephalus percae, Bothriocephalus claviceps, Glanitaenia osculata and the acanthocephalan Acanthocephalus lucii. All worms were juvenile or immature and were recovered from the intestinal lumen, with the exception of plerocercoids of Triaenophorus nodulosus, which were found in the body cavity or already encysted in the liver (the final site of infection of metacestodes). A marked difference was found in infection rates in the 3 spatially segregated subpopulations of perch fry. Parasites were found almost exclusively in LPF, which were heavily infected (overall prevalence = 30%) compared with the other studied subpopulations. Two species (C. lacustris and T. nodulosus) were found in 1 fish each (prevalence = 3%) in BPF, whereas EPF were uninfected. The species richness and prevalence of parasites in LPF increased from 20-24 d old fry (2 species of parasites; prevalence = 13%) to 106 d old fry (5 species of parasites; prevalence = 80%).

Density dependent attributes of fish aggregative behaviour.

Grouping behaviour, as fascinating as it is unclear, has lately drawn the attention of numerous researchers. While most of the authors focused their work on a mechanistic approach to the matter of schooling, this study explores the issue from a population point of view. Present camera observation study on the fish community carried out in the epipelagic habitat of a European temperate reservoir in the Czech Republic explored the relationship between density and aggregative features of predominantly cyprinid fish stock. Results demonstrated that schooling behaviour is triggered by the 'critical density' of fish in the habitat. School size as well as counts of schools and proportion of schooling individuals increased with the density of fish. Counts of clusters (observed units in time, including singletons, pairs and schools) and cluster size, on the other hand, showed a slowing tendency to increase. The slower increase implies the tendency of fish for not being frequent but rather to create larger groups. Altogether, our findings suggest that fish density is a triggering factor in the formation of large fish schools. As the tendency of cyprinid species for school formation could be an evolutional advantage responsible for dominance in later succession phases of water bodies, we suggest that more in situ studies should be encouraged for the proper understanding of the ecological interactions that drive the structure of aquatic ecosystems and for ensuring unbiased assessment.

Can species-specific prey responses to chemical cues explain prey susceptibility to predation?

The perception of danger represents an essential ability of prey for gaining an informational advantage over their natural enemies. Especially in complex environments or at night, animals strongly rely on chemoreception to avoid predators. The ability to recognize danger by chemical cues and subsequent adaptive responses to predation threats should generally increase prey survival. Recent findings suggest that European catfish (Silurus glanis) introduction induce changes in fish community and we tested whether the direction of change can be attributed to differences in chemical cue perception. We tested behavioral response to chemical cues using three species of freshwater fish common in European water: rudd (Scardinius erythrophthalmus), roach (Rutilus rutilus), and perch (Perca fluviatilis). Further, we conducted a prey selectivity experiment to evaluate the prey preferences of the European catfish. Roach exhibited the strongest reaction to chemical cues, rudd decreased use of refuge and perch did not alter any behavior in the experiment. These findings suggest that chemical cue perception might be behind community data change and we encourage collecting more community data of tested prey species before and after European catfish introduction to test the hypothesis. We conclude that used prey species can be used as a model species to verify whether chemical cue perception enhances prey survival.

Community-Driven Data Analysis Training for Biology.

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.

Thirty-Year-Old Paradigm about Unpalatable Perch Egg Strands Disclaimed by the Freshwater Top-Predator, the European Catfish (Silurus glanis).

So far, perch egg strands have been considered unpalatable biological material. However, we repeatedly found egg strands of European perch (Perca fluviatilis) in the diet of European catfish (Silurus glanis) caught by longlines in Milada and Most Lakes, Czech Republic. The finding proves that perch egg strands compose a standard food source for this large freshwater predatory fish. It extends the present knowledge on catfish foraging plasticity, showing it as an even more opportunistic feeder. Utilization of perch egg strands broadens the catfish diet niche width and represents an advantage against other fish predators. Comparison of datasets from extensive gillnet and SCUBA diver sampling campaigns gave the evidence that at least in localities where food sources are limited, multilevel predation by catfish may have an important impact on the perch population.

European catfish (Silurus glanis) as a freshwater apex predator drives ecosystem via its diet adaptability.

Apex predators play a key role in ecosystem stability across environments but their numbers in general are decreasing. By contrast, European catfish (Silurus glanis), the European freshwater apex predator, is on the increase. However, studies concerning apex predators in freshwaters are scarce in comparison to those in terrestrial and marine ecosystems. The present study combines stomach content and stable isotope analyses with diet preferences of catfish to reveal its impact on the ecosystem since stocking. Catfish niche width is extremely wide in comparison to the typical model predator, Northern pike (Esox lucius). Catfish and pike have different individual dietary specialization that results in different functional roles in coupling or compartmentalizing distinct food webs. The role of both species in the ecosystem is irreplaceable due to multiple predator effects. The impact of catfish is apparent across the entire aquatic ecosystem, but herbivores are the most affected ecological group. The key feature of catfish, and probably a common feature of apex predators in general, is utilization of several dietary strategies by individuals within a population: long-term generalism or specialization and also short-term specialization. Catfish, similar to other large-bodied apex predators, have two typical features: enormous generalism and adaptability to new prey sources.

Macrophytes shape trophic niche variation among generalist fishes.

Generalist species commonly have a fundamental role in ecosystems as they can integrate spatially distinct habitats and food-web compartments, as well as control the composition, abundance and behavior of organisms at different trophic levels. Generalist populations typically consist of specialized individuals, but the potential for and hence degree of individual niche variation can be largely determined by habitat complexity. We compared individual niche variation within three generalist fishes between two comparable lakes in the Czech Republic differing in macrophyte cover, i.e. macrophyte-rich Milada and macrophyte-poor Most. We tested the hypothesis that large individual niche variation among generalist fishes is facilitated by the presence of macrophytes, which provides niches and predation shelter for fish and their prey items. Based on results from stable nitrogen (δ15N) and carbon (δ13C) isotopic mixing models, perch (Perca fluviatilis L.) and rudd (Scardinius erythrophthalmus (L.)) showed larger individual variation (i.e., variance) in trophic position in Milada as compared to Most, whereas no significant between-lake differences were observed for roach (Rutilus rutilus (L.)). Contrary to our hypothesis, all the three species showed significantly lower individual variation in the relative reliance on littoral food resources in Milada than in Most. Rudd relied significantly more whereas perch and roach relied less on littoral food resources in Milada than in Most, likely due to prevalent herbivory by rudd and prevalent zooplanktivory by perch and roach in the macrophyte-rich Milada as compared to macrophyte-poor Most. Our study demonstrates how the succession of macrophyte vegetation, via its effects on the physical and biological complexity of the littoral zone and on the availability of small prey fish and zooplankton, can strongly influence individual niche variation among generalist fishes with different ontogenetic trajectories, and hence the overall food-web structures in lake ecosystems.