A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements

Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Divergence time estimation based upon 14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs, and euteleosts diverged from one another by 205 Ma during the Triassic. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes

QoS-Aware Resource Management for Multi-phase Serverless Workflows with Aquatope

Multi-stage serverless applications, i.e., workflows with many computation and I/O stages, are becoming increasingly representative of FaaS platforms. Despite their advantages in terms of fine-grained scalability and modular development, these applications are subject to suboptimal performance, resource inefficiency, and high costs to a larger degree than previous simple serverless functions. We present Aquatope, a QoS-and-uncertainty-aware resource scheduler for end-to-end serverless workflows that takes into account the inherent uncertainty present in FaaS platforms, and improves performance predictability and resource efficiency. Aquatope uses a set of scalable and validated Bayesian models to create pre-warmed containers ahead of function invocations, and to allocate appropriate resources at function granularity to meet a complex workflow's end-to-end QoS, while minimizing resource cost. Across a diverse set of analytics and interactive multi-stage serverless workloads, Aquatope significantly outperforms prior systems, reducing QoS violations by 5x, and cost by 34% on average and up to 52% compared to other QoS-meeting methods

Arquitectura, técnicas y modelos para posibilitar la Ciencia de Datos en el Archivo de la Misión Gaia

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Informática, Departamento de Arquitectura de Computadores y Automática, leída el 26/05/2017.The massive amounts of data that the world produces every day pose new challenges to modern societies in terms of how to leverage their inherent value. Social networks, instant messaging, video, smart devices and scientific missions are just mere examples of the vast number of sources generating data every second. As the world becomes more and more digitalized, new needs arise for organizing, archiving, sharing, analyzing, visualizing and protecting the ever-increasing data sets, so that we can truly develop into a data-driven economy that reduces inefficiencies and increases sustainability, creating new business opportunities on the way. Traditional approaches for harnessing data are not suitable any more as they lack the means for scaling to the larger volumes in a timely and cost efficient manner. This has somehow changed with the advent of Internet companies like Google and Facebook, which have devised new ways of tackling this issue. However, the variety and complexity of the value chains in the private sector as well as the increasing demands and constraints in which the public one operates, needs an ongoing research that can yield newer strategies for dealing with data, facilitate the integration of providers and consumers of information, and guarantee a smooth and prompt transition when adopting these cutting-edge technological advances. This thesis aims at providing novel architectures and techniques that will help perform this transition towards Big Data in massive scientific archives. It highlights the common pitfalls that must be faced when embracing it and how to overcome them, especially when the data sets, their transformation pipelines and the tools used for the analysis are already present in the organizations. Furthermore, a new perspective for facilitating a smoother transition is laid out. It involves the usage of higher-level and use case specific frameworks and models, which will naturally bridge the gap between the technological and scientific domains. This alternative will effectively widen the possibilities of scientific archives and therefore will contribute to the reduction of the time to science. The research will be applied to the European Space Agency cornerstone mission Gaia, whose final data archive will represent a tremendous discovery potential. It will create the largest and most precise three dimensional chart of our galaxy (the Milky Way), providing unprecedented position, parallax and proper motion measurements for about one billion stars. The successful exploitation of this data archive will depend to a large degree on the ability to offer the proper architecture, i.e. infrastructure and middleware, upon which scientists will be able to do exploration and modeling with this huge data set. In consequence, the approach taken needs to enable data fusion with other scientific archives, as this will produce the synergies leading to an increment in scientific outcome, both in volume and in quality. The set of novel techniques and frameworks presented in this work addresses these issues by contextualizing them with the data products that will be generated in the Gaia mission. All these considerations have led to the foundations of the architecture that will be leveraged by the Science Enabling Applications Work Package. Last but not least, the effectiveness of the proposed solution will be demonstrated through the implementation of some ambitious statistical problems that will require significant computational capabilities, and which will use Gaia-like simulated data (the first Gaia data release has recently taken place on September 14th, 2016). These ambitious problems will be referred to as the Grand Challenge, a somewhat grandiloquent name that consists in inferring a set of parameters from a probabilistic point of view for the Initial Mass Function (IMF) and Star Formation Rate (SFR) of a given set of stars (with a huge sample size), from noisy estimates of their masses and ages respectively. This will be achieved by using Hierarchical Bayesian Modeling (HBM). In principle, the HBM can incorporate stellar evolution models to infer the IMF and SFR directly, but in this first step presented in this thesis, we will start with a somewhat less ambitious goal: inferring the PDMF and PDAD. Moreover, the performance and scalability analyses carried out will also prove the suitability of the models for the large amounts of data that will be available in the Gaia data archive.Las grandes cantidades de datos que se producen en el mundo diariamente plantean nuevos retos a la sociedad en términos de cómo extraer su valor inherente. Las redes sociales, mensajería instantánea, los dispositivos inteligentes y las misiones científicas son meros ejemplos del gran número de fuentes generando datos en cada momento. Al mismo tiempo que el mundo se digitaliza cada vez más, aparecen nuevas necesidades para organizar, archivar, compartir, analizar, visualizar y proteger la creciente cantidad de datos, para que podamos desarrollar economías basadas en datos e información que sean capaces de reducir las ineficiencias e incrementar la sostenibilidad, creando nuevas oportunidades de negocio por el camino. La forma en la que se han manejado los datos tradicionalmente no es la adecuada hoy en día, ya que carece de los medios para escalar a los volúmenes más grandes de datos de una forma oportuna y eficiente. Esto ha cambiado de alguna manera con la llegada de compañías que operan en Internet como Google o Facebook, ya que han concebido nuevas aproximaciones para abordar el problema. Sin embargo, la variedad y complejidad de las cadenas de valor en el sector privado y las crecientes demandas y limitaciones en las que el sector público opera, necesitan una investigación continua en la materia que pueda proporcionar nuevas estrategias para procesar las enormes cantidades de datos, facilitar la integración de productores y consumidores de información, y garantizar una transición rápida y fluida a la hora de adoptar estos avances tecnológicos innovadores. Esta tesis tiene como objetivo proporcionar nuevas arquitecturas y técnicas que ayudarán a realizar esta transición hacia Big Data en archivos científicos masivos. La investigación destaca los escollos principales a encarar cuando se adoptan estas nuevas tecnologías y cómo afrontarlos, principalmente cuando los datos y las herramientas de transformación utilizadas en el análisis existen en la organización. Además, se exponen nuevas medidas para facilitar una transición más fluida. Éstas incluyen la utilización de software de alto nivel y específico al caso de uso en cuestión, que haga de puente entre el dominio científico y tecnológico. Esta alternativa ampliará de una forma efectiva las posibilidades de los archivos científicos y por tanto contribuirá a la reducción del tiempo necesario para generar resultados científicos a partir de los datos recogidos en las misiones de astronomía espacial y planetaria. La investigación se aplicará a la misión de la Agencia Espacial Europea (ESA) Gaia, cuyo archivo final de datos presentará un gran potencial para el descubrimiento y hallazgo desde el punto de vista científico. La misión creará el catálogo en tres dimensiones más grande y preciso de nuestra galaxia (la Vía Láctea), proporcionando medidas sin precedente acerca del posicionamiento, paralaje y movimiento propio de alrededor de mil millones de estrellas. Las oportunidades para la explotación exitosa de este archivo de datos dependerán en gran medida de la capacidad de ofrecer la arquitectura adecuada, es decir infraestructura y servicios, sobre la cual los científicos puedan realizar la exploración y modelado con esta inmensa cantidad de datos. Por tanto, la estrategia a realizar debe ser capaz de combinar los datos con otros archivos científicos, ya que esto producirá sinergias que contribuirán a un incremento en la ciencia producida, tanto en volumen como en calidad de la misma. El conjunto de técnicas e infraestructuras innovadoras presentadas en este trabajo aborda estos problemas, contextualizándolos con los productos de datos que se generarán en la misión Gaia. Todas estas consideraciones han conducido a los fundamentos de la arquitectura que se utilizará en el paquete de trabajo de aplicaciones que posibilitarán la ciencia en el archivo de la misión Gaia (Science Enabling Applications). Por último, la eficacia de la solución propuesta se demostrará a través de la implementación de dos problemas estadísticos que requerirán cantidades significativas de cómputo, y que usarán datos simulados en el mismo formato en el que se producirán en el archivo de la misión Gaia (la primera versión de datos recogidos por la misión está disponible desde el día 14 de Septiembre de 2016). Estos ambiciosos problemas representan el Gran Reto (Grand Challenge), un nombre grandilocuente que consiste en inferir una serie de parámetros desde un punto de vista probabilístico para la función de masa inicial (Initial Mass Function) y la tasa de formación estelar (Star Formation Rate) dado un conjunto de estrellas (con una muestra grande), desde estimaciones con ruido de sus masas y edades respectivamente. Esto se abordará utilizando modelos jerárquicos bayesianos (Hierarchical Bayesian Modeling). Enprincipio,losmodelospropuestos pueden incorporar otros modelos de evolución estelar para inferir directamente la función de masa inicial y la tasa de formación estelar, pero en este primer paso presentado en esta tesis, empezaremos con un objetivo algo menos ambicioso: la inferencia de la función de masa y distribución de edades actual (Present-Day Mass Function y Present-Day Age Distribution respectivamente). Además, se llevará a cabo el análisis de rendimiento y escalabilidad para probar la idoneidad de la implementación de dichos modelos dadas las enormes cantidades de datos que estarán disponibles en el archivo de la misión Gaia...Depto. de Arquitectura de Computadores y AutomáticaFac. de InformáticaTRUEunpu

New developments on the cheminformatics open workflow environment CDK-Taverna

<p>Abstract</p> <p>Background</p> <p>The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Lego™-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public.</p> <p>Results</p> <p>The CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios.</p> <p>Conclusions</p> <p>CDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Taverna community and published on myexperiment.org enables molecular scientists to quickly calculate, process and analyse molecular data as typically found in e.g. today's systems biology scenarios.</p

On-the-fly tracing for data-centric computing : parallelization, workflow and applications

As data-centric computing becomes the trend in science and engineering, more and more hardware systems, as well as middleware frameworks, are emerging to handle the intensive computations associated with big data. At the programming level, it is crucial to have corresponding programming paradigms for dealing with big data. Although MapReduce is now a known programming model for data-centric computing where parallelization is completely replaced by partitioning the computing task through data, not all programs particularly those using statistical computing and data mining algorithms with interdependence can be re-factorized in such a fashion. On the other hand, many traditional automatic parallelization methods put an emphasis on formalism and may not achieve optimal performance with the given limited computing resources. In this work we propose a cross-platform programming paradigm, called on-the-fly data tracing , to provide source-to-source transformation where the same framework also provides the functionality of workflow optimization on larger applications. Using a big-data approximation computations related to large-scale data input are identified in the code and workflow and a simplified core dependence graph is built based on the computational load taking in to account big data. The code can then be partitioned into sections for efficient parallelization; and at the workflow level, optimization can be performed by adjusting the scheduling for big-data considerations, including the I/O performance of the machine. Regarding each unit in both source code and workflow as a model, this framework enables model-based parallel programming that matches the available computing resources. The techniques used in model-based parallel programming as well as the design of the software framework for both parallelization and workflow optimization as well as its implementations with multiple programming languages are presented in the dissertation. Then, the following experiments are performed to validate the framework: i) the benchmarking of parallelization speed-up using typical examples in data analysis and machine learning (e.g. naive Bayes, k-means) and ii) three real-world applications in data-centric computing with the framework are also described to illustrate the efficiency: pattern detection from hurricane and storm surge simulations, road traffic flow prediction and text mining from social media data. In the applications, it illustrates how to build scalable workflows with the framework along with performance enhancements