Use of Solr and Xapian in the Invenio document repository software

Invenio is a free comprehensive web-based document repository and digital library software suite originally developed at CERN. It can serve a variety of use cases from an institutional repository or digital library to a web journal. In order to fully use full-text documents for efficient search and ranking, Solr was integrated into Invenio through a generic bridge. Solr indexes extracted full-texts and most relevant metadata. Consequently, Invenio takes advantage of Solr's efficient search and word similarity ranking capabilities. In this paper, we first give an overview of Invenio, its capabilities and features. We then present our open source Solr integration as well as scalability challenges that arose for an Invenio-based multi-million record repository: the CERN Document Server. We also compare our Solr adapter to an alternative Xapian adapter using the same generic bridge. Both integrations are distributed with the Invenio package and ready to be used by the institutions using or adopting Invenio

Optimizing insect metabarcoding using replicated mock communities

1. Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundance and biomass.2. Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization? and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins?3. We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Small insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike -in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike -in data generalize better across species for homogenates.4. We conclude that a nondestructive, mild lysis approach shows the highest promise for the presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogeniza- tion protocols perform better for characterizing community composition, in par- ticular in terms of biomass

ROOT - A C++ Framework for Petabyte Data Storage, Statistical Analysis and Visualization

ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, ROOT offers packages for complex data modeling and fitting, as well as multivariate classification based on machine learning techniques. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks - e.g. data mining in HEP - by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Supply System for Three-Level Inverters Using Multi-Pulse Rectifiers with Coupled Reactors

The paper presents a proposal of the multi-pulse AC/DC converter for providing supply for multilevel inverters and considerably reducing the line current distortion factor. It can be applied as a suitable source of DC voltage and is convenient to supply such inverters that need three or more voltage terminals to supply all sections of the inverter. The converter in question works as a multi-pulse rectifier supplying a three-level NPC (Neutral Point Clamped) inverter. The load introduced by the inverter is simulated as an impedance depended on a selected inverter state. All possible states are determined by using a set of three digits: 0, 1, 2. The sourcing converter is constructed from diode bridge rectifiers connected in parallel as well as the system of magnetically coupled reactors. The reactors are used to shift subsequent line voltages so that they create a multiphase voltage system supplying component rectifiers. The article presents two alternative rectifiers: A 12-pulse diode rectifier using one magnetically coupled reactor unit 3CRλ, and a 24-pulse one using three 3CRλ units. Simulation and experimental tests have been executed and selected results included. Conclusion and discussion are added

Active Filtering of Inverter Output Waveforms Based on Orthogonal Space Vector Theory

This paper presents a DC/AC converter consisting of two two-level inverters. The complex converter is built using two standard three-phase inverters: the main inverter (MI) and the auxiliary one (AI). The MI is controlled in a simple way to generate the stepped output voltage and the AI works as an active filter limiting the higher harmonics in the MI output voltage. The filtering process is based on the orthogonal space vector theory. A development and modification of the basic solution are presented here. The output voltage of the MI takes the shape of a stepped voltage comparable to the voltage generated by multilevel inverters. The AI operates as a very effective active power filter (APF) of the MI output voltage. The AI power is significantly lower in comparison to the MI power

Active Filtering of Inverter Output Waveforms Based on Orthogonal Space Vector Theory

This paper presents a DC/AC converter consisting of two two-level inverters. The complex converter is built using two standard three-phase inverters: the main inverter (MI) and the auxiliary one (AI). The MI is controlled in a simple way to generate the stepped output voltage and the AI works as an active filter limiting the higher harmonics in the MI output voltage. The filtering process is based on the orthogonal space vector theory. A development and modification of the basic solution are presented here. The output voltage of the MI takes the shape of a stepped voltage comparable to the voltage generated by multilevel inverters. The AI operates as a very effective active power filter (APF) of the MI output voltage. The AI power is significantly lower in comparison to the MI power

State and Space Vectors of the 5-Phase 2-Level VSI

The paper proposes a general description system of the five-phase two-level inverter. The two base methods are presented and discussed. The first one is based on the standard space vector transformation, while the other uses state vectors which enable the definition of the basic physical quantities of the inverter: current and voltage. The proposed notation system offers a general simplification of vector identification. It comprises a standardized proposal of notation and vector marking, which may be extremely useful for the specification of inverter states. The described notation system makes it possible to reach correlation between state and space vectors. It presents space and state vectors using the same digits. These properties suggest that the proposed notation system is a useful mathematical tool and may be really suitable in designing control algorithms. This mathematical tool was verified during simulation tests performed with the use of the Simulation Platform for Power Electronics Systems—PLECS

Polar Voltage Space Vectors of the Six-Phase Two-Level VSI

The paper recommends polar voltage space vectors of the six-phase and two-level inverter as a useful mathematical tool for vector control of the inverter. The inverter model is described using three mathematical tools: analytic expressions, voltage state, and space vectors. The analytic formulas allow for the determination of elementary physical inverter quantities: current and voltage. The state voltage vectors make it easy to define phase voltage distribution in every possible state of the inverter and voltage space vectors are the most important tool used for inverters’ control. The space vectors are defined using the standard voltage space vector transformation, while the state vectors are denoted by binary numbers and determine all voltage states of the inverter. The proposed notation system and vectors’ marking seem to be extremely useful in specifying the inverter states. This system certifies a deep correlation between the space and state vectors as they are described using the same digits. The properties of the system were confirmed during the simulation tests. Some examples of the inverter vector control based on polar voltage space vectors prove that the proposed solution is a useful mathematical tool and may be in fact suitable in designing inverter control algorithms. The simulation experiment described in this paper shows that the assumed control strategy allows for a significant reduction in the amount of switching compared to PWM. At the same time, the adopted vector strategy allows for the obtaining of a very favorable value of the current THD coefficient while maintaining the RMS values of the currents

The Precise Temperature Measurement System with Compensation of Measuring Cable Influence

The article presents an active bridge system that enables the solution of a significant problem consisting in ensuring correct indications of temperature values in a wide measuring range for a Pt100 temperature sensor with properties defined by the standard (EN-60751 + A2). The presented active bridge system combines the properties of the measuring amplifier with the stabilization of the current value in the branch in which the Pt100 sensor was placed. The article focuses on the comparison of the temperature measurement in a typical resistance bridge and the measurement made in the developed active bridge, which has also become the subject of a patent. For the performed tests, in which the correctness of the temperature measurement system operation was verified, and on the basis of the obtained results, the quality of temperature measurements was compared in a wide range of changes