Juan Falgueras

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

BackgroundHigh-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms.ResultsSeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming.ConclusionsSeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts.

AGILE Interface for ‘No-Learning Nor Experience Required’ Interaction

The wide variety of technological devices is a barrier to satisfactory usage and learning over all. Different types of interface element distribution and dissimilarities of their functionalities, even in the same category of products under the same brand, can steepen the learning curve to effective device operation. Interface design can be understood as a mechanism for the adequacy of the technological environment to substantially improve performance, satisfaction and life of the user with special requirements. Based on an inclusive paradigm, we aim to improve the usability, accessibility and satisfiability of the interface for a specific group of users, such as novice elderly, to benefit all types of users in their daily lives. The requirements derived from a holistic analysis of user, goals and context lead to the introduction of the AGILE Interface (Assisted Guided Interaction with no Learning nor Experience required). This interface is the pillar of a new interaction style designed to assist and guide users with specific needs owing to age and non-Information and Technology experience. In the context of present-day technology interactions, the ultimate goal of this work is to move beyond out of date user stereotypes to tailor appropriate interface design adapted to realistic and specific user demands.

Intuitive Bioinformatics for Genomics Applications: Omega-Brigid Workflow Framework

The recent developments in life sciences and technology have produced large amounts of data in an extremely fast and cost-efficient way which require the development of new algorithms, coupled with massively parallel computing. Besides, biologists are usually non-programmers, thus demanding intuitive computer applications that are easy to use by means of a friendly GUI. In addition, different algorithms, databases and other tools usually lie on incompatible file formats, applications, operating systems and hardware platforms. It is therefore of paramount importance to overcome such limitations, so that bioinformatics becomes much more widely used amongst biologists. The main goal of our research project is to unify many of these existing bioinformatics applications and resources (local and remote) in one easy-to-use environment, independent of the computing platform, being a concentrator resource tool with a friendly interface. To achieve this, we propose a tool based on a new, open, free and well-documented architecture called Biomniverso. Two main elements make up such a tool: its kernel (Omega), which supplies services specifically adapted to allow the addition of new bioinformatics functionalities by means of plugins (like Minerva, which makes easy to detect SNP amongst a set of genomic data to discover fraudulent olive oil), and the interface (Brigid), which allows even non-programmer laboratory scientists to chain different processes into workflows and customize them without code writing.

Oscillating annular liquid membranes

SummaryThe response of annular liquid membranes to sinusoidal mass flow rate fluctuations at the nozzle exit is analyzed as a function of the amplitude and frequency of the axial velocity fluctuations at the nozzle exit and thermodynamic compression of the gas enclosed by the membrane. It is shown that both the pressure of the gases enclosed by the annular membrane and the axial distance at which the annular membrane merges on the symmetry axis are periodic functions of time which have the same period as that of the mass flow rate fluctuations at the nozzle exit. They are also nearly sinusoidal functions of time for small amplitudes of the mass flow rate fluctuations at the nozzle exit, and exhibit delay and lag times with respect to the sinusoidal axial velocity fluctuations at the nozzle exit. Both the delay and the lag times are functions of the amplitude and frequency of the mass flow rate fluctuations at the nozzle exit and the polytropic exponent. The amplitudes of both the pressure of the gases enclosed by the annular liquid membrane and the convergence length increase and decrease, resp., as the amplitude and frequency of the mass flow rate fluctuations at the nozzle exit, resp., are increased. They also increase as the polytropic exponent is increased.ÜbersichtUntersucht wird das Verhalten rotationsschalenförmiger Flüssigkeitsmembranen in Abhängigkeit von der Amplitude und Frequenz der axialen Geschwindigkeitsschwankungen an der Düsenmündung und der thermodynamischen Verdichtung des eingeschlossenen Gases, wenn sich der Massestrom an der Düsenmündung sinusförmig ändert. Es wird gezeigt, daß der Druck des eingeschlossenen Gases und der axiale Mündungsabstand des Scheitels der geschlossenen Membran periodische Zeitfunktionen mit der Frequenz der Masseflußschwankung am Düsenaustritt sind. Für kleine Amplituden des Massestroms ist ihr Zeitverhalten ebenfalls fast-sinusförmig, wobei sie bezüglich der sinusförmigen axialen Geschwindigkeitsschwankungen an der Düsenmündung eine Ansprechzeit und Phasenverschiebung aufweisen. Ansprechzeit und Phasenverschiebung sind Funktionen von Amplitude und Frequenz der Massestromschwankung sowie des polytropen Exponenten. Die Amplitude von Gasdruck und Abstand des Membranscheitels von der Düse wächst bzw. fällt mit wachsender Amplitude und Frequenz des Massestroms. Beide nehmen außerdem mit dem polytropen Exponenten zu.

Response of annular liquid jets to mass loading

An adaptive, block-bidiagonal finite difference method is used to study the response of annular liquid jets to the injection of mass into the volume enclosed by the annular jet. It is shown that the annular jets response is characterized by damped oscillations in both the convergence length and the pressure of the gases enclosed by the jet, and that these oscillations are similar to those of an underdamped mass-spring-dashpot system. It is also shown that the maximum amplitude and the number of these oscillations increase as the nozzle exit angle, the initial pressure ratio across the annular jet, the pressure of the gases surrounding the jet, the Weber number, and the rate and duration of the mass injection are increased, are nearly independent of the annular jets thickness-to-radius ratio at the nozzle exit, and decrease as the Froude number is increased. The numerical calculations presented in this paper indicate that the pressure of the gases enclosed by the annular liquid jet responds instantaneously to the mass injection, whereas there is a lag in the response of the convergence length. This lag is due to the inertia of the jet and assumption that the gases enclosed by the jet are isothermal, and decreases as the injection duration is increased. The calculations also indicate that the critical pressure coefficient of unity determined from the solution of the steady state governing equations can be exceeded without affecting the stability of the annular jet.

SCBI_MapReduce, a New Ruby Task-Farm Skeleton for Automated Parallelisation and Distribution in Chunks of Sequences: The Implementation of a Boosted Blast

Current genomic analyses often require the managing and comparison of big data using desktop bioinformatic software that was not developed regarding multicore distribution. The task-farm SCBI_MAPREDUCE is intended to simplify the trivial parallelisation and distribution of new and legacy software and scripts for biologists who are interested in using computers but are not skilled programmers. In the case of legacy applications, there is no need of modification or rewriting the source code. It can be used from multicore workstations to heterogeneous grids. Tests have demonstrated that speed-up scales almost linearly and that distribution in small chunks increases it. It is also shown that SCBI_MAPREDUCE takes advantage of shared storage when necessary, is fault-tolerant, allows for resuming aborted jobs, does not need special hardware or virtual machine support, and provides the same results than a parallelised, legacy software. The same is true for interrupted and relaunched jobs. As proof-of-concept, distribution of a compiled version of BLAST

mORCA: sailing bioinformatics world with mobile devices

Motivation Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web‐based world and that mobile devices are endowed with web‐browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Results Throughout an in‐depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy‐to‐use web‐based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the services metadata stored in catalogs or repositories. Availability and implementation mORCA is available at http://bitlab‐es.com/morca/app as a web‐app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. Contact ortrelles@uma.es Supplementary information Source code, final web‐app, training material and documentation is available at http://bitlab‐es.com/morca

A reflective characterisation of occasional user

This work revisits established user classifications and aims to characterise a historically unspecified user category, the Occasional User (OU). Three user categories, novice, intermediate and expert, have dominated the work of user interface (UI) designers, researchers and educators for decades. These categories were created to conceptualise users needs, strategies and goals around the 80s. Since then, UI paradigm shifts, such as direct manipulation and touch, along with other advances in technology, gave new access to people with little computer knowledge. This fact produced a diversification of the existing user categories not observed in the literature review of traditional classification of users. The findings of this work include a new characterisation of the occasional user, distinguished by users uncertainty of repetitive use of an interface and little knowledge about its functioning. In addition, the specification of the OU, together with principles and recommendations will help UI community to informatively design for users without requiring a prospective use and previous knowledge of the UI. The OU is an essential type of user to apply user-centred design approach to understand the interaction with technology as universal, accessible and transparent for the user, independently of accumulated experience and technological era that users live in. Significance of user classification for the design of interactive systems.Analysis of user classifications, identifying common definition parameters.Notification of the absence of the Occasional User in previous classifications.Presentation of specific parameters and examples of Occasional Users.Enumeration of main implications of the Occasional User in user interface design.

mORCA: ubiquitous access to life science web services

BackgroundTechnical advances in mobile devices such as smartphones and tablets have produced an extraordinary increase in their use around the world and have become part of our daily lives. The possibility of carrying these devices in a pocket, particularly mobile phones, has enabled ubiquitous access to Internet resources. Furthermore, in the life sciences world there has been a vast proliferation of data types and services that finish as Web Services. This suggests the need for research into mobile clients to deal with life sciences applications for effective usage and exploitation.ResultsAnalysing the current features in existing bioinformatics applications managing Web Services, we have devised, implemented, and deployed an easy-to-use web-based lightweight mobile client. This client is able to browse, select, compose parameters, invoke, and monitor the execution of Web Services stored in catalogues or central repositories. The client is also able to deal with huge amounts of data between external storage mounts. In addition, we also present a validation use case, which illustrates the usage of the application while executing, monitoring, and exploring the results of a registered workflow. The software its available in the Apple Store and Android Market and the source code is publicly available in Github.ConclusionsMobile devices are becoming increasingly important in the scientific world due to their strong potential impact on scientific applications.Bioinformatics should not fall behind this trend. We present an original software client that deals with the intrinsic limitations of such devices and propose different guidelines to provide location-independent access to computational resources in bioinformatics and biomedicine. Its modular design makes it easily expandable with the inclusion of new repositories, tools, types of visualization, etc.

SeqTrim07: a pipeline for preprocessing sequence reads

SeqTrim is a pipeline designed to preprocessing sequence reads. It is easy to install and configure, flexible even if default parameters are accurate for most purposes and usable as a web interface or a standalone command line application. It identifies the sequence insert by removing low quality sequences, cloning vector, poly-A or poly-T tails, adaptors and any contaminant sequence or unwanted feature. Several input and output formats are available, which enables its inclusion in already or newly defined sequence processing work flows. It outperforms preprocessors implemented in other web servers and standalone applications at least in detecting adaptors and chimeric clones. SeqTrim is under continuous refinement to deal with most sequence events due to collaboration between biologists and computer scientists.