SYLI - an external workflow system for DSpace

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Integration of JINR Information Resources

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Big Data Processing in the Cloud: a Hydra/Sufia Experience

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

DSpace for Data Revisited

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Tag Cloud of Search Queries for Repository System

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

SimpleREST -RESTful DSpace API

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Development of remote monitoring process tools for biomass fired bubbling fluidized bed boilers

Remote monitoring of a power boiler allows the supplying company to make sure that equipment is used as supposed to and gives a good chance for process optimization. This improves co-operation between the supplier and the customer and creates an aura of trust that helps securing future contracts. Remote monitoring is already in use with recovery boilers but the goal is to expand especially to biomass-fired BFB-boilers. To make remote monitoring possible, data has to be measured reliably on site and the link between the power plant and supplying company’s server has to work reliably. Data can be gathered either with the supplier’s sensors or with measurements originally installed in the power plant if the plant in question is not originally built by the supplying company. Main goal in remote monitoring is process optimization and avoiding unnecessary accidents. This can be achieved for instance by following the efficiency curves and fouling in different parts of the process and comparing them to past values. The final amount of calculations depends on the amount of data gathered. Sudden changes in efficiency or fouling require further notice and in such a case it’s important that dialogue toward the power plant in question also works.

Cost-efficient virtual machine management : provisioning, admission control, and consolidation

One of the main challenges in Software Engineering is to cope with the transition from an industry based on software as a product to software as a service. The field of Software Engineering should provide the necessary methods and tools to develop and deploy new cost-efficient and scalable digital services. In this thesis, we focus on deployment platforms to ensure cost-efficient scalability of multi-tier web applications and on-demand video transcoding service for different types of load conditions. Infrastructure as a Service (IaaS) clouds provide Virtual Machines (VMs) under the pay-per-use business model. Dynamically provisioning VMs on demand allows service providers to cope with fluctuations on the number of service users. However, VM provisioning must be done carefully, because over-provisioning results in an increased operational cost, while underprovisioning leads to a subpar service. Therefore, our main focus in this thesis is on cost-efficient VM provisioning for multi-tier web applications and on-demand video transcoding. Moreover, to prevent provisioned VMs from becoming overloaded, we augment VM provisioning with an admission control mechanism. Similarly, to ensure efficient use of provisioned VMs, web applications on the under-utilized VMs are consolidated periodically. Thus, the main problem that we address is cost-efficient VM provisioning augmented with server consolidation and admission control on the provisioned VMs. We seek solutions for two types of applications: multi-tier web applications that follow the request-response paradigm and on-demand video transcoding that is based on video streams with soft realtime constraints. Our first contribution is a cost-efficient VM provisioning approach for multi-tier web applications. The proposed approach comprises two subapproaches: a reactive VM provisioning approach called ARVUE and a hybrid reactive-proactive VM provisioning approach called Cost-efficient Resource Allocation for Multiple web applications with Proactive scaling. Our second contribution is a prediction-based VM provisioning approach for on-demand video transcoding in the cloud. Moreover, to prevent virtualized servers from becoming overloaded, the proposed VM provisioning approaches are augmented with admission control approaches. Therefore, our third contribution is a session-based admission control approach for multi-tier web applications called adaptive Admission Control for Virtualized Application Servers. Similarly, the fourth contribution in this thesis is a stream-based admission control and scheduling approach for on-demand video transcoding called Stream-Based Admission Control and Scheduling. Our fifth contribution is a computation and storage trade-o strategy for cost-efficient video transcoding in cloud computing. Finally, the sixth and the last contribution is a web application consolidation approach, which uses Ant Colony System to minimize the under-utilization of the virtualized application servers.

Replikoitavan palvelinjärjestelmän toteuttaminen julkisen liikenteen avoimen datan jakeluun

Tässä diplomityössä tutkittiin, miten toteuttaa replikoitava palvelinjärjestelmä julkisen liikenteen avoimen datan jakeluun. Tutkimuksessa selvitettiin, onko vastaavanlaisia järjestelmiä suunniteltu aiemmin, vai pitääkö järjestelmä suunnitella itse. Projektissa käytettiin avoimen lähdekoodin OneBusAway-ohjelmistokokonaisuutta. Projektin avulla osoitettiin, että kyseinen ohjelmisto toimi yliopiston testikäytössä hyvin. Ohjelmiston avulla pystytään jakelemaan staattista ja reaaliaikaista dataa, ja se on replikoitavissa kunnasta toiseen maailmanlaajuisesti. Tulevaisuudessa olisi kuitenkin hyvä selvittää, miten ohjelmistosta puuttuva reittihakuominaisuus kannattaisi toteuttaa, sekä olisiko REST- rajapinta mahdollista muuttaa sellaiseksi, että se noudattaisi julkisen liikenteen standardeja.

The GATO gene annotation tool for research laboratories

Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

Accuracy in book papers' sales forecasting

The main objective of this thesis was to study if the quantitative sales forecasting methods will enhance the accuracy of the sales forecast in comparison to qualitative sales forecasting method. A literature review in the field of forecasting was conducted, including general sales forecasting process, forecasting methods and techniques and forecasting accuracy measurement. In the empirical part of the study the accuracy of the forecasts provided by both qualitative and quantitative methods is being studied and compared in the case of short, medium and long term forecasts. The SAS® Forecast Server –tool was used in creating the quantitative forecasts.

Cloning, sequence analysis, and expression of cDNA coding for the major house dust mite allergen, Der f 1, in Escherichia coli

Our objective was to clone, express and characterize adult Dermatophagoides farinae group 1 (Der f 1) allergens to further produce recombinant allergens for future clinical applications in order to eliminate side reactions from crude extracts of mites. Based on GenBank data, we designed primers and amplified the cDNA fragment coding for Der f 1 by nested-PCR. After purification and recovery, the cDNA fragment was cloned into the pMD19-T vector. The fragment was then sequenced, subcloned into the plasmid pET28a(+), expressed in Escherichia coli BL21 and identified by Western blotting. The cDNA coding for Der f 1 was cloned, sequenced and expressed successfully. Sequence analysis showed the presence of an open reading frame containing 966 bp that encodes a protein of 321 amino acids. Interestingly, homology analysis showed that the Der p 1 shared more than 87% identity in amino acid sequence with Eur m 1 but only 80% with Der f 1. Furthermore, phylogenetic analyses suggested that D. pteronyssinus was evolutionarily closer to Euroglyphus maynei than to D. farinae, even though D. pteronyssinus and D. farinae belong to the same Dermatophagoides genus. A total of three cysteine peptidase active sites were found in the predicted amino acid sequence, including 127-138 (QGGCGSCWAFSG), 267-277 (NYHAVNIVGYG) and 284-303 (YWIVRNSWDTTWGDSGYGYF). Moreover, secondary structure analysis revealed that Der f 1 contained an a helix (33.96%), an extended strand (17.13%), a ß turn (5.61%), and a random coil (43.30%). A simple three-dimensional model of this protein was constructed using a Swiss-model server. The cDNA coding for Der f 1 was cloned, sequenced and expressed successfully. Alignment and phylogenetic analysis suggests that D. pteronyssinus is evolutionarily more similar to E. maynei than to D. farinae.

Telemedicina: Desenvolvimento de um sistema para atendimento à distância de pacientes com doença renal crônica pré-dialítica

ResumoIntrodução:O foco no tratamento da doença renal crônica (DRC) é evitar a sua progressão com o uso do controle clínico otimizado. O uso de tecnologias leves apresenta-se como forma promissora de cuidado em saúde. A internet oferece a oportunidade de instrumentalizar o médico em seu contato profissional com o usuário.Objetivo:Desenvolver um sistema web para o atendimento a distância de pacientes com DRC nos estágios não dialíticos e clinicamente estáveis.Métodos:Desenvolvido um sistema utilizando a linguagem Java, banco de dados MySQL e framework PrimeFaces; disponibilizado em um servidor de aplicações Glassfish.Resultados:O acesso inicial é realizado pelo nefrologista, que cadastra os pacientes com suas informações pessoais e dados de acesso. Após ser cadastrado, o paciente (ou médico de família) pode inserir os dados de sua consulta e estes serão, na sequência, repassados ao nefrologista para avaliação. O formulário com os dados de interesse é pré-determinado, mas ainda há possibilidade de acrescentar informações de forma livre. O sistema possibilita, adicionalmente, que haja troca de mensagens entre os médicos e os pacientes. Além disso, os usuários recebem mensagens via e-mail alertando-os de suas tarefas. O sigilo é garantido por senhas individuais para médicos e pacientes.Conclusão:Essa ferramenta possibilitará aumentar a área de abrangência dos nefrologistas, diminuir os custos e aproximar o paciente ao seu médico da atenção básica, utilizando o Programa de Saúde de Família como interface entre o paciente e a atenção secundária nefrológica.

Energy aware software for many-core systems

Many-core systems provide a great potential in application performance with the massively parallel structure. Such systems are currently being integrated into most parts of daily life from high-end server farms to desktop systems, laptops and mobile devices. Yet, these systems are facing increasing challenges such as high temperature causing physical damage, high electrical bills both for servers and individual users, unpleasant noise levels due to active cooling and unrealistic battery drainage in mobile devices; factors caused directly by poor energy efficiency. Power management has traditionally been an area of research providing hardware solutions or runtime power management in the operating system in form of frequency governors. Energy awareness in application software is currently non-existent. This means that applications are not involved in the power management decisions, nor does any interface between the applications and the runtime system to provide such facilities exist. Power management in the operating system is therefore performed purely based on indirect implications of software execution, usually referred to as the workload. It often results in over-allocation of resources, hence power waste. This thesis discusses power management strategies in many-core systems in the form of increasing application software awareness of energy efficiency. The presented approach allows meta-data descriptions in the applications and is manifested in two design recommendations: 1) Energy-aware mapping 2) Energy-aware execution which allow the applications to directly influence the power management decisions. The recommendations eliminate over-allocation of resources and increase the energy efficiency of the computing system. Both recommendations are fully supported in a provided interface in combination with a novel power management runtime system called Bricktop. The work presented in this thesis allows both new- and legacy software to execute with the most energy efficient mapping on a many-core CPU and with the most energy efficient performance level. A set of case study examples demonstrate realworld energy savings in a wide range of applications without performance degradation.

Adopting the Vaadin Java framework to rebuild VTT’s Web Interfaces and Database Applications

With the growth in new technologies, using online tools have become an everyday lifestyle. It has a greater impact on researchers as the data obtained from various experiments needs to be analyzed and knowledge of programming has become mandatory even for pure biologists. Hence, VTT came up with a new tool, R Executables (REX) which is a web application designed to provide a graphical interface for biological data functions like Image analysis, Gene expression data analysis, plotting, disease and control studies etc., which employs R functions to provide results. REX provides a user interactive application for the biologists to directly enter the values and run the required analysis with a single click. The program processes the given data in the background and prints results rapidly. Due to growth of data and load on server, the interface has gained problems concerning time consumption, poor GUI, data storage issues, security, minimal user interactive experience and crashes with large amount of data. This thesis handles the methods by which these problems were resolved and made REX a better application for the future. The old REX was developed using Python Django and now, a new programming language, Vaadin has been implemented. Vaadin is a Java framework for developing web applications and the programming language is extremely similar to Java with new rich components. Vaadin provides better security, better speed, good and interactive interface. In this thesis, subset functionalities of REX was selected which includes IST bulk plotting and image segmentation and implemented those using Vaadin. A code of 662 lines was programmed by me which included Vaadin as the front-end handler while R language was used for back-end data retrieval, computing and plotting. The application is optimized to allow further functionalities to be migrated with ease from old REX. Future development is focused on including Hight throughput screening functions along with gene expression database handling