Machine-readable Data Files Research Articles

An Online Nanoinformatics Platform Empowering Computational Modeling of Nanomaterials by Nanostructure Annotations and Machine Learning Toolkits.

Modern nanotechnology has generated numerous datasets from in vitro and in vivo studies on nanomaterials, with some available on nanoinformatics portals. However, these existing databases lack the digital data and tools suitable for machine learning studies. Here, we report a nanoinformatics platform that accurately annotates nanostructures into machine-readable data files and provides modeling toolkits. This platform, accessible to the public at https://vinas-toolbox.com/, has annotated nanostructures of 14 material types. The associated nanodescriptor data and assay test results are appropriate for modeling purposes. The modeling toolkits enable data standardization, data visualization, and machine learning model development to predict properties and bioactivities of new nanomaterials. Moreover, a library of virtual nanostructures with their predicted properties and bioactivities is available, directing the synthesis of new nanomaterials. This platform provides a data-driven computational modeling platform for the nanoscience community, significantly aiding in the development of safe and effective nanomaterials.

Massive Warm/Hot Galaxy Coronae. II. Isentropic Model

Abstract We construct a new analytic phenomenological model for the extended circumgalactic material (CGM) of L* galaxies. Our model reproduces the O vii/O viii absorption observations of the Milky Way (MW) and the O vi measurements reported by the COS-Halos and eCGM surveys. The warm/hot gas is in hydrostatic equilibrium in an MW gravitational potential, and we adopt a barotropic equation of state, resulting in a temperature variation as a function of radius. A pressure component with an adiabatic index of is included to approximate the effects of a magnetic field and cosmic rays. We introduce a metallicity gradient motivated by the enrichment of the inner CGM by the Galaxy. We then present our fiducial model for the corona, tuned to reproduce the observed O vi–O viii column densities and with a total mass of inside . The gas densities in the CGM are low ( cm−3), and its collisional ionization state is modified by the metagalactic radiation field. We show that for O vi-bearing warm/hot gas with typical observed column densities cm−2 at large ( kpc) impact parameters from the central galaxies, the ratio of the cooling to dynamical times, / , has a model-independent upper limit of . In our model, / at large radii is . We present predictions for a wide range of future observations of the warm/hot CGM, from UV/X-ray absorption and emission spectroscopy to dispersion measure and Sunyaev–Zel’dovich cosmic microwave background measurements. We provide the model outputs in machine-readable data files for easy comparison and analysis.

GMOL: An Interactive Tool for 3D Genome Structure Visualization.

It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome structures so that researchers may better analyze genomic data. GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function.

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

On providing client support for machine readable data files

209 With the increased power of the microcomputer, there is growing use made of Machine Readable Data Files (MRDFs) for data analysis by data users. Data providers use distribution systems ranging from 9-track tape, diskettes, CD-ROM, transmission of data via on-line networks or access to data from on-line systems. As the quantity and complexity of MRDFs increases, and as the medium for access becomes computer-to-computer linkage, there is a urgent need to improve the quality of both the supporting documentation and the software that is included with these files. We concentrate in this paper on the issues of how and what meta-information should be provided to users of public use microdata MRDFs. As the marketing and sale of such data become increasingly important to statistical agencies, it is essential to view these issues from the external client's perspec­ tive. Indeed, the meta-information can be seen to play an indispensable role in advertising the availability of the product and in supporting the client's use of the product.

Compensation Policy and Firm Performance: An Annotated Bibliography of Machine-Readable Data Files

This paper presents detailed descriptions of 24 machine-readable data files that could be used in empirical studies of the relationship between compensation policy and firm performance. Also included are the addresses of the organizations (mostly government agencies) that create and distribute the files and, in most cases, of specific persons to contact in order to obtain the data. The author also provides information on data available from six private consulting firms.

MRDF

Cataloging machine-readable data files (MRDF) is a new challenge to librarians. At the University of Florida, several months were spent on the development of procedures for cataloging computer files. Problems are identified and the University of Florida's solutions to these problems are provided. Our goal was to provide model research library approaches for handling MRDF, specifically magnetic tape computer files.

Compensation Policy and Firm Performance: An Annotated Bibliography of Machine-Readable Data Files

Compensation Policy and Firm Performance: An Annotated Bibliography of Machine-Readable Data Files

Academic Libraries and Collection Development of Nonbibliographic Machine-Readable Data Files

Academic Libraries and Collection Development of Nonbibliographic Machine-Readable Data Files

Optical disks: Are archivists repeating the mistakes of the past?

Practical, workable, and relatively inexpensive optical wstems have piqued the interest of ~me archivists In the capabiIitles of this new technolo~.l. Promises of rapid ~arch and retrieval capabilities with cheap storage costs and a stable medium seem especially tempting to repositories with large ~IIections of graphic images, maps, drawings, and textual ck~cuments. As archivlsts debate using optical .~/stems for storage and retrieval of records already in archives, we must not avoid the question of how to Identify, acc~ess... and preserve information created elsewhere and stored m optical based systems. Archivlsts have rarely stopped to consider what we wi II do with information from optical disk systems that are created outside archives by government age.holes, corporations, institutions, and mdlvlduals. But we should r~.c)gnlze that the same features which make optical disk te~hnolog/,, appealing for use in archives ( high density storage, rapid access, imaoe enhancement, easy reproduction, etc. ) also make this technology., attractive and cosleffective for many applications in oraanizations with ~tive records systems The records that offices are ~annlng onto optlcal disks t_ndav will confront archivists .~oner or later as another information technol .ogy problem unless we beoln developing strategies now to preserve information in this format. No standards, guidelines, or procedures exist to held archivists handle records stored on optical disk .~/stems, but there are important similarities between optical and m~netic e/stems. Archlv)sts can apply some lessons learned from our previous exDerlence with magnetic medla systems to respond more effectiveIv to the Introduction of optical disks. The first los, son to learn from our experience with maanetm electronic records is that the ;mort life span of storage media, although an important problem, is not the most challenging asp~t of preserving records of modern information s./stems. Archivists who perceive me threeto ten-year useful life o[ magnetic media as the main problem of electronic. records are likely to consider the lon~r proje~cted life of optical dlsF:s as a s]~niflc~nt advance or even as a posslble solutlon to many of the problems that archivists confront ',vhen pr~ervmgcomputer-generated records The optical medium m~¢ last 30 years or lancer, thus reducing the frequenc¢ at wnlcn tne mformatlon must be c~pled onto a new storo~ device, and optical disks cannot be erased m the .:arise that magrletlc media can. To be sanguine about optically stored mformatlon as a consequence, however, over ]oaks the much more crucial Issue of system dependency which opticaland magnetm systems share. Optical ~stems pose many of the same access and preservation problerns,~s m~netIo systems and they rai~ some new issues of t.nelr own. Because both types of systems rely on software to retrleve information, archivists must preserve both the medium on which the records are stored and the means to access me records ( hardware & software). Even if, indeed especially because, optical media may last for fifly years, there is no assurance that the hardware and software necessary to retrieve rec~)rds from that medium will be usable or available in fifty years. Anyone who has encountered wire recordings, wa× cylinders, punched paper tape or Mc~,ee cards, to name only a few obsolete information storage technologms, can apprecmte this problem on a small scale. Archivists who work with magnetic electron;c records try to mlnlmlze the need for software by reformatting electromc mformatlon into a softwareindependent format. In the ab~nce ofwldely adopted data and document Interchange standards, this approach has been effective for certain types of machine-readable data files. '~et some archivists are becoming uncomfortable with this practice. The strategy, of creating software-lndependent data for arcnlval preservation is increasingly hmlted because information from most document-based and m~a~le-based systems cannot be retrieved or interpreted In a .~ftware-Independent format. Thi.~ problem is even more apparent with optlcal systems because there Is no such thing as a ~ftwareindependent for m at for

Expanding Networks: Reference Services for MRDF

Machine‐readable data files (MRDF) are now a basic part of the information revolution. Reference librarians can learn to play a major role in disseminating information about MRDF and in helping patrons to use them to retrieve information. A major library may have access to computer tapes or cartridges of numeric and statistical databases. Other MRDF may be available through various online services, electronic bulletin boards, flexible diskettes and optical disks. Since many statistical data are available only in machine‐readable format, reference librarians will need to integrate MRDF into their normal approach to information retrieval. One must concur with Ms. Bliss Beckman Siman who wrote in 1986 that “there is probably too little attention paid either by the literature or the professional organizations to the areas of reference and bibliographic instruction with machine‐readable data files.” Further, she stated “clearly the first necessity is to meet the technical demands of this new media but without more attention to the techniques of public service the expected use of this information resource simply won't develop.” Greater emphasis must be placed on the importance of the reference transaction in expanding the use of MRDF in both teaching and research. This article will discuss some of the major issues concerned with providing reference services for MRDF.

Government information in machine-readable data files: Implications for libraries and librarians

It is the purpose of this article to describe government information in machine-readable data files in relation to other formats and to examine requirements for their acquisition, preservation, and utilization in retrieval and reference services. Skill and knowledge adjustments on the part of librarians are also discussed. The primary emphasis is on computer tapes.

The Development of a Canadian Union List of Machine Readable Data Files (CULDAT)

The Development of a Canadian Union List of Machine Readable Data Files (CULDAT)

Archives Law and Machine-readable Data Files: A Look at the United States

Archives Law and Machine-readable Data Files: A Look at the United States

Machine-Readable Data Files in the Social Sciences:

The problems in making machine-readable data files (MRDFs) accessible as well as in using them are basically the same for all social scientists. There are two kinds of problem: the quality of the data in the MRDFs themselves and accessibility. The social scientists' concern is quality control; the librarians' is accessibility. Clean datasets make it possible to ask questions that could not be asked in the past. In analyzing large amounts of data, social scientists can detect the weak signals of important relationships. Three problems confronting librarians are: availability of bibliographic control; the quality of documentation; and level of user skills.

Reference use of state government information in academic libraries

To gather data on the reference use of state government information, and in particular machine-readable data files, a questionnaire was sent to selected academic libraries that are depositories for their home state government publications. Results indicate that librarians are beginning to make use of these online sources but will need to take the initiative in expanding these services. Information is also presented on reference services and sources for state government information.

The impact of information technology on public access to social science databases

An examination of four trends in American society and their impact on public libraries, librarians and public access to information. The trends examined include: the rapid increase in the availability of microcomputers; the existence of a telecommunications network; the tendency for more information to appear in machine-readable form; and an increase in the number of individuals familiar with and inclined to utilize machine-readable data files.

Machine-readable data files of government publications : Data files from the National Center for Health Statistics

Machine-readable data files of government publications : Data files from the National Center for Health Statistics

Approaches to Information about Census Bureau Machine-readable Data Files

Approaches to Information about Census Bureau Machine-readable Data Files

Machine-readable data files of government publications

Machine-readable data files of government publications