Introducing the Internet.

The benefits to medical practitioners of using the Internet are growing rapidly as the Internet becomes easier to use and ever more biomedical resources become available on line. The Internet is the largest computer network in the world; it is also a virtual community, larger than many nation states, with its own rules of behaviour or "netiquette." There are several types of Internet connection and various ways of acquiring a connection. Once connected, you can obtain, free of charge, programs that allow easy use of the Internet''s resources and help on how to use these resources; you can access many of these resources through the hypertext references in the on line version of this series (go to http:@www.bmj.com/bmj/ to reach the electronic version). You can then explore the various methods for accessing, manipulating, or disseminating data on the Internet, such as electronic mail, telnet, file transfer protocol, and the world wide web. Results from a search of the world wide web for information on the rare condition of Recklinghausen''s neurofibromatosis illustrate the breadth of medical information available on the Internet.     

The current status and portability of our sequence handling software.

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX.     

Human genomes as email attachments

SUMMARY: The amount of genomic sequence data being generated and made available through public databases continues to increase at an ever-expanding rate. Downloading, copying, sharing and manipulating these large datasets are becoming difficult and time consuming for researchers. We need to consider using advanced compression techniques as part of a standard data format for genomic data. The inherent structure of genome data allows for more efficient lossless compression than can be obtained through the use of generic compression programs. We apply a series of techniques to James Watson's genome that in combination reduce it to a mere 4MB, small enough to be sent as an email attachment.     

MacSECPROT: Two programs in basic to evaluate protein secondary structure

Two interactive programs in BASIC are described, which provide useful tools to evaluate protein secondary structure. Output is given in two formats: (1) graphics are displayed on screen, which can be printed immediately, and (2) textfiles are saved to disk as permanent records and can be printed with a word-processing program. The programs are fast and easy to use and could be a valuable teaching aid in biochemical and molecular biology courses. Program lists are written in Microsoft® BASIC for the Apple® Macintosh™, but can be adapted to other machines accepting graphic commands.     

Distributed computing in bioinformatics

This paper provides an overview of methods and current applications of distributed computing in bioinformatics. Distributed computing is a strategy of dividing a large workload among multiple computers to reduce processing time, or to make use of resources such as programs and databases that are not available on all computers. Participating computers may be connected either through a local high-speed network or through the Internet.     

Communication in plastic surgery by means of e-mail: experiences and recommendations for clinical use

The Internet is a global network of computers with a broad variety of services and options. Electronic mail (email) is the most frequently used service. For a plastic surgeon, this mode is the fastest and the most cost-effective way of transferring data of any kind. The critical aim of this study was to assess the transfer of confidential data by means of e-mail and to present general conditions for the use of e-mail. Therefore, experiences with this means of communication are described to point to the possibilities, but also to indicate problems and weak points of this medium. Some rules should be obeyed for the transfer of confidential patient data by means of e-mail to satisfy the demand for data-security standards. Also, medicolegal aspects must be considered. These recommendations or rules and aspects will be discussed to offer a guideline to plastic surgeons for their e-mail applications.     

Microarray data assembler

SUMMARY: Large volumes of microarray data are generated and deposited in public databases. Most of this data is in the form of tab-delimited text files or Excel spreadsheets. Combining data from several of these files to reanalyze these data sets is time consuming. Microarray Data Assembler is specifically designed to simplify this task. The program can list files and data sources, convert selected text files into Excel files and assemble data across multiple Excel worksheets and workbooks. This program thus makes data assembling easy, saves time and helps avoid manual error. AVAILABILITY: The program is freely available for non-profit use, via email request from the author, after signing a Material Transfer Agreement with Johns Hopkins University.     

SDAR: a practical tool for graphical analysis of two-dimensional data

ABSTRACT: BACKGROUND: Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionally, more complex software packages typically require more time by the individual user to understand and operate. Practical and convenient graphical data analysis software in Java with a user-friendly interface are rare. RESULTS: We have developed SDAR, a Java application to analyse two-dimensional data with an intuitive graphical user interface. A smart ASCII parser allows import of data into SDAR without particular format requirements. The centre piece of SDAR is the Java class GraphPanel which provides methods for generic tasks of data visualisation. Data can be manipulated and analysed with respect to the most common operations experienced in an experimental biochemical laboratory. Images of the data plots can be generated in SVG-, TIFF- or PNG-format. Data exported by SDAR is annotated with commands compatible with the Grace software. CONCLUSION: Since SDAR is implemented in Java, it is truly cross-platform compatible. The software is easy to install, and very convenient to use judging by experience in our own laboratories. It is freely available to academic users at http://www.structuralchemistry.org/pcsb/. To download SDAR, users will be asked for their name, institution and email address. A manual, as well as the source code of the GraphPanel class can also be downloaded from this site.     

Diagnostic Criteria for Problematic Internet Use among U.S. University Students: A Mixed-Methods Evaluation

Empirical studies have identified increasing rates of problematic Internet use worldwide and a host of related negative consequences. However, researchers disagree as to whether problematic Internet use is a subtype of behavioral addiction. Thus, there are not yet widely accepted and validated diagnostic criteria for problematic Internet use. To address this gap, we used mixed-methods to examine the extent to which signs and symptoms of problematic Internet use mirror DSM-5 diagnostic criteria for substance use disorder, gambling disorder, and Internet gaming disorder. A total of 27 university students, who self-identified as intensive Internet users and who reported Internet-use-associated health and/or psychosocial problems were recruited. Students completed two measures that assess problematic Internet use (Young’s Diagnostic Questionnaire and the Compulsive Internet Use Scale) and participated in focus groups exploring their experiences with problematic Internet use. Results of standardized measures and focus group discussions indicated substantial overlap between students’ experiences of problematic Internet use and the signs and symptoms reflected in the DSM-5 criteria for substance use disorder, gambling disorder, and Internet gaming disorder. These signs and symptoms included: a) use Internet longer than intended, b) preoccupation with the Internet, c) withdrawal symptoms when unable to access the Internet, d) unsuccessful attempts to stop or reduce Internet use, e) craving, f) loss of interest in hobbies or activities other than the Internet, g) excessive Internet use despite the knowledge of related problems, g) use of the Internet to escape or relieve a negative mood, and h) lying about Internet use. Tolerance, withdrawal symptoms, and recurrent Internet use in hazardous situations were uniquely manifested in the context of problematic Internet use. Implications for research and practice are discussed.     

Programs,databases, and expert systems for human geneticists — a survey

We present an overview of the variety of databases and programs that offer substantial aid to medical and molecular geneticists. Databases and expert systems for genetic diseases and birth defects, programs for segregation and linkage analysis, certain DNA and protein sequence databases, and information resources in general for molecular biology are addressed. These systems cannot be used effectively without the newly developed techniques of information exchange based on international computer networks. A short introduction is given to the Internet and to European institutions and organizations that offer help with the aquisition and use of bioinformatic resources.     

Guide to the Internet. The world wide web.

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals.     

The Mesh of Civilizations in the Global Network of Digital Communication

Conflicts fueled by popular religious mobilization have rekindled the controversy surrounding Samuel Huntington’s theory of changing international alignments in the Post-Cold War era. In The Clash of Civilizations, Huntington challenged Fukuyama’s “end of history” thesis that liberal democracy had emerged victorious out of Post-war ideological and economic rivalries. Based on a top-down analysis of the alignments of nation states, Huntington famously concluded that the axes of international geo-political conflicts had reverted to the ancient cultural divisions that had characterized most of human history. Until recently, however, the debate has had to rely more on polemics than empirical evidence. Moreover, Huntington made this prediction in 1993, before social media connected the world’s population. Do digital communications attenuate or echo the cultural, religious, and ethnic “fault lines” posited by Huntington prior to the global diffusion of social media? We revisit Huntington''s thesis using hundreds of millions of anonymized email and Twitter communications among tens of millions of worldwide users to map the global alignment of interpersonal relations. Contrary to the supposedly borderless world of cyberspace, a bottom-up analysis confirms the persistence of the eight culturally differentiated civilizations posited by Huntington, with the divisions corresponding to differences in language, religion, economic development, and spatial distance.Have social media created a global village that spans cultural differences and traditional borders? For most of the postwar period, research on international alignments was informed by World Systems Theory, an approach that emphasized the influence of North-South economic divisions and East-West ideological divisions [1]. Following the collapse of the Soviet Union, Fukuyama [2] proposed that those divisions had culminated in the triumph of liberal democratic systems, signaling the “end of history.” In The Clash of Civilizations [3], Fukuyama’s mentor, Samuel Huntington, acknowledged that “the fundamental source of conflict in this new world will not be primarily ideological or primarily economic,” but he challenged Fukyama’s prediction of global consensus:The great divisions among humankind and the dominating source of conflict will be cultural. Nation states will remain the most powerful actors in world affairs, but the principal conflicts of global politics will occur between nations and groups of different civilizations. The clash of civilizations will dominate global politics. The fault lines between civilizations will be the battle lines of the future.The world has undergone substantial changes since Huntington made this prediction in 1993, including rapid economic growth in South Asia and South America and global diffusion of social media connecting the world’s population. Moreover, the evidence for Huntington''s theory of international global alignment was largely top-down, based on the political and economic relations among culturally differentiated nation states. The growing availability of digital traces of human communications now makes it possible to revisit Huntington''s thesis by taking a bottom-up view, based on interpersonal interactions among millions of individuals instead of the alignments of state actors. Have these online interactions created a global village that spans not only the old Cold War divisions but Huntington’s cultural fault lines as well?To find out, we used hundreds of millions of anonymized email and Twitter communications among tens of millions of worldwide users to map global patterns of transnational interpersonal communication. We measure the density, not the content, of interpersonal communication, and our findings do not address Huntington’s highly controversial warning of the potential for conflict between cultures. Nevertheless, the observed patterns provide a unique angle on changing global alignments in the Post-Cold War era.Our work builds on a study by Leskovec and Horvitz of the global flows of online Instant Messaging (IM) [4], extending that research in four important ways. First, we measure the density of social ties, not the density of message traffic. The “fault lines of civilizations” are indicated not by the number of messages two people exchange across borders but by the number of individuals in each country who exchange messages with one another. Second, we measure the density of social ties after taking into account differences in language, geo-location, Cold War alignment, economic development, and religion. (NB: In addition to analyzing communication densities between country pairs, Leskovec and Horvitz also measured global properties of the social network among pairs of individuals, but they did not use the latter to analyze social densities between country pairs. They also found that between-country communication densities were highly correlated with language and spatial distance, but they did not measure communication densities relative to the expected density given similarities of language and geo-location.) Third, we use multiple platforms (Yahoo! email and Twitter) to provide greater robustness and to avoid the possibility that our results are artifacts of the idiosyncrasies of a particular service. Twitter differs from email in two ways that are relevant to our study: most email exchanges are dyadic while Twitter messages are publicly visible, and the Twitter platform makes it much easier for users to discover one another, thereby reducing the tendency for online interactions to reflect pre-existing relationships. Fourth, we correct for internet access and market penetration, without which online traffic flows confound the strength of interpersonal ties with the popularity of a given communication medium. By taking into account differences in Internet access and market penetration, we are able to estimate the global network of social ties derived from the interpersonal flows of Internet communications.We measured communication density based on the number of observed bi-directed ties between users in two countries, relative to the maximum possible number of such ties, given the number of users in each country and the number of people with Internet access. (NB: The email analysis was based on anonymized geo-tagged edge lists. Prior to the analysis, the edge lists were anonymized as follows: Individual email accounts were assigned a random numeric identifier, after which the original email addresses were deleted. The email message content was not accessed or used for this study. Other than country, the edge lists we analyzed contained no individually identifiable information. The project was approved by the Cornell University IRB. The Twitter dataset was provided to us already anonymized by the team that collected it [5]. Scripts for the processing of that dataset are available from http://dx.doi.org/10.6084/m9.figshare.1304572.)A bi-directed email tie exists between two users if at least two messages are exchanged, one in each direction. A bi-directed Twitter tie exists if two users each follow the other. We defined pairwise communication density as the ratio between the observed number of bi-directed ties and the number of expected ties, given the number of subscribers and the number of Internet users.We obtained qualitatively similar results for email and Twitter communication densities and therefore report only the combined density measures for the two platforms. We also measured densities net of geographic proximity, shared language, population size, economic development, and colonial history.     

FERN – a Java framework for stochastic simulation and evaluation of reaction networks

Background  

Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary.     

Location Selection for Active Services

Active services are application-specified programs that are executed inside the network. The location where the active service is executed plays an important role. The dynamic behavior of networks requires that the selection of the most suitable location to instantiate a service is done at run time. To dynamically place an active service, information about the network (topology, bandwidth) and the application (type of the service) is necessary. This paper describes a method to dynamically search for available active service locations in the Internet. To be deployed in the current Internet, a solution is required to scale well to large networks, and to demand as little changes to the Internet as possible, especially not at lower network layers. Finally, the solution must be flexible and customizable to take application requirements into account. The proposed solution makes use of the routing path between two end systems. Active service locations that are located close to the routing path are then found via DNS queries. The evaluation shows that the application pays an overhead at start up time. For applications that can tolerate a start up delay, we show with three experiments using a video and an image application that the quality of the application can be increased by a dynamic placement of active services.     

Concentration of Access to Information and Communication Technologies in the Municipalities of the Brazilian Legal Amazon

This study fills demand for data on access and use of information and communication technologies (ICT) in the Brazilian legal Amazon, a region of localities with identical economic, political, and social problems. We use the 2010 Brazilian Demographic Census to compile data on urban and rural households (i) with computers and Internet access, (ii) with mobile phones, and (iii) with fixed phones. To compare the concentration of access to ICT in the municipalities of the Brazilian Amazon with other regions of Brazil, we use a concentration index to quantify the concentration of households in the following classes: with computers and Internet access, with mobile phones, with fixed phones, and no access. These data are analyzed along with municipal indicators on income, education, electricity, and population size. The results show that for urban households, the average concentration in the municipalities of the Amazon for computers and Internet access and for fixed phones is lower than in other regions of the country; meanwhile, that for no access and mobile phones is higher than in any other region. For rural households, the average concentration in the municipalities of the Amazon for computers and Internet access, mobile phones, and fixed phones is lower than in any other region of the country; meanwhile, that for no access is higher than in any other region. In addition, the study shows that education and income are determinants of inequality in accessing ICT in Brazilian municipalities and that the existence of electricity in rural households is directly associated with the ownership of ICT resources.     

medplot: A Web Application for Dynamic Summary and Analysis of Longitudinal Medical Data Based on R

In biomedical studies the patients are often evaluated numerous times and a large number of variables are recorded at each time-point. Data entry and manipulation of longitudinal data can be performed using spreadsheet programs, which usually include some data plotting and analysis capabilities and are straightforward to use, but are not designed for the analyses of complex longitudinal data. Specialized statistical software offers more flexibility and capabilities, but first time users with biomedical background often find its use difficult. We developed medplot, an interactive web application that simplifies the exploration and analysis of longitudinal data. The application can be used to summarize, visualize and analyze data by researchers that are not familiar with statistical programs and whose knowledge of statistics is limited. The summary tools produce publication-ready tables and graphs. The analysis tools include features that are seldom available in spreadsheet software, such as correction for multiple testing, repeated measurement analyses and flexible non-linear modeling of the association of the numerical variables with the outcome. medplot is freely available and open source, it has an intuitive graphical user interface (GUI), it is accessible via the Internet and can be used within a web browser, without the need for installing and maintaining programs locally on the user’s computer. This paper describes the application and gives detailed examples describing how to use the application on real data from a clinical study including patients with early Lyme borreliosis.     

The SpikerBox: a low cost, open-source bioamplifier for increasing public participation in neuroscience inquiry

Although people are generally interested in how the brain functions, neuroscience education for the public is hampered by a lack of low cost and engaging teaching materials. To address this, we developed an open-source tool, the SpikerBox, which is appropriate for use in middle/high school educational programs and by amateurs. This device can be used in easy experiments in which students insert sewing pins into the leg of a cockroach, or other invertebrate, to amplify and listen to the electrical activity of neurons. With the cockroach leg preparation, students can hear and see (using a smartphone oscilloscope app we have developed) the dramatic changes in activity caused by touching the mechanosensitive barbs. Students can also experiment with other manipulations such as temperature, drugs, and microstimulation that affect the neural activity. We include teaching guides and other resources in the supplemental materials. These hands-on lessons with the SpikerBox have proven to be effective in teaching basic neuroscience.