GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

Knowledge management in intelligent tutoring systems

In the last years, Intelligent Tutoring Systems have been a very successful way for improving learning experience. Many issues must be addressed until this technology can be defined mature. One of the main problems within the Intelligent Tutoring Systems is the process of contents authoring: knowledge acquisition and manipulation processes are difficult tasks because they require a specialised skills on computer programming and knowledge engineering. In this thesis we discuss a general framework for knowledge management in an Intelligent Tutoring System and propose a mechanism based on first order data mining to partially automate the process of knowledge acquisition that have to be used in the ITS during the tutoring process. Such a mechanism can be applied in Constraint Based Tutor and in the Pseudo-Cognitive Tutor. We design and implement a part of the proposed architecture, mainly the module of knowledge acquisition from examples based on first order data mining. We then show that the algorithm can be applied at least two different domains: first order algebra equation and some topics of C programming language. Finally we discuss the limitation of current approach and the possible improvements of the whole framework.

Permutation classes, sorting algorithms, and lattice paths

A permutation is said to avoid a pattern if it does not contain any subsequence which is order-isomorphic to it. Donald Knuth, in the first volume of his celebrated book "The art of Computer Programming", observed that the permutations that can be computed (or, equivalently, sorted) by some particular data structures can be characterized in terms of pattern avoidance. In more recent years, the topic was reopened several times, while often in terms of sortable permutations rather than computable ones. The idea to sort permutations by using one of Knuth���s devices suggests to look for a deterministic procedure that decides, in linear time, if there exists a sequence of operations which is able to convert a given permutation into the identical one. In this thesis we show that, for the stack and the restricted deques, there exists an unique way to implement such a procedure. Moreover, we use these sorting procedures to create new sorting algorithms, and we prove some unexpected commutation properties between these procedures and the base step of bubblesort. We also show that the permutations that can be sorted by a combination of the base steps of bubblesort and its dual can be expressed, once again, in terms of pattern avoidance. In the final chapter we give an alternative proof of some enumerative results, in particular for the classes of permutations that can be sorted by the two restricted deques. It is well-known that the permutations that can be sorted through a restricted deque are counted by the Schr��der numbers. In the thesis, we show how the deterministic sorting procedures yield a bijection between sortable permutations and Schr��der paths.

The Small Project Observatory: Visualizing Software Ecosystems

Software evolution research has focused mostly on analyzing the evolution of single software systems. However, it is rarely the case that a project exists as standalone, independent of others. Rather, projects exist in parallel within larger contexts in companies, research groups or even the open-source communities. We call these contexts software ecosystems, and on this paper we present The Small Project Observatory, a prototype tool which aims to support the analysis of project ecosystems through interactive visualization and exploration. We present a case-study of exploring an ecosystem using our tool, we describe about the architecture of the tool, and we distill the lessons learned during the tool-building experience.

Discrete element methods for asphalt concrete : development and application of user-defined microstructural models and a viscoelastic micromechanical model

As an important Civil Engineering material, asphalt concrete (AC) is commonly used to build road surfaces, airports, and parking lots. With traditional laboratory tests and theoretical equations, it is a challenge to fully understand such a random composite material. Based on the discrete element method (DEM), this research seeks to develop and implement computer models as research approaches for improving understandings of AC microstructure-based mechanics. In this research, three categories of approaches were developed or employed to simulate microstructures of AC materials, namely the randomly-generated models, the idealized models, and image-based models. The image-based models were recommended for accurately predicting AC performance, while the other models were recommended as research tools to obtain deep insight into the AC microstructure-based mechanics. A viscoelastic micromechanical model was developed to capture viscoelastic interactions within the AC microstructure. Four types of constitutive models were built to address the four categories of interactions within an AC specimen. Each of the constitutive models consists of three parts which represent three different interaction behaviors: a stiffness model (force-displace relation), a bonding model (shear and tensile strengths), and a slip model (frictional property). Three techniques were developed to reduce the computational time for AC viscoelastic simulations. It was found that the computational time was significantly reduced to days or hours from years or months for typical three-dimensional models. Dynamic modulus and creep stiffness tests were simulated and methodologies were developed to determine the viscoelastic parameters. It was found that the DE models could successfully predict dynamic modulus, phase angles, and creep stiffness in a wide range of frequencies, temperatures, and time spans. Mineral aggregate morphology characteristics (sphericity, orientation, and angularity) were studied to investigate their impacts on AC creep stiffness. It was found that aggregate characteristics significantly impact creep stiffness. Pavement responses and pavement-vehicle interactions were investigated by simulating pavement sections under a rolling wheel. It was found that wheel acceleration, steadily moving, and deceleration significantly impact contact forces. Additionally, summary and recommendations were provided in the last chapter and part of computer programming codes wree provided in the appendixes.

The Amplifier - v. 9, no. 9

In this issue...computer programming course, Butte Elks Club, IBM, summer jobs, John F. Kennedy, New York World Fair, Butte YMCA, weightlifting, Staghorn Ranch

Parsing for agile modeling

In order to analyze software systems, it is necessary to model them. Static software models are commonly imported by parsing source code and related data. Unfortunately, building custom parsers for most programming languages is a non-trivial endeavour. This poses a major bottleneck for analyzing software systems programmed in languages for which importers do not already exist. Luckily, initial software models do not require detailed parsers, so it is possible to start analysis with a coarse-grained importer, which is then gradually refined. In this paper we propose an approach to "agile modeling" that exploits island grammars to extract initial coarse-grained models, parser combinators to enable gradual refinement of model importers, and various heuristics to recognize language structure, keywords and other language artifacts.

Assessment of work performed by paired students: a pedagogical experience

���Teamwork��� is one of the abilities most valued by employers. In [16] we describe the process of adapting to the ECTS methodologies (for ongoing assessment), a course in computer programming for students in a technical degree (Marine Engineering, UPM) not specifically dedicated to computing. As a further step in this process we have emphasized cooperative learning. For this, the students were paired and the work of each pair was evaluated via surprise tests taken and graded jointly, and constituting a substantial part of the final grade. Here we document this experience, discussing methodological aspects, describing indicators for measuring the impact of these methodologies on the educational experience, and reporting on the students��� opinion of it.

Slabsim: Simulador de dispositivos ��pticos integrados

En los dise��os y desarrollos de ingenier��a, antes de comenzar la construcci��n e implementaci��n de los objetivos de un proyecto, es necesario realizar una serie de an��lisis previos y simulaciones que corroboren las expectativas de la hip��tesis inicial, con el fin de obtener una referencia emp��rica que satisfaga las condiciones de trabajo o funcionamiento de los objetivos de dicho proyecto. A menudo, los resultados que satisfacen las caracter��sticas deseadas se obtienen mediante la iteraci��n de m��todos de ensayo y error. Generalmente, ��stos m��todos utilizan el mismo procedimiento de an��lisis con la variaci��n de una serie de par��metros que permiten adaptar una tecnolog��a a la finalidad deseada. Hoy en d��a se dispone de computadoras potentes, as�� como algoritmos de resoluci��n matem��tica que permiten resolver de forma veloz y eficiente diferentes tipos de problemas de c��lculo. Resulta interesante el desarrollo de aplicaciones que permiten la resoluci��n de ��stos problemas de forma r��pida y precisa en el an��lisis y s��ntesis de soluciones de ingenier��a, especialmente cuando se tratan expresiones similares con variaciones de constantes, dado que se pueden desarrollar instrucciones de resoluci��n con la capacidad de inserci��n de par��metros que definan el problema. Adem��s, mediante la implementaci��n de un c��digo de acuerdo a la base te��rica de una tecnolog��a, se puede lograr un c��digo v��lido para el estudio de cualquier problema relacionado con dicha tecnolog��a. El desarrollo del presente proyecto pretende implementar la primera fase del simulador de dispositivos ��pticos Slabsim, en cual se puede representar la distribuci��n de la energ��a de una onda electromagn��tica en frecuencias ��pticas guiada a trav��s de una una gu��a diel��ctrica plana, tambi��n conocida como slab. Este simulador esta constituido por una interfaz gr��fica generada con el entorno de desarrollo de interfaces gr��ficas de usuario Matlab GUIDE, propiedad de Mathworks��, de forma que su manejo resulte sencillo e intuitivo para la ejecuci��n de simulaciones con un bajo conocimiento de la base te��rica de este tipo de estructuras por parte del usuario. De este modo se logra que el ingeniero requiera menor intervalo de tiempo para encontrar una soluci��n que satisfaga los requisitos de un proyecto relacionado con las gu��as diel��ctricas planas, e incluso utilizarlo para una amplia diversidad de objetivos basados en esta tecnolog��a. Uno de los principales objetivos de este proyecto es la resoluci��n de la base te��rica de las gu��as slab a partir de m��todos num��ricos computacionales, cuyos procedimientos son extrapolables a otros problemas matem��ticos y ofrecen al autor una contundente base conceptual de los mismos. Por este motivo, las resoluciones de las ecuaciones diferenciales y caracter��sticas que constituyen los problemas de este tipo de estructuras se realizan por estos medios de c��lculo en el n��cleo de la aplicaci��n, dado que en algunos casos, no existe la alternativa de uso de expresiones anal��ticas ��tiles. ABSTRACT. The first step in engineering design and development is an analysis and simulation process which will successfully corroborate the initial hypothesis that was made and find solutions for a particular. In this way, it is possible to obtain empirical evidence which suitably substantiate the purposes of the project. Commonly, the characteristics to reach a particular target are found through iterative trial and error methods. These kinds of methods are based on the same theoretical analysis but with a variation of some parameters, with the objective to adapt the results for a particular aim. At present, powerful computers and mathematical algorithms are available to solve different kinds of calculation problems in a fast and efficient way. Computing application development is useful as it gives a high level of accurate results for engineering analysis and synthesis in short periods of time. This is more notable in cases where the mathematical expressions on a theoretical base are similar but with small variations of constant values. This is due to the ease of adaptation of the computer programming code into a parameter request system that defines a particular solution on each execution. Additionally, it is possible to code an application suitable to simulate any issue related to the studied technology. The aim of the present project consists of the construction of the first stage of an optoelectronics simulator named Slabsim. Slabism is capable of representing the energetic distribution of a light wave guided in the volume of a slab waveguide. The mentioned simulator is made through the graphic user interface development environment Matlab GUIDE, property of Mathworks��. It is designed for an easy and intuitive management by the user to execute simulations with a low knowledge of the technology theoretical bases. With this software it is possible to achieve several aims related to the slab waveguides by the user in low interval of time. One of the main purposes of this project is the mathematical solving of theoretical bases of slab structures through computing numerical analysis. This is due to the capability of adapting its criterion to other mathematical issues and provides a strong knowledge of its process. Based on these advantages, numerical solving methods are used in the core of the simulator to obtain differential and characteristic equations results that become represented on it.

KATS: A Knowledge Acquisition Tool Based on Electronic Document Processing

This paper describes a particular knowledge acquisition tool for the construction and maintenance of the knowledge model of an intelligent system for emergency management in the field of hydrology. This tool has been developed following an innovative approach directed to end-users non familiarized in computer oriented terminology. According to this approach, the tool is conceived as a document processor specialized in a particular domain (hydrology) in such a way that the whole knowledge model is viewed by the user as an electronic document. The paper first describes the characteristics of the knowledge model of the intelligent system and summarizes the problems that we found during the development and maintenance of such type of model. Then, the paper describes the KATS tool, a software application that we have designed to help in this task to be used by users who are not experts in computer programming. Finally, the paper shows a comparison between KATS and other approaches for knowledge acquisition.

Simultaneous assessment of loss of heterozygosity at multiple microsatellite loci using semi-automated fluorescence-based detection: subregional mapping of chromosome 4 in cervical carcinoma.

Detection of loss of heterozygosity (LOH) by comparison of normal and tumor genotypes using PCR-based microsatellite loci provides considerable advantages over traditional Southern blotting-based approaches. However, current methodologies are limited by several factors, including the numbers of loci that can be evaluated for LOH in a single experiment, the discrimination of true alleles versus "stutter bands," and the use of radionucleotides in detecting PCR products. Here we describe methods for high throughput simultaneous assessment of LOH at multiple loci in human tumors; these methods rely on the detection of amplified microsatellite loci by fluorescence-based DNA sequencing technology. Data generated by this approach are processed by several computer software programs that enable the automated linear quantitation and calculation of allelic ratios, allowing rapid ascertainment of LOH. As a test of this approach, genotypes at a series of loci on chromosome 4 were determined for 58 carcinomas of the uterine cervix. The results underscore the efficacy, sensitivity, and remarkable reproducibility of this approach to LOH detection and provide subchromosomal localization of two regions of chromosome 4 commonly altered in cervical tumors.

Ense��ando a programar: un camino directo para desarrollar el pensamiento computacional

Est�� ampliamente aceptado que es fundamental desarrollar la habilidad de resolver problemas. El pensamiento computacional se basa en resolver problemas haciendo uso de conceptos fundamentales de la inform��tica. Nada mejor para desarrollar la habilidad de resolver problemas usando conceptos inform��ticos que una asignatura de introducci��n a la programaci��n. Este trabajo presenta nuestras reflexiones acerca de c��mo iniciar a un estudiante en el campo de la programaci��n de computadores. El trabajo no detalla los contenidos a impartir, sino que se centra en aspectos metodol��gicos, con la inclusi��n de experiencias y ejemplos concretos, a la vez que generales, extensibles a cualquier ense��anza de programaci��n. En general, aunque se van desarrollado lenguajes cada vez m��s cercanos al lenguaje humano, la programaci��n de ordenadores utilizando lenguajes formales no es una materia intuitiva y de f��cil comprensi��n por parte de los estudiantes. A la persona que ya sabe programar le parece una tarea sencilla, pero al ne��fito no. Es m��s, dominar el arte de la programaci��n es complejo. Por esta raz��n es indispensable utilizar todas las t��cnicas y herramientas posibles que faciliten dicha labor.

Efficacy of an Internet-based, individually tailored smoking cessation program: A randomized trial

Introduction: Self-help computer-based programs are easily accessible and cost-effective interventions with a great recruitment potential. However, each program is different and results of meta-analyses may not apply to each new program; therefore, evaluations of new programs are warranted. The aim of this study was to assess the marginal efficacy of a computer-based, individually tailored program (the Coach) over and above the use of a comprehensive Internet smoking cessation website. Methods: A two-group randomized controlled trial was conducted. The control group only accessed the website, whereas the intervention group received the Coach in addition. Follow-up was conducted by e-mail after three and six months (self-administrated questionnaires). Of 1120 participants, 579 (51.7%) responded after three months and 436 (38.9%) after six months. The primary outcome was self-reported smoking abstinence over four weeks. Results: Counting dropouts as smokers, there were no statistically significant differences between intervention and control groups in smoking cessation rates after three months (20.2% vs. 17.5%, p��0.25, odds ratio (OR)��1.20) and six months (17% vs. 15.5%, p��0.52, OR��1.12). Excluding dropouts from the analysis, there were statistically significant differences after three months (42% vs. 31.6%, p��0.01, OR��1.57), but not after six months (46.1% vs. 37.8%, p��0.081, OR��1.41). The program also significantly increased motivation to quit after three months and self-efficacy after three and six months. Discussion: An individually tailored program delivered via the Internet and by e-mail in addition to a smoking cessation website did not significantly increase smoking cessation rates, but it increased motivation to quit and self-efficacy.

Financial planning in transit: use of commercially available microcomputer software. Final report.

Urban Mass Transportation Administration, Washington, D.C.