Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Aquaculture production in areas with high seasonal temperature variations: Development of planning tools

Postprint (published version)

Tailored Jeffamine molecular tools for ordering mesoporous Silica

Herein, we report the formation of organized mesoporous silica materials prepared from a novel nonionic gemini surfactant, myristoyl-end capped Jeffamine, synthesized from a polyoxyalkyleneamine (ED900). The behavior of the modified Jeffamine in water was first investigated. A direct micellar phase (L1) and a hexagonal (H1) liquid crystal were found. The structure of the micelles was investigated from the SAXS and the analysis by Generalized Indirect Fourier Transformation (GIFT), which show that the particles are globular of coreshell type. The myristoyl chains, located at the ends of the amphiphile molecule are assembled to form the core of the micelles and, as a consequence, the molecules are folded over on themselves. Mesoporous materials were then synthesized from the self-assembly mechanism. The recovered materials were characterized by SAXS measurements, nitrogen adsorptiondesorption analysis, transmission and scanning electron microscopy. The results clearly evidence that by modifying the synthesis parameters, such as the surfactant/silica precursor molar ratio and the hydrothermal conditions, one can control the size and the nanostructuring of the resulting material. It was observed that, the lower the temperature of the hydrothermal treatment, the better the mesopore ordering.

Cleaning of ceramic filter plates

In this thesis, cleaning of ceramic filter plates clogged by iron oxides was studied. Oxalic acid is considered as the most effective cleaning agent for the plates fouled by iron oxides, but when using oxalic acid, sparingly soluble calcium oxalate may be formed and it can blind the filter media. Suitability of another chemical for cleaning the plates clogged by iron oxides was studied in this thesis. The literature part was mostly about the properties of the chemical, about its reactions, industrial uses, safety issues etc. In the experimental part, the efficiency of the chemical for cleaning of the ceramic plates clogged by iron oxides was studied. Two kinds of plates were used in the experiments; the others were clogged by hematite and the others by magnetite. Both soaking and flow-through experiments were done. A suitable concentration, pH and temperature were tried to find in the experiments. Also the effect of ultrasound was studied. The efficiency of the cleaning was examined by measuring the permeability of the plates during the experiments. ICP-OES analysis was performed for determining the amount of dissolved iron in the washing solution. Some experiments were also done with oxalic acid. The results from the oxalic acid experiments were compared to the results from the experiments with the other chemical. In the experiments with the other chemical, the permeability increased more and the amounts of dissolved iron were larger. According to the results from the experiments, the method of application of the washing solutions had an impact on the washing results.

Empowering local democracy in Catalonia: tools and policy domains to implement a top-down solution

This article is the result of an ongoing research into a variety of features of Spanish local government. It aims, in particular, at providing a profile of the tools implemented by local authorities to improve local democracy in Catalonia. The main hypothesis of the work is that, even though the Spanish local model is constrained by a shared and unique set of legal regulations, local institutions in Catalonia have developed their own model of local participation. And the range of instruments like these is still now increasing. More specifically, the scope of this research is twofold. On the one hand, different types of instruments for public deliberation in the Catalan local administration system are identified and presented, based on the place they take in the policy cycle. On the other hand, we focus on policy domains and the quality of the decision-making processes. Researching the stability of the participation tools or whether local democracy prefers more 'ad hoc' processes allows us to analyze the boundaries/limits of local democracy in Catalonia. The main idea underlying this paper is that, despite the existence of a single legal model regulating municipalities in Catalonia, local authorities tend to use their legally granted selfmanagement capacities to design their own instruments which end up presenting perceivable distinct features, stressing democracy in different policy domains, and in diverse policy cycles. Therefore, this paper is intended to identify such models and to provide factors (variables) so that an explanatory model can be built.

The Effect of Operational Disturbances on Reliability and Operation Time Distribution of NCmachine Tools in FMS

This thesis concentrates on studying the operational disturbance behavior of machine tools integrated into FMS. Operational disturbances are short term failures of machine tools which are especially disruptive to unattended or unmanned operation of FMS. The main objective was to examine the effect of operational disturbances on reliability and operation time distribution for machine tools. The theoretical part of the thesis covers the fimdamentals of FMS relating to the subject of this study. The concept of FMS, its benefits and operator's role in FMS operation are reviewed. The importance of reliability is presented. The terms describing the operation time of machine tools are formed by adopting standards and references. The concept of failure and indicators describing reliability and operational performance for machine tools in FMSs are presented. The empirical part of the thesis describes the research methodology which is a combination of automated (ADC) and manual data collection. By using this methodology it is possible to have a complete view of the operation time distribution for studied machine tools. Data collection was carried out in four FMSs consisting of a total of 17 machine tools. Each FMS's basic features and the signals of ADC are described. The indicators describing the reliability and operation time distribution of machine tools were calculated according to collected data. The results showed that operational disturbances have a significant influence on machine tool reliability and operational performance. On average, an operational disturbance occurs every 8,6 hours of operation time and has a down time of 0,53 hours. Operational disturbances cause a 9,4% loss in operation time which is twice the amount of losses caused by technical failures (4,3%). Operational disturbances have a decreasing influence on the utilization rate. A poor operational disturbance behavior decreases the utilization rate. It was found that the features of a part family to be machined and the method technology related to it are defining the operational disturbance behavior of the machine tool. Main causes for operational disturbances were related to material quality variations, tool maintenance, NC program errors, ATC and machine tool control. Operator's role was emphasized. It was found that failure recording activity of the operators correlates with the utilization rate. The more precisely the operators record the failure, the higher is the utilization rate. Also the FMS organizations which record failures more precisely have fewer operational disturbances.

Building the map of innovation for membrane materials (Ceramic membranes)

This work proposes a method of visualizing the trend of research in the field of ceramic membranes from 1999 to 2006. The presented approach involves identifying problems encountered during research in the field of ceramic membranes. Patents from US patent database and articles from Science Direct(& by ELSEVIER was analyzed for this work. The identification of problems was achieved with software Knowledgist which focuses on the semantic nature of a sentence to generate series of subject action object structures. The identified problems are classified into major research issues. This classification was used for the visualization of the intensity of research. The image produced gives the relation between the number of patents, with time and the major research issues. The identification of the most cited papers which strongly influence the research of the previously identified major issues in the given field was also carried out. The relations between these papers are presented using the metaphor of social network. The final result of this work are two figures, a diagram showing the change in the studied problems a specified period of time and a figure showing the relations between the major papers and groups of the problems

Groupware and Workflow Tools - A Case study of SAP Business Workflow Supporting System Integration in a Global Telecommunication Company

Workflow management systems aim at the controlled execution of complex application processes in distributed and heterogeneous environments. These systems will shape the structure of information systems in business and non-business environments. E business and system integration is a fertile soil for WF and groupware tools. This thesis aims to study WF and groupware tools in order to gather in house knowledge of WF to better utilize WF solutions in future, and to focus on SAP Business Workflow in order to find a global solution for Application Link Enabling support for system integration. Piloting this solution in Nokia collects the experience of SAP R/3 WF tool for other development projects in future. The literary part of this study will guide to the world of business process automation providing a general description of the history, use and potentials of WF & groupware software. The empirical part of this study begins with the background of the case study describing the IT environment initiating the case by introducing SAP R/3 in Nokia, the communication technique in use and WF tool. Case study is focused in one solution with SAP Business Workflow. This study provides a concept to monitor communication between ERP systems and to increase the quality of system integration. Case study describes a way create support model for ALE/EDI interfaces. Support model includes monitoring organization and the workflow processes to solve the most common IDoc related errors.

Study of ligand-based virtual screening tools in computer-aided drug design

Virtual screening is a central technique in drug discovery today. Millions of molecules can be tested in silico with the aim to only select the most promising and test them experimentally. The topic of this thesis is ligand-based virtual screening tools which take existing active molecules as starting point for finding new drug candidates. One goal of this thesis was to build a model that gives the probability that two molecules are biologically similar as function of one or more chemical similarity scores. Another important goal was to evaluate how well different ligand-based virtual screening tools are able to distinguish active molecules from inactives. One more criterion set for the virtual screening tools was their applicability in scaffold-hopping, i.e. finding new active chemotypes. In the first part of the work, a link was defined between the abstract chemical similarity score given by a screening tool and the probability that the two molecules are biologically similar. These results help to decide objectively which virtual screening hits to test experimentally. The work also resulted in a new type of data fusion method when using two or more tools. In the second part, five ligand-based virtual screening tools were evaluated and their performance was found to be generally poor. Three reasons for this were proposed: false negatives in the benchmark sets, active molecules that do not share the binding mode, and activity cliffs. In the third part of the study, a novel visualization and quantification method is presented for evaluation of the scaffold-hopping ability of virtual screening tools.

A Survey and Classification of Software Testing Tools

Software testing is one of the essential parts in software engineering process. The objective of the study was to describe software testing tools and the corresponding use. The thesis contains examples of software testing tools usage. The study was conducted as a literature study, with focus on current software testing practices and quality assurance standards. In the paper a tool classifier was employed, and testing tools presented in study were classified according to it. We found that it is difficult to distinguish current available tools by certain testing activities as many of them contain functionality that exceeds scopes of a single testing type.

Synthesis and characterization of Fe(III)-doped ceramic membranes of titanium dioxide and its application in photoelectrocatalysis of a textile dye

Pure and Fe(III)-doped TiO2 suspensions were prepared by the sol gel method with the use of titanium isopropoxide (Ti(OPri)4) as precursor material. The properties of doped materials were compared to TiO2 properties based on the characterization by thermal analysis (TG-DTA and DSC), X-ray powder diffractometry and spectroscopy measurements (FTIR). Both undoped and doped TiO2 suspensions were used to coat metallic substrate as a mean to make thin-film electrodes. Thermal treatment of the precursors at 400ºC for 2 h in air resulted in the formation of nanocrystalline anatase TiO2. The thin-film electrodes were tested with respect to their photocatalytic performance for degradation of a textile dye in aqueous solution. The plain TiO2 remains as the best catalyst at the conditions used in this report.

Influence of topography and surface chemistry on the wetting properties of TiO2-based ceramic coatings

Vätning av fasta ytor är ett viktigt fenomen i såväl naturen som i en lång rad av industriella tillämpningar. Det är allmänt känt att vätningen av en fast yta styrs av ytans kemi samt struktur. Målsättningen med avhandlingen var att studera hur kemisk heterogenitet och ytråhet på nanometernivå påverkar vätningsegenskaperna hos en fast yta. Ytorna som studerades var titandioxid-baserade kerama ytor som framställdes med hjälp av en sol-gel process. Vätningstudierna utfördes genom kontaktvinkelmätningar, vilket innebär att man mäter vinkeln som vätska/luft-gränsskiktet hos en vätskedroppe bildar mot en fast yta. Ytråheten hos materialen studerades främst genom atomkraftsmikroskopi (AFM). I AFM detekteras ytans struktur av en mycket skarp nål som skannar ytan. Resultaten i avhandlingen kunde framgångsrikt modelleras med existerande teorier för vätning av heterogena ytor.

Vibration free machining tools

Appearance of the vibration is the very important problem in long tool turning and milling. Current solutions of minimizing vibrations provided by different tool suppliers are very expensive. This Master’s Thesis is presenting the new type of vibration free machining tools produced by Konepaja ASTEX Gear Oy that have cheaper production costs compare to competitors’ products. Vibration problems in machining and their today’s solutions are analyzed in this work. The new vibration damping invention is presented and described. Moreover, the production, laboratory experimental modal analysis and practical testing of the new vibration free prototypes are observed and analyzed on the pages of this Thesis. Based on the testing results the new invention is acknowledged to be successful and approved for further studies and developments.

Applications of graph transformation in tools for domain-specific modeling languages

The use of domain-specific languages (DSLs) has been proposed as an approach to cost-e ectively develop families of software systems in a restricted application domain. Domain-specific languages in combination with the accumulated knowledge and experience of previous implementations, can in turn be used to generate new applications with unique sets of requirements. For this reason, DSLs are considered to be an important approach for software reuse. However, the toolset supporting a particular domain-specific language is also domain-specific and is per definition not reusable. Therefore, creating and maintaining a DSL requires additional resources that could be even larger than the savings associated with using them. As a solution, di erent tool frameworks have been proposed to simplify and reduce the cost of developments of DSLs. Developers of tool support for DSLs need to instantiate, customize or configure the framework for a particular DSL. There are di erent approaches for this. An approach is to use an application programming interface (API) and to extend the basic framework using an imperative programming language. An example of a tools which is based on this approach is Eclipse GEF. Another approach is to configure the framework using declarative languages that are independent of the underlying framework implementation. We believe this second approach can bring important benefits as this brings focus to specifying what should the tool be like instead of writing a program specifying how the tool achieves this functionality. In this thesis we explore this second approach. We use graph transformation as the basic approach to customize a domain-specific modeling (DSM) tool framework. The contributions of this thesis includes a comparison of di erent approaches for defining, representing and interchanging software modeling languages and models and a tool architecture for an open domain-specific modeling framework that e ciently integrates several model transformation components and visual editors. We also present several specific algorithms and tool components for DSM framework. These include an approach for graph query based on region operators and the star operator and an approach for reconciling models and diagrams after executing model transformation programs. We exemplify our approach with two case studies MICAS and EFCO. In these studies we show how our experimental modeling tool framework has been used to define tool environments for domain-specific languages.