CiteULike: lmichan's library [54 articles]

US regional health information organizations and the nationwide health information network: any lessons for Canadians?

D Protti — 2008-08-18T13:53:57-00:00

Healthcare quarterly (Toronto, Ont.), Vol. 11, No. 2. (2008)

The creation of regional clinical data exchanges (usually referred to as RHIOs) is a centerpiece of the US national healthcare information technology strategy. How well are they doing and what lessons can we learn that might be applied here in Canada?

Facebook for scientists: requirements and services for optimizing how scientific collaborations are established.

T Schleyer — 2008-08-18T13:52:53-00:00

Journal of medical Internet research, Vol. 10, No. 3. (2008)

BACKGROUND: As biomedical research projects become increasingly interdisciplinary and complex, collaboration with appropriate individuals, teams, and institutions becomes ever more crucial to project success. While social networks are extremely important in determining how scientific collaborations are formed, social networking technologies have not yet been studied as a tool to help form scientific collaborations. Many currently emerging expertise locating systems include social networking technologies, but it is unclear whether they make the process of finding collaborators more efficient and effective. OBJECTIVE: This study was conducted to answer the following questions: (1) Which requirements should systems for finding collaborators in biomedical science fulfill? and (2) Which information technology services can address these requirements? METHODS: The background research phase encompassed a thorough review of the literature, affinity diagramming, contextual inquiry, and semistructured interviews. This phase yielded five themes suggestive of requirements for systems to support the formation of collaborations. In the next phase, the generative phase, we brainstormed and selected design ideas for formal concept validation with end users. Then, three related, well-validated ideas were selected for implementation and evaluation in a prototype. RESULTS: Five main themes of systems requirements emerged: (1) beyond expertise, successful collaborations require compatibility with respect to personality, work style, productivity, and many other factors (compatibility); (2) finding appropriate collaborators requires the ability to effectively search in domains other than your own using information that is comprehensive and descriptive (communication); (3) social networks are important for finding potential collaborators, assessing their suitability and compatibility, and establishing contact with them (intermediation); (4) information profiles must be complete, correct, up-to-date, and comprehensive and allow fine-grained control over access to information by different audiences (information quality and access); (5) keeping online profiles up-to-date should require little or no effort and be integrated into the scientist's existing workflow (motivation). Based on the requirements, 16 design ideas underwent formal validation with end users. Of those, three were chosen to be implemented and evaluated in a system prototype, "Digital|Vita": maintaining, formatting, and semi-automated updating of biographical information; searching for experts; and building and maintaining the social network and managing document flow. CONCLUSIONS: In addition to quantitative and factual information about potential collaborators, social connectedness, personal and professional compatibility, and power differentials also influence whether collaborations are formed. Current systems only partially model these requirements. Services in Digital|Vita combine an existing workflow, maintaining and formatting biographical information, with collaboration-searching functions in a novel way. Several barriers to the adoption of systems such as Digital|Vita exist, such as potential adoption asymmetries between junior and senior researchers and the tension between public and private information. Developers and researchers may consider one or more of the services described in this paper for implementation in their own expertise locating systems.

Sources of information used by nurses to inform practice: An integrative review.

SM Spenceley — 2008-08-13T15:45:00-00:00

International journal of nursing studies, Vol. 45, No. 6. (June 2008), pp. 954-970.

BACKGROUND: We present an integrative review of the literature about sources of information nurses use to inform practice. The demand for access to more and better information has been fueled by the evidence-based healthcare movement. Although the expectations for evidence-based practice have never been higher, the demands on care environments have never been greater. The goals of professional nursing are served by using the best available information to inform practice. To influence such activity, we must understand what sources of information nurses rely on for guidance. DATA SOURCES: We examined studies of any research design published between 1985 and 2006, as well as research dissertations in the same time frame. Databases searched included the Cumulative Index of Nursing and Allied Health Literature (CINAHL), Medline, the Educational Resources Information Center, the Library and Information Science Abstracts and the Library Literature and Information Science databases. REVIEW METHODS: The review question: what information sources do registered nurses turn to, to support direct patient care? Analysis included an overview of study design and practice setting, and an examination of sources accessed most frequently by nurses to guide practice. RESULTS: We present, in ranked order, the sources nurses accessed in order to guide practice. We note the high reliance on informal, interactive sources. An unexpected finding of high reliance on journals is explored in greater detail and found to be equivocal at best. We conclude with a critical discussion of what we see as embedded assumptions and expectations about how information-seeking supports nursing practice. CONCLUSION: Expectations embedded in the scope and context of nursing practice have influenced knowledge development in the area of information-seeking to support practice. It is important that future research in this area takes into account the expectations and information needs arising in emerging roles for nurses within evolving healthcare systems.

Exploring e-Science: An Introduction

2007-11-06T12:41:20-00:00

URL decay in MEDLINE - a 4-year follow-up study

Jonathan Wren — 2008-04-16T08:15:26-00:00

Bioinformatics (15 April 2008), btn127.

Motivation: Internet-based electronic resources, as given by Uniform Resource Locators (URLs), are being increasingly used in scientific publications but are also becoming inaccessible in a time-dependant manner, a phenomenon documented across disciplines. Initial reports brought attention to the problem, spawning methods of effectively preserving URL content while some journals adopted policies regarding URL publication and begun storing supplementary information on journal websites. Thus, a re-examination of URL growth and decay in the literature is merited to see if the problem has grown or been mitigated by any of these changes Results: After the 2003 study, three follow-up studies were conducted in 2004, 2005 and 2007. Unfortunately, no significant change was found in the rate of URL decay among any of the studies. However, only 5% of URLs cited more than twice have decayed versus 20% of URLs cited once or twice. The most common types of lost content were computer programs (43%), followed by scholarly content (38%) and databases (19%). Compared to URLs still available, no lost content type was significantly over or under-represented. Searching for 30 of these websites using Google, 11 (37%) were found relocated to different URLs. Conclusions: URL decay continues unabated, but URLs published by organizations tend to be more stable. Repeated citation of URLs suggests calculation of an electronic impact factor (eIF) would be an objective, quantitative way to measure the impact of Internet-based resources on scientific research. Contact: Jonathan-Wren@OMRF.org 10.1093/bioinformatics/btn127

US NSF - NSB-05-40, Long-Lived Digital Data Collections Enabling Research and Education in the 21st Century

2008-06-16T17:05:47-00:00

(2005)

Three options for citation tracking: Google Scholar, Scopus and Web of Science

Nisa Bakkalbasi — 2006-06-29T21:13:39-00:00

Biomedical Digital Libraries, Vol. 3 (29 June 2006), 7.

Zoology www guide

Georg Hemmrich — 2008-06-04T23:46:33-00:00

Zoology, Vol. 108, No. 2. (24 June 2005), pp. 179-180.

Information navigation on the web by clustering and summarizing query results

Dmitri Roussinov — 2008-06-01T14:15:13-00:00

Information Processing & Management, Vol. 37, No. 6. (November 2001), pp. 789-816.

Information retrieval on the Internet: a guide for dental practitioners

Heiko Spallek — 2008-06-01T14:13:16-00:00

Dental Clinics of North America, Vol. 46, No. 3. (July 2002), pp. 435-462.

Tagging and searching: Search retrieval effectiveness of folksonomies on the World Wide Web

Jason — 2008-03-05T16:37:15-00:00

Information Processing & Management, Vol. In Press, Corrected Proof

Many Web sites have begun allowing users to submit items to a collection and tag them with keywords. The folksonomies built from these tags are an interesting topic that has seen little empirical research. This study compared the search information retrieval (IR) performance of folksonomies from social bookmarking Web sites against search engines and subject directories. Thirty-four participants created 103 queries for various information needs. Results from each IR system were collected and participants judged relevance. Folksonomy search results overlapped with those from the other systems, and documents found by both search engines and folksonomies were significantly more likely to be judged relevant than those returned by any single IR system type. The search engines in the study had the highest precision and recall, but the folksonomies fared surprisingly well. Del.icio.us was statistically indistinguishable from the directories in many cases. Overall the directories were more precise than the folksonomies but they had similar recall scores. Better query handling may enhance folksonomy IR performance further. The folksonomies studied were promising, and may be able to improve Web search performance.

Gene Ontology annotations: what they mean and where they come from.

DP Hill — 2008-05-11T16:21:46-00:00

BMC bioinformatics, Vol. 9 Suppl 5 (2008)

To address the challenges of information integration and retrieval, the computational genomics community increasingly has come to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). Here we address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations, in the hope that this will lead both to better representations of biological reality through annotation and ontology development and to more informed use of GO resources by experimental scientists.

Introduction to cheminformatics.

DS Wishart — 2008-05-31T23:44:07-00:00

Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], Vol. Chapter 14 (June 2007)

Cheminformatics is a relatively new field of information technology that focuses on the collection, storage, analysis, and manipulation of chemical data. The chemical data of interest typically includes information on small molecule formulas, structures, properties, spectra, and activities (biological or industrial). Cheminformatics originally emerged as a vehicle to help the drug discovery and development process, however cheminformatics now plays an increasingly important role in many areas of biology, chemistry, and biochemistry. The intent of this unit is to give readers some introduction into the field of cheminformatics and to show how cheminformatics not only shares many similarities with the field of bioinformatics, but that it can also enhance much of what is currently done in bioinformatics.

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

Dean Cheng — 2008-05-16T14:44:25-00:00

Nucl. Acids Res. (16 May 2008), gkn296.

A particular challenge in biomedical text mining is to find ways of handling comprehensive' or associative' queries such as Find all genes associated with breast cancer'. Given that many queries in genomics, proteomics or metabolomics involve these kind of comprehensive searches we believe that a web-based tool that could support these searches would be quite useful. In response to this need, we have developed the PolySearch web server. PolySearch supports >50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is Given X, find all Y's' where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences. PolySearch's performance has been assessed in tasks such as gene synonym identification, protein-protein interaction identification and disease gene identification using a variety of manually assembled gold standard' text corpuses. Its f-measure on these tasks is 88, 81 and 79%, respectively. These values are between 5 and 50% better than other published tools. The server is freely available at http://wishart.biology.ualberta.ca/polysearch 10.1093/nar/gkn296

PLoS ONE: iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

2008-05-29T01:49:10-00:00

Science 2.0.

MM Waldrop — 2008-05-31T23:27:58-00:00

Scientific American, Vol. 298, No. 5. (May 2008), pp. 68-73.

Science 2.0 generally refers to new practices of scientists who post raw experimental results, nascent theories, claims of discovery and draft papers on the Web for others to see and comment on. Proponents say these "open access" practices make scientific progress more collaborative and therefore more productive. Critics say scientists who put preliminary findings online risk having others copy or exploit the work to gain credit or even patents. Despite pros and cons, Science 2.0 sites are beginning to proliferate; one notable example is the OpenWetWare project started by biological engineers at the Massachusetts Institute of Technology.

[Evaluation of scientific quality using citation analysis and other bibliometric methods]

PO Seglen — 2008-05-31T22:56:13-00:00

Nordisk medicin, Vol. 104, No. 12. (1989)

Bibliometric methods for scientific evaluation are examined. The citation frequency for scientific publications, as given in the Science Citation Index, is influenced by various forms of citation bias as well as by the characteristic dynamics and citation practices of the various scientific fields, and therefore cannot be taken as an unequivocal measure of scientific quality. Even for single authors the citation frequency is very variable; therefore this parameter should not be used for graded evaluation of individual scientists or research groups. At higher aggregate levels (large institutes etc) bibliometric indicators may, as part of a more general evaluation, give relevant information about research activity, provided due corrections are made for variable research field effects. The journal impact factor, i e the mean citation frequency of all articles in a journal, has been suggested as a rapid indicator of article quality. However, the distribution of citation frequency values within a journal is extremely broad and skewed; therefore assigning the same value to all articles would not seem to serve the purpose of evaluation particularly well. Furthermore the citation frequencies of articles published by individual authors or research groups are found to correlate extremely poorly with the corresponding journal impact factors. The latter parameter would thus appear to be unsuitable as an indicator of scientific quality.

Citation indexing and evaluation of scientific papers.

J Margolis — 2007-12-05T15:03:06-00:00

Science, Vol. 155, No. 767. (10 March 1967), pp. 1213-1219.

Evaluation by means of citation patterns can be successful only insofar as published papers and their bibliographies reflect scientific activity and nothing else. Such an innocent descrip tion is becoming less and less tenable. The present scientific explosion gave rise to more than a proportional pub lication explosion, which not only re flects the scientific explosion but has its own dynamics and vicious circles. Publication of results is probably the main means of accomplishing the al most impossible task of accounting for time and money spent on research. Inevitably, this puts a premium on quantity at the expense of quality, and, as with any other type of inflation, the problem worsens: the more papers are written, the less they count for and the greater is the pressure to publish more. What makes matters worse is the fact that the sheer volume of the"litera ture" makes it increasingly difficult to separate what is worthwhile from the rest. Critical reviews have become somewhat of a rarity, and editorial judgment is usually relegated to ref erees, who are contemporaries and, per haps, competitors of the authors-a situation which has its own undesirable implications (11, 18). It requires little imagination to discover other vicious circles, all arising from distortion of the primary reasons for publishing the results of scientific inquiry. There are, it is true, signs of ad justment to this crisis, partly due to some easing of the pressure to pub lish at all costs, and partly due to the readers' changing attitudes toward the flood of publications. An increasing amount of research is now being car ried out in the form of collective proj ects in large institutions where publica tion is no longer the standard method of accounting for individual work. At the same time there is apparent an in creasing tendency for scientific journals to polarize into the relatively few leading ones which carry important informa tion and the many subsidiary journals which serve as vehicles for interim lo cal accounting and, in a way, sub stitute for detailed intradepartmental re ports. This division is a result not of some arbitrary decree but of normal competition between journals, as a re sult of which, however, the strong usual ly get stronger and the weak get weaker. Were it not for these changes and also for a striking improvement in abstracting, indexing, and alerting serv ices, most research workers would have found long ago that, even in their own specialized fields, new information is accumulating faster than it can be sorted out. These developments can pro vide only a temporary reprieve, so long as there remains a strong incentive to publish the greatest possible number of papers. A new scale of values based on citations is by no means infallible or, in many cases, even fair, but at least it provides an alternative to the existing one, which is at the root of the crisis. It might, of course, be asked whether wide acceptance of such new stand ards would not lead to deliberate abuses. A little reflection shows that the system is less open to manipula tion than might appear. First, the ref erees are expected to see to it that the submitted papers cite work which is pertinent to the subject. An increased awareness of the usefulness of citation indexing as a tool for retrieval and evaluation will make this aspect of refereeing more important, and what now passes for minor carelessness or discourtesy could easily come to be regarded as serious malpractice. Sec ond, as noted above, careful selection of references is in the author's own interest, because it helps him to reach his readers. There is, therefore, some room for hope that healthy feedback in the system will tend to keep it viable. At the basis of this hope lies the supposition that, in the long run, only good work can ensure recognition. As Martyn (2) has pointed out, as an information-retrieval method, cita tion indexing is rather "noisy." The word noisy may apply even more to the problem of evaluation. Whereas in information retrieval much of the unwanted information can be filtered out by suitable search strategy (2, 6), this is not so easy to do for the pur pose of evaluation, because a simple descendence relationship between papers is still an ideal far removed from actuality (7). The situation would be much better if we could at will exclude all citations which do not indi cate real indebtedness. A scheme of citation relationship indicators, first men tioned by Garfield (12) and elaborated by Lipetz (17), would be a help, but, even if it were technically feasible, to provide such indicators would greatly add to the production costs of the Index. Another possible way to minimize the effects of "noise" is to increase the size of the samples on which the reckon ing is based. Now that research has be come a rather popular occupation, it seems that a kind of public vote may have to be accepted as a factor in evaluation. Since this is the case, there is something to be said for extending the "franchise" to minimize acciden tal effects. An index which attempted to process all scientific publications would be several times the size of the present Index, and, what is more, it would not necessarily be an improve ment as a tool for information retrieval because most of the significant work is already concentrated in the present Index. Whether this attempt will ever be considered worthwhile remains pri marily a matter of policy and eco nomics. In the meantime there is an urgent need for more experience with the existing services. It is not the purpose of this article to advocate evaluation of scientific work by some kind of public opinion poll; its purpose is to recognize a pos sible trend in this direction. Any judg ment by public acclaim is subject to obvious fallacies, but we must not be carried away by the analogy to the Stock Exchange or to electoral prac tices. The fact that, in this case, the "public" consists of authors whose con tributions are generally linked creates quite a new pattern of organization. In this discussion some of the aspects of this pattern have been explored through analogy to idealized genetic or mechani cal network models, but the very uniqueness of the system, with its many self-organizing ramifications, makes it a new field which deserves close study, since these developments may have pro found effects on the future of scientific communication.

Research paper citation record keeping: It is not for whimps.

M V Dodson — 2008-05-31T22:54:53-00:00

Journal of animal science (23 May 2008)

In an era in which academic institutions are held more accountable, a problem, which does not seem to have an immediate resolution exists: how does one demonstrate the quality of one's work? Specifically, how does one show that his/her research is making an impact and is thought to be important? A variety of measures of scientific journal article importance, reflected mostly by citation analyses, have been focused on as being potential "gold standards." However, while a number of measures have been reported, keeping a record of citation of individual research papers, primarily due to the effort involved in finding accurate information, is not for whimps.

teoria de redes - Buscar con Google

2008-05-23T01:33:19-00:00

Scientific communication at the beginning of the 21st century

JM Russell — 2008-05-21T03:51:24-00:00

International Social Science Journal, Vol. 168 (2001), pp. 271-282.

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.

D Thieffry — 2008-02-20T17:52:27-00:00

Bioessays, Vol. 20, No. 5. (May 1998), pp. 433-440.

Because a large number of molecular mechanisms involved in gene regulation have been described during the last decades, it is now becoming possible to address questions about the global structure of gene regulatory networks, at least in the case of some of the best-characterized organisms. This paper presents a global characterization of the transcriptional regulation in Escherichia coli on the basis of the current data. The connectivity of the corresponding network was evaluated by analyzing the distribution of the number of genes regulated by a given regulatory protein, and the distribution of the number of regulatory genes regulating a given regulated gene. The mean connectivity found (between 2 and 3) shows a rather loosely interconnected structure. Special emphasis is given to circular sequences of interactions ("circuits") because of their critical dynamical properties. Only one-element circuits were found, in which negative autoregulation is the dominant architecture. These global properties are discussed in light of several pertinent theoretical approaches, as well as in terms of physiological and evolutionary considerations.

[Coauthorship networks and institutional collaboration in Revista Española de Cardiología publications]

JC Valderrama-Zurián — 2007-03-11T13:54:39-00:00

Rev Esp Cardiol, Vol. 60, No. 2. (February 2007), pp. 117-130.

INTRODUCTION AND OBJECTIVES: The aim of this study was to analyze the patterns of investigator and institutional collaboration in papers published in the Revista Española de Cardiología. METHODS: Details of coauthorship and institutional collaboration involved in articles published in the Revista Española de Cardiología in the period 2000-2005 were recorded and a collaboration index was derived. Collaboration networks were identified using the TextToPajek and PAJEK software tools. RESULTS: Of the 980 papers analyzed, 95.1% had been authored by two or more individuals and 51.43% involved institutional collaboration. The overall collaboration index was 6.23 (standard deviation [SD] 3.1). There was a significant statistical relationship (P< .02) between the collaboration index and the journal section in which the article was published: the Original Articles and Special Reports sections had the highest collaboration indices (mean 7.87 [2.88]; and mean 6.59 [5.02], respectively). The 44 authors who had the highest publication rates were identified. In addition, 25 coauthorship networks involving 112 investigators were observed. CONCLUSIONS: An analysis of collaboration networks led to the identification of a number of author networks in cardiovascular medicine in Spain, and highlighted the interrelationships between them in terms of both scientific research and scientific publications. The most significant aspect of institutional collaboration was the predominance of collaboration within institutions and within Spanish autonomous regions (i.e., 80.57% of collaborations). Possible topics for future study include an analysis of the scientific productivity of the networks identified and of changes in the pattern of collaboration over time.

PAJEK -- Program for large network analysis

V Batagelj — 2008-01-30T04:27:39-00:00

(1998)

Large networks, having thousands of vertices and lines, can be found in many different areas, e. g: genealogies, flow graphs of programs, molecule, computer networks, transportation networks, social networks, intra/inter organisational networks ... Many standard network algorithms are very time and space consuming and therefore unsuitable for analysis of such networks. In the article we present some approaches to analysis and visualisation of large networks implemented in program Pajek. Some...

Pajek - Analysis and Visualization of Large Networks

Vladimir Batagelj — 2005-07-18T12:13:51-00:00

Lecture Notes in Computer Science, Vol. 2265 (January 2002), 477.

<TT>Pajek</TT> (spider, in Slovene) is a program package, for Windows (32 bit), for analysis and visualization of large networks (having thousands of vertices). It is freely available, for noncommercial use, at its home page: <TT>http://vlado.fmf.uni-lj.si/pub/networks/pajek/</TT>

An Identity Crisis in the Life Sciences

Jun Zhao — 2007-11-07T18:05:00-00:00

Provenance and Annotation of Data (2006), pp. 254-269.

myGrid is an e-Science project assisting life scientists to build workflows that gather data from distributed, autonomous, replicated and heterogeneous resources. The provenance logs of workflow executions are recorded as RDF graphs. The log of one workflow run is used to trace the history of its execution process. However, by aggregating provenance logs of many workflow runs, one may gather the provenance of a common data product shared in multiple derivation paths. A successful aggregation relies on accurate and universal identification of each data product. The nature of bioinformatics data and services, however, makes this difficult. We describe the identity problem in bioinformatics data, and present a protocol for managing identity co-references and allocating identity to gathered and computed data products. The ability to overcome this problem means that the provenance of workflows in bioinformatics and other domains can be exploited to enhance the practice of e-Science.

Service-Oriented Science

Ian Foster — 2005-06-28T17:29:12-00:00

Science, Vol. 308, No. 5723. (06 May 2005), pp. 814-817.

New information architectures enable new approaches to publishing and accessing valuable data and programs. So-called service-oriented architectures define standard interfaces and protocols that allow developers to encapsulate information tools as services that clients can access without knowledge of, or control over, their internal workings. Thus, tools formerly accessible only to the specialist can be made available to all; previously manual data-processing and analysis tasks can be automated by having services access services. Such service-oriented approaches to science are already being applied successfully, in some cases at substantial scales, but much more effort is required before these approaches are applied routinely across many disciplines. Grid technologies can accelerate the development and adoption of service-oriented science by enabling a separation of concerns between discipline-specific content and domain-independent software and hardware infrastructure.

Cyberinfrastructure: Empowering a "Third Way" in Biomedical Research

Kenneth Buetow — 2005-06-28T17:32:32-00:00

Science, Vol. 308, No. 5723. (06 May 2005), pp. 821-824.

Biomedicine has experienced explosive growth, fueled in parts by the substantial increase of government support, continued development of the biotechnology industry, and the increasing adoption of molecular-based medicine. At its core, it is composed of fiercely independent, innovative, entrepreneurial individuals, organizations, and institutions. The field has developed unprecedented capacity to characterize biologic systems at their most fundamental levels with the use of tools and technologies almost unimaginable a generation ago. Biomedicine is at the precipice of unlocking the very essence of biologic life and enabling a new generation of medicine. Development and deployment of cyberinfrastructure may prove to be on the critical path to obtaining these goals.

Special Issue: Grids and Web Services for e-Science: Editorials

Tony Hey — 2005-12-27T14:22:30-00:00

Concurr. Comput. : Pract. Exper., Vol. 17, No. 2-4. (2005), pp. 317-322.

e-Science perspectives in Venezuela

G Diaz — 2008-01-31T08:29:43-00:00

(27 Jan 2008)

We describe the e-Science strategy in Venezuela, in particular initiatives by the Centro Nacional de Calculo Cientifico Universidad de Los Andes (CECALCULA), Merida, the Universidad de Los Andes (ULA), Merida, and the Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas. We present the plans for the Venezuelan Academic Grid and the current status of Grid ULA supported by Internet2. We show different web-based scientific applications that are being developed in quantum chemistry, atomic physics, structural damage analysis, biomedicine and bioclimate within the framework of the E-Infrastructure shared between Europe and Latin America (EELA)

E-Science Meets Computational Science and Information Technology

Geoffrey Fox — 2005-12-26T17:40:54-00:00

Computing in Science and Engg., Vol. 4, No. 4. (July 2002), pp. 84-85.

e-Science and its implications.

T Hey — 2007-10-25T13:54:41-00:00

Philosophical Transactions A Math Phys Eng Sci, Vol. 361, No. 1809. (15 August 2003), pp. 1809-1825.

After a definition of e-science and the Grid, the paper begins with an overview of the technological context of Grid developments. NASA's Information Power Grid is described as an early example of a 'prototype production Grid'. The discussion of e-science and the Grid is then set in the context of the UK e-Science Programme and is illustrated with reference to some UK e-science projects in science, engineering and medicine. The Open Standards approach to Grid middleware adopted by the community in the Global Grid Forum is described and compared with community-based standardization processes used for the Internet, MPI, Linux and the Web. Some implications of the imminent data deluge that will arise from the new generation of e-science experiments in terms of archiving and curation are then considered. The paper concludes with remarks about social and technological issues posed by Grid-enabled 'collaboratories' in both scientific and commercial contexts.

Cyberinfrastructure for e-Science

Tony Hey — 2005-06-28T17:30:32-00:00

Science, Vol. 308, No. 5723. (06 May 2005), pp. 817-821.

Here we describe the requirements of an e-Infrastructure to enable faster, better, and different scientific research capabilities. We use two application exemplars taken from the United Kingdom's e-Science Programme to illustrate these requirements and make the case for a service-oriented infrastructure. We provide a brief overview of the UK "plug-and-play composable services" vision and the role of semantics in such an e-Infrastructure.

Maps of random walks on complex networks reveal community structure

Martin Rosvall — 2008-01-24T08:30:08-00:00

Proceedings of the National Academy of Sciences (23 January 2008), 0706851105.

To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the networkincluding physics, chemistry, molecular biology, and medicineinformation flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences. 10.1073/pnas.0706851105

Social network analysis: An approach and technique for the study of information exchange

Caroline Haythornthwaite — 2006-04-26T02:43:14-00:00

Library & Information Science Research, Vol. 18, No. 4. ( 1996), pp. 323-342.

Social network analysis is an approach and set of techniques used to study the exchange of resources among actors (i.e., individuals, groups, or organizations). One such resource is information. Regular patterns of information exchange reveal themselves as social networks, with actors as nodes in the network and information exchange relationships as connectors between nodes. Just as roads structure the flow of resources among cities, information exchange relationships structure the flow of information among actors. Social network analysis assesses information opportunities for individuals or groups of individuals in terms of exposure to and control of information. By gaining awareness of existing information exchange routes, information providers can act on information opportunities and make changes to information routes to improve the delivery of information services.

Social Network Analysis: A Handbook

John Scott — 2005-07-04T17:17:30-00:00

(26 January 2000)

The revised and updated edition of this bestselling text provides an accessible introduction to the theory and practice of network analysis in the social sciences. It gives a clear and authoritative guide to the general framework of network analysis, explaining the basic concepts, technical measures and reviewing the available computer programs.The book outlines both the theoretical basis of network analysis and the key techniques for using it as a research tool. Building upon definitions of points, lines and paths, John Scott demonstrates their use in clarifying such measures as density, fragmentation and centralization. He identifies the various cliques, components and circles into which networks are formed, and outlines an approach to the study of socially structured positions. He also discusses the use of multidimensional methods for investigating social networks.Social Network Analysis is an invaluable resource for researchers across the social sciences and for students of social theory and research methods.

Analysis and Visualization of Social Networks

Dorothea Wagner — 2005-06-06T20:53:10-00:00

Lecture Notes in Computer Science, Vol. 2647 (January 2003), pp. 261-266.

Social network analysis is a subdiscipline of the social sciences using graph-theoretic concepts to understand and explain social structure. We describe the main issues in social network analysis. General principles are laid out for visualizing network data in a way that conveys structural information relevant to specific research questions. Based on these innovative graph drawing techniques integrating the analysis and visualization of social networks are introduced.

Linked: The New Science of Networks

Albert-László Barabási — 2005-03-21T13:12:54-00:00

(02 May 2002)

How is the human brain like the AIDS epidemic? Ask physicist Albert-László Barabási and he'll explain them both in terms of networks of individual nodes connected via complex but understandable relationships. Linked: The New Science of Networks is his bright, accessible guide to the fundamentals underlying neurology, epidemiology, Internet traffic, and many other fields united by complexity. Barabási's gift for concrete, nonmathematical explanations and penchant for eccentric humor would make the book thoroughly enjoyable even if the content weren't engaging. But the results of Barabási's research into the behavior of networks are deeply compelling. Not all networks are created equal, he says, and he shows how even fairly robust systems like the Internet could be crippled by taking out a few super-connected nodes, or hubs. His mathematical descriptions of this behavior are helping doctors, programmers, and security professionals design systems better suited to their needs. Linked presents the next step in complexity theory--from understanding chaos to practical applications. --Rob Lightner The first book to explore the hot new science of networks and their impact on nature, business, medicine, and everyday life. In the 1980's, James Gleick's Chaos introduced the world to complexity. Now, Albert-László Barabási's Linked reveals the next major scientific leap: the study of networks. We've long suspected that we live in a small world, where everything is connected to everything else. Indeed, networks are pervasive--from the human brain to the Internet to the economy to our group of friends. These linkages, it turns out, aren't random. All networks, to the great surprise of scientists, have an underlying order and follow simple laws. Understanding the structure and behavior of these networks will help us do some amazing things, from designing the optimal organization of a firm to stopping a disease outbreak before it spreads catastrophically. In Linked, Barabási, a physicist whose work has revolutionized the study of networks, traces the development of this rapidly unfolding science and introduces us to the scientists carrying out this pioneering work. These "new cartographers" are mapping networks in a wide range of scientific disciplines, proving that social networks, corporations, and cells are more similar than they are different, and providing important new insights into the interconnected world around us. This knowledge, says Barabási, can shed light on the robustness of the Internet, the spread of fads and viruses, even the future of democracy. Engaging and authoritative, Linked provides an exciting preview of the next century in science, guaranteed to be transformed by these amazing discoveries. From Linked: This book has a simple message: think networks. It is about how networks emerge, what they look like, and how they evolve. It aims to develop a web-based view of nature, society, and technology, providing a unified framework to better understand issues ranging from the vulnerability of the Internet to the spread of diseases. Networks are present everywhere. All we need is an eye for them...We will see the challenges doctors face when they attempt to cure a disease by focusing on a single molecule or gene, disregarding the complex interconnected nature of the living matter. We will see that hackers are not alone in attacking networks: we all play Goliath, firing shots at a fragile ecological network that, without further support, could soon replicate our worst nightmares by turning us into an isolated group of species...Linked is meant to be an eye-opening trip that challenges you to walk across disciplines by stepping out of the box of reductionism. It is an invitation to explore link by link the next scientific revolution: the new science of networks.

Why social networks are different from other types of networks

MEJ Newman — 2005-09-30T09:20:29-00:00

(26 May 2003)

We argue that social networks differ from most other types of networks, including technological and biological networks, in two important ways. First, they have non-trivial clustering or network transitivity, and second, they show positive correlations, also called assortative mixing, between the degrees of adjacent vertices. Social networks are often divided into groups or communities, and it has recently been suggested that this division could account for the observed clustering. We demonstrate that group structure in networks can also account for degree correlations. We show using a simple model that we should expect assortative mixing in such networks whenever there is variation in the sizes of the groups and that the predicted level of assortative mixing compares well with that observed in real-world networks.

Uncovering the overlapping community structure of complex networks in nature and society

Gergely Palla — 2005-06-08T20:26:31-00:00

Nature, Vol. 435, No. 7043., pp. 814-818.

Knowledge Networks: Innovation Through Communities of Practice

2005-03-23T10:33:58-00:00

(01 February 2004)

Knowledge Networks: Innovations Through Communities of Practice draws on the experience of people who have worked with CoPs in the real world and to present their combined wisdom in a form that is accessible to a wide audience. CoPs are examined from a practical, rather than a purely academic point of view. The book also examines the benefits that CoPs can bring to an organization, provides a number of case studies, lessons learned and sets of guidelines. It also looks at virtual CoPs and to the future by asking 'what next?' This book is a resource for all people who work with CoPs - both in academia and in the real world.

prefuse: a toolkit for interactive information visualization

Jeffrey Heer — 2005-06-01T19:26:04-00:00

(2005), pp. 421-430.

Knowledge Management: are we missing something

P Hildreth — 2005-04-27T01:32:00-00:00

(1999)

As commercial organisations face up to modern pressures to downsize and outsource they have lost knowledge as people leave and take with them what they know. This knowledge is increasingly being recognised as an important resource and organisations are now taking steps to manage it. In addition, as the pressures for globalisation increase, collaboration and co-operation are becoming more distributed and international. Knowledge sharing in a distributed international environment is becoming an...

Preferential attachment in the growth of social networks: the case of Wikipedia

A Capocci — 2006-03-01T16:18:10-00:00

(27 Feb 2006)

We present an analysis of the statistical properties and growth of the free on-line encyclopedia Wikipedia. By describing topics by vertices and hyperlinks between them as edges, we can represent this encyclopedia as a directed graph. The topological properties of this graph are in close analogy with that of the World Wide Web, despite the very different growth mechanism. In particular we measure a scale--invariant distribution of the in-- and out-- degree and we are able to reproduce these features by means of a simple statistical model. As a major consequence, Wikipedia growth can be described by local rules such as the preferential attachment mechanism, though users can act globally on the network.

Introduction: networking technology, networking society, networking nature

Erik van der Vleuten — 2004-12-28T17:28:08-00:00

History and Technology, Vol. 20, No. 3., 195.

To know or not to know: archiving and the under-appreciated historical value of data

David Covarrubias — 2008-02-12T13:22:52-00:00

Molecular Cancer, Vol. 7 (11 February 2008), 18.

Coauthorship networks and patterns of scientific collaboration.

ME Newman — 2006-07-16T18:42:36-00:00

Proc Natl Acad Sci U S A, Vol. 101 Suppl 1 (6 April 2004), pp. 5200-5205.

By using data from three bibliographic databases in biology, physics, and mathematics, respectively, networks are constructed in which the nodes are scientists, and two scientists are connected if they have coauthored a paper. We use these networks to answer a broad variety of questions about collaboration patterns, such as the numbers of papers authors write, how many people they write them with, what the typical distance between scientists is through the network, and how patterns of collaboration vary between subjects and over time. We also summarize a number of recent results by other authors on coauthorship patterns.

Similarity measures, author cocitation analysis, and information theory

Loet Leydesdorff — 2006-12-05T07:46:57-00:00

Journal of the American Society for Information Science and Technology, Vol. 56, No. 7. (2005), pp. 769-772.

The use of Pearson's correlation coefficient in Author Cocitation Analysis was compared with Salton's cosine measure in a number of recent contributions. Unlike the Pearson correlation, the cosine is insensitive to the number of zeros. However, one has the option of applying a logarithmic transformation in correlation analysis. Information calculus is based on both the logarithmic transformation and provides a non-parametric statistics. Using this methodology, one can cluster a document set in a precise way and express the differences in terms of bits of information. The algorithm is explained and used on the data set, which was made the subject of this discussion.

Collaboration, peer review and open source software

Justin Johnson — 2008-02-18T20:39:40-00:00

Information Economics and Policy, Vol. 18, No. 4. (November 2006), pp. 477-497.

Open source software development may be superior to proprietary development because the open source organizational form naturally minimizes transactions costs associated with privately distributed information. This manifests itself in the ability of open source communities to encourage critical peer review and the sharing of ideas. When these activities are important, the open source organizational form may do better than a proprietary organizational form. My results suggest why open source is particularly powerful when maintainability of software is critical, and also suggest that the founder of a software project may be more likely to choose open source if there is an existing dominant proprietary software project.

Cognitive Changes in Scientometrics during the 1980s, as Reflected by the Reference Patterns of Its Core Journal

András Schubert — 2008-02-18T20:06:41-00:00

Social Studies of Science, Vol. 23, No. 3. (1993), pp. 571-581.

The journal Scientometrics (and the research field it represents) has moved slightly from the 'soft' towards the 'harder' sciences. This proposition has been tested and supported by analyzing the references of the research articles published in the journal in the periods 1980-81 and 1990-91, respectively.