Disaggregating non-volatile memory for throughput-oriented genomics workloads

Massive exploitation of next-generation sequencing technologies requires dealing with both: huge amounts of data and complex bioinformatics pipelines. Computing architectures have evolved to deal with these problems, enabling approaches that were unfeasible years ago: accelerators and Non-Volatile Memories (NVM) are becoming widely used to enhance the most demanding workloads. However, bioinformatics workloads are usually part of bigger pipelines with different and dynamic needs in terms of resources. The introduction of Software Defined Infrastructures (SDI) for data centers provides roots to dramatically increase the efficiency in the management of infrastructures. SDI enables new ways to structure hardware resources through disaggregation, and provides new hardware composability and sharing mechanisms to deploy workloads in more flexible ways. In this paper we study a state-of-the-art genomics application, SMUFIN, aiming to address the challenges of future HPC facilities.This work is partially supported by the European Research Council (ERC) under the EU Horizon 2020 programme (GA 639595), the Spanish Ministry of Economy, Industry and Competitivity (TIN2015-65316-P) and the Generalitat de Catalunya (2014-SGR-1051).Peer ReviewedPostprint (author's final draft

Nanostructured thermoelectric generator for energy harvesting

This paper presents the development processes towards a new generation of nanostructured thermoelectric generators for power harvesting from small temperature gradients by using a combination of traditional silicon microfabrication techniques, electroplating and submicron ion-track nanolithography. Polyimide nanotemplates with pore diameters ranging from 30nm to 120 nm were fabricated. Preliminary results for Bi2Te3 nanowires (50 and 120 nm diameter) electroplated into polycarbonate ion-track commercial membranes are presented. Bi2Te3 nanowires of R ̄ 3m structure, with preferential orientation in the (015) and (110) crystallographic plans with nearly stoichiometric composition were electroplated. The fine-grained observed microstructure (6-10 nm) and (110) crystalline orientation appear extremely promising for improving thermoelectric material properties

Closing the sea surface mixed layer temperature budget from in situ observations alone: Operation Advection during BoBBLE

Sea surface temperature (SST) is a fundamental driver of tropical weather systems such as monsoon rainfall and tropical cyclones. However, understanding of the factors that control SST variability is lacking, especially during the monsoons when in situ observations are sparse. Here we use a ground-breaking observational approach to determine the controls on the SST variability in the southern Bay of Bengal. We achieve this through the first full closure of the ocean mixed layer energy budget derived entirely from in situ observations during the Bay of Bengal Boundary Layer Experiment (BoBBLE). Locally measured horizontal advection and entrainment contribute more significantly than expected to SST evolution and thus oceanic variability during the observation period. These processes are poorly resolved by state-of-the-art climate models, which may contribute to poor representation of monsoon rainfall variability. The novel techniques presented here provide a blueprint for future observational experiments to quantify the mixed layer heat budget on longer time scales and to evaluate these processes in models

Software that goes with the flow in systems biology

A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists

Leaf-applied sodium chloride promotes cadmium accumulation in durum wheat grain

Cadmium (Cd) accumulation in durum wheat grain is a growing concern. Among the factors affecting Cd accumulation in plants, soil chloride (Cl) concentration plays a critical role. The effect of leaf NaCl application on grain Cd was studied in greenhouse-grown durum wheat (Triticum turgidum L. durum, cv. Balcali-2000) by immersing (10 s) intact flag leaves into Cd and/or NaCl-containing solutions for 14 times during heading and dough stages. Immersing flag leaves in solutions containing increasing amount of Cd resulted in substantial increases in grain Cd concentration. Adding NaCl alone or in combination with the Cd-containing immersion solution promoted accumulation of Cd in the grains, by up to 41%. In contrast, Zn concentrations of grains were not affected or even decreased by the NaCl treatments. This is likely due to the effect of Cl complexing Cd and reducing positive charge on the metal ion, an effect that is much smaller for Zn. Charge reduction or removal (CdCl2 0 species) would increase the diffusivity/lipophilicity of Cd and enhance its capability to penetrate the leaf epidermis and across membranes. Of even more significance to human health was the ability of Cl alone to penetrate leaf tissue and mobilize and enhance shoot Cd transfer to grains, yet reducing or not affecting Zn transfer

Contribution of an alveolar cell of origin to the high-grade malignant phenotype of pregnancy-associated breast cancer.

Pregnancy-associated breast cancers (PABCs) are tumors diagnosed during pregnancy or up to 5 years following parturition, and are usually high-grade, connective tissue-rich, and estrogen receptor (ER)/progesterone receptor-negative. Little is known about the cellular origin of PABCs or the mechanisms by which PABCs are initiated. Using the RCAS retrovirus to deliver the ErbB2 oncogene into the mammary epithelium of our previously reported MMTV-tva transgenic mice, we detected high-grade, poorly differentiated, stroma-rich and ER-negative tumors during pregnancy and lactation. These high-grade and stroma-rich tumors were less frequent in involuted mice or in age-matched nulliparous mice. More importantly, by generating a WAP-tva transgenic line for expression of ErbB2 selectively in WAP(+) mammary alveolar cells, we found that tumors had similar morphological phenotypes (high grade, poorly differentiated, stroma-rich and ER-negative), irrespective of the time since pregnancy and even in the absence of pregnancy. These data suggest that PABCs arise preferentially from an alveolar cell population that expands during pregnancy and lactation. This somatic mouse model may also be useful for preclinical testing of new prophylactic and therapeutic strategies against PABC

Effects of detuning, gain-guiding, and index antiguiding on the dynamics of two laterally coupled semiconductor lasers

Four examples of laterally coupled semiconductor lasers with different waveguiding structures have been studied using coupled mode theory and allowing for frequency detuning between the lasers. The structures include purely real index guiding, pure gain-guiding, and combinations of index guiding and antiguiding with gain-guiding. The dynamics of these four systems have been explored using AUTO software (standard numerical continuation package), linear stability analysis, and direct integration of the rate equations. Convincing agreement between results obtained by these three methods has been demonstrated, including effects due to variation of laser pumping rate, detuning, and linewidth enhancement factor. A periodicity of behavior with laser separation has been revealed that was previously overlooked. This periodicity has increasing influence on the bifurcations of the system as the structures develop from those with purely real guidance to a combination of index antiguiding and gain-guiding. The laser design and operating parameters used are realistic for a wide range of edge-emitting and surface-emitting lasers of practical importance, so that the dynamics studied here are relevant to real systems of coupled lasers

Mapping bifurcation structure and parameter dependence in quantum dot spin-VCSELs

We consider a modified version of the spin-flip model (SFM) that describes optically pumped quantum dot (QD) spin-polarized vertical-cavity surface-emitting lasers (VCSELs). Maps showing different dynamical regions and those consisting of various key bifurcations are constructed by direct numerical simulations and a numerical path continuation technique, respectively. A comparison between them clarifies the physical mechanism that governs the underlying dynamics as well as routes to chaos in QD spin-VCSELs. Detailed numerical simulations illustrate the role played by the capture rate from wetting layer (WL) to QD ground state, the gain parameter, and the amplitude-phase coupling. By tuning the aforementioned key parameters in turn we show how the dynamical regions evolve as a function of the intensity and polarization of the optical pump, as well as in the plane of the spin relaxation rate and linear birefringence rate, which is of importance in the design of spin lasers promising potential applications. By increasing the capture rate from WL to QD our simulation accurately describes the transition from the QD spin-VCSEL to the quantum well case, in agreement with a previous mathematical derivation, and thus validates the modified SFM equations

ChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

Chromatin immunoprecipitation (ChIP) coupled with high-throughput techniques (ChIP-X), such as next generation sequencing (ChIP-Seq) and microarray (ChIP-chip), has been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). The targeted genes can be activated or suppressed by the TF, or are unresponsive to the TF. Microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but is unable to determine if the affected genes are direct or indirect targets of the TF. Furthermore, both ChIP-X and microarray methods produce a large number of false positives. Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly and Arabidopsis. This server will assist biologists to detect direct and indirect target genes regulated by a TF of interest and to aid in the functional characterization of the TF. ChIP-Array is available at http://jjwanglab.hku.hk/ChIP-Array, with free access to academic users. © 2011 The Author(s).published_or_final_versio