The underground city: the tourism potential of water and sewage infrastructure: the example of Poland

Industrial tourism and technical facilities are a fast-growing branch of tourism that contains areas of great growth potential. The article deals with one of them. The tourist potential of water and sewage infrastructure in selected Polish cities was analysed and assessed. The study covered 11 cities of diverse socioeconomic potentials around the country. For each city, data were collected that had various levels of detail with regard to visitor numbers, tourist types, facilities made available, events and other special celebrations. For supplementary data, unstructured interviews were also conducted with relevant employees identified in businesses. The analysis showed the studied form of tourism to have very high tourism potential. The work focuses on factors and features accounting for its currently low level of development. It is also emphasised that, based on current tourism trends, it should be expected to continue to grow rapidly in the coming years, and thus warrants further research.

AMAW: automated gene annotation for non-model eukaryotic genomes

SummaryTo support small and large-scale genome annotation projects, we present AMAW (Automated MAKER2 Annotation Wrapper), a program devised to annotate non-model unicellular eukaryotic genomes by automating the acquisition of evidence data (transcripts and proteins) and facilitating the use of MAKER2, a widely adopted software suite for the annotation of eukaryotic genomes. Moreover, AMAW exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2.AvailabilityAMAW is released both as a Singularity container recipe and a standalone Perl script (https://bitbucket.org/phylogeno/amaw/)[email protected] or [email protected] informationSupplementary data are available at Bioinformatics online.

Modeling Qualitative Outcomes by Supplementing Participant Data with General Population Data: A New and More Versatile Approach

Although one often has detailed information about participants in a program, the lack of comparable information on non-participants precludes standard qualitative choice estimation. This challenge can be overcome by incorporating a supplementary sample of covariate values from the general population. This paper presents new estimators based on this sampling strategy, which perform comparably to the best existing supplementary sampling estimators. The key advantage of the new estimators is that they readily incorporate sample weights, so that they can be applied to Census surveys and other supplementary data sources that have been generated using complex sample designs. This substantially widens the range of problems that can be addressed under a supplementary sampling estimation framework. The potential for improving precision by incorporating imperfect knowledge of the population prevalence rate is also explored.

PELAKSANAAN PENINGKATAN HAK GUNA BANGUNAN MENJADI HAK MILIK UNTUK RUMAH TINGGAL DI KANTOR PERTANAHAN KARAWANG DITINJAU DARI KEPUTUSAN MENTERI NEGARA AGRARIA / KEPALA BADAN PERTANAHAN NASIONAL NOMOR 6 TAHUN 1998 TENTANG PEMBERIAN HAK MILIK ATAS TANAH

Tanah merupakan faktor yang sangat penting dalam kehidupan masyarakat. Selain sandangdan pangan, manusia juga membutuhkan tanah sebagai tempat tinggal mereka. Untukmemberikan kepastian hukum dan menjamin kepemilikan tanah kepada pemegang hak atastanah, maka mereka harus mempunyai bukti yang disebut sertipikat. Bahwa rumah tinggaldiperlukan masyarakat, maka tanah digunakan sebagai rumah tinggal dari status HakGuna Bangunan menjadi Hak Milik untuk rumah tinggal. Masalah yang dikaji dalampenelitian ini adalah bagaimana pelaksanaan peningkatan Hak Guna Bangunan menjadiHak Milik untuk rumah tinggal di Kantor Pertanahan Kabupaten Karawang? dan apa sajasyarat-syarat yang harus dipenuhi dalam pendaftaran peningkatan Hak Guna Bangunanmenjadi Hak Milik untuk rumah tinggal?. Berkaitan dengan masalah tersebut, penelitianini bertujuan untuk mengetahui pelaksanaan peningkatan Hak Guna Bangunan menjadiHak Milik untuk rumah tinggal di Kantor Pertanahan Kabupaten Karawang. Metodependekatan yang digunakan dalam penelitian ini adalah Yuridis empiris yaitu pendekatanyang menitik beratkan pada pengumpulan data dari studi lapangan sebagai data utama danstudi kepustakaan sebagai data pelengkap. Adapun hipotesa dari penulis adalah perihalpelaksanaan Peningkatan Hak Guna Bangunan menjadi Hak Milik adalah seringditemuinya pemohon yang mendaftarkan peningkatan dengan berkas yang kurang lengkapdikarenakan kurangnya pengetahuan terkait proses tersebut sehingga menunda prosespeningkatan hak dan membutuhkan waktu yang lama. Kata Kunci : Peningkatan Hak, Hak Guna Bangunan, Hak Land is a very important factor in people's lives. In addition to clothing and food, humansalso need land as their residence. To provide legal certainty and guarantee ownership ofland to holders of land rights, they must have evidence called certificates. Whereas aresidence is needed by the community, the land is used as a residence from the status ofBuilding Use Rights to become Ownership Rights for the residence. The problem examinedin this study is how to implement an increase in Building Use Rights to Property Rights forresidences in the Karawang Regency Land Of ice? and what are the conditions that must bemet in registering an increase in the Right to Build into Ownership Rights for residences?In connection with these problems, this study aims to determine the implementation of theincrease in Building Use Rights to Property Rights for residences in the Karawang RegencyLand Of ice. The method of approach used in this study is empirical juridical, which is anapproach that focuses on collecting data from field studies as the main data and librarystudies as supplementary data. The hypothesis of the author is that regarding theimplementation of the Improvement of Building Rights to Ownership Rights, it is often thecase that an applicant registers an increase with an incomplete file due to lack ofknowledge related to the process, thus delaying the process of increasing rights and takes along time. Keywords: Increased Rights, Building Rights, Ownership Right

PATO: Pangenome Analysis Toolkit

Motivation We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment. Results PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20–30x times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Lastly, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R. Availability The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license. Supplementary information Supplementary data are available at Bioinformatics online.

RCytoGPS: An R Package for Reading and Visualizing Cytogenetics Data

Summary Cytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology. Availability and Implementation Freely available at https://CRAN.R-project.org/package=RCytoGPS. The code for the underlying CytoGPS software can be found at https://github.com/i2-wustl/CytoGPS. Supplementary information There is no supplementary data.

CNN-PepPred: An open-source tool to create convolutional NN models for the discovery of patterns in peptide sets. Application to peptide-MHC class II binding prediction

Summary The ability to unveil binding patterns in peptide sets has important applications in several biomedical areas, including the development of vaccines. We present an open-source tool, CNN-PepPred, that uses convolutional neural networks to discover such patterns, along with its application to peptide-HLA class II binding prediction. The tool can be used locally on different operating systems, with CPUs or GPUs, to train, evaluate, apply and visualize models. Availability and Implementation CNN-PepPred is freely available as a Python tool with a detailed User’s Guide at: https://github.com/ComputBiol-IBB/CNN-PepPred Supplementary information Supplementary data are available at Bioinformatics online.

LRez: C ++ API and toolkit for analyzing and managing Linked-Reads data

Motivation Linked-Reads technologies combine both the high-quality and low cost of short-reads sequencing and long-range information, through the use of barcodes tagging reads which originate from a common long DNA molecule. This technology has been employed in a broad range of applications including genome assembly, phasing and scaffolding, as well as structural variant calling. However, to date, no tool or API dedicated to the manipulation of Linked-Reads data exist. Results We introduce LRez, a C ++ API and toolkit which allows easy management of Linked-Reads data. LRez includes various functionalities, for computing numbers of common barcodes between genomic regions, extracting barcodes from BAM files, as well as indexing and querying BAM, FASTQ and gzipped FASTQ files to quickly fetch all reads or alignments containing a given barcode. LRez is compatible with a wide range of Linked-Reads sequencing technologies, and can thus be used in any tool or pipeline requiring barcode processing or indexing, in order to improve their performances. Availability and implementation LRez is implemented in C ++, supported on Unix-based platforms, and available under AGPL-3.0 License at https://github.com/morispi/LRez, and as a bioconda module. Supplementary information Supplementary data are available at Bioinformatics Advances

PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method

Motivation Drug repositioning reveals novel indications for existing drugs and in particular, diseases with no available drugs. Diverse computational drug repositioning methods have been proposed by measuring either drug-treated gene expression signatures or the proximity of drug targets and disease proteins found in prior networks. However, these methods do not explain which signaling subparts allow potential drugs to be selected, and do not consider polypharmacology, i.e. multiple targets of a known drug, in specific subparts. Results Here, to address the limitations, we developed a subpathway-based polypharmacology drug repositioning method, PATHOME-Drug, based on drug-associated transcriptomes. Specifically, this tool locates subparts of signaling cascading related to phenotype changes (e.g. disease status changes), and identifies existing approved drugs such that their multiple targets are enriched in the subparts. We show that our method demonstrated better performance for detecting signaling context and specific drugs/compounds, compared to WebGestalt and clusterProfiler, for both real biological and simulated datasets. We believe that our tool can successfully address the current shortage of targeted therapy agents. Availability and implementation The web-service is available at http://statgen.snu.ac.kr/software/pathome. The source codes and data are available at https://github.com/labnams/pathome-drug. Supplementary information Supplementary data are available at Bioinformatics online.