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BACKGROUND: Structural biomolecular data are commonly stored in the PDB format. The PDB format is widely supported by software vendors because of its simplicity and readability. However, the PDB format cannot fully address many informatics challenges related to the growing amount of structural data. To overcome the limitations of the PDB format, a new textual format mmCIF was released in June 1997 in its version 1.0. mmCIF provides extra information which has the advantage of being in a computer readable form. However, this advantage becomes a disadvantage if a human must read and understand the stored data. While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited. FINDINGS: In this paper we present mmView - a cross-platform web-based application that allows to explore comfortably the structural data of biomacromolecules stored in the mmCIF format. The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form. The application also allows to display and investigate biomolecular structures via an integrated Java application Jmol. CONCLUSIONS: The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool. The mmView application is offered in two flavors: as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user's computer, and as a publicly available web server.
- Publikační typ
- časopisecké články MeSH
PURPOSE: Multiple data formats in the MRS community currently hinder data sharing and integration. NIfTI-MRS is proposed as a standard spectroscopy data format, implemented as an extension to the Neuroimaging informatics technology initiative (NIfTI) format. This standardized format can facilitate data sharing and algorithm development as well as ease integration of MRS analysis alongside other imaging modalities. METHODS: A file format using the NIfTI header extension framework incorporates essential spectroscopic metadata and additional encoding dimensions. A detailed description of the specification is provided. An open-source command-line conversion program is implemented to convert single-voxel and spectroscopic imaging data to NIfTI-MRS. Visualization of data in NIfTI-MRS is provided by development of a dedicated plugin for FSLeyes, the FMRIB Software Library (FSL) image viewer. RESULTS: Online documentation and 10 example datasets in the proposed format are provided. Code examples of NIfTI-MRS readers are implemented in common programming languages. Conversion software, spec2nii, currently converts 14 formats where data is stored in image-space to NIfTI-MRS, including Digital Imaging and Communications in Medicine (DICOM) and vendor proprietary formats. CONCLUSION: NIfTI-MRS aims to solve issues arising from multiple data formats being used in the MRS community. Through a single conversion point, processing and analysis of MRS data are simplified, thereby lowering the barrier to use of MRS. Furthermore, it can serve as the basis for open data sharing, collaboration, and interoperability of analysis programs. Greater standardization and harmonization become possible. By aligning with the dominant format in neuroimaging, NIfTI-MRS enables the use of mature tools present in the imaging community, demonstrated in this work by using a dedicated imaging tool, FSLeyes, for visualization.
Background: Electronic health record (EHR) systems are necessary for sharing medical information between care delivery organizations (CDOs). While many standardized data can be shared, it is still difficult to share nonstandardized clinical data. Furthermore, there remains the problem that the EHR system cannot finely control the disclosure status. We have been operating a documentbased electronic medical record system called the Document Archiving and Communication System (DACS) in which printed images of all medical records are stored in PDF format. Objectives: To develop a document-based EHR system that can disclose selected clinical documents in PDF format. Methods: With a document-based EHR system, any documents stored in the DACS can be opened to a designated CDO. These open documents can be selected by the service CDO staff. In order to manage the disclosure status, an access control list (ACL) file was designed based on the HL7 clinical document architecture header. The PDF file and its ACL file were transiently stored in the Japanese standard repository, SS-MIX2. The doctor of the designated CDO was then able to access the documents according to the information in the ACL file. Results: From March 2017 to September 2017, 308 documents of 20 patients were disclosed to 3 CDOs using this document-based EHR system. These documents included examination reports, agreement forms concerning the EHR, progress notes, summaries and surgical reports generated from five different systems. Conclusions: The document-based EHR system was able to reveal clinical documents from the EMR to medical staff under a controlled disclosure environment..
10 s. : grafy ; 34 cm
- MeSH
- informační systémy MeSH
- informatika MeSH
- ukládání a vyhledávání informací MeSH
- Publikační typ
- směrnice MeSH
- Konspekt
- Knihovnictví. Informatika
- NLK Obory
- knihovnictví, informační věda a muzeologie
The Neurodata Without Borders (abbreviation NWB) format is a current technology for storing neurophysiology data along with the associated metadata. Data stored in the format is organized into separate HDF5 files, each file usually storing the data associated with a single recording session. While the NWB format provides a structured method for storing data, so far there have not been tools which enable searching a collection of NWB files in order to find data of interest for a particular purpose. We describe here three tools to enable searching NWB files. The tools have different features making each of them most useful for a particular task. The first tool, called the NWB Query Engine, is written in Java. It allows searching the complete content of NWB files. It was designed for the first version of NWB (NWB 1) and supports most (but not all) features of the most recent version (NWB 2). For some searches, it is the fastest tool. The second tool, called "search_nwb" is written in Python and also allow searching the complete contents of NWB files. It works with both NWB 1 and NWB 2, as does the third tool. The third tool, called "nwbindexer" enables searching a collection of NWB files using a two-step process. In the first step, a utility is run which creates an SQLite database containing the metadata in a collection of NWB files. This database is then searched in the second step, using another utility. Once the index is built, this two-step processes allows faster searches than are done by the other tools, but does not enable as complete of searches. All three tools use a simple query language which was developed for this project. Software integrating the three tools into a web-interface is provided which enables searching NWB files by submitting a web form.
- Publikační typ
- časopisecké články MeSH
3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.
- MeSH
- anatomické modely MeSH
- automatizované zpracování dat MeSH
- komprese dat statistika a číselné údaje MeSH
- lebka anatomie a histologie embryologie MeSH
- myši MeSH
- obličejové kosti anatomie a histologie embryologie MeSH
- rentgenová mikrotomografie statistika a číselné údaje MeSH
- rentgenový obraz - interpretace počítačová MeSH
- šíření informací metody MeSH
- software * MeSH
- zobrazování trojrozměrné statistika a číselné údaje MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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1.vyd. 159 s.
UNLABELLED: ABIF Manager is simple application for low-level access to ABIF formatted files. Those are produced by Data Collection software based on the data, collected from capillary sequencing machine. The application shows all the data as readable text, which can be easily edited. AVAILABILITY AND IMPLEMENTATION: The program source code and compiled executable is freely available at: https://sourceforge.net/projects/abifmanager/.
- MeSH
- software * MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
