A Framework for Verifying Scalability and Performance of Cloud Based Web Applications

Antud magistritöö uurib võimalusi, kuidas kasutada veebirakendust MediaWiki, mida kasutatakse Wikipedia rakendamiseks, ja kuidas kasutada antud teenust mitme serveri peal nii, et see oleks kõige optimaalsem ja samas kõik veebikülastajad saaks teenusele ligi mõistliku ajaga. Amazon küsib raha pilves toimivate masinate ajalise kasutamise eest, ümardades pooleldi kasutatud tunnid täistundideks. Antud töö sisaldab vahendeid kuidas mõõta pilves olevate serverite jõudlust ning võimekust ja skaleerida antud veebirakendust. Amazon EC2 pilvesüsteemis on võimalik kasutajatel koostada virtuaalseid tõmmiseid operatsiooni süsteemidest, mida saab pilves rakendada XEN virtualiseerimise keskkonnas, kui eraldiseisvat serverit. Antud virtuaalse tõmmise peale sai paigaldatud tööks vaja minev keskkond, et koguda andmeid serverite kasutuse kohta ja võimaldada platvormi, mis lubab dünaamiliselt ajas lisada servereid ja eemaldada neid. Magistritöö uurib Amazon EC2 pilvesüsteemi kasutusvõimalusi, mille hulka kuulub Auto Scale, mis aitab skaleerida pilves kasutatavaid rakendusi horisontaalselt. Amazon pilve kasutatakse antud töös MediaWiki seadistamiseks ja suuremahuliste eksperimentide rakendamiseks. Vajalik on teha palju optimiseerimisi ja seadistamisi, et suurendada teenuse läbilaske võimsust. Antud töö raames loodud raamistik aitab mõõta serverite kasutust, kogudes andmeid protsessori, mälu ja võrgu kasutamise kohta. See aitab leida süsteemis olevaid kitsaskohti, mis võivad põhjustada süsteemi olulist aeglustumist. Antud töö raames sai tehtud erinevaid teste, et selgitada välja parim võimalik paigutus ja seadistus. Saavutatud seadistust kontrolliti hiljem 2 suuremahulise eksperimentiga, mis kestis üks päev ja mille käigus tekitati 22 miljonit päringut, leidmaks kuidas raamistik võimaldab teenust pilves skaleerida ülesse päringute arvu tõusmisel ja vähendada servereid, kui päringute arv väheneb. Ühes eksperimendis kasutati optimaalset heuristikat, et selgitada välja optimaalne serverite arv, mida on vaja pilves rakendada. Teine eksperimentidest kasutas Amazon Auto Scale teenust, mis kasutas serverite keskmist protsessori kasutamist, et selgitada välja, kas pilves on vaja servereid lisada või eemaldada. Antud eksperimendid näitavad selgelt, et kasutades dünaamilist arvu servereid, olenevalt päringute arvust, on võimalik teenuse üleval hoidmiseks säästa raha.Network usage and bandwidth speeds have increased massively and vast majority of people are using Internet on daily bases. This has increased CPU utilization on servers meaning that sites with large visits are using hundreds of computers to accommodate increasing traffic rates to the services. Making plans for hardware ordering to upgrade old servers or to add new servers is not a straightforward process and has to be carefully considered. There is a need to predict traffic rate for future usage. Buying too many servers can mean revenue loss and buying too few servers can result in losing clients. To overcome this problem, it is wise to consider moving services into virtual cloud and make server provisioning as an automatic step. One of the popular cloud service providers, Amazon is giving possibility to use large amounts of computing power for running servers in virtual environment with single click. They are providing services to provision as many servers as needed to run, depending how loaded the servers are and whatever we need to do, to add new servers or to remove existing ones. This will eliminate problems associated with ordering new hardware. Adding new servers is an automatic process and will follow the demand, like adding more servers for peak hours and removing unnecessary servers at night or when the traffic is low. Customer pays only for the used resources on the cloud. This thesis focuses on setting up a testbed for the cloud that will run web application, which will be scaled horizontally (by replicating already running servers) and will use the benchmark tool for stressing out the web application, by simulating huge number of concurrent requests and proper load-balancing mechanisms. This study gives us a proper picture how servers in the cloud are scaled and whole process remains transparent for the end user, as it sees the web application as one server. In conclusion, the framework is helpful in analyzing the performance of cloud based applications, in several of our research activities

Bioinformaatilise programmi gDAT arendus arbuskulaarset mükoriisat moodustavate seente määramiseks erinevate pärilikkusaine markerpiirkondade põhjal

Väitekirja elektrooniline versioon ei sisalda publikatsiooneMullas on palju mikroorganisme, ning neil on oluline roll ökosüsteemide toimimisel. Üheks oluliseks mikroorganismide rühmaks on arbuskulaarset mükoriisat (AM) moodustavad seened (krohmseened). AM on seenjuure vorm, mida moodustavad krohmseened enamuse roht- ja puittaimedega, sealhulgas paljude kultuurtaimedega. Mükoriisses kooselus saab peremeestaim seene abil kasvuks vajalikke mineraalaineid ja vett, seen omakorda taimelt fotosünteesil tekkinud süsivesikuid. Lisaks parandavad AM seened taimede toimetulekut stressitingimustega, näiteks veepuuduse ja haigustekitajatega. Antud doktoritöös uuriti AM seente määramise efektiivsust kasutades kolme mikroorganismide määramiseks enim kasutatud genoomset markerpiirkonda (SSU, ITS, LSU) ja erinevate sekveneerimisplatvormide sobivust AM seente määramiseks ökoloogilistest proovidest. Doktoritöö raames valmis graafilise liidesega bioinformaatiline töövahend gDAT (graphical downstream analyse tool), mis aitab ökoloogidel analüüsida suuremahulisi DNA järjestusandmeid. Doktoritöö peamised tulemused ja järeldused on: 1) SSU markerpiirkond on piisavalt varieeruv AM seeneliikide määramiseks. Teisisõnu, selle markeri liigisisene varieeruvus on AM seentel väiksem kui liikidevaheline varieeruvus; 2) uute sekveneerimisplatvormide tulekuga on järjestuste maht proovi kohta mitmekordistunud, kuid liigirikkus proovi kohta püsib sama ja saadud ökoloogiline teave (elurikkuse hinnang) on võrreldav eelmise põlvkonna sekveneerimisplatvormil saaduga. Seega on metoodiliselt optimaalne proovipõhine järjestuste arv saavutatud AM seeneliikide määramiseks ning elurikkuse hindamiseks looduskeskkonnast; 3) lisaks SSU markerpiirkonnale saab arvukamaid AM seeni edukalt määrata ka järjestades koguseenekooslust ITS piirkonna praimersüsteeme kasutades; 4) arendatud bioinformaatiline töövahend gDAT võimaldab kiirelt, tõhusalt teostada AM seente uurimusi pärilikkusaine põhjal. See töövahend on kasutatav ka teiste organismide DNA-põhiseks määramiseks.Soils harbour vast numbers of microorganisms that play important roles in ecosystems. One important group of microorganisms is the arbuscular mycorrhizal (AM) fungi. AM is a type of mycorrhiza, where fungi forms a symbiosis with most of the herbaceous and woody plants including crop plants. AM fungi provide nutrients and water that are needed for plant growth and in exchange receive carbon fixed by the plant in photosynthesis. AM fungi also improve plant tolerance to stress, such as drought and pathogen attacks. This thesis analysed the efficiency of popular DNA sequencing marker regions (SSU, ITS, LSU) used with microorganisms and different sequencing platforms to identify AM fungi in environmental samples. Outcome of the thesis is a bioinformatics tool gDAT (graphical downstream analysis tool) with graphical interface that allows ecologists to easily analyse vast amounts of DNA sequence data. The main results and conclusions of the thesis are the following: 1) the SSU marker region is sufficiently variable to identify AM fungi; and the variation within species is lower than the variation between species; 2) newer sequencing technologies provide increased sequencing depth, but this does not increase species richness estimates per sample and produces similar community patterns compared to previous generation sequencing. Thus, the optimal sample sequencing depth has been achieved for AM fungal diversity assessments; 3) the ITS region can be used successfully to identify abundant AM fungal species; 4) the newly developed bioinformatics tool gDAT allows rapid and efficient analysis of AM fungi from sequenced DNA. This tool is not limited to AM fungi and is applicable for other organisms to be identified through DNA sequencing.https://www.ester.ee/record=b535617

Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety

Background and aim sSupporting arbuscular mycorrhizal (AM) nutrient acquisition in crops may reduce the need for fertilizer inputs, leading to more cost effective and sustainable crop production. In wheat, AM fungal responsiveness and benefits of symbiosis vary among varieties. This study explored the role of soil compaction in this variation.Methods We examined in a field experiment how soil compaction affects AM fungal colonization and biomass in five spring wheat varieties, and how these varieties differ in their AM-mediated phosphorus (P) uptake. We also studied soil properties, and AM fungal community composition in roots and soil.Results Soil compaction increased AM fungal colonization in the variety Alderon, characterized by root traits that indicate inefficient P uptake. Wheat P concentration and P:N ratio in Alderon and Diskett increased with increased root AM fungal colonization and biomass. In Diskett, which is the most cultivated spring wheat variety in Sweden and has intermediate root traits, total P content per m2 also increased with root AM fungal colonization and biomass.Conclusions Some wheat varieties, potentially those characterized by P inefficient root traits, such as Alderon, may depend more on AM-mediated P uptake in compacted than in non-compacted soil. Increased P uptake with increased AM fungal colonization in Diskett suggests that efficient root and AM-mediated nutrient uptake can occur simultaneously in a modern variety. Breeding varieties that use roots and AM symbiosis as complementary strategies for nutrient uptake could improve nutrient uptake efficiency and help farmers achieve stable yields in varying conditions

Land-use intensity and host plant simultaneously shape the composition of arbuscular mycorrhizal fungal communities in a Mediterranean drained peatland

Land-use change is known to be a major threat to biodiversity and ecosystem services in Mediterranean areas. However, the potential for different host plants to modulate the effect of land-use intensification on community composition of arbuscular mycorrhizal fungi (AMF) is still poorly understood. To test the hypothesis that low land-use intensity promotes AMF diversity at different taxonomic scales and to determine whether any response is dependent upon host plant species identity, we characterised AMF communities in the roots of 10 plant species across four land use types of differing intensity in a Mediterranean peatland system. AMF were identified using 454 pyrosequencing. This revealed an overall low level of AMF richness in the peaty soils; lowest AMF richness in the intense cropping system at both virtual taxa and family level; strong modulation by the host plant of the impact of land-use intensification on AMF communities at the virtual taxa level; and a significant effect of land-use intensification on AMF communities at the family level. These findings have implications for understanding ecosystem stability and productivity and should be considered when developing soil-improvement strategies in fragile ecosystems, such as Mediterranean peatlands

Hedgerows increase the diversity and modify the composition of arbuscular mycorrhizal fungi in Mediterranean agricultural landscapes

Sustainable agriculture is essential to address global challenges such as climate change and biodiversity loss. Hedgerows enhance aboveground biodiversity and provide ecosystem services, but little is known about their impact on soil biota. Arbuscular mycorrhizal (AM) fungi are one of the key components of belowground biodiversity. We compared the diversity and composition of AM fungal communities at four farmland sites located in Central Spain, where 132 soil samples in total were collected to assess soil physical and chemical properties and the AM fungal communities. We compared the richness (number of AM fungal taxa), taxonomic, functional, and phylogenetic diversity, and structure of the AM fungal communities across three farmland habitat types, namely hedgerows, woody crops (olive groves and vineyard), and herbaceous crops (barley, sunfower, and wheat). Our results showed positive efects of hedgerows on most diversity metrics. Almost 60% of the AM fungal taxa were shared among the three farmland habitat types. Hedgerows increased AM fungal taxonomic richness (31%) and alpha diversity (25%), and especially so compared to herbaceous crops (45% and 28%, respectively). Hedgerows harbored elevated proportions of AM fungi with non-ruderal life-history strategies. AM fungal communities were more similar between hedgerows and woody crops than between hedgerows and adjacent herbaceous crops, possibly because of diferences in tillage and fertilization. Unexpectedly, hedgerows reduced phylogenetic diversity, which might be related to more selective associations of AM fungi with woody plants than with herbaceous crops. Overall, the results suggest that planting hedgerows contributes to maintain belowground diversity. Thus, European farmers should plant more hedgerows to attain the goals of the EU Biodiversity Strategy for 2030.Ministerio de Educación y Formación ProfesionalComunidad de Madrid, REMEDINALUniversidad de AlcaláFondo Europeo de Desarrollo Regional-FEDEREstonian Research Counci

Metabarcoding of soil environmental DNA to estimate plant diversity globally

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region

Global diversity and distribution of nitrogen-fixing bacteria in the soil

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold