dirHub: a trackHub configurator with directory structure projection

SummaryTrack Data Hub is a mechanism enabling us to visualize genomics data as tracks along genome coordinates and share them over the Internet, relying on a web server hosting data files and genome browsers offering graphical representations. It requires an accessible configuration file specifying all graphical parameters and track hierarchy, in addition to the data files. Here dirHub is developed to assist generation of the configuration file by projection of a file directory structure, which makes it possible to set up trackHub visualization mostly by file operations.Availability and implementationIt is implemented in ruby and the source code is available at https://github.com/hkawaji/dirHub/. It is tested on the UCSC Genome Browser and the Hub Track Database Definition (v2).

Experimental Directory Structure (Exdir): An alternative to HDF5 without introducing a new file format

ABSTRACTNatural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available specifications which facilitate data sharing and reproducible research. Hierarchical Data Format 5 (HDF5) is a popular open format widely used in neuroscience, often as a foundation for other, more specialized formats. However, drawbacks related to HDF5’s complex specification have initiated a discussion for an improved replacement. We propose a novel alternative, the Experimental Directory Structure (Exdir), an open standard for data storage in experimental pipelines which amends drawbacks associated with HDF5 while retaining its advantages. HDF5 stores data and metadata in a hierarchy within a complex binary file which, among other things, is not human-readable, not optimal for version control systems, and lacks support for storing raw data. Exdir, one the other hand, uses file system directories to represent the hierarchy, with metadata stored in human-readable YAML files, datasets stored in binary NumPy files, and raw data stored directly in subdirectories. Furthermore, storing data in multiple files makes it easier to track for version control systems. Exdir is not a file format in itself, but a standard for organizing files in a directory structure. Exdir uses the same abstractions as HDF5 and is compatible with the HDF5 Abstract Data Model. Several research groups are already using data stored in a directory hierarchy as an alternative to HDF5, but no common standard exists in the field. This complicates and limits the opportunity for data sharing and development of common tools for reading, writing, and analyzing data. Exdir facilitates improved data storage, data sharing, reproducible research, and novel insight from interdisciplinary collaboration. With the publication of Exdir, we invite the scientific community to join the development to create an open standard that will serve as many needs as possible and that will serve as a foundation for open access to and exchange of data.SIGNIFICANCE STATEMENTExperimental Directory Structure (Exdir) is a proposal to standardize a storage solution that has become an increasingly popular alternative to Hierarchical Data Format 5 (HDF5), namely to use directories to define a hierarchy, store data in binary files, and metadata in text files. While this strategy is deployed locally by several research groups, no common standard exists. We envision the establishment of such a standard and present Exdir to the community as a starting point.

An Analysis of the File System for Linux

This paper discusses about types of file structures in Linux, points out that EXT2 is the most commonly used file system in Linux, analyzes the disk layout, index point and directory structure of EXT2, and studies the method to access files in EXT2 by name, which makes the access faster and more efficient.

Analysis for HFS+ on Windows Platform and its Application in Computer Forensics

HFS+ is the main file system of Mac OS. With the popularity of Apple computer, more and more security specialists pay attention to the computer forensics in Mac OS. As computer forensics technology on Windows Platforms is quite mature and can pass the limit of authority, when get the HFS+ disk or mirror from Apple computer, we can achieve data manipulation for further computer forensics through analyzing the file system on Windows platform. This paper proposed an efficient method to analyze HFS+ file system on Windows to build directory structure and get the unallocated space. This work is the important beginning of computer forensics in Mac OS.

Information Hiding of MS-Office Compound Document

Propose an information hiding method to embed information into the FIB, directory structure, short stream, Document Summary Information stream and Data stream of Microsoft Office Word, Excel and PowerPoint documents. Experiment results show that the method has high volume of information hiding and good invisibility. The maximum information hiding rate can reach 30 percent. As the robustness of this algorithm is to be improved, the algorithm can be just applied to detect the change of the original document.

Applying Skill Technology to Aid Cadence Allegro Part Management

Library construction is a fundamental work in Cadence Allegro’s schematic and PCB (printed circuit board) constructing process. Existing part libraries are normally organized in directory structure. With the increment of the amount of library files, part management becomes slow and error-prone which is carried out on manual basis. A new method is given by designing part management software through applying the SKILL technology to aid Cadence Allegro part management. Application results show that the new method is effective in the library construction.