MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

Growth of unstable interfaces in disordered media

The effects of a disordered medium in the growth of unstable interfaces are studied by means of two local models with multiplicative and additive quenched disorder, respectively. For short times and large pushing the multiplicative quenched disorder is equivalent to a time-dependent noise. In this regime, the linear dispersion relation contains a destabilizing contribution introduced by the noise. For long times, the interface always gets pinned. We model the systematics of the pinned shapes by means of an effective nonlinear model. These results show good agreement with numerical simulations. For the additive noise we find numerically that a depinning transition occurs.

Magnetoresistance at artificial interfaces in the itinerant SrRuO3 ferromagnet

The magnetoresistance across interfaces in the itinerant ferromagnetic oxide SrRuO3 have been studied. To define appropriately the interfaces, epitaxial thin films have been grown on bicrystalline and laser-patterned SrTiO3 substrates. Comparison is made with results obtained on similar experiments using the double-exchange ferromagnetic oxide La2/3Sr1/3MnO3. It is found that in SrRuO3, interfaces induce a substantial negative magnetoresistance, although no traces of the low-field spin tunneling magnetoresistance are found. We discuss these results on the basis of the distinct degree of spin polarization in ruthenates and manganites and the different nature of the surface magnetic layer formed at interfaces.

User cost of capital with delayed investment grants

The usual assumption when considering investment grants is that grant payments are automatic when investments are undertaken. However, evidence from case studies shows that there can exist some time lag until funds are received by granted firms. In this paper the effects of delays in grant payments on the optimal investment policy of the firm are analyzed. It is shown how these delays lead not only to a higher financing cost but to an effective reduction in the investment grant rate, and in some cases, how benefits from investment grants could be canceled due to interactions with tax effects.

The Raccoon River Valley Trail user study: summary and recommendations,1992.

This study is a concise summary of a study of trail users on the Raccoon River Valley Trail commissioned by the Dallas County Conservation Board. It provides information associated with natural and cultural resources.

Iowa DOT staff waterway user charge proposal,1976.

The Iowa DOT reviewed Corps of Engineers accounting records to determine the costs of operating and maintaining a 300 mile section of the Mississippi River. This document reviews the details the study.

Interfaces entre a ciência da informação e a ciência cognitiva

Estudo panorâmico sobre aspectos da ciência da informação (CI) e da ciência cognitiva (CC), apontando recentes contribuições em quatro de suas possíveis interseções: categorização, indexação, recuperação da informação (RI) e interação homem-computador.

Development of a New Process for Determining Design Year Traffic Demands, TR-528, 2007

Researchers should continuously ask how to improve the models we rely on to make financial decisions in terms of the planning, design, construction, and maintenance of roadways. This project presents an alternative tool that will supplement local decision making but maintain a full appreciation of the complexity and sophistication of today’s regional model and local traffic impact study methodologies. This alternative method is tailored to the desires of local agencies, which requested a better, faster, and easier way to evaluate land uses and their impact on future traffic demands at the sub-area or project corridor levels. A particular emphasis was placed on scenario planning for currently undeveloped areas. The scenario planning tool was developed using actual land use and roadway information for the communities of Johnston and West Des Moines, Iowa. Both communities used the output from this process to make regular decisions regarding infrastructure investment, design, and land use planning. The City of Johnston case study included forecasting future traffic for the western portion of the city within a 2,600-acre area, which included 42 intersections. The City of West Des Moines case study included forecasting future traffic for the city’s western growth area covering over 30,000 acres and 331 intersections. Both studies included forecasting a.m. and p.m. peak-hour traffic volumes based upon a variety of different land use scenarios. The tool developed took goegraphic information system (GIS)-based parcel and roadway information, converted the data into a graphical spreadsheet tool, allowed the user to conduct trip generation, distribution, and assignment, and then to automatically convert the data into a Synchro roadway network which allows for capacity analysis and visualization. The operational delay outputs were converted back into a GIS thematic format for contrast and further scenario planning. This project has laid the groundwork for improving both planning and civil transportation decision making at the sub-regional, super-project level.

Construction Automation Using Pen-Based Computers, HR-368, 1996

The Iowa Department of Transportation is committed to improved management systems, which in turn has led to increased automation to record and manage construction data. A possible improvement to the current data management system can be found with pen-based computers. Pen-based computers coupled with user friendly software are now to the point where an individual's handwriting can be captured and converted to typed text to be used for data collection. It would appear pen-based computers are sufficiently advanced to be used by construction inspectors to record daily project data. The objective of this research was to determine: (1) if pen-based computers are durable enough to allow maintenance-free operation for field work during Iowa's construction season; and (2) if pen-based computers can be used effectively by inspectors with little computer experience. The pen-based computer's handwriting recognition was not fast or accurate enough to be successfully utilized. The IBM Thinkpad with the pen pointing device did prove useful for working in Windows' graphical environment. The pen was used for pointing, selecting and scrolling in the Windows applications because of its intuitive nature.

Evaluation of the user-friendliness of seven new generation intensive care ventilators.

OBJECTIVE: To explore the user-friendliness and ergonomics of seven new generation intensive care ventilators. DESIGN: Prospective task-performing study. SETTING: Intensive care research laboratory, university hospital. METHODS: Ten physicians experienced in mechanical ventilation, but without prior knowledge of the ventilators, were asked to perform eight specific tasks [turning the ventilator on; recognizing mode and parameters; recognizing and setting alarms; mode change; finding and activating the pre-oxygenation function; pressure support setting; stand-by; finding and activating non-invasive ventilation (NIV) mode]. The time needed for each task was compared to a reference time (by trained physiotherapist familiar with the devices). A time >180 s was considered a task failure. RESULTS: For each of the tests on the ventilators, all physicians' times were significantly higher than the reference time (P < 0.001). A mean of 13 +/- 8 task failures (16%) was observed by the ventilator. The most frequently failed tasks were mode and parameter recognition, starting pressure support and finding the NIV mode. Least often failed tasks were turning on the pre-oxygenation function and alarm recognition and management. Overall, there was substantial heterogeneity between machines, some exhibiting better user-friendliness than others for certain tasks, but no ventilator was clearly better that the others on all points tested. CONCLUSIONS: The present study adds to the available literature outlining the ergonomic shortcomings of mechanical ventilators. These results suggest that closer ties between end-users and manufacturers should be promoted, at an early development phase of these machines, based on the scientific evaluation of the cognitive processes involved by users in the clinical setting.

User's Manual for the County Road Evaluation Program - Volume I, HR-242, 1986

Provides instructions for using the computer program which was developed under the research project, "The Economics of Reducing the County Road System: Three Case Studies In Iowa". This program operates on an IBP personal computer with 300K storage. A fixed disk is required with at least 3 megabytes of storage. The computer must be equipped with DOS version 3.0; the programs are written in Fortran. The user's manual describes all data requirements including network preparation, trip information, cost for maintenance, reconstruction, etc. Program operation instructions are presented, as well as sample solution output and a listing of the computer programs.

EuroPhenome: a repository for high-throughput mouse phenotyping data.

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

User experience strategy

L'objectiu d'aquest projecte era desenvolupar una metodologia de user experience strategy per aconseguir que el client d'una pàgina web tingui una mateixa experiència tant si fa servir una plataforma com una altra, aplicant diferents tècniques de disseny centrades en l'usuari.