Assessing and assuring interoperability of a genomics file format

Background: Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, and only rarely do the creators of these tools robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results. Methods: We sought (1) to assess the interoperability of a wide range of bioinformatics software using a shared genomics file format and (2) to provide a simple, reproducible method for enhancing interoperability. As a focus, we selected the popular BED file format for genomic interval data. Based on the file format's original documentation, we created a formal specification. We developed a new verification system, Acidbio (https://github.com/hoffmangroup/acidbio), which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the BED format. We also used a fuzzing approach to automatically perform additional testing. Results: Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software's performance on the test suite. Discussion: Acidbio makes it easy to assess interoperability of software using the BED format, and therefore to identify areas for improvement in individual software packages. Applying our approach to other file formats would increase the reliability of bioinformatics software and data.

Fast nanopore sequencing data analysis with SLOW5

Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the example of DNA methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. SLOW5 is approximately 25% smaller than FAST5 and delivers consistent improvements on different computer architectures.

Meta-Analysis the Root of Terrorism from the Perspektif Islamic Movement in Indonesia

This paper aims to map the root of terrorism in Indonesia from the Islamic movement perspective. The authors want to know how the root of terrorism has strengthened in Indonesia. A qualitative method approach was taken through a literature study regarding the delivery of research map information while the data was exported in the RIS Export file format. Then, the authors exported the data and processed it using VOSviewer to find out a bibliometric map of research development based on significant themes of Indonesian terrorism cases. Nvivo 12 plus provided exploration and description of terrorism in Indonesia to get an efficient explanation of the data. The findings are, the first to map the issue of terrorism in Indonesia. First, there was a correlation between terrorism, radicalism, and Islam. Different views of religious teachings eventually led to the terrorism movement. Several radical Islamic organizations in Indonesia have portrayed Islam as a terrorist religion. Second, the factors causing the strengthening of terrorism in Indonesia were due to injustice, oppression, and discrimination leading to terrorism and radicalism using the concept of jihad. This research suggests that the government can handle terrorism cases in Indonesia and neutralize ideas that are considered radical with a de-radicalization approach. (Tulisan ini bertujuan memetakan akar terorisme di Indonesia dari aspek gerakan Islam. Penulis ingin mengetahui bagaimana akar terorisme menguat di Indonesia. Pendekatan metode kualitatif ditempuh melalui studi pustaka sedangkan untuk penyampaian informasi peta penelitian, data diekspor dalam format file Ekspor RIS. Kemudian, penulis mengekspor data dalam format (RIS), mengolahnya menggunakan VOS viewer untuk mengetahui peta bibliometrik pengembangan penelitian berdasarkan tema signifikan kasus terorisme di Indonesia dan menggunakan Nvivo 12 plus untuk memberikan eksplorasi dan deskripsi terorisme di Indonesia demi mendapatkan penjelasan yang efisien dari data. Temuan penelitian ini adalah; Pertama, pada tahap pemetaan isu terorisme di Indonesia, terdapat korelasi antara terorisme, radikalisme, dan Islam. Perbedaan pandangan terhadap ajaran agama pada akhirnya memunculkan gerakan terorisme. Beberapa organisasi Islam radikal di Indonesia telah mencitrakan Islam sebagai agama teroris. Kedua, diketahui faktor penyebab menguatnya terorisme di Indonesia adalah rasa ketidakadilan, penindasan dan diskriminasi yang berujung pada gerakan terorisme dan radikalisme dengan mengusung konsep jihad. Saran dari penelitian ini adalah agar pemerintah dapat menangani kasus terorisme di Indonesia dan menetralisir ide-ide yang dianggap radikal dengan pendekatan deradikalisasi.

Implementation of reengineering technology to ensure the predefined geometric accuracy of a light aircraft keel

The subject of this research is the technology of reengineering and control of parts of aircraft objects (AOs) and technological equipment for their manufacture. The predefined accuracy of the keel of a light aircraft and molding surfaces of technological equipment for its manufacture has been ensured by using reengineering technology and CAD systems. A portrait of the actual physically existing keel of a light aircraft was built in the *.stl file format using the software Artec Studio (USA). The control and comparison of the geometry of the shapes of the analytical standard with the actual physically existing keel of a light aircraft based on its portrait have been implemented. The methods used are the analysis and synthesis of the experimental geometry of shapes, the method of expert evaluations. The following results were obtained: based on the analysis and synthesis, the presence of significant errors in the accuracy of the manufacture of the keel for a light aircraft in the range from −5.26 mm to +5.39 mm was detected. It has been shown that the key factor is the keel's relative plane indicator, which is outside the tolerance margin and is 85 %. It was decided to fabricate new technological equipment from another material – organic plastics. Control of the technological equipment made from organic plastics for the keel of a light aircraft showed that the shape-forming surfaces of the equipment have appropriate shapes and sizes corresponding to the existing analytical standard and are devoid of inaccuracies that occurred in the previous version. The range of keel margins that was made using the new technological equipment from organic plastics is from –0.51 mm to +0.34 mm while the relative plane of the keel outside the tolerance margin does not exceed 15 %. The study results showed the adequacy of the decisions taken, ensuring the predefined accuracy for the keel of a light aircraft and molding surfaces of technological equipment for its manufacture.

Unified Nanotechnology Format: One Way to Store Them All

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

Improving software metadata conversion by adding CFF support

In August GitHub added enhanced support for citation-file-format (CFF) to all GitHub repositories. As you can see in the chart below (kindly provided by Stephan Druskat and based on GitHub queries for CFF files), ...

Ontology of Heterogeneous Image File Formats and their Disparate Applications

Different image formats are available in the world today which are used for various purposes, this paper elaborates the Ontology of different Image File Formats and their various applications. Digital images are saved in various Image File Formats which have different properties and features which are ideal for a particular use. A digital image is primarily classified into two types, raster or vector type. Image format elucidate how the information in the image will be stored. Image file format is a systematic way of storing and arranging digital images. Image file format can store data in compressed format (which may be lossy or lossless), uncompressed format or a vector format. Some Image format are suitable for a particular purpose while some are not. TIFF Image type is good for printing whereas PNG or JPG, are best for web. Analysis of the basic Image File Format have been carried out practically and the result is displayed in the coming section

Regional hematology service registration system for the Russian Federation

Introduction. The hematology service registration system describes actual indicators of hematology service infrastructure and target objects of both assigned and affiliated organizations of Russian Federation regions along with its correlations. This system data base makes it possible to collect, save, and analyze information, creating a data storage library about all current existing resources and taking into account concrete, specific conditions of specialized and high-tech hematological medical assistance organizations at the local levels and formed quality and availability optimization proposals.Aim — description and justification of the need to create a unified, complex, available to all users, informational reference system with the possibility of up-to-date maintenance and accounting that allows for the keep and control of the regional characteristics and hematology service indicators of the Russian Federation.General findings. The creation of and development of the hematology service registration system began in 2018, and work on the project continues. Four main phases were selected as the key stages of the hematology service pasportisation: analyses of the current data, verification of information, creation of a user-friendly tool, system updating. Objects to monitor: medical key and related institutions, universities, affiliated organizations, laboratory service. The data working stages: data collection, manual updating, package uploading. The information sources: official websites, data high-tech medical treatment web portal, web portals of the public health authorities, Compulsory Medical Insurance Fund website, The Unified Data Health Care System, license register of the Federal Service for Healthcare Surveillance, data of the Federal State Statistics Service, official documents of Ministry of Public Health. Based on the developed checklists and forms for entering additional information for specialists of the subjects of the Russian Federation, a reference book of the Ministry of Defense (Excel file format) was created. However, in the course of further remote interaction and conducting field events in the regions of the Russian Federation during 2019–2020 new data needs for evaluating hematology services were determined. The increase of additional data inputs and its structure complication became the main reasons for further developing a new platform design concept and data conversion in database framework of the hematology service registration system (Access file format). The current objectives are as follows: authentication of the internal objects identifiers, implementation of the relational database codifier, modification of cartographic display and objects routing. The hematology service registration system contains data both for the key infrastructure nodes of Russian Federation hematology service and correlations within routing of all key system objects. Based on the positive results, the hematology service registration system is planned to be used by experts of specialized medical organizations, regional executive authorities on public health and professional communities, who will be able to accumulate all changes and indicators in dynamics within one system. The expected result is to provide the Ministry of Defense of the Russian Federation regions with methodological and informational support in specialized and high-tech medical care administration.