Efficient Open Source Research Articles

Critical success factors for open source innovation in pharma industry: learning from two case studies

PurposeThe study aims to add to the body of knowledge of open source tangible product management (also called open design). The objective is also to develop a guideline for efficient open source tangible product development and adoption.Design/methodology/approachThe exploratory research design using secondary data (like newspapers, magazines, research articles, bogs, papers, etc.) is used to analyze open source tangible product design challenges and enablers. The success stories of Open Source Software projects (OSS) were studied for identification of critical success factors and further their relevancy was tested in the two popular cases of open source drug discovery (malaria and tuberculosis)FindingsOpen innovation has become a part of competitive strategy of current businesses. It requires an efficient intellectual property protection regime for its implementation. However, in a market dominated by proprietary benefits, the open source technology development can serve as remedy for innovation needs of neglected sectors. The OSS literature revealed managing two classes of factors, namely technology sponsor level factors and environmental factors for efficiency and effectiveness. The case study analysis in the context of applicability of these OSS critical factors showed their limitations in open source tangible products, and highlighted understanding additional challenges and remedies.Research limitations/implicationsOpen source innovation is a collaborative effort involving inputs from various/diverse players, hence monitoring the effort and motivation level of the contributors is a cumbersome task. Only the information that is available online and in print media is taken as research inputs in this work. Also the data taken were from two case studies; a lot more case studies in the open design domain can progress the theory. The implications of this study are far-reaching in the areas where profit motivated proprietary efforts lack in addressing societal need. It provides guidelines for addressing those unmet needs by developing products in a collaborative way without intellectual property hurdles.Originality/valueThe essence of open design is becoming more vital, and there is a pressing need to build theory to support it, which still is elusive and dispersed. The study fills the gap using secondary data and case study approach.

Fast and exact quantification of motif occurrences in biological sequences

BackgroundIdentification of motifs and quantification of their occurrences are important for the study of genetic diseases, gene evolution, transcription sites, and other biological mechanisms. Exact formulae for estimating count distributions of motifs under Markovian assumptions have high computational complexity and are impractical to be used on large motif sets. Approximated formulae, e.g. based on compound Poisson, are faster, but reliable p value calculation remains challenging. Here, we introduce ‘motif_prob’, a fast implementation of an exact formula for motif count distribution through progressive approximation with arbitrary precision. Our implementation speeds up the exact calculation, usually impractical, making it feasible and posit to substitute currently employed heuristics.ResultsWe implement motif_prob in both Perl and C+ + languages, using an efficient error-bound iterative process for the exact formula, providing comparison with state-of-the-art tools (e.g. MoSDi) in terms of precision, run time benchmarks, along with a real-world use case on bacterial motif characterization. Our software is able to process a million of motifs (13–31 bases) over genome lengths of 5 million bases within the minute on a regular laptop, and the run times for both the Perl and C+ + code are several orders of magnitude smaller (50–1000× faster) than MoSDi, even when using their fast compound Poisson approximation (60–120× faster). In the real-world use cases, we first show the consistency of motif_prob with MoSDi, and then how the p-value quantification is crucial for enrichment quantification when bacteria have different GC content, using motifs found in antimicrobial resistance genes. The software and the code sources are available under the MIT license at https://github.com/DataIntellSystLab/motif_prob.ConclusionsThe motif_prob software is a multi-platform and efficient open source solution for calculating exact frequency distributions of motifs. It can be integrated with motif discovery/characterization tools for quantifying enrichment and deviation from expected frequency ranges with exact p values, without loss in data processing efficiency.

Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

We present open-source implementations of the linear-scaling fast multipole method (FMM) within the polarizable embedding (PE) model for efficient treatment of large polarizable environments in computational spectroscopy simulations. The implementations are tested for accuracy, efficiency, and usability on model systems as well as more realistic biomolecular systems. We explain how FMM parameters affect the calculation of molecular properties and show that PE calculations employing FMM can be carried out in a black-box manner. The efficiency of the linear-scaling approach is demonstrated by simulating the UV/vis spectrum of a chromophore in an environment of more than 1 million polarizable sites. Our implementations are interfaced to several open-source quantum chemistry programs, making computational spectroscopy simulations within the PE model and FMM available to a large variety of methods and a broad user base.

Back-end porting of FT_MX based on LLVM compilation architecture

The processor FT_MX is a high-performance chip independently developed by the National University of Defense Technology, with an innovative architecture and instruction set. LLVM architecture is a widely used and efficient open source compiler framework initiated by the University of Illinois. This paper introduces the basic architecture and functions of LLVM, analyzes the back-end migration mechanism of the architecture in detail, and gives the specific process of implementing FT_MX back-end migration, and realizes the support of LLVM architecture to the back-end of FT_MX processor.

Stacked Hybrid Discrete Choice Models for Airline Itinerary Choice

This study develops a methodology to train and apply a hybrid stacked discrete choice model for airline itinerary choice. This stacked model framework includes a data-driven component (i.e., gradient boosting machines) as well as a theory-driven component (i.e., utility maximization using generalized extreme value models). The resulting ensemble model combines attractive features of each, including the ability to conform to complex nonlinear relationships among itinerary characteristics, as well as the ability to leverage an analyst’s understanding of travel behavior tendencies and the natural relationship among itineraries. Using a real industry dataset containing purchase information for approximately 10 million air travelers, it is demonstrated that the resulting model outperforms either the gradient boosting or utility maximization modeling paradigm alone in forecasting air traveler choice behavior. Implementation of this model can be achieved using efficient open source tools including XGBoost and Larch, and requires relatively modest additional effort by an analyst above and beyond the effort to use either tool alone.

GGraph: An Efficient Structure-Aware Approach for Iterative Graph Processing

Many iterative graph processing systems have recently been developed to analyze graphs. Although they are effective from different aspects, there is an important issue that has not been addressed yet. A real-world graph follows the power-law property, in which a small number of vertices have high degrees (i.e., are connected to most other vertices in the graph). These vertices are called <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">hot-vertices</i> and usually require more iterations to converge. In the existing solutions, these hot-vertices may be allocated to many or even all graph partitions along with other vertices that are easy to converge. As the result, the partitions with hot-vertices have to be loaded repeatedly (and consequently the system suffers from high data access cost), although perhaps only a few vertices in these partitions are active. To cope with this issue, we develop an efficient open source graph partition manager, called GGraph, which can be integrated into the existing graph processing systems to efficiently support iterative graph processing, by taking into account the power-law property of the graph structure. It uses a novel graph repartitioning scheme with low overhead to dynamically partition the hot-vertices together, so as to avoid loading the inactive vertices in the same partition as the repeatedly processed hot-vertices. By such means, it not only enables less data access cost, but also enables the privileged processing of the hot-vertices. In order to further increase the convergence speed, a scheduling algorithm is further proposed in this work to prioritize the processing of the hot-vertices with low overhead. To demonstrate the efficiency of GGraph, we plug it into four state-of-the-art graph processing systems, i.e., Gemini, GraphChi, Chaos, and GridGraph, and experimental results show that GGraph improves their performance by up to 3.2 times, 3.8 times, 3.9 times, 3.5 times, respectively.

Streamlining Processing and Utilization of EM Data - An Efficient Open-source Solution

Streamlining Processing and Utilization of EM Data - An Efficient Open-source Solution

Efficient Open Source Software Radio on Heterogeneous Multicore Embedded Platforms

Software radio is a common technique in modern communications equipment, and it is frequently implemented using heterogeneous multicore processors because of its high computational requirements. Programming such systems is still a challenging task and developers rely often on standard parallel APIs and frameworks such as OpenMP and OpenCL. These tools, however, present some limitations when more than one algorithm has to be accelerated. The typical workload of a software radio usually includes several compute-intensive algorithms so it might be still better served by more specific tools, especially on embedded platforms. In this article, a development methodology for implementing software radio applications in heterogeneous multicore embedded platforms is proposed. The methodology is based on GNU radio, a free and open source software toolkit. To validate the methodology, a DVB–T receiver has been ported to an embedded heterogeneous multicore platform as a proof-of-concept. The results show that two different compute-intensive algorithms, Viterbi decoder, and FFT, can be simultaneously accelerated, improving the DVB–T receiver performance by 63%.

A minimal Tersoff potential for diamond silicon with improved descriptions of elastic and phonon transport properties

Silicon is an important material and many empirical interatomic potentials have been developed for atomistic simulations of it. Among them, the Tersoff potential and its variants are the most popular ones. However, all the existing Tersoff-like potentials fail to reproduce the experimentally measured thermal conductivity of diamond silicon. Here we propose a modified Tersoff potential and develop an efficient open source code called GPUGA (graphics processing units genetic algorithm) based on the genetic algorithm and use it to fit the potential parameters against energy, virial and force data from quantum density functional theory calculations. This potential, which is implemented in the efficient open source GPUMD (graphics processing units molecular dynamics) code, gives significantly improved descriptions of the thermal conductivity and phonon dispersion of diamond silicon as compared to previous Tersoff potentials and at the same time well reproduces the elastic constants. Furthermore, we find that quantum effects on the thermal conductivity of diamond silicon at room temperature are non-negligible but small: using classical statistics underestimates the thermal conductivity by about 10% as compared to using quantum statistics.

Vulnerability Assessment of Web Applications using Penetration Testing

In recent years, utilization of web applications, web hacking exercises have grown exponentially. Organizations are confronting extremely critical difficulties in anchoring their web applications from rising cyber threats, as bargain with the assurance issues don't appear to be the right approach. Vulnerability Assessment and Penetration Testing (VAPT) methods help us find these vulnerabilities / security loopholes in our systems even before an intruder could find a way to get it. This helps avoid zero-day exploits. This paper aims to elucidate the overview of Vulnerability Assessment and Penetration Testing and introduce the most efficient open source tools used to perform these tests. This paper also presents a combined VAPT testing methodology that incorporates strengths of several existing approaches, with the goal to understand their utility and benefit the most from the tests.

What Is Needed for the Sustainable Success of OSS Projects: Efficiency Analysis of Commit Production Process via Git

The purpose of this study is to investigate the relative efficiency of open source software projects, and to analyze what is needed for their sustainable success. The success of open source software is known to be attributable to a massive number of contributors engaging in the development process. However, an efficient open source software project is not guaranteed simply by active participation by many; a coordination mechanism is needed to seamlessly manage the multi-party collaboration. On this basis, this study aimed to examine the internal regulatory processes based on Git and GitHub, which serve as such a mechanism, and redefine the efficiency of open source software projects to fully reflect them. For this purpose, a two-stage data envelopment analysis was used to measure the project efficiency reflecting the internal processes. Moreover, this study considered the Kruskal–Wallis test and Tobit regression analysis to examine the effects of the participation by many on an open source software project based on the newly defined efficiency. Results show that a simple increase in contributors can be poisonous in terms of the efficiency of open source software projects.

Turbulence closure for mixing length theories

We present an approach to turbulence closure based on mixing length theory with three-dimensional fluctuations against a two-dimensional background. This model is intended to be rapidly computable for implementation in stellar evolution software and to capture a wide range of relevant phenomena with just a single free parameter, namely the mixing length. We incorporate magnetic, rotational, baroclinic and buoyancy effects exactly within the formalism of linear growth theories with nonlinear decay. We treat differential rotation effects perturbatively in the corotating frame using a novel controlled approximation which matches the time evolution of the reference frame to arbitrary order. We then implement this model in an efficient open source code and discuss the resulting turbulent stresses and transport coefficients. We demonstrate that this model exhibits convective, baroclinic and shear instabilities as well as the magnetorotational instability (MRI). It also exhibits non-linear saturation behaviour, and we use this to extract the asymptotic scaling of various transport coefficients in physically interesting limits.

OpenLabs - Collaborative Industrialization with Distributed and Open Source Microfactories

Technical progress in production technology, the advancement of ICTs as well as increasing social and economic imbalances and ever-scarce resources ask for new means of value creation. . With the spill over of the highly efficient and innovative open source principles to the world of physical goods and products new modes of value creation appear that put traditional economic strategies and assumptions into question by stressing collaboration instead of competition, knowledge sharing engineering and fostering the empowerment of the people to participate and get engaged.The here presented multidisciplinary OpenLabs concept takes into account these new patterns of value creation based on open source principles and is a suitable approach to increase the overall empowerment and participation in local communities in developing, but also in developed countries.

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database

BackgroundThe NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different organisms. The NCBI Entrez online web-search interface is convenient for simple manual search for a small number of genes but impractical for the kinds of outputs seen in typical genomics projects.ResultsWe have developed an efficient open source tool implemented in Python called Annokey, which annotates gene lists with the results of a keyword search of the NCBI Entrez Gene database and linked Pubmed article information. The user steers the search by specifying a ranked list of keywords (including multi-word phrases and regular expressions) that are correlated with their topic of interest. Rank information of matched terms allows the user to guide further investigation.We applied Annokey to the entire human Entrez Gene database using the key-term “DNA repair” and assessed its performance in identifying the 176 members of a published “gold standard” list of genes established to be involved in this pathway. For this test case we observed a sensitivity and specificity of 97% and 96%, respectively.ConclusionsAnnokey facilitates the identification of genes related to an area of interest, a task which can be onerous if performed manually on a large number of genes. Annokey provides a way to capitalize on the high quality information provided by the Entrez Gene database allowing both scalability and compatibility with automated analysis pipelines, thus offering the potential to significantly enhance research productivity.

Sampling from Dirichlet process mixture models with unknown concentration parameter: mixing issues in large data implementations.

We consider the question of Markov chain Monte Carlo sampling from a general stick-breaking Dirichlet process mixture model, with concentration parameter alpha . This paper introduces a Gibbs sampling algorithm that combines the slice sampling approach of Walker (Communications in Statistics - Simulation and Computation 36:45–54, 2007) and the retrospective sampling approach of Papaspiliopoulos and Roberts (Biometrika 95(1):169–186, 2008). Our general algorithm is implemented as efficient open source C++ software, available as an R package, and is based on a blocking strategy similar to that suggested by Papaspiliopoulos (A note on posterior sampling from Dirichlet mixture models, 2008) and implemented by Yau et al. (Journal of the Royal Statistical Society, Series B (Statistical Methodology) 73:37–57, 2011). We discuss the difficulties of achieving good mixing in MCMC samplers of this nature in large data sets and investigate sensitivity to initialisation. We additionally consider the challenges when an additional layer of hierarchy is added such that joint inference is to be made on alpha . We introduce a new label-switching move and compute the marginal partition posterior to help to surmount these difficulties. Our work is illustrated using a profile regression (Molitor et al. Biostatistics 11(3):484–498, 2010) application, where we demonstrate good mixing behaviour for both synthetic and real examples.Electronic supplementary materialThe online version of this article (doi:10.1007/s11222-014-9471-3) contains supplementary material, which is available to authorized users.

TUIT, a BLAST-Based Tool for Taxonomic Classification of Nucleotide Sequences

Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. The routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. The taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classification; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina. Stand-alone TUIT is available online at http://sourceforge.net/projects/tuit/.

Smart sensor/actuator node reprogramming in changing environments using a neural network model

The techniques currently developed for updating software in sensor nodes located in changing environments require usually the use of reprogramming procedures, which clearly increments the costs in terms of time and energy consumption. This work presents an alternative to the traditional reprogramming approach based on an on-chip learning scheme in order to adapt the node behaviour to the environment conditions. The proposed learning scheme is based on C-Mantec, a novel constructive neural network algorithm especially suitable for microcontroller implementations as it generates very compact size architectures. The Arduino UNO board was selected to implement this learning algorithm as it is a popular, economic and efficient open source single-board microcontroller. C-Mantec has been successfully implemented in a microcontroller board by adapting it in order to overcome the limitations imposed by the limited resources of memory and computing speed of the hardware device. Also, this work brings an in-depth analysis of the solutions adopted to overcome hardware resource limitations in the learning algorithm implementation (e.g., data type), together with an efficiency assessment of this approach when the algorithm is tested on a set of circuit design benchmark functions. Finally, the utility, efficiency and versatility of the system is tested in three different-nature case studies in which the environmental conditions change its behaviour over time.

Open sources three-dimensional ultrasound volumetric rendering in object oriented approach

On account of the advanced technology in recent years, the increasing demand for an effective medical imaging system has addressed its significance in diagnosis especially in the development of three-dimensional medical image reconstruction. Based on literature revise on various computational investigated, none of them show efficiency in terms of cost and computing performance. Owing to this fact, a method of 3D ultrasound volume reconstruction and rendering using Visualization Toolkit (VTK) has been proposed in this paper. The 3D reconstruction has been achieved through a series of computerized processes includes DICOM sources manipulation, grey interpolations, ray casting and volume rendering. Volunteered subject scanned on carotid arteries were collected. Experimental simulations were taking place on a maximum 256 numbers of two dimensional ultrasonic slices in DICOM storage. The result obtained indicates that VTK is an efficient open source library in performing 3D restoration especially in the matter of volume rendering. Internal structure of carotid arteries can be examined explicitly in any orientation. Within several virtual slicing features, such as slider, double side slider and box widget, it allows certain region-of-interest (ROI) visualization. The method proposed has shown its future utilities in clinical application especially in CT, MRI and Ultrasound images, in order to provide a more informative view for hospital personnel performing a more significant diagnosis. Key words: Three dimensional, reconstruction, visualization toolkit (VTK), volume, rendering, medical imaging, ultrasound, open sources.

HDDM: Hierarchical Bayesian estimation of the Drift-Diffusion Model in Python

The diffusion model is a commonly used tool to infer latent psychological processes underlying decision-making, and to link them to neural mechanisms based on response times. Although efficient open source software has been made available to quantitatively fit the model to data, current estimation methods require an abundance of response time measurements to recover meaningful parameters, and only provide point estimates of each parameter. In contrast, hierarchical Bayesian parameter estimation methods are useful for enhancing statistical power, allowing for simultaneous estimation of individual subject parameters and the group distribution that they are drawn from, while also providing measures of uncertainty in these parameters in the posterior distribution. Here, we present a novel Python-based toolbox called HDDM (hierarchical drift diffusion model), which allows fast and flexible estimation of the the drift-diffusion model and the related linear ballistic accumulator model. HDDM requires fewer data per subject/condition than non-hierarchical methods, allows for full Bayesian data analysis, and can handle outliers in the data. Finally, HDDM supports the estimation of how trial-by-trial measurements (e.g., fMRI) influence decision-making parameters. This paper will first describe the theoretical background of the drift diffusion model and Bayesian inference. We then illustrate usage of the toolbox on a real-world data set from our lab. Finally, parameter recovery studies show that HDDM beats alternative fitting methods like the χ2-quantile method as well as maximum likelihood estimation. The software and documentation can be downloaded at: http://ski.clps.brown.edu/hddm_docs/

Shirorekha Chopping Integrated Tesseract OCR Engine for Enhanced Hindi Language Recognition

OCR Engine is one of the most efficient open source OCR engines currently available. Recently, Tesseract OCR 3.01 is capable of recognizing Hindi language but still it needs some enhancement to improve the performance. The Hindi language recognition accuracy is quite low even for the printed text, as the conjunct character combinations of Hindi Language are not easily separable due to partial overlapping. The proposed approach solves this problem, so that Devanagari conjunct characters can easily be segmented and recognized using Tesseract OCR Engine. This paper presents a complete methodology to improve The Hindi Language Recognition accuracy. This paper also presents comparison with other Devanagari OCR engines available on the basis of recognition accuracy, processing time, font variations and database size.