A data management infrastructure for the integration of imaging and omics data in life sciences.

BACKGROUND: As technical developments in omics and biomedical imaging increase the throughput of data generation in life sciences, the need for information systems capable of managing heterogeneous digital assets is increasing. In particular, systems supporting the findability, accessibility, interoperability, and reusability (FAIR) principles of scientific data management. RESULTS: We propose a Service Oriented Architecture approach for integrated management and analysis of multi-omics and biomedical imaging data. Our architecture introduces an image management system into a FAIR-supporting, web-based platform for omics data management. Interoperable metadata models and middleware components implement the required data management operations. The resulting architecture allows for FAIR management of omics and imaging data, facilitating metadata queries from software applications. The applicability of the proposed architecture is demonstrated using two technical proofs of concept and a use case, aimed at molecular plant biology and clinical liver cancer research, which integrate various imaging and omics modalities. CONCLUSIONS: We describe a data management architecture for integrated, FAIR-supporting management of omics and biomedical imaging data, and exemplify its applicability for basic biology research and clinical studies. We anticipate that FAIR data management systems for multi-modal data repositories will play a pivotal role in data-driven research, including studies which leverage advanced machine learning methods, as the joint analysis of omics and imaging data, in conjunction with phenotypic metadata, becomes not only desirable but necessary to derive novel insights into biological processes.

Applications of Plasmon-Enhanced Nanocatalysis to Organic Transformations.

Localized surface plasmon resonance (LSPR) is a physical phenomenon exhibited by nanoparticles of metals including coinage metals, alkali metals, aluminum, and some semiconductors which translates into electromagnetic, thermal, and chemical properties. In the past decade, LSPR has been taken advantage of in the context of catalysis. While plasmonic nanoparticles (PNPs) have been successfully applied toward enhancing catalysis of inorganic reactions such as water splitting, they have also demonstrated exciting performance in the catalysis of organic transformations with potential applications in synthesis of molecules from commodity to pharmaceutical compounds. The advantages of this approach include improved selectivity, enhanced reaction rates, and milder reaction conditions. This review provides the basics of LSPR theory, details the mechanisms at play in plasmon-enhanced nanocatalysis, sheds light onto such nanocatalyst design, and finally systematically presents the breadth of organic reactions hence catalyzed.

Challenges of big data integration in the life sciences.

Big data has been reported to be revolutionizing many areas of life, including science. It summarizes data that is unprecedentedly large, rapidly generated, heterogeneous, and hard to accurately interpret. This availability has also brought new challenges: How to properly annotate data to make it searchable? What are the legal and ethical hurdles when sharing data? How to store data securely, preventing loss and corruption? The life sciences are not the only disciplines that must align themselves with big data requirements to keep up with the latest developments. The large hadron collider, for instance, generates research data at a pace beyond any current biomedical research center. There are three recent major coinciding events that explain the emergence of big data in the context of research: the technological revolution for data generation, the development of tools for data analysis, and a conceptual change towards open science and data. The true potential of big data lies in pattern discovery in large datasets, as well as the formulation of new models and hypotheses. Confirmation of the existence of the Higgs boson, for instance, is one of the most recent triumphs of big data analysis in physics. Digital representations of biological systems have become more comprehensive. This, in combination with advances in machine learning, creates exciting new research possibilities. In this paper, we review the state of big data in bioanalytical research and provide an overview of the guidelines for its proper usage.

ImmunoNodes - graphical development of complex immunoinformatics workflows.

BACKGROUND: Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the other hand, are difficult to integrate with other tools, which is typically required for the complex analysis and prediction pipelines required for advanced applications. RESULT: We present ImmunoNodes, an immunoinformatics toolbox that is fully integrated into the visual workflow environment KNIME. By dragging and dropping tools and connecting them to indicate the data flow through the pipeline, it is possible to construct very complex workflows without the need for coding. CONCLUSION: ImmunoNodes allows users to build complex workflows with an easy to use and intuitive interface with a few clicks on any desktop computer.

From the desktop to the grid: scalable bioinformatics via workflow conversion.

BACKGROUND: Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization, among others. Workflows rest upon the notion of splitting complex work into the joint effort of several manageable tasks. There are several engines that give users the ability to design and execute workflows. Each engine was created to address certain problems of a specific community, therefore each one has its advantages and shortcomings. Furthermore, not all features of all workflow engines are royalty-free -an aspect that could potentially drive away members of the scientific community. RESULTS: We have developed a set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor documents. We have also overcome the shortcomings and combined the features of two royalty-free workflow engines with a substantial user community: the Konstanz Information Miner, an engine which we see as a formidable workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources. We have thus created a free and highly accessible way to design workflows on a desktop computer and execute them on high-performance computing resources. CONCLUSIONS: Our work will not only reduce time spent on designing scientific workflows, but also make executing workflows on remote high-performance computing resources more accessible to technically inexperienced users. We strongly believe that our efforts not only decrease the turnaround time to obtain scientific results but also have a positive impact on reproducibility, thus elevating the quality of obtained scientific results.

ballaxy: web services for structural bioinformatics.

MOTIVATION: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. RESULTS: In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling. AVAILABILITY AND IMPLEMENTATION: ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL.

Performance studies on distributed virtual screening.

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other. The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infrastructures (DCIs). We have conducted thorough performance studies accounting not only for the runtime of the docking itself, but also for structure preparation. Performance studies were conducted via the workflow-enabled science gateway MoSGrid (Molecular Simulation Grid). As input we used benchmark datasets for protein kinases. Our performance studies show that docking workflows can be made to scale almost linearly up to 500 concurrent processes distributed even over large DCIs, thus accelerating vHTS campaigns significantly.

The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations.

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user-friendly Web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. The MoSGrid science gateway supports applications in the domains quantum chemistry (QC), molecular dynamics (MD), and docking. This paper presents the open-source MoSGrid architecture as well as lessons learned from its design.

Siringomielia y embarazo: informe de un caso / Syringomielia and pregnancy. Report of a case

Este informe relata el caso de una mujer de 39 años de edad, cuarta gesta, que durante su primer embarazo desarrolló déficit neurológico de la mano izquierda, lentamente progresivo llegando a afectar en el curso de siete años, todo el miembro superior izquierdo y mano derecha. Durante este tiempo, tiene dos abortos y entre el tercero y cuarto embarazo, por la sospecha clínica, se realizan estudios de laboratorio y gabinete encontrándose en la electromiografía, lesión de las astas anteriores de la médula espinal a nivel cervical. Durante este cuarto embarazo, el déficit neurológico se acentuó y se decide su interrupción en forma electiva por medio de operación cesárea bajo bloque epidural a las 38 semanas de gestación. Según nuestro conocimiento, este caso de siringomielia y embarazo, es el primero comunicado en nuestro medio

Incidencia de macrosomía fetal. Morbilidad materna y fetal / Fetal macrosomia incidence: Maternal and fetal morbility

La macrosomía fetal es una eventualidad obstétrica que se asocia con una elevada morbimortalidad materno-fetal. Con el objetivo de saber la incidencia de la macrosomía en nuestra institutción, conocer las cifras de los nacimientos por vía vaginal y abdominal materno-fetal, se diseñó el presente estudio. Al revisar 3,590 expedientes, encontramos una incidencia de macrosomía fetal de 5.6 por ciento de la población obstétrica global. Se resolvieron por la vía vaginal 58 por ciento, 68 por ciento de los recién nacidos era del sexo masculino. Las principales complicaciones maternas fueron, en las cesáreas, dos desgarros del labio inferior de la histerectomía y dos atonías transoperatorias. En los partos, los desgarros de III y IV fueron nueve de cada grado. Las principales complicaciones fetales fueron cinco de asfixia de leve a severa y cuatro distocias de hombro. Este estudio permite concluir que la incidencia de macrosomía fetal en nuestro servicio, es semejante a lo publicado, que se obtuvo 42 por ciento en el índice de cesárea y que la morbilidad materno-fetal fue baja

Versiónb externa en presentación pélvica / External version in pelvic presentation

En el servicio de obstetricia del Hospital, Clínica y Maternidad Conchita de Monterrey, N.L., se realizó un estudio prospectivo de intento de versión externa en 45 pacientes con diagnóstico de presentación pélvica, conforme a un protocolo establecido en la institución, con la finalidad de determinar el porcentaje de éxito y su reprercusión en reducir el índice de operación cesárea primaria por esta indicación. De las 45 pacientes, la mayoría fueron primigestas (48.9 por ciento). El éxito en la versión se logró en 17 pacientes (60 por ciento), culminando en parto en presentación cefálica y en cesárea 81.4 por ciento respectivamente. Ninguno de los casos de operación cesárea fue por presentación pélvica. Durante el periodo de estudio se redujo la incidencia de cesárea primaria en pacientes con presentación pélvica de 15.3 a 9.3 por ciento, respectivamente una disminución real de 39.2 por ciento. No se presentaron complicaciones atribuibles al procedimiento. Con los resultados obtenidos se concluye que el intento de versión externa en presentación pélvica tiene menos riesgo para la madre y el feto que la atención de un parto pélvico logrando una disminución de índice de cesárea primaria por tal indicación.