Library Code Research Articles

High-Capacity Digital Polymers: Storing Images in Single Molecules

High-capacity digital poly(phosphodiester)s were synthesized by stepwise automated phosphoramidite chemistry. Coding libraries containing either 4 or 8 phosphoramidite monomers of different mass we...

ROBUSTNESS IMPROVEMENT USING OPEN SOURCE CODE LIBRARIES

AbstractComputer tools are commonly used to assess designs. We develop a toolchain using open source code libraries in Python to provide an open source, interactive robust design improvement toolchain. A reference folder contains a script that reads an input parameter value file and runs the simulation. The toolchain executes uncertainty quantification steps by replicating the reference folder. This is repeated for design points, and mean and sigma graphs generated versus each design variable. This fits within a workflow of defining variation modes, design variables, and toolchain execution.

Reaction rate analyses of high-energy neutrons by injection of 100 MeV protons onto lead–bismuth target

Reaction rate analyses of high-energy neutrons and 100 MeV protons are conducted experimentally by combining the Monte Carlo codes and the nuclear data libraries, in the proton beam transport facility at the Kyoto University Critical Assembly. For the number of neutrons per proton, the ratio of high-energy neutrons for threshold energy under 20 MeV and 100 MeV protons is successfully reconstructed by combining JENDL-4.0 and the INCL model of the PHITS3.0 code with a relative difference about 10% between the experiments and the calculations. The MCNP6.1 code significantly demonstrates with the suitability of combining JENDL/HE-2007 (for high-energy neutrons) and LAHET150 (for protons) for analyzing the 209Bi(n, xn)210-xBi reaction rates of the high-energy neutrons over 20 MeV. In further studies, reaction rate analyses of neutrons over 20 MeV, such as 209Bi(n, 7n)203Bi reactions, still remain to be improved by combining the Monte Carlo code and nuclear data libraries.

A Virtualized Tier-3g Facility Installation for WLCG Network of CERN

A Tier-3g Facility within the computing resources of Istanbul Aydin University has been planned and installed with the TR-ULAKBIM national Tier-2 center. The facility is intended to provide an upgraded data analysis infrastructure to CERN researchers who are the members in the recent nation-wide projects and international projects such as ATLAS and CMS experiments. The fundamental design of Tier-3g has been detailed in this work with an emphasis on technical implementations of the following parts: Virtualization of all nodes, VOMS usage for reaching fast experimental data in the WLCG network, batch cluster / multicore computing with HTCONDOR and PROOF systems, usage of grid proxies to access code libraries in AFS and CVMFS, dynamic disk space allocation and remote system mounting of EOS. We also present the interpretation of test results that was obtained by the simulation of typical analysis codes.

Librarianship at the Turn of the Century: Contribution of Y.A. Grikhanov

The article analyses the contribution of Y.A. Grikhanov to the development of librarianship and library science. The main activity trends of Y.A. Grikhanov were driven by the development tasks of the library sphere since the 1970s. The author highlights the key problems of library stocks knowledge and determines contribution of Y.A. Grikhanov to their resolution. He was one of the organizers of the system of Depository storage of library collections in the libraries of Russia; he worked in the Department of Libraries of the Ministry of Culture of the Russian Federation. The main priorities of the Department activities in 1991—1999 were the creation of the All-Russian information-library computer network, the formation of “National Program for the preservation of library stocks”, the determination of priorities of the state library policy. Y.A. Grikhanov is one of the founders of the Federal Law “On Librarianship” and “The Model Library Code for the CIS Member States”. “The Library Encyclopaedia”, prepared under the guidance of Y.A. Grikhanov, reflects the holistic period of development of library science in Russia. Contribution of Y.A. Grikhanov to library stocks knowledge, library law and philosophical basis of library theory is huge. He is the leading scientist and organizer who has influenced the development of librarianship in Russia and the CIS countries.

DBTree: Very large phylogenies in portable databases

Abstract Growing numbers of large phylogenetic syntheses are being published. Sometimes as part of a hypothesis testing framework, sometimes to present novel methods of phylogenetic inference, and sometimes as a snapshot of the diversity within a database. Commonly used methods to reuse these trees in scripting environments have their limitations. I present a toolkit that transforms data presented in the most commonly used format for such trees into a database schema that facilitates quick topological queries. Specifically, the need for recursive traversal commonly presented by schemata based on adjacency lists is largely obviated. This is accomplished by computing pre‐ and post‐order indexes and node heights on the topology as it is being ingested. The resulting toolkit provides several command line tools to do the transformation and to extract subtrees from the resulting database files. In addition, reusable library code with object–relational mappings for programmatic access is provided. To demonstrate the utility of the general approach I also provide database files for trees published by Open Tree of Life, Greengenes, D‐PLACE, PhyloTree, the NCBI taxonomy and a recent estimate of plant phylogeny. The database files that the toolkit produces are highly portable (either as SQLite or tabular text) and can readily be queried, for example, in the R environment. Programming languages with mature frameworks for object‐relational mapping and phylogenetic tree analysis, such as Python, can use these facilities to make much larger phylogenies conveniently accessible to researcher programmers.

Morphisms of Neural Codes

We define a notion of morphism between combinatorial codes, making the class of all combinatorial codes into a category $\mathbf{Code}$. We show that morphisms can be used to remove redundant information from a code, and that morphisms preserve convexity. This fact leads us to define "minimally non-convex" codes. We propose a program to characterize these minimal obstructions to convexity and hence characterize all convex codes. We implement a library of Sage code to perform computation with morphisms. These computational methods yield the smallest to-date example of a non-convex code with no local obstructions. We conclude by giving an algebraic formulation of our results.

MLLBC: A Machine Learning Toolbox for Modeling the Loss Rate of the Lining Bearing Capacity

Testing the health of tunnels, as a branch of highway operation, has an extremely important application in public property and even life safety. Among them, there are many factors that cause the tunnel to deform or collapse. The conventional methods use the finite element method (FEM) which are to simulate the bearing capacity loss rate of the lining by using the mechanical method. However, it takes a long time to calculate the stress-strain-situation of the lining model under each condition. This paper explores the machine learning to calculate the loss rate of the lining bearing capacity under more conditions based on FEM simulation data. Here, we establish a machine learning toolbox for modeling the loss rate of the lining bearing capacity named “MLLBC”, which contains three main components: 1) data loading; 2) machine learning model deployment; 3) performance evaluation. To ensure the fairness of model evaluation, ten machine learning models use a unified code library. We also conduct experiments on our new dataset which is the loss rate of the lining bearing capacity with different data amounts, as well as experiments on the goodness of model fitting under different ranges of various variables.

Building Uncertainty Models on Top of Black-Box Predictive APIs

With the commoditization of machine learning, more and more off-the-shelf models are available as part of code libraries or cloud services. Typically, data scientists and other users apply these models as “black boxes”within larger projects. In the case of regressing a scalar quantity, such APIs typically offer a predict() function, which outputs the estimated target variable (often referred to as ŷ or, in code, y_hat). However, many real-world problems may require some sort of deviation interval or uncertainty score rather than a single point-wise estimate. In other words, a mechanism is needed with which to answer the question “How confident is the system about that prediction?” Motivated by the lack of this characteristic in most predictive APIs designed for regression purposes, we propose a method that adds an uncertainty score to every black-box prediction. Since the underlying model is not accessible, and therefore standard Bayesian approaches are not applicable, we adopt an empirical approach and fit an uncertainty model using a labelled dataset (x, y) and the outputs ŷ of the black box. In order to be able to use any predictive system as a black box and adapt to its complex behaviours, we propose three variants of an uncertainty model based on deep networks. The first adds a heteroscedastic noise component to the black-box output, the second predicts the residuals of the black box, and the third performs quantile regression using deep networks. Experiments using real financial data that contain an in-production black-box system and two public datasets (energy forecasting and biology responses) illustrate and quantify how uncertainty scores can be added to black-box outputs.

Repeatable Research Infrastructure Enabling Administrative Data Analysis

Background/RationaleLinked administrative datasets offer great potential for research, but also present major challenges—including the preparation of operational data into a form suitable for efficient research, complex and computationally demanding analysis, and the need to capture and share information about dataset contents and research methods.
 Main AimThe analytical services team in the Secure Anonymised Information Linkage (SAIL) Databank is creating interconnected tools and systems to automate the preparation and analysis of research data and to curate information about datasets and research methods. Our underlying goal is to make linked data research orders of magnitude faster and cheaper, as well as improve its consistency and quality.
 MethodsSeveral key developments are ongoing:
 
 Automation of data quality checking.
 Management of dataset metadata.
 Processing of raw source datasets into cleaned, research-ready data assets.
 The Concept Library, an application for creating, using, and sharing knowledge about research definitions and methods.
 A suite of R packages for analysis.
 
 Web Application Programming Interfaces will allow these pieces to work together as an integrated system enabling efficient research.
 ResultsInitial versions of dataset quality checking, cleaned datasets, and R code to implement common tasks are already in day-to-day use by researchers within SAIL. An advisory group has been convened to help guide the work.
 For example, shared library code that flags conditions within health data has been used across multiple projects; a cleaned dataset measuring follow-up within primary care has been used by more than 100 projects.
 ConclusionOur proof-of-concept work demonstrates the ability of shared code and cleaned data to meet needs across multiple projects, saving effort and standardizing results. Ongoing work to develop and integrate these tools should further streamline the research process, increasing the output and public benefit of SAIL and other data sources.

Intelligent Electronic Management of Library by Radio Frequency Identification Technology

In the information era, the knowledge learned in the campus can hardly meet the needs of the society, so the library has become one of the choices for people to supplement their knowledge. With the increasing demand for libraries, the traditional library management method has been difficult to support the demand. In order to promote the intelligent transformation of the library, the basic structure and principle of Radio Frequency Identification Devices (RFID) technology were briefly introduced in this paper, and the intelligent library management system based on RFID was also introduced. Then the library of Huaqiao University was divided into two regions, and the performance of collection counting, book query and passage efficiency of traditional library management based on magnetic stripe together with bar code and intelligent library management based on RFID were compared. The results showed that the collection counting efficiency of intelligent libraries was much higher than that of traditional libraries, the high accuracy and stability of book query avoided the dislocation and chaos like traditional libraries, and there was no congestion even during rush hours because of the higher passing efficiency.

The Geodynamic World Builder: a solution for complex initial conditions in numerical modeling

Abstract. The Geodynamic World Builder is an open-source code library intended to set up initial conditions for computational geodynamic models in both Cartesian and spherical geometries. The inputs for the JavaScript Object Notation (JSON)-style parameter file are not mathematical but rather a structured nested list describing tectonic features, e.g., a continental, an oceanic or a subducting plate. Each of these tectonic features can be assigned a specific temperature profile (e.g., plate model) or composition label (e.g., uniform). For each point in space, the Geodynamic World Builder can return the composition and/or temperature. It is written in C++ but can be used in almost any language through its C and Fortran wrappers. Various examples of 2-D and 3-D subduction settings are presented. The Geodynamic World Builder comes with an extensive online user manual.

Standard model parameters in the tadpole-free pure MS¯ scheme

We present an implementation and numerical study of the Standard Model couplings, masses, and vacuum expectation value (VEV), using the pure $\overline{\mathrm{MS}}$ renormalization scheme based on dimensional regularization. Here, the $\overline{\mathrm{MS}}$ Lagrangian parameters are treated as the fundamental inputs, and the VEV is defined as the minimum of the Landau gauge effective potential, so that tadpole diagrams vanish, resulting in improved convergence of perturbation theory. State-of-the-art calculations relating the $\overline{\mathrm{MS}}$ inputs to on-shell observables are implemented in a consistent way within a public computer code library, smdr (standard model in dimensional regularization), which can be run interactively or called by other programs. Included here for the first time are the full two-loop contributions to the Fermi constant within this scheme and studies of the minimization condition for the VEV at three-loop order with four-loop QCD effects. We also implement and study the scale dependence of all known multiloop contributions to the physical masses of the Higgs boson, the $W$ and $Z$ bosons, and the top quark, the fine structure constant and weak mixing angle, and the renormalization group equations and threshold matching relations for the gauge couplings, fermion masses, and Yukawa couplings.

МЕТОДИЧНІ АСПЕКТИ НАВЧАННЯ СТУДЕНТІВ СТВОРЕННЮ ЦИФРОВИХ ЧАСТОТНИХ СЛОВНИКІВ

Частотні словники створюються для виявлення найбільш використовуваних слів у природній мові, мові письменника, певному творі тощо. Цими словниками послуговуються при вивченні іноземних мов; розробці інших видів словників; проектуванні мовних експериментів; проведенні досліджень у галузях лексичної семантики, психолінгвістики, морфології та інших; створенні прикладних програм, орієнтованих на опрацювання природної мови. Інформаційно-комунікаційні технології, доступ до величезних електронних лінгвістичних корпусів, національних баз даних слів, заснованих на субтитрах телевізійних програм та фільмів, значно прискорили дослідження в галузі статистичного опрацювання текстів. Зважаючи на те, що частотні словники широко використовуються в різних сферах діяльності, а їх побудова передбачає розв’язання широкого кола лінгвістичних задач, доцільно розглянути технологію створення таких словників у процесі підготовки фахівців з прикладної лінгвістики та комп’ютерних наук, учителів інформатики. У статті розглядається методика навчання студентів створенню частотних словників. Запропоновано алгоритм побудови частотного словника. Аналізуються особливості реалізації кожного кроку алгоритму з використанням мови Python, яка є популярною мовою програмування з відкритим кодом та великими бібліотеками. Автор наводить програмні коди та обґрунтовує використання відповідних модулів, методів опрацювання рядків, функцій, констант, структур даних, регулярних виразів. Запропонована методика спрямована на: 1) підвищення мотивації студентів до навчання та 2) розкриття практичної значущості засвоєних ними методів та прийомів програмування. Автор вважає, що підхід, представлений у цій статті, може бути корисним викладачам дисциплін інформатичного циклу.

Survey Confirms Strong Support for Intellectual Freedom in Public Collection Development Librarians

A Review of:
 Oltmann, S. M. (2019). Important Factors in Midwestern Public Librarians’ Views on Intellectual Freedom and Collection Development: Part 1. The Library Quarterly, 89(1), 2-15. https://doi.org/10.1086/700659
 Abstract
 Objective – The article sought to explore whether librarian attitudes regarding intellectual freedom conform to the stance of the American Library Association (ALA).
 Design – Electronic survey.
 Setting – Public libraries in the Midwestern United States.
 Subjects – Subjects were 645 collection development library professionals employed in public libraries.
 Methods – An electronic survey was distributed to public library directors in nine Midwestern states and was completed by the library professional primarily responsible for collection development. The survey focused on community information and probed the participants for their stances on several intellectual freedom topics. 
 Main Results – The survey was sent to 3,018 participants via each state’s librarian and had a response rate of 21.37%. The first section of the survey focused on broad strokes statements representing the ALA’s stance on intellectual freedom for public libraries. The results revealed widespread agreement on these issues. More than 88% of participants agreed with statements like “public libraries should provide their clients with access to information from a variety of sources.” Despite strong agreement among participants, particular demographic characteristics were more likely to lead to disagreement with all statements including working in rural communities and not holding a master’s degree in library science.
 The next section of the survey focused on how strongly participants’ personal beliefs conformed to the intellectual freedom statements in the ALA’s Library Code of Ethics. Again, there was widespread agreement, with 94.9% of participants indicating that they agreed with the statement “we uphold the principles of intellectual freedom and resist all efforts to censor library materials.” Only one participant disagreed with the statement “it is the right of every individual to both seek and receive information from all points of view without restriction.” When asked whether the ALA’s stance on intellectual freedom ever conflicted with their personal beliefs, 39.8% of participants indicated that it did, 22% were unsure, and 40% had never experienced conflict. Participants holding a master's degree in library science and librarians in large cities were less likely to experience conflict between their personal beliefs and the ALA’s stance on intellectual freedom. In the free text comments, several participants indicated that they experienced conflict when the ALA’s stance did not reflect their personal beliefs or community values.
 Conclusion – While the overwhelming majority of respondents indicated that they agreed with the ALA’s stance on intellectual freedom, a minority of participants experienced some conflict. Respondents indicated that personal belief could create conflict when librarians committed to intellectual freedom were required to make choices in their professional work that conflicted with their own views. Conflict could also arise when collection choices made to support intellectual freedom were not supported by patrons in the community.

Food Service Guideline Policies on Local Government-Controlled Properties.

Local governments can implement food service guideline (FSG) policies, which, in large cities, may reach millions of people. This study identified FSG policies among the 20 largest US cities and analyzed them for key FSG policy attributes. Quantitative research. Local government facilities. Twenty largest US cities. Frequency of FSG policies and percent alignment to tool. Using municipal legal code libraries and other data sources, FSG policies enacted as of December 31, 2016, were identified. Full-text reviews were conducted of identified policies to determine whether they met inclusion criteria. Included policies were analyzed for key policy attributes specific to nutrition, behavioral design, implementation, and facility efficiency. Searches identified 469 potential FSG policies, of which 6 policies across 5 cities met inclusion criteria. Five policies met a majority of criteria assessed by the classification tool. Overall alignment to the tool ranged from 17% to 88%. Of the 6 policies, 5 met a majority of the nutrition attributes and 5 met at least 50% of attributes associated with implementation. No policies met the attributes associated with facility efficiency. The FSG policies were identified in 5 of the 20 US cities. Policy alignment was high for nutrition and implementation attributes. This analysis suggests that when cities adopt FSG policies, many develop policies that align with key policy attributes. These policies can serve as models for other jurisdictions to create healthier food access through FSGs.

Towards the ethical librarian

PurposeThe purpose of this paper is to examine the perspectives and viewpoints of professional staff of the Sam Jonah Library in as much as the ethical aspects of their profession are concerned. The paper also seeks to determine the common ethical issues that confront these professionals and their default courses of action in dealing with these issues.Design/methodology/approachThe descriptive survey design was used as the research methodology with the population of the study being all professional (post-graduate diploma and above) and para-professional (certificate, diploma and first degree) staff of the library. Due to the small number of professional staff (43) in the library, the census sampling technique was used.FindingsResults indicated the existence of ethical dilemmas in the working lives of these professionals with guidance for dealing with these dilemmas emanating mostly from consultation of senior colleagues. Although the findings showed that the Ghana Library Association (GLA) had an ethics handbook, it was revealed that majority of the staff were not aware of its existence. It was also discovered that one of the major challenges of these professionals is the absence of a specific library code of ethics handbook to guide staff in case they are confronted with these ethical dilemmas. The study recommends a strong awareness creation initiative from the GLA to bring to the notice of members, the existence of a formal code of ethics document.Originality/valueThe paper provides information on specific ethical issues confronting staff of the library and their current modes of dealing with the dilemmas they encounter.

The Application Programmer Interface (API) in Modern Cartography: Development and Prospects

Abstract. Application Programmer Interfaces have been a part of the cartographic landscape since 2006 with the introduction of the Google Maps API. Essentially a library of code that provides access to a variety of mapping functions, APIs have since been the basis of online, tile-based, Multiscale Pannable (MSP) mapping. While the Google Maps API is still the most widely used with more than 4.6 billion websites embedding a Google Map, a variety of other mapping APIs have been introduced primarily to circumvent Google’s pricing structure.The cost for using Google Maps on websites has changed over the years. From 2005 to 2011, the use of Google Maps was free no matter how many maps were referenced by a website. From then to 2016, Google limited map downloads to 25,000 map loads a day for 90 consecutive days. In 2016, the 90 consecutive days was removed so the number of maps downloaded could not exceed 25,000 on any given day. If it did, the website developer needed to register their site and pay a fee for maps produced over this limit.In April 2018, Google announced the launch of a new name for the Google Maps API – Google Maps Platform – and a new pricing plan. A free tier continues to be offered through a US $200 monthly credit but now requires creating an account and entering a credit card number. In this new online platform, it is still possible to use the Google Maps API without incurring any cost by limiting the number of daily downloads so that the monthly quota of 28,000 map downloads is not exceeded.The problem is not the use of the Google Maps API but the Google map tiles. The look of maps from Google and the associated interface have become so popular that users avoid using other kinds of maps – even those from Apple. Users complain that the tiles from other vendors implement a different color scheme or highlight different features. They also complain that these maps appear more slowly. While other APIs can use Google Map tiles, including the popular Leaflet API, their use is still subject to the same pricing structure.With the help of the Internet, maps from Google have become the standard maps. All other renditions of the world are seen to be inferior and not worthy of examination. They are simply interesting oddities. While some can adapt to alternative representations, most choose not to. This Google Map phenomena is examined along with lessons from the historical progression of online mapping.

Using Open Source Code Libraries for Robust Design Analysis

AbstractThe design of systems today often involves computer simulation to assess performance and design margins. Understanding how variability erases design margin is important to assure adequacy of margins, especially in optimization efforts. In this paper, we develop a toolchain using open source code libraries in Python, and encapsulate it in Jupyter notebooks, to provide an open source, interactive uncertainty quantification and sensitivity analysis toolchain. This works generally with simulation tools, where a reference folder is created containing a script that reads an input file of parameter values and runs the simulation. With that easily created, the toolchain executes the necessary uncertainty quantification steps with replicates of that reference folder. This approach fits within a broader workflow outlined that defines the variation modes to study, maps to simulation inputs, and screens the variables for sensitivity before conducting an uncertainty quantification. An example is shown in the simulation analysis of a Stirling engine.

Processing of the multigroup cross-sections for MCNP calculations

Stochastic Monte Carlo (MC) neutron transport codes are widely used in various reactorphysics applications, traditionally related to criticality safety analyses, radiation shielding and validation of deterministic transport codes. The main advantage of Monte Carlo codes lies in their ability to model complex and detail geometries without the need of simplifications. Currently, one of the most accurate and developed stochastic MC code for particle transport simulation is MCNP. To achieve the best real world approximations, continuous-energy (CE) cross-section (XS) libraries are often used. These CE libraries consider the rapid changes of XS in the resonance energy range; however, computing-intensive simulations must be performed to utilize this feature. To broaden ourcomputation abilities for industrial application and partially to allow the comparison withdeterministic codes, the CE cross section library of the MCNP code is replaced by the multigroup (MG) cross-section data. This paper is devoted to the cross-section processing scheme involving modified versions of TRANSX and CRSRD codes. Following this approach, the same data may be used in deterministic and stochastic codes. Moreover, using formerly developed and upgraded crosssection processing scheme, new MG libraries may be tailored to the user specific applications. For demonstration of the proposed cross-section processing scheme, the VVER-440 benchmark devoted to fuel assembly and pip-by-pin power distribution was selected. The obtained results are compared with continues energy MCNP calculation and multigroup KENO-VI calculation.