Exploring storage technologies for HPSS disk caches

At KIT we operate HPSS as a tape system for the GridKa WLCG Tier-1 and for the Baden-Württemberg Data Archive service. Performance limitations of the HPSS disk cache systems led us to explore new technology options for the disk cache, based on classic storage systems with SSDs, storage servers with local NVMe devices, and also options based on IBM Storage Scale. We will present details on the different possible solutions, including benchmarks

Inverse Methods: a Powerful Tool for Evaluating Aerosol Data, Exemplified on Cases With Relevance for the Atmosphere and the Aerosol Climate Effect

For a complete description of a given aerosol, more than one parameter is necessary, e.g. parameters concerning size distribution, chemical composition, and particle morphology. On the other hand, most instruments measuring aerosol properties are sensitive mostly to one parameter, but cross-sensitive to others. These cross-sensitivities are often eliminated by assumptions during data evaluation, inducing systematic uncertainties in the results. The use of assumptions can be reduced by combining the information of several instruments on the same aerosol and using inverse methods for interpretation of the data. The presentation focuses on two application examples of these methods. The first example concerns a size distribution inversion algorithm that combines data from several instruments into one size distribution. The second example deals with an algorithm that retrieves the aerosol asymmetry parameter (with respect to particle scattering) from measurements of the aerosol absorption and spectral scattering and hemispheric backscattering coefficients, thereby providing a set of parameters that completely describes an aerosol with respect to its direct climate effect

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

Reaction rates for mesoscopic reaction-diffusion kinetics

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework, frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a mixed boundary condition at the reaction radius of two molecules. We also establish fundamental limits for the range of mesh resolutions for which this approach yields accurate results, and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics

Transcriptome analysis of the short-lived fish Nothobranchius furzeri

Altersforschung wird erschwert durch die lange Lebensspanne der verwendeten Modellorganismen. Der türkise Prachtgrundkärpfling Nothobranchius furzeri hat die kürzeste Lebensspanne, die je für Wirbeltiere in Gefangenschaft ermittelt wurde. Weiterhin zeigen Populationen aus Gebieten mit verschiedenen klimatischen Bedingungen große Unterschiede, welche auch bei den abgeleiteten Laborstämmen beobachtet werden können Daher eignet sich N. furzeri als Modellorganismus für die Altersforschung. Das erste Ziel dieser Arbeit war, einen umfassenden Katalog aller Transkripte der Protein-kodierenden Gene von N. furzeri zu erstellen. Dafür wurden 13 cDNA-Banken mit Sanger, 454/Roche und Solexa/Illumina sequenziert. Insgesamt 47 Gb an Sequenzdaten wurden erzeugt. Der resultierende Transkriptkatalog enthält Sequenzen für 19.875 Proteinkodierende Gene, davon 71% mit dem vollständigen Proteinkodierenden Bereich. Der zweite Teil dieser Arbeit beschreibt Untersuchungen zu Veränderungen der Genexpression in alternden N. furzeri. Dabei wurden junge und alte N. furzeri des Laborstammes GRZ sowie des Laborstammes MZM-0403, welcher fast doppelt so alt wie GRZ wird, mittels RNA-seq untersucht. Es konnten in Gehirn und Haut 86 Gene mit signifikanten Veränderungen in der Expressionshöhe nachgewiesen werden. Diese spielen dabei eine Rolle in biologischen Prozessen mit bekanntem Alternsbezug. Für eine große Zahl (41%) dieser Gene konnten zudem ähnliche Veränderungen auch im alternden Zebrafisch nachgewiesen werden. Der Vergleich der Veränderungen zwischen den beiden Stämmen legt nahe, dass der Alterungsprozess in GRZ schneller verläuft als in MZM-0403. Zusammengefasst habe ich in dieser Arbeit einen umfassenden N. furzeri Transkriptkatalog erstellt und erste Einblicke in die Veränderungen der Genexpression alternder N. furzeri gegeben.Age research is hindered by the long lifespan of the current vertebrate model organisms. The African killifish Nothobranchius furzeri has the shortest lifespan recorded for vertebrates in captivity. Furthermore, populations living in regions with different climatic conditions show large differences in lifespan, and derived strains maintain these differences even in captivity. For these reasons, N. furzeri has been established as a new model organism for age research. The first aim of this thesis was to build a comprehensive transcript catalogue of protein-coding N. furzeri genes. To this end, Sanger, 454/Roche and Solexa/Illumina sequencing was used to sequence 13 cDNA libraries from different transcriptomes, yielding 46 Gb sequence data. Assembly and annotation resulted in a transcript catalogue containing transcript contigs for 19,875 protein-coding genes, thereof 71% with a complete coding sequence. The second aim was to study gene expression changes in ageing N. furzeri. A RNA-seq experiment was conducted to study transcript levels in brain and skin of young and old fish of the strains GRZ and MZM-0403, which differ in lifespan by 100%. Eighty-six differentially expressed genes were detected, which play a role in several ageing-relevant processes. A significant fraction (41%) of the N. furzeri genes was also found to be differentially regulated in ageing zebrafish, thus confirming their relevance in ageing. Finally, comparisons of fold changes of the two strains suggested that ageing is accelerated in the short-lived N. furzeri strain GRZ, compared to the longer-lived strain MZM-0403. In summary, in this thesis, I describe the development of a comprehensive, annotated N. furzeri transcript catalogue and give first insights into transcriptome-wide changes during N. furzeri ageing

Black Carbon Contribution to the Aerosol Phase and its Scavenged Fraction in Mixed Phase Clouds at the High Alpine Site Jungfraujoch (3580m asl)

The mass fraction of black carbon (BC) in the atmospheric aerosol and its mixing state are important for the direct aerosol climate effect. These properties also determine if BC is incorporated into cloud hydrometeors (i.e. droplets and ice crystals) and are important because the microphysical and optical properties of the cloud are altered (indirect aerosol effect). Measurements were performed during several Cloud and Aerosol Characterization Experiments, in winter 2004 (CLACE3), summer 2004 (CLACE3.5), winter 2005 (CLACE4) and summer 2005 (CLACE4.5) at the high Alpine research station Jungfraujoch (3580 m asl)