1. COMUNICACIÓN
CIENTÍTICA

3. 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)

4. 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.

5. • 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

6. 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".

7. 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)

8. 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.

9. 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").

10. 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.

11. 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.

12. 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.

13. 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.

14. 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:

15. 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

16. 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.

17. 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)

18. 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

19. 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.