Mozilla Public License Research Articles

BROADCAST: A high-order compressible CFD toolbox for stability and sensitivity using Algorithmic Differentiation

The evolution of any complex dynamical system is described by its state derivative operators. However, the extraction of the exact N-order state derivative operators is often inaccurate and requires approximations. The open-source CFD (Computational Fluid Dynamics) code called BROADCAST discretises the compressible Navier-Stokes equations and then extracts the linearised N-derivative operators through Algorithmic Differentiation (AD) providing a toolbox for laminar flow dynamics. Furthermore, the gradients through adjoint derivation are extracted either by transposition of the linearised operator or through the backward mode of the AD tool. The software includes base-flow computation and linear global stability analysis via eigen-decomposition of the linearised operator or via singular value decomposition of the resolvent operator. Sensitivity tools as well as weakly nonlinear analysis complete the package. The numerical method for the spatial discretisation of the equations consists of a finite-difference high-order shock-capturing scheme applied within a finite volume framework on 2D curvilinear structured grids. The stability and sensitivity tools are demonstrated on two cases: a cylinder flow at low Mach number and a hypersonic boundary layer. Program summaryProgram Title: BROADCASTCPC Library link to program files:https://doi.org/10.17632/hcf893cr2n.1Developer's repository link:https://github.com/OneraHub/BroadcastLicensing provisions: Mozilla Public License 2.0Programming language: Python, FortranNature of problem: The extraction of the exact N-order state derivative operators useful to study complex dynamical systems is often inaccurate and requires approximations from the user.Solution method: This program discretises the compressible Navier-Stokes equations and then extracts the linearised state derivative operators through Algorithmic Differentiation providing a toolbox for laminar flow dynamics.

Correction of sexual dysfunction in postmenopausal women

Annotation. In the postmenopausal age, the quality of sexual life deteriorates significantly. To date, there are no effective methods for correcting sexual dysfunction (SD) in women of this age. The aim of the study was to compare the clinical efficacy of traditional drugs for menopausal hormone therapy (MHT) – tibolone and a complex drug containing 1 mg of estradiol and 5 mg of dydrogesterone for SD in postmenopausal women. 69 postmenopausal women with SD were monitored: 37 – the main group (MG), 32 – the comparison group (CG). MG women were treated a drug’s containing tibolone, 1 pill once a day. Women with CG were prescribed traditional menopausal hormone therapy (MHT) with a drug containing 1 mg of estradiol and 5 mg of dydrogesterone. The quality of sexual life was determined before treatment and 1 month after treatment using a specially designed questionnaire and menopause rating scale (MRS). Statistics were processed using LibreOffice Calc (Mozilla Public License v 2.0). Quantitative data from the two related groups (before and after treatment) were compared using the Wilcoxon signed rank test. When considering the results in an alternative form (the presence or absence of a certain feature used Fisher's angular transformation. Pairwise comparisons of groups were performed using the Mann-Whitney test at p <0,05. In the treatment of SD in women with MG there was a reduction of all symptoms; in patients with CG - improvement of only one indicator was observed. In MG, after 1month treatment of SD, the number of women satisfied with their sexual life increased 2.4 times (p<0.05), and in CG – 1.4 times (p>0.05). Significant reduction in most menopausal symptoms was observed in both groups of women after treatment. According to psychoneurological indicators and atrophic changes of the vagina, the difference between MG and CG after treatment was not detected (p>0.05). Besides, the best correction of climacteric vegetative disorders in CG was found in comparison with MG (p<0.05). In MG has been noted significant improvement in physical and mental health disorders and joint and muscle discomfort compared with СG (p <0.05). Recovery of urinary disorders during a month of therapy with MHT drugs was not observed in any group of studied women. Thus, the drug based on tibolone can be recommended for the correction of sexual dysfunction in postmenopausal women.

OpenBravo ERP in Enterprise Company

This paper aims to find out the extent of the use of OpenBravo software in an enterprise's ERP. Then compare OpenBravo with other Open Source ERP applications like Odoo. Enterprise Resource Planning (ERP) plays an important role in organizational management. especially in the field of information systems, to produce precise and accurate data. OpenBravo is web-based software and open-source web-based ERP solution for small and medium-sized enterprises and is released under the OpenBravo PublicLicense, under the Mozilla Public License. Openbravo provides a web-based interface, where users can view production, inventory, customer information, order tracking, and workflow information. The modules contained in Openbravo software include general settings, master data management, warehouse management, procurement management, project and service management, production management, sales management, and financial management. In this case, the ERP used is OpenBravo. Comparison with other types of ERP will be carried out and will be discussed in more detail related to the advantages and disadvantages of each ERP discussed. After the comparison and the advantages and disadvantages are discussed, then finally conclusions are made from all the discussions carried out. In this case, the writing methodology used to complete this paper comes from a literature study which contains several things such as the concept of OpenBravo, how OpenBravo works, and the advantages and disadvantages of OpenBravo when compared to other ERPs.

OpenBravo ERP in Enterprise Company

This paper aims to find out the extent of the use of OpenBravo software in an enterprise's ERP. Then compare OpenBravo with other Open Source ERP applications like Odoo. Enterprise Resource Planning (ERP) plays an important role in organizational management. especially in the field of information systems, to produce precise and accurate data. OpenBravo is web-based software and open-source web-based ERP solution for small and medium-sized enterprises and is released under the OpenBravo PublicLicense, under the Mozilla Public License. Openbravo provides a web-based interface, where users can view production, inventory, customer information, order tracking, and workflow information. The modules contained in Openbravo software include general settings, master data management, warehouse management, procurement management, project and service management, production management, sales management, and financial management. In this case, the ERP used is OpenBravo. Comparison with other types of ERP will be carried out and will be discussed in more detail related to the advantages and disadvantages of each ERP discussed. After the comparison and the advantages and disadvantages are discussed, then finally conclusions are made from all the discussions carried out. In this case, the writing methodology used to complete this paper comes from a literature study which contains several things such as the concept of OpenBravo, how OpenBravo works, and the advantages and disadvantages of OpenBravo when compared to other ERPs.

Using pentoxifylline, arginine hydrochloride, levocarnitine and rheosorbilact solutions for correction of fetoplacental dysfunction in pregnant women with preeclampsia

Annotation. As of today, there is no effective method for treating the fetoplacental dysfunction (FPD) in pregnant women with preeclampsia. The aim of research was the study of the method proposed by the authors for restoring the functional activity of the fetoplacental complex in pregnant women with FPD on the background of treatment of preeclampsia. А randomized controlled study of the effect proposed treatment (intravenous solution of pentoxifylline; solution containing arginine hydrochloride and levocarnitine; rheosorbilact) of 37 pregnant women at 35-40 weeks of gestation with FPD on the background of moderate preeclampsia, was performed. Such ultrasound doppler measurements have been studied: systolic-diastolic ratio, resistance index, pulsation index in the umbilical arteries, right and left uterine arteries, fetal middle cerebral artery, fetal internal carotid artery and fetal aorta before and after the performed treatment. Statistics were processed using LibreOffice Calc (Mozilla Public License v 2.0), adapted for medical and biological research. We used nonparametric Wilcoxon criteria, Mann-Whitney criteria at a significance level of p <0.05. After the performed treatment, stabilization of the fetoplacental blood circulation in women of the main group was observed, which manifested by decrease in S/D in umbilical artery in 1.3 times, in the left uterine artery in 1.4 times and in the fetal aorta in 1,1 times, and decrease in RI indices in the umbilical artery in 1.1 times, in the right uterine artery in 1.3 times, and increase in the middle cerebral artery in 1.4 times. So, in the course of the proposed treatment, the restoration of the blood flow velocity and the stabilization of vascular resistance in uterine arteries and the umbilical artery were observed in the women of the main group. The research of the possibility of using the above methodology in earlier gestational age and in the risk group for the prevention of preeclampsia is prospective and requires further attention.

Open-Source Coprocessor for Integer Multiple Precision Arithmetic

This paper presents an open-source digital circuit of the coprocessor for an integer multiple-precision arithmetic (MPA). The purpose of this coprocessor is to support a central processing unit (CPU) by offloading computations requiring integer precision higher than 32/64 bits. The coprocessor is developed using the very high speed integrated circuit hardware description language (VHDL) as an intellectual property (IP) core. Therefore, it can be implemented within field programmable gate arrays (FPGAs) at various scales, e.g., within a system on chip (SoC), combining CPU cores and FPGA within a single chip as well as FPGA acceleration cards. The coprocessor handles integer numbers with precisions in the range 64 bits–32 kbits, with the limb size set to 64 bits. In our solution, the sign-magnitude representation is used to increase the efficiency of the multiplication operation as well as to provide compatibility with existing software libraries for MPA. The coprocessor is benchmarked in factorial ( n ! ), exponentiation ( n n ) and discrete Green’s function (DGF) computations on Xilinx Zynq-7000 SoC on TySOM-1 board from Aldec. In all benchmarks, the coprocessor demonstrates better runtimes than a CPU core (ARM Cortex A9) executing the same computations using a software MPA library. For sufficiently large input parameters, our coprocessor is up to three times faster when implemented in FPGA on SoC, rising to a factor of ten in DGF computations. The open-source coprocessor code is licensed under the Mozilla Public License.

LabxDB: versatile databases for genomic sequencing and lab management.

Experimental laboratory management and data-driven science require centralized software for sharing information, such as lab collections or genomic sequencing datasets. Although database servers such as PostgreSQL can store such information with multiple-user access, they lack user-friendly graphical and programmatic interfaces for easy data access and inputting. We developed LabxDB, a versatile open-source solution for organizing and sharing structured data. We provide several out-of-the-box databases for deployment in the cloud including simple mutant or plasmid collections and purchase-tracking databases. We also developed a high-throughput sequencing (HTS) database, LabxDB seq, dedicated to storage of hierarchical sample annotations. Scientists can import their own or publicly available HTS data into LabxDB seq to manage them from production to publication. Using LabxDB's programmatic access (REST API), annotations can be easily integrated into bioinformatics pipelines. LabxDB is modular, offering a flexible framework that scientists can leverage to build new database interfaces adapted to their needs. LabxDB is available at https://gitlab.com/vejnar/labxdb and https://labxdb.vejnar.org for documentation. LabxDB is licensed under the terms of the Mozilla Public License 2.0. Supplementary data are available at Bioinformatics online.

High-performance sampling of generic determinantal point processes.

Determinantal point processes (DPPs) were introduced by Macchi (Macchi 1975 Adv. Appl. Probab. 7, 83-122) as a model for repulsive (fermionic) particle distributions. But their recent popularization is largely due to their usefulness for encouraging diversity in the final stage of a recommender system (Kulesza & Taskar 2012 Found. Trends Mach. Learn. 5, 123-286). The standard sampling scheme for finite DPPs is a spectral decomposition followed by an equivalent of a randomly diagonally pivoted Cholesky factorization of an orthogonal projection, which is only applicable to Hermitian kernels and has an expensive set-up cost. Researchers Launay et al. 2018 (http://arxiv.org/abs/1802.08429); Chen & Zhang 2018 NeurIPS (https://papers.nips.cc/paper/7805-fast-greedy-map-inference-for-determinantal-point-process-to-improve-recommendation-diversity.pdf) have begun to connect DPP sampling to LDLH factorizations as a means of avoiding the initial spectral decomposition, but existing approaches have only outperformed the spectral decomposition approach in special circumstances, where the number of kept modes is a small percentage of the ground set size. This article proves that trivial modifications of LU and LDLH factorizations yield efficient direct sampling schemes for non-Hermitian and Hermitian DPP kernels, respectively. Furthermore, it is experimentally shown that even dynamically scheduled, shared-memory parallelizations of high-performance dense and sparse-direct factorizations can be trivially modified to yield DPP sampling schemes with essentially identical performance. The software developed as part of this research, Catamari (hodgestar.com/catamari) is released under the Mozilla Public License v.2.0. It contains header-only, C++14 plus OpenMP 4.0 implementations of dense and sparse-direct, Hermitian and non-Hermitian DPP samplers. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'.

Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.

SummaryOrdino is a web-based analysis tool for cancer genomics that allows users to flexibly rank, filter and explore genes, cell lines and tissue samples based on pre-loaded data, including The Cancer Genome Atlas, the Cancer Cell Line Encyclopedia and manually uploaded information. Interactive tabular data visualization that facilitates the user-driven prioritization process forms a core component of Ordino. Detail views of selected items complement the exploration. Findings can be stored, shared and reproduced via the integrated session management.Availability and implementationOrdino is publicly available at https://ordino.caleydoapp.org. The source code is released at https://github.com/Caleydo/ordino under the Mozilla Public License 2.0.Supplementary information Supplementary data are available at Bioinformatics online.

Error-Free Data Visualization and Processing through imzML and mzML Validation.

Open data formats are key to facilitating data processing, sharing, and integration. The imzML format ( http://imzml.org/ ) has drastically improved these aspects of mass spectrometry imaging data. Efficient processing of data depends on data sets which are consistent and adhere to the specifications; however, this is not always the case. Here we present a validation tool for data stored in both imzML and the HUPO-PSI mass spectrometery counterpart, mzML, to identify any deviations from the published (i)mzML standard which could cause issues for the user when visualizing or processing data. The tool is released in two forms, a graphical user interface (GUI) for ease of use, and a command line version to fit into existing workflows and pipelines. When certain known issues are encountered, such as the presence of negative values for the location of the binary data, the validator resolves the issue automatically upon saving. The GUI version of the validator also allows editing of the metadata included within the (i)mzML files in order to resolve inconsistencies. We also present a means of performing conditional validation on the metadata within (i)mzML files, where user-defined rules are validated against depending on whether specific metadata are present (or not). For example, if the MALDI term is present, then additional rules related to MALDI (such as the requirement of inclusion of laser parameters) can be validated against this. This enables a flexible and more thorough automated validation of (i)mzML data. Such a system is necessary for validating data against more comprehensive sets of metadata such as minimum reporting guidelines or metadata requirements prior to submission and acceptance of data to data repositories. We demonstrate how this tool can be used to validate against the proposed minimum reporting guidelines in MSI as well as institute specific metadata criteria. The validator tool is endorsed for validation of imzML ( http://imzml.org/ ) and mzML ( http://www.psidev.info/mzml ) and is made available through the respective Web sites. The validator is also released as open source under Mozilla Public License 2.0 at https://gitlab.com/imzML/imzMLValidator .

AnaCoDa: analyzing codon data with Bayesian mixture models

AnaCoDa is an R package for estimating biologically relevant parameters of mixture models, such as selection against translation inefficiency, non-sense errors and ribosome pausing time, from genomic and high throughput datasets. AnaCoDa provides an adaptive Bayesian MCMC algorithm, fully implemented in C++ for high performance with an ergonomic R interface to improve usability. AnaCoDa employs a generic object-oriented design to allow users to extend the framework and implement their own models. Current models implemented in AnaCoDa can accurately estimate biologically relevant parameters given either protein coding sequences or ribosome foot-printing data. Optionally, AnaCoDa can utilize additional data sources, such as gene expression measurements, to aid model fitting and parameter estimation. By utilizing a hierarchical object structure, some parameters can vary between sets of genes while others can be shared. Genes may be assigned to clusters or membership may be estimated by AnaCoDa. This flexibility allows users to estimate the same model parameter under different biological conditions and categorize genes into different sets based on shared model properties embedded within the data. AnaCoDa also allows users to generate simulated data which can be used to aid model development and model analysis as well as evaluate model adequacy. Finally, AnaCoDa contains a set of visualization routines and the ability to revisit or re-initiate previous model fitting, providing researchers with a well rounded easy to use framework to analyze genome scale data. AnaCoDa is freely available under the Mozilla Public License 2.0 on CRAN (https://cran.r-project.org/web/packages/AnaCoDa/).

Implementation of a single sign-on system between practice, research and learning systems.

Multiple specialized electronic medical systems are utilized in the health enterprise. Each of these systems has their own user management, authentication and authorization process, which makes it a complex web for navigation and use without a coherent process workflow. Users often have to remember multiple passwords, login/logout between systems that disrupt their clinical workflow. Challenges exist in managing permissions for various cadres of health care providers. This case report describes our experience of implementing a single sign-on system, used between an electronic medical records system and a learning management system at a large academic institution with an informatics department responsible for student education and a medical school affiliated with a hospital system caring for patients and conducting research. At our institution, we use OpenMRS for research registry tracking of interventional radiology patients as well as to provide access to medical records to students studying health informatics. To provide authentication across different users of the system with different permissions, we developed a Central Authentication Service (CAS) module for OpenMRS, released under the Mozilla Public License and deployed it for single sign-on across the academic enterprise. The module has been in implementation since August 2015 to present, and we assessed usability of the registry and education system before and after implementation of the CAS module. 54 students and 3 researchers were interviewed. The module authenticates users with appropriate privileges in the medical records system, providing secure access with minimal disruption to their workflow. No passwords requests were sent and users reported ease of use, with streamlined workflow. The project demonstrates that enterprise-wide single sign-on systems should be used in healthcare to reduce complexity like "password hell", improve usability and user navigation. We plan to extend this to work with other systems used in the health care enterprise.

NES: a free software to manage data from neuroscience experiments

NES: a free software to manage data from neuroscience experiments

Characterizing rate limiting steps in transcription from RNA production times in live cells.

Single-molecule measurements of live Escherichia coli transcription dynamics suggest that this process ranges from sub- to super-Poissonian, depending on the conditions and on the promoter. For its accurate quantification, we propose a model that accommodates all these settings, and statistical methods to estimate the model parameters and to select the relevant components. The new methodology has improved accuracy and avoids overestimating the transcription rate due to finite measurement time, by exploiting unobserved data and by accounting for the effects of discrete sampling. First, we use Monte Carlo simulations of models based on measurements to show that the methods are reliable and offer substantial improvements over previous methods. Next, we apply the methods on measurements of transcription intervals of different promoters in live E. coli, and show that they produce significantly different results, both in low- and high-noise settings, and that, in the latter case, they even lead to qualitatively different results. Finally, we demonstrate that the methods can be generalized for other similar purposes, such as for estimating gene activation kinetics. In this case, the new methods allow quantifying the inducer uptake dynamics as opposed to just comparing them between cases, which was not previously possible. We expect this new methodology to be a valuable tool for functional analysis of cellular processes using single-molecule or single-event microscopy measurements in live cells. Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7Ehakkin22/censored/ andre.ribeiro@tut.fi or andre.sanchesribeiro@tut.fi Supplementary data are available at Bioinformatics online.

Open Source Software (OSS) Quality Assurance: A Survey Paper

Open source software (OSS) is a software product with the source code made public so that anyone can read, analyze, and change or improve the code. The use of this software is under a license, like Apache, GNU, MIT, Mozilla Public, and Eclipse Public License. Open source software development (OSSD) provides high quality assurance through user testing and peer reviews. The quality of these products depends on the size of the product community. This paper discusses the stakeholders of the OSS community, the quality assurance frameworks and models proposed in some studies, some statistics about OSS, the problems that affect the quality of OSSD, and the advantages and disadvantages of OSS compared to closed source software. This allows us to understand how we can achieve and improve the quality assurance and quality control of OSSD.

Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data.

MS2-GFP-tagging of RNA is currently the only method to measure intervals between consecutive transcription events in live cells. For this, new transcripts must be accurately detected from intensity time traces. We present a novel method for automatically estimating RNA numbers and production intervals from temporal data of cell fluorescence intensities that reduces uncertainty by exploiting temporal information. We also derive a robust variant, more resistant to outliers caused e.g. by RNAs moving out of focus. Using Monte Carlo simulations, we show that the quantification of RNA numbers and production intervals is generally improved compared with previous methods. Finally, we analyze data from live Escherichia coli and show statistically significant differences to previous methods. The new methods can be used to quantify numbers and production intervals of any fluorescent probes, which are present in low copy numbers, are brighter than the cell background and degrade slowly. Source code is available under Mozilla Public License at http://www.cs.tut.fi/%7ehakkin22/jumpdet/.

Estimation of fluorescence-tagged RNA numbers from spot intensities

Present research on gene expression using live cell imaging and fluorescent proteins or tagged RNA requires accurate automated methods of quantification of these molecules from the images. Here, we propose a novel automated method for classifying pixel intensities of fluorescent spots to RNA numbers. The method relies on a new model of intensity distributions of tagged RNAs, for which we estimated parameter values in maximum likelihood sense from measurement data, and constructed a maximum a posteriori classifier to estimate RNA numbers in fluorescent RNA spots. We applied the method to estimate the number of tagged RNAs in individual live Escherichia coli cells containing a gene coding for an RNA with MS2-GFP binding sites. We tested the method using two constructs, coding for either 96 or 48 binding sites, and obtained similar distributions of RNA numbers, showing that the method is adaptive. We further show that the results agree with a method that uses time series data and with quantitative polymerase chain reaction measurements. Lastly, using simulated data, we show that the method is accurate in realistic parameter ranges. This method should, in general, be applicable to live single-cell measurements of low-copy number fluorescence-tagged molecules. MATLAB extensions written in C for parameter estimation and finding decision boundaries are available under Mozilla public license at http://www.cs.tut.fi/%7ehakkin22/estrna/ CONTACT: andre.ribeiro@tut.fi.

A C library for retrieving specific reactions from the BioModels database

We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple string searches. Our goal is to provide a useful tool for quantitative modelers who seek to accelerate modeling efforts through the reuse of previously published representations of specific chemical reactions. The library is open-source and dual licensed under the Mozilla Public License Version 2.0 and GNU General Public License Version 2.0. Project source code, downloads and documentation are available at http://code.google.com/p/lib-sbml-reaction-finder.

Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams

Scientists conducting microarray and other experiments use circular Venn and Euler diagrams to analyze and illustrate their results. As one solution to this problem, this paper introduces a statistical model for fitting area-proportional Venn and Euler diagrams to observed data. The statistical model outlined in this paper includes a statistical loss function and a minimization procedure that enables formal estimation of the Venn/Euler area-proportional model for the first time. A significance test of the null hypothesis is computed for the solution. Residuals from the model are available for inspection. As a result, this algorithm can be used for both exploration and inference on real data sets. A Java program implementing this algorithm is available under the Mozilla Public License. An R function venneuler() is available as a package in CRAN and a plugin is available in Cytoscape.

The Cardiac Atlas Project—an imaging database for computational modeling and statistical atlases of the heart

Motivation: Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape and wall motion and characterize cardiac function among and within population groups.Results: Three main open-source software components were developed: (i) a database with web-interface; (ii) a modeling client for 3D + time visualization and parametric description of shape and motion; and (iii) open data formats for semantic characterization of models and annotations. The database was implemented using a three-tier architecture utilizing MySQL, JBoss and Dcm4chee, in compliance with the DICOM standard to provide compatibility with existing clinical networks and devices. Parts of Dcm4chee were extended to access image specific attributes as search parameters. To date, approximately 3000 de-identified cardiac imaging examinations are available in the database. All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (http://www.mozilla.org/MPL/MPL-1.1.txt).Availability: http://www.cardiacatlas.orgContact: a.young@auckland.ac.nzSupplementary information: Supplementary data are available at Bioinformatics online.