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  • 1. COMUNICACIÓN CIENTÍTICA
  • 2. El poster científico  OBJETIVOS: 1.-Aprender a realizar un poster cientítico 2.-Simular estrategias de comunicación científica 3.-Aprender a resumir ideas y trabajos. PRODUCTOS FINALES: 1.-Realización de un poster científico 2.-Hacer un "congreso" científico sobre temas ambientales. 3.-Depositar los resultados en la sección “Biblioteca” del Aula virtual de ECOURBAN (cuando se hayan hecho en formato electrónico)
  • 3. CONSIDERACIONES  Con el objetivo de dar difusión a nuestro trabajo, vamos a realizar un póster donde se resuma de forma gráfica todo lo anterior, con diseño original y vistoso, igual que lo harían los científicos en sus congresos, donde se explique en qué consiste la problemática estudiada, la investigación realizada, las principales conclusiones que se han extrraído y las soluciones posibles para mejorar esa problemática ambiental. El póster podrá estar realizado a mano, escrito de puño y letra o a ordenador.  Antes de hacer un poster hay que saber que es un instrumento científico de primer orden, y como tal es de gran importancia para la comunicación entre los profesionales de la ciencia. Por eso hay que dedicarle un tiempo a saber cómo hacerlo, para ello hemos puesto varios recursos que pueden ser de utilidad para todos.
  • 4. • Estructura  La estructura del resumen del póster es la misma que la de las comunicaciones orales y, siempre que el trabajo o estudio que hayamos realizado lo permita, debe incluir:  - Título  - Autor(es)  - Centro(s)  - Introducción, hipótesis y objetivo  - Metodología (materiales y métodos)  - Resultados  - Conclusiones
  • 5. EL TEXTO  • Ha de comprenderse per se (para entenderlo no hace falta recurrir a otra fuente).  • Ha de contener los puntos esenciales del trabajo, estudio, experiencia...  • Tiene una extensión limitada (la organización indica el número máximo de caracteres o palabras).  • Ha de ser claro y breve, exacto y conciso; por este motivo, deben emplearse frases cortas, hay que seleccionar las palabras más adecuadas y cuidar al máximo el lenguaje.  • Tenemos que pensar que el resumen es "un artículo en pequeño".
  • 6. Introducción  Debe ser corta. Sirve para familiarizar al lector con el tema. Losaspectos que debe contemplar son:  - Antecedentes, revisión (muy corta) del tema  - Importancia teórica y/o práctica del tema  - Hipótesis  - Objetivos del trabajo  - Definiciones (en algunos casos puede ser necesario definir algún término)
  • 7. Metodología (materiales y métodos)  Este apartado le ha de permitir al lector la evaluación de la forma en la que se llevó a cabo el trabajo.  Debe describirse qué se hizo para obtener, recoger y analizar los datos; es decir, el diseño del estudio, cómo se llevó a cabo, si tuvo distintas fases, qué variables se consideraron, cómo se analizaron los datos (análisis estadístico, si lo hubo), etc.
  • 8. Resultados  En el póster incluiremos un resumen de los resultados, una vez  analizados, tanto si la hipótesis que formulábamos se ha podido probar como si no ha sido así.  Seleccionaremos los datos más relevantes y que estén más relacionados con el/los objetivo/s del estudio.  Procuraremos evitar textos demasiado largos, con demasiados datos.  La utilización de tablas y figuras en este apartado es muy útil y procuraremos usarlas (como ya hemos dicho "una imagen vale más que mil palabras").
  • 9. Conclusiones  En general, en el póster se incluye un apartado específico con las conclusiones del trabajo (de hecho, en muchas ocasiones, después de leer el título, el lector va directamente a las conclusiones).  Además, según el caso, puede también incluirse una pequeña discusión de los resultados, una interpretación de los mismos, recomendaciones para futuros trabajos, sugerencias, etc.
  • 10. Referencias bibliográficas  No es obligatorio incluir referencias bibliográficas en un póster y podemos prescindir de este apartado (el espacio destinado a la bibliografía lo podemos aprovechar para incluir información de nuestro propio trabajo).  Dependiendo del tipo de estudio, experiencia, etc. estará indicado incluir referencias; en este caso, seleccionaremos las más importantes, las que consideremos imprescindibles en relación con el tema.
  • 11. Agradecimientos  No es obligatorio, pero debemos considerar si incluimos un pequeño apartado en el que se mencione a personas que han participado en el trabajo pero que no pueden considerarse autores, a organizaciones, empresas o sociedades que han financiado el trabajo o que han contribuido al mismo de alguna forma, etc.
  • 12. Tablas, fotografías, ilustraciones, ...  El póster es un medio muy adecuado para la utilización de recursos gráficos. Por este motivo, son pocos los pósters en los que se utiliza sólo texto. Hallar el justo equilibrio entre texto e imágenes contribuye en gran parte al "éxito" del póster.
  • 13. Pon aquí el título con letra grande y legible Tu nombre aquí1,2 y tus compañeros o profesor aquí 1 , Departamento escolar2 , Nombre del colegio o instituto INTRODUCCIÓN Y ANTECEDENTES RESUMEN METODOLOGÍA RESULTADOS METODOLOGÍA RESULTADOS CONCLUSIONES PROPUESTAS DE FUTURO AGRADECIMIENTOS:
  • 14. Conclusions In summary, this analysis of the topside sounder data from ISS-b leads to the following preliminary conclusions:  There is no apparent preference for midlatitude spread echoes to occur over continental land masses.  There are very large seasonal variations in the occurrence probability of midlatitude spreading over distinct geographic domains. These seasonal variations are largest over the oceanic regions.  The highest occurrence probability for midlatitude spread echoes is over the north Atlantic in the November-January period. The smallest occurrence probability is over the north Pacific, in the same interval.  Occurrence probabilities up to about 30% are quite common at all locales. Acknowledgments We thank Dr. T. Maruyama for the ISS-b data. The first author thanks Patrick Roddy for assistance. This work was supported by NASA grant NNG04WC19G Introduction Ionosonde signatures of spread echo conditions are not strictly limited to regions near the magnetic equator. A number of radar and satellite studies have shown that radio scintillation and large scale density irregularities in the F region plasma also occur at midlatitudes, although less frequently. Fukao et al. [1991] observed spread F type ionograms quite far from the magnetic equator, and Hanson and Johnson [1992] observed mid-latitude density perturbations at dip latitudes as high as 40 degrees using the AE-E satellite. Our focus in this work is to determine whether midlatitude spread echoes have any statistically significant seasonal or geographical variability. Future Work It may be interesting to compare the statistics we have derived here to global weather patterns. For example, the existence of monsoon zones in the equatorial zone in southeast Asia can be expected to launch copious quantities of gravity waves, which might in turn be expected to trigger outbreaks of spreading events. It may be fruitful to compare satellite observations of midlatitude gravity waves at F region heights to the occurrence probability plots shown here. We have begun a study of this nature using DE-2 data, but the results are not yet ready for such a detailed comparison. Seasonal and Longitudinal Variations of Midlatitude Topside Spread Echoes Based on ISS-b Observations A. M. Mwene, G. D. Earle, J. P. McClure William. B. Hanson Center for Space Sciences, University of Texas at Dallas References [1]Fukao, S., et al., Turbulent upwelling of the mid-latitude ionosphere: 1.Observational results by the MU radar, J. Geophys.Res., 96, 3725, 1991. [2]Hanson, W. B. and F. S. Johnson, Lower midlatitude ionospheric disturbances and the Perkins instability, Planet. Space Sci., 40,1615, 1992. [3]Maruyama, T., and N. Matuura, Global distribution of occurrence probability of spread echoes based on ISS-b observation, J. Radio Res. Lab., 27, 201, 1980. [4]McClure, J.P. S. Singh, D.K. Bamgboye, F.S. Johnson, and H. Kil,Occurrence of equatorial F region irregularities: Evidence for tropospheric seeding, J. Geophys. Res., 103, 29,119, 1998. Instrumentation and Coverage The topside sounder instrument from the ISS-b satellite is used as our diagnostic tool. The satellite provided useful data from August 1978 through December 1980, with intermittent tape recorder outages and data dump intervals resulting in roughly a 30% duty cycle. The satellite was inserted into a 70 degree inclination orbit, with apogee and perigee at 1220 km and 972 km, respectively. The 150 W topside sounder instrument used for this study covered the frequency range from 0.5-14.8 MHz in 0.1 MHz steps, with a receiver bandwidth of 6 kHz. Figure 1 shows the satellite coverage over the course of one season. The points on the map correspond to the locations at which topside ionograms were obtained. Midlatitude coverage is relatively good for all seasons except for the May-July solstice period. We have therefore omitted this interval from our analysis. Data Presentation Figures 2-4 show logarithmically scaled histogram plots of the Maruyama index values for each of the geographic regions defined in Table 1. Each of the figures corresponds to a different season; logarithmic axes have been used in order to highlight the regions on each graph for which the index value is greater than four. It is important to remember that the regions defined in Table 1 correspond to very different geographic areas (in km2 ). However, it is valid to compare the seasonal variations for a given geographic area. In Figures 2-4 the left column of histograms corresponds to oceanic regions, and the right column corresponds to land masses. The seasonal variations become more apparent when the data from Figures 2-4 are presented as occurrence probabilities. These have been calculated as follows for each region: The occurrence probabilities as a function of season and geographic domain are presented in Figure 5. Discussion With reference to Figure 5, there are very large seasonal differences in occurrence probabilities for midlatitude spread echoes in the north Atlantic, south Atlantic, and north Pacific regions. Somewhat less striking seasonal variations are evident in Asia and Europe. The other geographic domains have much less pronounced seasonal variations. The occurrence of spread echoes over the north Atlantic region is particularly variable. This region shows the highest (November-January) and second lowest (August- September) occurrence probabilities. The overall occurrence probabilities for MSF are quite large when classified using the Maruyama and Matuura [1980] index. This may be caused by incursion of high and/or low latitude irregularities into the midlatitude domain. In general there are no differences between the number of spreading events occurring over land masses and over oceans. Table. 1.Definitions of the regions of interest. Fig . 1.Satellite coverage map showing regions of interest. 1 10 100 NORTHPACIFIC 1 10 100 SOUTHPACIFIC 1 10 100 NORTHATLANTIC 1 10 100 SOUTHATLANTIC 0 5 10 15 20 1 10 100 Spread F index INDIAN OCEAN 1 10 100 NORTHAMERICA 1 10 100 ASIA 1 10 100 AUSTRALIA 1 10 100 AFRICA 0 5 10 15 20 10 0 10 2 Spread F index EURASIA AND N.AFRICA NOV-DEC-JAN OccurencesinLogscale Fig. 5. Topside spread echo occurrence probabilities as a function of season and location. -20-5050-1100Indian Ocean -20-50315-100South Atlantic +20-50285-3450North Atlantic -20-50155-2800South Pacific +20-50140-2250North Pacific -20-50110-1550Australia +20-5010-500Africa +20-5060-1400Asia +20-50345-600Eurasia +20-50225-2850North America Mag LatitudeGeog LongitudeRegion Name -20-5050-1100Indian Ocean -20-50315-100South Atlantic +20-50285-3450North Atlantic -20-50155-2800South Pacific +20-50140-2250North Pacific -20-50110-1550Australia +20-5010-500Africa +20-5060-1400Asia +20-50345-600Eurasia +20-50225-2850North America Mag LatitudeGeog LongitudeRegion Name 1 10 100 NORTH PACIFIC 1 10 100 SOUTH PACIFIC 1 10 100 NORTH ATLANTIC 1 10 100 SOUTH ATLANTIC 0 5 10 15 20 1 10 100 Spread F index INDIAN OCEAN 1 10 100 NORTH AMERICA 1 10 100 ASIA 1 10 100 AUSTRALIA 1 10 AFRICA 0 5 10 15 20 1 10 100 Spread F index EURASIA AND NORTH AFRICA FEB-MARCH-APRIL OccurencesinLogscale Fig . 2. Maruyama and Matuura’s [1980] spread echo index variations for each region in Feb-Apr. Procedure Maruyama and Matuura [1980] describe the process of inferring a simple index corresponding to spread echo conditions from the ISS-b topside sounder data. Index values greater than four correspond to widespread regions of spread echoes. McClure et al. [1998] offer a good overview of this classification method, particularly as it applies to equatorial spread F. We use the Maruyama index in our analysis to identify regions at magnetic latitudes between ±20 and ± 50 degrees that have significant spreading. Table 1 shows the breakdown of the various geographic regions, and Figure 1 shows these regions on a world map. 1 10 100 NORTHPACIFIC 1 10 100 SOUTHPACIFIC 1 10 100 NORTH ATLANTIC 1 10 100 SOUTH ATLANTIC 0 5 10 15 20 1 10 100 Spread F index INDIAN OCEAN 1 10 100 NORTH AMERICA 1 10 100 ASIA 1 10 100 AUSTRALIA 1 10 100 AFRICA 0 5 10 15 20 1 10 100 Spread F index EURASIA ANDN.AFRICA AUG-SEPT-OCTOBER OccurencesinLogscale Fig. 4. Same format as Figure 2 for Nov- Jan. Fig. 3. Same format as Figure 2 for Aug-Oct. %100 nsobservatioofnumberTotal 5indexwitheventsofNumberyProbabilit ×≥= This is surprising, since it might be expected that more thunderstorms and subsequently more gravity wave seeding for spreading would be expected over land masses, where orographic features exist. The lack of such a correlation may be due to the fact that gravity waves can be ducted over very large horizontal distances, so that waves generated over land masses may propagate for thousands of kilometers before generating perturbations that lead to midlatitude spread echoes. Abstract A preliminary study of the seasonal and longitudinal variations of spread echoes from the Ionosphere Sounding Satellite (ISS) using the topside sounding data has been undertaken. Significant longitudinal and seasonal variations in midlatitude spread echoes are observed. The north Atlantic region has the highest occurrence probability in the winter solstice. The smallest occurrence is in the north Pacific in the same interval. Occurrence probabilities of up to about 30% are quite common. 0 20 40 60 % FEB MAR APR SEASONAL OCCURRENCE PROBABILITIES FOR SPREADING EVENTS 0 20 40 60 % AUG SEPT OCT 0 20 40 60 NOV DEC JAN % Npacific Spacfic Natlantic Satlantic Indianocean Africa Namerica Eurasia Asia Australia
  • 15. The importance of trust: Science, policy, and the publics Jenny Dyck Brian School of Life Sciences, Arizona State University, Tempe, AZ 85287-4601 Photo courtesy of Su-Chun Zhang, University of Wisconsin-Madison (Borrowed from http://www.news.wisc.edu/packages/stemcells/images/Zhang_neural_stem_cell1_01.jpg) We are facing a complex, multi-faceted, and seemingly intractable crisis of confidence: Scientists alternate between bravado, secrecy, and defensiveness; they sometimes seek advice from ethicists and lawyers, who, of course, disagree with one another, and have vested interests of their own; politicians, seemingly concerned as much with re-election as with promoting the public good, try to reconcile competing values by seeking advice from these dysfunctional communities of experts; not surprisingly, then, ‘expert’ opinions are put to partisan uses, members of the lay public feel ignored, and, at bottom, we all end up practicing politics, not democracy. Public interest in science is high, but public trust is waning. Scientists are sometimes seen as self-interested rather than as serving the greater good. Moreover, in public debates over science, scientists often seem to believe that any hostility toward scientific research must be based in misunderstanding of facts, rather than differences in values and interests. Public interest and public trust must be fostered through effective public dialogue and openness, the outcome of proactive collaboration between ethicists, scientists, and policy-makers. Both the form and the content of that dialogue will be important, and to be effective it cannot be controlled by any one group or single interest. In the context of stem cell research, policy decisions will reflect a balance of competing values and interests. Sound policy decisions will emerge from an effective public dialogue, within which scientists have an important role to play. But policy decisions are not scientific decisions: “science can alert us to problems, and can help us understand how to achieve our goals once we have decided them; but the goals can emerge only from a political process in which science should have no special privilege” (Sarewitz, 2004b). How, then, should we connect the dots between science, policy, and the public good? Science can progress responsibly when: Scientists • Are not trying to hide or to downplay the controversies and risks associated with their research; • Participate in open public debate about the research they want to do and why such research is justified. Ethicists • Are scientifically well-informed without treating the science as unassailable; • Do a better job structuring the ethical debate so it remains focused on important substantive issues rather than ideology, false dichotomies, and polemics. Policy-makers • Engage with the scientists, ethicists, and publics to fairly balance competing interests in line with the democratically ascertained public good. California’s Proposition 71 In November 2004, California voters passed the California Stem Cell Research and Cures Initiative (Proposition 71), approving $3 billion of government funding for stem cell research. As an amendment to the state constitution, it created an unprecedented “right to conduct stem cell research.” In doing so, Proposition 71 turned the “privilege of conducting publicly funded research into an absolute legal protection for stem cell researchers, while offering no equivalent protection for the citizens who would be the voluntary subjects of that research” (Sarewitz, 2004). For instance, the Independent Citizens Oversight Committee that was formed as part of the California Institute for Regenerative Medicine (CIRM) consists entirely of people who have a stake in the success of stem cell research. A success story? Proposition 71 was touted as “one of the most transparent and democratic scientific processes in U.S. history” (Magnus, 2004). It is more accurate to depict the campaign for Proposition 71 as propaganda designed to persuade rather than inform or educate California voters. Television commercials and websites dramatically underplayed the complexity of the science, offering instead a very simplistic presentation of deeply complex philosophical and ethical questions. The campaign succeeded in painting opponents of Proposition 71 as religious conservatives – despite many liberal detractors concerned about the lack of transparency and accountability implicit in the ballot measure. Fast forward one year and none of the $295 million earmarked for stem cell research this year has been spent. Why? Legal challenges have prevented CIRM from borrowing any of the money. Lawsuits questioning the legality of the stem cell institute have been filed to address issues of royalties and intellectual property rights as well as standards of public accountability and transparency. Stem cell scientists can learn an important lesson: hype and hubris are two-edged swords. Democratizing science When democratic debate is impoverished and uninformed, as it was in California, important issues and values are ignored. Well-informed and well-intentioned public dialogue is a conversation neither science nor society can afford to sacrifice. How do we make science and democracy fit together? “Democratizing science does not mean settling questions about Nature by plebiscite any more than democratizing politics means settling the prime rate by referendum. What democratization does mean, in science as elsewhere, is creating institutions and practices that fully incorporate principles of accessibility, transparency, and accountability. It means considering the societal outcomes of research at least as attentively as the scientific or technological outputs. It means insisting that in addition to being rigorous, science be popular, relevant, and participatory.” (Guston, 2004) For further reading Cash, D.W., et al. Knowledge Systems for Sustainable Development. Proceedings of the National Academy of Science 100(14): 8086-8091. Center for Genetics and Society. 2005. Statement on teaching evolution. <http://www.genetics- and-society.org>. Accessed 2006 Feb 1. Guston, D., and D. Sarewitz. 2002. Real Time Technology Assessment. Technology in Society 24(1-2):93-109. Guston, D. 2004. Forget Politicizing Science. Let’s Democratize Science! Issues in Science and Technology Fall 2004: 25-28. Greenfield, D. 2004. Impatient Proponents. Hastings Center Report 34(5):32-35. House of Lords, Science and Technology Committee. 2000. Report: Science and Society. The United Kingdom Parliament. Kitcher, P. 2001. Science, Truth, and Democracy. Oxford University Press, New York. Krimsky, S. 2003. Science in the Private Interest: Has the Lure of Profits Corrupted Biomedical Research? Rowman & Littlefield Publishers, Lanham, MD. Magnus, D. 2004. Stem Cell Research Should Be More Than a Promise. Hastings Center Report 34(5): 35-36. Sarewitz, D. 2003. Scientizing the Soul: Research as a Substitute for Moral Discourse in Modern Society. BA Festival of Science, Salford, UK. Sarewitz, D. Stepping Out of Line in Stem Cell Research. LA Times 2004 Oct 25, B11. Sarewitz, D. Hiding Behind Science. Newsday.com 2004 May 23. O’Neill, O. 2002. A Question of Trust: The BBC Reith Lectures 2002. University Press, Cambridge. Wack, P. 1984. Scenarios: The Gentle Art of Re-Perceiving.” [Working Paper] Cambridge, MA. Acknowledgments I would like to thank Jason Scott Robert for his insightful ideas and valuable feedback. Funding for this project was provided by the School of Life Sciences at Arizona State University. For further information Please contact jennifer.brian@asu.edu. More information on this and related projects can be obtained at www.cspo.org and www.public.asu.edu/~jrobert6. A recipe for science and society Accountability: One who is accountable is one who may be called to answer for her actions, and so one who assumes responsibility. To whom are scientists and ethicists accountable, and for what? Transparency: Transparency is the converse of privacy. Transparency permits the exercise of accountability. But while transparency may prevent secrecy, it may not limit deception and deliberate misinformation. Hence the need for accessibility. Accessibility: Meaningful and informed debate can take place only when people have access to knowledge. Accessibility therefore involves providing resources explaining proposed or ongoing research, including its goals, complexities, and attendant risks. Deliberation: Science qua science does not trump all other interests, but reliable and benevolent science is an important consideration in public deliberation about the direction and governance of scientific research. Baking tips: • Science is not trustworthy just because it is science, but rather only when it is trustworthy science. Trustworthy science is credible, salient, and legitimate (Cash et al. 2001). • “Well placed trust grows out of active inquiry rather than blind acceptance” (O’Neill, 2002). Finding meaning in innovation Today’s society is characterized by uncertainty and rapid change. How should decisions about science and society be made in the face of many unknowns and multiple conflicting values? The relationship between science and politics is complex and difficult, and science can never save us from politics, just as it should not subvert important political processes. Scientists, social scientists, ethicists must come up with new strategies for collaborative engagement. Debates must be structured such that evaluations of particular values are not overshadowed by fights about the likelihood of future possibilities, rather than their desirability. Science, technology, and ethics all contribute to the construction of society together, but their efforts are not always collaborative. Ideas for enhancing the linkages between those domains include: • Scenario development and deliberation • “Scenario planning is a discipline for rediscovering the… power of creative foresight in contexts of accelerated change, greater complexity and genuine uncertainty” (Wack, 1984). • Scenario development and deliberation serve many ends, but will be successful if those involved learn from the deliberations, and the quality and focus of public and bioethical discourse about the future of biotechnology is improved. • Real time technology assessment (RTTA) (Guston and Sarewitz, 2001) • Through empirical, conceptual, and historical studies as well as public engagement exercises, the goals of RTTA are: to assess possible societal impacts and outcomes; develop deliberative processes to identify potential impacts and chart paths to enhance desirable impacts and mitigate undesirable ones; and evaluate how the research agenda evolves.
  • 16. Abstract Visualization of protein structural data is an important aspect of protein research. Incorporation of genomic annotations into a protein structural context is a challenging problem, because genomic data is too large and dynamic to store on the client and mapping to protein structures is often nontrivial. To overcome these difficulties we have developed a suite of SOAP- based Web services and extended the commonly used structural visualization tools UCSF Chimera and Delano Scientific PyMOL via plugins. The initial services focus on (1) displaying both polymorphism and disease associated mutation data mapped to protein structures from arbitrary genes and (2) structural and functional analysis of protein structures using residue environment vectors. With these tools, users can perform sequence and structure based alignments, visualize conserved residues in protein structures using BLAST, predict catalytic residues using an SVM, predict protein function from structure, and visualize mutation data in SWISS-PROT and dbSNP. The plugins are distributed to academics, government and nonprofit organizations under a restricted open source license. The Web services are easily accessible from most programming languages using a standard SOAP API. Our services feature secure communication over SSL and high performance multi-threaded execution. They are built upon a mature networking library, Twisted, that allow for new services to easily be integrated. Services are self-described and documented automatically enabling rapid application development. The plugin extensions are developed completely in the Python programming language and are distributed at http://www.lifescienceweb.org/ The LSW Website contains developer tools and mailing lists, and we encourage other developers to extend their applications using our services. LifeScienceWeb Services: Integrated Analysis of Protein Structural Data Charles Moad*, Randy Heiland*, Sean D. Mooney *Pervasive Technology Labs Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics Indiana University, Indianapolis, Indiana 46202 Updates The annotations are currently updated every 2-3 months. Internally, we provide services for annotating genes or coordinates not in the PDB usually through a collaboration. For information on how to do this please contact Sean Mooney, sdmooney@iupui.edu. Acknowledgements CM and RH are funded through the IPCRES Initiative grant from the Lilly Endowment. SDM is funded from a grant from the Showalter Trust, an Indiana University Biomedical Research Grant and startup funds provided through INGEN. The Indiana Genomics Initiative (INGEN) is funded in part by the Lilly Endowment. The authors would like to thank the authors of UCSF Chimera and PyMOL for their help in extending their applications. You can download these tools from the following: • UCSF Chimera: http://www.cgl.ucsf.edu/chimera/ • Delano Scientific PyMOL: http://pymol.sourceforge.net Project Goals Web services are an efficient way to provide genomic data in the context of protein structural visualization tools. Our goal is to define a series of bioinformatic web services that can be used to extend protein structural visualization tools, and other extensible computational biology desktop applications. Our current focus is on extending UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) and Delano Scientific PyMOL(http://pymol.sourceforge.net). Figure 1: Screen grab of the current services list from http://www.lifescienceweb.org/. Services currently offered include: • ClustalW alignments • Mutation <-> PDB mapping • SVM based catalytic residue prediction • Sequence conservation based on PSI-BLAST PSSM Services Model Web services are an efficient way to provide genomic data in the context of protein structural visualization tools. Our goal is to define a set of bioinformatic web services that can be used to extend protein structural visualization tools, and other extensible computational biology desktop applications. We are currently focused on extending UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) and Delano Scientific PyMOL (http://pymol.sourceforge.net). Our services use the SOAP protocol and are currently developed using open source Python-based projects. Software Plugin Extensions We have extended UCSF Chimera and Delano Scientific PyMOL to access our services. The three primary services we provide now are: 1. Disease associated mutation and SNP to protein structure mapping and visualization 2. Protein sequence and structure residue analysis with PSI-BLAST and S- BLEST 3. Catalytic residue prediction using a support vector machine (Youn, E., et al. submitted) Installation Plugin installation is easy and can be performed for a user without root privileges. Currently, all platforms supported by UCSF Chimera and PyMOL are supported and include UNIX platforms, LINUX, Mac OS X and Windows XP. For either of the two clients supported (PyMOL or UCSF Chimera), simply follow the directions linked on the download page at http://www.lifescienceweb.org/. They will thereafter be available from the menu, as shown below. Figure 2: Running our tools from the client application, shown using PyMOL. Automated Sequence and Structural Analysis of Protein Structures Using PSI-BLAST and S-BLEST, we provide analysis of residue environments that match between protein structures in a queried database. Additionally, if the found environments represent similar structure or function classes, the environments that are most structurally associated to those environments are returned. This service is authenticated and SSL encrypted, and all coordinate data and analysis data are stored on our servers. Currently, users can query the ASTRAL 40 v1.69 and ASTRAL 95 v1.69 nonredundant domain datasets, as well as other commonly used nonredundant protein structure databases. Figure 3: MutDB controller window , shown using PyMOL. Controller features include (from the top): • Tabbed selection of query type and controller options. • Query entry text box and resulting hits from PDB shown below, with PDB ID, chain, residues, and TITLE of PDB. • Once a PDB ID above is selected, the coordinates are downloaded and the mutations from Swiss-Prot (SP) and dbSNP (SNP) are retrieved. The database source, type, position, mutation and wildtype flag are displayed. Upon selection, the mutation is highlighted in the coordinate visualization window. • Status window that displays the number of mutations or PDB coordinates found. • Mutation information window displays a link to the source (which opens in the browser), the position and annotations in that may be available, including PubMed ID (as link), phenotype and a link to MutDB.org. Figure 4: MutDB structure visualization window showing a highlighted mutation using PyMOL. Citations Dantzer J, Moad C, Heiland R, Mooney S. (2005) "MutDB services: interactive structural analysis of mutation data". Nucleic Acids Res., 33, W311-4. Peters B, Moad C, Youn E, Buffington K, Heiland R, Mooney S, “Identification of Similar Regions of Protein Structures Using Integrated Sequence and Structure Analysis Tools”. Submitted. Mooney, S.D., Liang, H.P., DeConde, R., Altman, R.B., Structural characterization of proteins using residue environments. Proteins, 2005. 61(4): p. 741-7. Figure 5: S-BLEST controller window shown using UCSF Chimera. On the right, the control box has (from top): • Tabs for selecting hits in database with matching environments (or significant sequence similarity using PSI-BLAST) or common functional annotations in the hits. • A pull down selection box showing the PDB ID’s with matching environments and the Z-score between the best environments. Upon selection the hit is downloaded and displayed in the visualization window (left). • A button to retrieve a ClustalW alignment between the the selected hit structure and the query. • The most significantly matched residue environments between the query and the hit. Displays Z-score, the matched residues, the ranking of that match (overall for that query residue environment) and the Manhattan distance. When residues are selected from this list, the coordinates in the visualization window are aligned using a the Chimera match command. • Below the windows a ClustalW alignment is shown Visualization of Mutations on Protein Structures We provide mapping between mutations and SNPs and protein structures. The mutations are mapped using Smith-Waterman based alignments. Swiss-Prot mutations and nonsynonymous SNPs in dbSNP are currently supported. See http://mutdb.org/ for a current list of the versions of each dataset we provide. Figure 6: S-BLEST controller window showing the function analysis tab using UCSF Chimera. LSW server client client WSDLs Twisted (twistedmatrix.com) pywebsvcs.sf.net SOAP (We will address service discovery in the future)
  • 17. Case-Macy Institute for Health Communications Curriculum Development A Dissemination Project Kathy Cole-Kelly, MS, MSW, Amy Friedman, Ted Parran, MD, Case Western Reserve University School of Medicine Introduction For the first time in a generation, all of the major licensure organizations in Medical Education have identified Doctor/Patient Communication Skills to be a core competency that education institutions need to be responsible for teaching and assessing. The LCME, AAMC, ACGME, and Institute of Medicine have each released reports in the past two years stressing the necessity for a longitudinally consistent, developmentally appropriate curriculum in physician/patient communications. In 1999, the Josiah Macy, Jr. Foundation funded a three-school consortium (Case, NYU and U. Mass) to conduct a demonstration project in health communications curriculum, implemented and evaluated across all four years of undergraduate medical education. The demonstration project proved to be so successful that the Macy Foundation has provided additional grant support to Case to design this faculty development program for medical educators. The purpose of this course is to disseminate principles regarding the teaching and evaluation of health communication skills to as many medical schools and teaching hospitals as possible. Target audience The program is designed for: • Leaders in undergraduate and graduate medical education with major responsibilities for communication skills training • Those working with curriculum development, implementation and evaluation • Faculty teams that represent both undergraduate (UGME) and graduate (GME) teaching Educational Design and Methodology Teaching and learning formats included: • Interactive presentations • Case studies • Small group discussions • Role-plays • Bedside and ambulatory communication skills teaching • Individual tutorials • Step-back exercises • Video taping and review • Focused feedback • Resources utilized included a clinical skills lab with standardized simulated patients and real patients Evaluation • The completion of a curriculum project in health communication at the UME or GME level. • The effectiveness of workshop participants as necessary skills in curriculum development, implementation and assessment in health communications. Workshop Goals After this program participants will be able to : Workshop #1 • Practice using various educational technologies (standardized patients, role play, OSCEs) in teaching and assessing communication skills • Develop educational approaches for assessing communications competencies • Develop strategies for fostering institutional endorsement of communication curriculum • Critique the major established models of doctor- patient communication Workshop #2 • Describe and develop effective methods for faculty development in the design and execution of communication curriculum • Critique strategies aimed at integrating health communications curriculum • Share participants communication curriculum products PRESENTATIONS RATED MOST HIGHLY Identifying Core Competencies to the Medical Interview Introduction to Assessment Strategies Regarding Communication Skills Individual consultation and project development sessions OSTE- Resident as Teacher Faculty Development – The Resident as Teacher Advanced Communication Skills Evaluation Strategies #2 TESTIMONIALS "Role-play session gave a new perspective that I think will be very useful.” “Wonderfully practical points and tools for encouragement.” “Great! Fun speakers to watch and listen to.” “Good interactive session (objective writing with a script).” "Role play was effective-shared 'practical' aspects of teaching patients.” “Great combination of enthusiasm, knowledge, and demonstration of knowing what you know and honestly of knowing what you don't know”. “An atmosphere of like-minded people.” "I appreciated having a huge amount of totally on topic resources gathered by organization and handed to me in a binder”. “I liked the small groups, loosely organized to meet individual learning goals”. “Really enjoyed the sharing of resources/ideas…thank you! “Loved it! Loved it! Thank you”! 2003/2004 Curricular Projects • Case Macy Institute for Health Communications Curriculum Development • Incorporating Professional Communication Training into the Medical School Curriculum • Start Early and Start Strong: Teaching Communication Skills in the Formative Pre-Clinical Years • Residents as Teachers • Graphic web-based information for low literacy sarcoidosis patients: a parallel group randomized trial • Knowledge Map Promotes Integration of Medical School Communication Skills Training • A Faculty Development Workshop: Communication and Interpersonal Skills • Healing Voices Project of the New River Health Association • A Proposed Basic Interviewing Communication Curriculum for a Multicultural Primary Care Residency Program • Doctor Patient Communication Competencies Institutions Enrolled To Date Georgetown University Medical Center Henry Ford Health Systems MetroHealth Medical Center Michigan State University Ohio State University Oregon Health and Sciences University University of Miami University of South Dakota SOM University of West Virginia Vancouver University Vanderbilt University Washington University Albert Einstein College of Medicine Geisinger Health System Christiana Care Health System Medical College of Georgia The Cleveland Clinic Foundation Geisinger Medical Center SUNY Upstate Medical University Wright State University UCSD School of Medicine University of British Columbia Medical School Cook County Hospital/Rush Medical College Stroger Hospital of Cook County Genesys Regional Medical Center Jefferson Medical College New Jersey Medical School Northern Ontario School of Medicine Faculty Theodore V. Parran Jr., MD Kathy Cole-Kelly, MS, MSW Philip A. Anderson, MD Holly Gerzina, MEd Marianna G. Hewson, PhD J. Harry Isaacson, MD, FACP Klara Papp, PhD Clint W. Snyder, PhD
  • 18. Acknowledgments We thank Miss Keren Mishra for her contribution in the knowledge management research for this project, Harry Koponen for gathering data requirements, Leo Kwok and Hashank Thilakawardhana for the assistance of the CBT development and Andrew Cazzaniga for his work on the Knowledge Audit Framework. Introduction Most research in cost estimating mainly focus on improving costing models and methodologies. The ICOST Project is about the integration of internal Costing practices within industry, primarily Commercial Cost Estimation with Technical Cost Engineering. Conclusions • Identified the issues within internal costing practices •Assisted in integrating commercial and engineering disciplines • Successful three years of Strategic research • Improved scientific understanding about cost estimating • Active industry participation • Contributed to improve collaboration and further research and development opportunities. ICOST-Improving the Internal Cost Estimating Practices at Conceptual Design Stage PhD Researcher: Petros Souchoroukov, Supervisor: Dr. Rajkumar Roy — Enterprise Integration, School of Industrial and Manufacturing Systems, Cranfield University Fig. 7. The Functional-Based Costing Framework. For further information Please contact p.souchoroukov@cranfield.ac.uk and r.roy@cranfield.ac.uk. More information on this and related projects can be obtained at http://www.cranfield.ac.uk/sims/cim/people/roy.htm Fig. 1. Involvement of Commercial and Engineering Disciplines in the Product Life Cycle. Product Life cycle Involvement Concept Design Manufacture Operation Disposal Commercial Discipline Engineering Discipline 80% Cost Commitment Deliverables 1. AS-IS Industry Best Practice Report (Fig. 2); 2. Materials Cost Estimating Hand Book; 3. Two CBTs on cost estimating of injection moulding and metal forming operations. (Fig. 3); 4. A framework on lateral transfer of cost estimating knowledge between engineers and people with commercial background (Fig.4); 5. Data and Information requirement for Cost Engineering (Fig 5) 6. Functional-based costing framework (Fig 6 & 7) Fig. 2. Best Practice in Cost Estimating. Raw Materials + Raw Material Specification Bough Out Parts + Standard Bought Out Part Specification + Subcontract Item Specification Raw Material Scrap + Raw Material Scrap Resale Value Raw Material Rate + Volatility of the Raw Material Bough Out Part Rate + Standard Bought Out Part Rate + Subcontract Item Rate Bough Out Part Scrap Material Overhead Cost + Bought Out Material Inventory Cost + Raw Material Inventory Cost Material Usage + Part Dimensions + Raw Materials Usage + Standard Bought Out Part Quantity + Subcontract Item Quantity + Weigh of the Part Materials Fig. 3: CBT template created for Impression-die drop hammer forging operations. Fig. 4. Lateral Transfer of Costing Knowledge. Building knowledge base Knowledge Type Traditional Categorisation Process knowledge Engineering Supplier knowledge Commercial Risk knowledge Commercial Material knowledge Engineering Costing process knowledge Commercial Product knowledge Engineering Company strategy knowledge Commercial Design knowledge Engineering Market trend knowledge Commercial Contact knowledge Engineering/Commercial. Ref: ICOST. Roy, Souchoroukov, Mishra Commercial Engineering Hybrid Variable and fixed price components Rental, lease or buy contracts Activity Based Costing Unit price bid unbalancing, 'front-end loading' Earned value WBS and Accounting codes Manadatory government legistlation Capitalequipment tax law Key cost controltechniques Leadership and nagotiation skills Learning curves, Contract arrangement and adminsitration. Project control methods. Opportunity costing Terminology, Questioning Quotation analysis form trading Optimisation Parametric estimating Service to purchase Converstion units Pricing Change control Mechanics of compensation Proposalmemorandum Tooling cost Fringe and burdens Scope of work Earned value management Factored estimates Forecasting Labour productivity Estimating Rules Regression analysis Process knowledge Abilityto read engineering documents Environmental costing Material Knowledge Accounts and WBS codes Planning knowledge, Product knowledge Office software Bid and contractor selection Designknowledge Workload reporting Supplier knowledge Enterprise software, Risk knowledge Report writing Costing process knowledge Presentationskills, Knowledge of company strategy decision making, Market trend knowledge Resourcefulness and problem solving Team working Assumption and exclusions compilation Model development throughsoftware Budgeting Estimationmarketing skills, Benchmarking Knowledge capture and representation Generating CERs (Cost Estimating Relationships) sensitivity analysis Managing data flows through applicationof costing software problem areas in cost esimating, indirect costs. Contact knowledge Product Lifecyles phases Accuracy of estimationthrough product lifecycle and suitable estimationmethods Data collection and management, Step 1 15 Knowledge Areas In Cost Estimating 1 Supplier Knowledge 2 Risk Knowledge 3 Costing Process Knowledge 4 Company Strategy Knowledge 5 Contact Knowledge 6 Process Knowledge 7 Material Knowledge 8 Product Knowledge 9 Design Knowledge 10 Market Trends Knowledge 11 Project Management Knowledge 12 Standard and Legal Knowledge 13 Methods and Tools Knowledge 14 IT. and Communications Skills Knowledge 15 Product Lifecycle Knowledge Requirements derived through audit Step2 Step 3 MIN Requirements Function 1 Function 2 Function 3 MAX MAX MINMIN MAX COST OF FUNCTIONCOST OF FUNCTION Estimate Estimate Estimate DATA ACQUISITIONDATA ACQUISITION Fig. 5. Data Infrastructure for Cost Estimating in Manufacture Fig. 6. Using Functional Decomposition Techniques and Value Engineering to create relationships between functions and product components to assist cost estimating.