Transcription factor map alignment of promoter regions

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels—to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human–mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments.

PENELOPE-2008: A Code System for Monte Carlo Simulation of Electron and Photon Transport

The computer code system PENELOPE (version 2008) performs Monte Carlo simulation of coupledelectron-photon transport in arbitrary materials for a wide energy range, from a few hundred eV toabout 1 GeV. Photon transport is simulated by means of the standard, detailed simulation scheme.Electron and positron histories are generated on the basis of a mixed procedure, which combinesdetailed simulation of hard events with condensed simulation of soft interactions. A geometry packagecalled PENGEOM permits the generation of random electron-photon showers in material systemsconsisting of homogeneous bodies limited by quadric surfaces, i.e., planes, spheres, cylinders, etc. Thisreport is intended not only to serve as a manual of the PENELOPE code system, but also to provide theuser with the necessary information to understand the details of the Monte Carlo algorithm.

Optimal management of microgrids

Desenvolupament dels models matemàtics necessaris per a controlar de forma òptima la microxarxa existent als laboratoris del Institut de Recerca en Energia de Catalunya. Els algoritmes s'implementaran per tal de simular el comportament i posteriorment es programaran directament sobre els elements de la microxarxa per verificar el seu correcte funcionament.. Desenvolupament dels models matemàtics necessaris per a controlar de forma òptima la microxarxa existent als laboratoris del Institut de Recerca en Energia de Catalunya. Els algoritmes s'implementaran per tal de simular el comportament i posteriorment es programaran directament sobre els elements de la microxarxa per verificar el seu correcte funcionament.

Improving energy access in rural sub-Saharan Africa

XVII Convocatòria d’ajuts a accions de cooperació - 2009GRECDH – UPC. Improving Energy Access In Rural sub- Saharan Africa. O-006/09. Informe

Open licensing's impact on higher education resources colombian and catalan approaches

A new initiative has sprung on the path created by the Open Access (OA) movement: Open Education (OE). The initiative's aim is to open up all educational resources at all learning levels. In order to achieve this goal, several international institutions, like UNESCO and the OECD, have published reports, surveys and documents to help educational institutions in this endeavor. This global initiative needs a legal framework; as a result, efforts thus far have usually resorted to Open Licensing (OL), especially Creative Commons (CC) licensing. In fact, as a response to this new movement, Creative Commons launched a new program, ccLearn , which recognizes open licensing's impact on education and directly supports the idea of open educational resources (OER). However, there still remain a good amount of open questions: What is happening locally with OL in higher education? How are educational institutions receiving the initiative? How is it that the OL initiative relates to educational resources? Are there local examples of open educational resources (OER)? How do these local instances incorporate CC into their educational frameworks?. To this effect, this analysis aims to focus on the legal approach and specifically on the way the educational sector is using open licenses outside the English speaking world. It will do so by looking at the current situation in two specific scenarios, the Colombian and the Catalan experiences with open educational projects at the higher education level.

Explaining Open Courseware Europe

Since two years ago, five European universities are working together with Creative Commons and the Open Courseware Consortium in an EU funded project aimed at supporting student virtual mobility on the basis of OCW. During those two years, there have been several workshops dedicated to different topics and some documents have been produced, among them about the use of CC licenses. The final goal of the project is to establish an European branch of the OCW Consortium as the existing ones in other regions. More information about the project: http://opencourseware.eu/

Accessing Legal Information in Catalonia. Open Acces to Legislation and Case Law

The article outlines free online legal resources to conduct research on Catalan and Spanish legislation and case-law. Most of these resources are primary sources made public by government bodies. The list shows how the Spanish and Catalan governments, in their attempt to promote equal access to legislation and case-law, cover the different jurisdictions. The text also mentions some resources to conduct historical legal research about legislation and case law, and some free legal private websites.

Promoting the Creation, Share and Use of OERs through Open Repositories and Social Networks

In this paper we discuss and analyze the process of using a learning object repository and building a social network on the top of it, including aspects related to open source technologies, promoting the use of the repository by means of social networks and helping learners to develop their own learning paths.

Open Educational Resources: an opportunity for virtual learning institutions

The Universitat Oberta de Catalunya (UOC, Open University of Catalonia) is involved inseveral research projects and educational activities related to the use of Open Educational Resources (OER). Some of the discussed issues in the concept of OER are research issues which are being tackled in two EC projects (OLCOS and SELF). Besides the research part, the UOC aims at developing a virtual centre for analysing and promoting the concept of OERin Europe in the sector of Higher and Further Education. The objectives are to makeinformation and learning services available to provide university management staff,eLearning support centres, faculty and learners with practical information required to create, share and re-use such interoperable digital content, tools and licensing schemes. In the realisation of these objectives, the main activities are the following: to provide organisationaland individual e-learning end-users with orientation; to develop perspectives and useful recommendations in the form of a medium-term Roadmap 2010 for OER in Higher and Further Education in Europe; to offer practical information and support services about how to create, share and re-use open educational content by means of tutorials, guidelines, best practices, and specimen of exemplary open e-learning content; to establish a larger group ofcommitted experts throughout Europe and other continents who not only share theirexpertise but also steer networking, workshops, and clustering efforts; and to foster and support a community of practice in open e-learning content know-how and experiences.

Open Apps: Opening Teaching Experiences and Applications

The Universitat Oberta de Catalunya (Open University of Catalonia, UOC) is an online university that makes extensive use of information and communication technologies to provide education. Ever since its establishment in 1995, the UOC has developed and tested methodologies and technological support services to meet the educational challenges posed by its student community and its teaching and management staff. The know-how it has acquired in doing so is the basis on which it has created the Open Apps platform, which is designed to provide access to open source technical applications, information on successful learning and teaching experiences, resources and other solutions, all in a single environment. Open Apps is an open, online catalogue, the content of which is available to all students for learning purposes, all IT professionals for downloading and all teachers for reusing.To contribute to the transfer of knowledge, experience and technology, each of the platform¿s apps comes with full documentation, plus information on cases in which it has been used and related tools. It is hoped that such transfer will lead to the growth of an external partner network, and that this, in turn, will result in improvements to the applications and teaching/learning practices, and in greater scope for collaboration.Open Apps is a strategic project that has arisen from the UOC's commitment to the open access movement and to giving knowledge and technology back to society, as well as its firm belief that sustainability depends on communities of interest.

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

UPCommons: global access to Universitat Politècnica de Catalunya (UPC) knowledge

Programa de mà lliurat en la presentació del pòster 'UPCommons', exposat al primer COMMUNIA Workshop on Technology and the Public Domain, celebrat a Torí (Itàlia) el 18 de gener de 2008.

Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses

Background: Optimization methods allow designing changes in a system so that specific goals are attained. These techniques are fundamental for metabolic engineering. However, they are not directly applicable for investigating the evolution of metabolic adaptation to environmental changes. Although biological systems have evolved by natural selection and result in well-adapted systems, we can hardly expect that actual metabolic processes are at the theoretical optimum that could result from an optimization analysis. More likely, natural systems are to be found in a feasible region compatible with global physiological requirements. Results: We first present a new method for globally optimizing nonlinear models of metabolic pathways that are based on the Generalized Mass Action (GMA) representation. The optimization task is posed as a nonconvex nonlinear programming (NLP) problem that is solved by an outer- approximation algorithm. This method relies on solving iteratively reduced NLP slave subproblems and mixed-integer linear programming (MILP) master problems that provide valid upper and lower bounds, respectively, on the global solution to the original NLP. The capabilities of this method are illustrated through its application to the anaerobic fermentation pathway in Saccharomyces cerevisiae. We next introduce a method to identify the feasibility parametric regions that allow a system to meet a set of physiological constraints that can be represented in mathematical terms through algebraic equations. This technique is based on applying the outer-approximation based algorithm iteratively over a reduced search space in order to identify regions that contain feasible solutions to the problem and discard others in which no feasible solution exists. As an example, we characterize the feasible enzyme activity changes that are compatible with an appropriate adaptive response of yeast Saccharomyces cerevisiae to heat shock Conclusion: Our results show the utility of the suggested approach for investigating the evolution of adaptive responses to environmental changes. The proposed method can be used in other important applications such as the evaluation of parameter changes that are compatible with health and disease states.

Coscheduling techniques and monitoring tools for non-dedicated cluster computing

Our efforts are directed towards the understanding of the coscheduling mechanism in a NOW system when a parallel job is executed jointly with local workloads, balancing parallel performance against the local interactive response. Explicit and implicit coscheduling techniques in a PVM-Linux NOW (or cluster) have been implemented. Furthermore, dynamic coscheduling remains an open question when parallel jobs are executed in a non-dedicated Cluster. A basis model for dynamic coscheduling in Cluster systems is presented in this paper. Also, one dynamic coscheduling algorithm for this model is proposed. The applicability of this algorithm has been proved and its performance analyzed by simulation. Finally, a new tool (named Monito) for monitoring the different queues of messages in such an environments is presented. The main aim of implementing this facility is to provide a mean of capturing the bottlenecks and overheads of the communication system in a PVM-Linux cluster.

Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities

We have analyzed the heat stress response in the yeast Saccharomyces cerevisiae by determining mRNA levels and transcription rates for the whole transcriptome after a shift from 25uC to 37uC. Using an established mathematical algorithm, theoretical mRNA decay rates have also been calculated from the experimental data. We have verified the mathematical predictions for selected genes by determining their mRNA decay rates at different times during heat stress response using the regulatable tetO promoter. This study indicates that the yeast response to heat shock is not only due to changes in transcription rates, but also to changes in the mRNA stabilities. mRNA stability is affected in 62% of the yeast genes and it is particularly important in shaping the mRNA profile of the genes belonging to the environmental stress response. In most cases, changes in transcription rates and mRNA stabilities are homodirectional for both parameters, although some interesting cases of antagonist behavior are found. The statistical analysis of gene targets and sequence motifs within the clusters of genes with similar behaviors shows that both transcriptional and post-transcriptional regulons apparently contribute to the general heat stress response by means of transcriptional factors and RNA binding proteins.