SODAR Core: a Django-based framework for scientific data management and analysis web apps

Modern life science is generating large data sets at a unprecedented speed. A major source of data are so-called omics (e.g., genomics, metabolomics, or proteomics) experiments. Consequently, management and analysis of scientific data has become a major challenge. Further, the heterogeneity of projects makes "one size fits all" data analysis systems infeasible and calls for specialized data analysis platforms. The authors are actively developing applications for the FAIR (findable, accessible, interoperable, and reuseable) data management of omics data and their analysis. In order to prevent duplication of work, we have extracted the commonly useful components into SODAR Core, a Python framework on top of Django. It is used in our actively developed applications and also proved useful in internal web app prototypes. Examples for using SODAR Core in the development of scientific data management web apps is Digestiflow and the Filesfolders module shipping with SODAR Core. An example for using SODAR Core in the development of scientific data analysis web apps is VarFis

SODAR: managing multiomics study data and metadata

Scientists employing omics in life science studies face challenges such as the modeling of multiassay studies, recording of all relevant parameters, and managing many samples with their metadata. They must manage many large files that are the results of the assays or subsequent computation. Users with diverse backgrounds, ranging from computational scientists to wet-lab scientists, have dissimilar needs when it comes to data access, with programmatic interfaces being favored by the former and graphical ones by the latter. We introduce SODAR, the system for omics data access and retrieval. SODAR is a software package that addresses these challenges by providing a web-based graphical user interface for managing multiassay studies and describing them using the ISA (Investigation, Study, Assay) data model and the ISA-Tab file format. Data storage is handled using the iRODS data management system, which handles large quantities of files and substantial amounts of data. SODAR also offers programmable APIs and command-line access for metadata and file storage. SODAR supports complex omics integration studies and can be easily installed. The software is written in Python 3 and freely available at https://github.com/bihealth/sodar-server under the MIT license

VarFish - Collaborative and comprehensive variant analysis for diagnosis and research

VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of panel and exome variant data for rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Filtered variants are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows user to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software’s extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g., after update of genotype or phenotype databases

Femtosecond multimodal imaging with a laser-driven X-ray source

Laser-plasma accelerators are compact linear accelerators based on the interaction of high-power lasers with plasma to form accelerating structures up to 1000 times smaller than standard radiofrequency cavities, and they come with an embedded X-ray source, namely betatron source, with unique properties: small source size and femtosecond pulse duration. A still unexplored possibility to exploit the betatron source comes from combining it with imaging methods able to encode multiple information like transmission and phase into a single-shot acquisition approach. In this work, we combine edge illumination-beam tracking (EI-BT) with a betatron X-ray source and present the demonstration of multimodal imaging (transmission, refraction, and scattering) with a compact light source down to the femtosecond timescale. The advantage of EI-BT is that it allows multimodal X-ray imaging technique, granting access to transmission, refraction and scattering signals from standard low-coherence laboratory X-ray sources in a single shot

Wave vector dependence of the dynamics in supercooled metallic liquids

We present a detailed investigation of the wave vector dependence of collective atomic motion in Au49Cu26.9Si16.3Ag5.5Pd2.3 and Pd42.5Cu27Ni9.5P21 supercooled liquids close to the glass transition temperature. Using x-ray photon correlation spectroscopy in a precedent uncovered spatial range of only few interatomic distances, we show that the microscopic structural relaxation process follows in phase the structure with a marked slowing down at the main average inter-particle distance. This behavior is accompanied by dramatic changes in the shape of the intermediate scattering functions which suggest the presence of large dynamical heterogeneities at length-scales corresponding to few particle diameters. A ballistic-like mechanism of particle motion seems to govern the structural relaxation of the two systems in the highly viscous phase, likely associated to hopping of caged particles in agreement with theoretical studies

Fail-safe optimization of viscous dampers for seismic retrofitting

This paper presents a new optimization approach for designing minimum-cost fail-safe distributions of fluid viscous dampers for seismic retrofitting. Failure is modeled as either complete damage of the dampers or partial degradation of the dampers' properties. In general, this leads to optimization problems with large number of constraints. Thus, the use of a working-set optimization algorithm is proposed. The main idea is to solve a sequence of relaxed optimization sub-problems with a small sub-set of all constraints. The algorithm terminates once a solution of a sub-problem is found that satisfies all the constraints of the problem. The retrofitting cost is minimized with constraints on the inter-story drifts at the peripheries of frame structures. The structures considered are subjected to a realistic ensemble of ground motions, and their response is evaluated with time-history analyses. The transient optimization problem is efficiently solved with a gradient-based sequential linear programming algorithm. The gradients of the response functions are calculated with a consistent adjoint sensitivity analysis procedure. Promising results attained for 3-D irregular frames are presented and discussed. The numerical results highlight the fact that the optimized layout and size of the dampers can change significantly even for moderate levels of damage

A Regularized Discrete Laminate Parametrization Technique with Applications to Wing-Box Design Optimization

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97055/1/AIAA2012-1519.pd

Polarization of photospheric lines from turbulent dynamo simulations

We employ the magnetic and velocity fields from turbulent dynamo simulations to synthesize the polarization of a typical photospheric line. The synthetic Stokes profiles have properties in common with those observed in the quiet Sun. The simulated magnetograms present a level of signal similar to that of the Inter-Network regions. Asymmetric Stokes V profiles with two, three and more lobes appear in a natural way. The intensity profiles are broadened by the magnetic fields in fair agreement with observational limits. Furthermore, the Hanle depolarization signals of the Sr I 4607 A line turn out to be within the solar values. Differences between synthetic and observed polarized spectra can also be found. There is a shortage of Stokes V asymmetries, that we attribute to a deficit of structuring in the magnetic and velocity fields from the simulations as compared to the Sun This deficit may reflect the fact that the Reynolds numbers of the numerical data are still far from solar values. We consider the possibility that intense and tangled magnetic fields, like those in the simulations, exist in the Sun. This scenario has several important consequences. For example, less than 10% of the existing unsigned magnetic flux would be detected in present magnetograms. The existing flux would exceed by far that carried by active regions during the maximum of the solar cycle. Detecting these magnetic fields would involve improving the angular resolution, the techniques to interpret the polarization signals, and to a less extent, the polarimetric sensitivity.Comment: Accepted for publication in ApJ. 20 pag. 11 fig