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baoilleach committed Jun 3, 2011
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12 changes: 6 additions & 6 deletions paper.tex
Expand Up @@ -330,7 +330,7 @@ \section*{Background}
availability of the underlying scientific data, standards (to exchange availability of the underlying scientific data, standards (to exchange
data), and code (to reproduce results). All three of these goals stem data), and code (to reproduce results). All three of these goals stem
from the fundamental tenants of the scientific method for data sharing from the fundamental tenants of the scientific method for data sharing
and reproducibilty. and reproducibility.


The Blue Obelisk was first described in the CDK News \cite{CDKNewsBO} and The Blue Obelisk was first described in the CDK News \cite{CDKNewsBO} and
later as a formal paper by Guha et al.\cite{Guha2006} in later as a formal paper by Guha et al.\cite{Guha2006} in
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graphical editors while Avogadro is a 3D molecular editor and viewer aimed at graphical editors while Avogadro is a 3D molecular editor and viewer aimed at
preparing and analysing computational chemistry calculations. Both preparing and analysing computational chemistry calculations. Both
projects are designed to be extended or scripted by users through projects are designed to be extended or scripted by users through
the provision of a plugin architective and scripting support (using the provision of a plugin architecture and scripting support (using
Bioclipse Scripting Language~\cite{Bioclipse2}, or Python in the case Bioclipse Scripting Language~\cite{Bioclipse2}, or Python in the case
of Avogadro). An interesting aspect of both Avogadro and Bioclipse is of Avogadro). An interesting aspect of both Avogadro and Bioclipse is
that they share some developers with the underlying toolkits and this that they share some developers with the underlying toolkits and this
Expand All @@ -527,7 +527,7 @@ \subsection*{Second-generation tools}


\subsection*{Computational chemistry analysis} \subsection*{Computational chemistry analysis}


Another area where the Blue Obelisk has had a signficant impact in the Another area where the Blue Obelisk has had a significant impact in the
past five years is in supporting past five years is in supporting
quantum chemistry calculations and in interpreting their results. quantum chemistry calculations and in interpreting their results.
Electronic structure calculations have a long tradition in the Electronic structure calculations have a long tradition in the
Expand Down Expand Up @@ -572,7 +572,7 @@ \subsection*{Computational chemistry analysis}
comparison to experimental data. QMForge~\cite{WebQMForge} provides comparison to experimental data. QMForge~\cite{WebQMForge} provides
a GUI for various electronic structure analyses such as Frenking's charge a GUI for various electronic structure analyses such as Frenking's charge
decomposition analysis~\cite{Frenking} and Mulliken or C-squared analyses decomposition analysis~\cite{Frenking} and Mulliken or C-squared analyses
on user-defined molecular fragments. QMForge also provides a rudamentary on user-defined molecular fragments. QMForge also provides a rudimentary
Cartesian coordinate editor allowing molecular structures to be saved via Open Babel. Cartesian coordinate editor allowing molecular structures to be saved via Open Babel.


The Quixote project epitomises the full use of the Blue Obelisk The Quixote project epitomises the full use of the Blue Obelisk
Expand Down Expand Up @@ -742,7 +742,7 @@ \subsection*{The business end}
mechanisms for releasing Open Source software mechanisms for releasing Open Source software
without violating confidentiality or incurring liability. without violating confidentiality or incurring liability.
A phrase from the meeting A phrase from the meeting
summed it up: ``The ice is beginning to melt'', signifiying that we can summed it up: ``The ice is beginning to melt'', signifying that we can
expect a rapid increase in industry's interest expect a rapid increase in industry's interest
in Open Source. in Open Source.


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literature retrieval), there are many RDF tools literature retrieval), there are many RDF tools
(e.g. SIMILE, Apache Jena) which can operate in machine memory and provide (e.g. SIMILE, Apache Jena) which can operate in machine memory and provide
the flexibility that RDF offers. For larger the flexibility that RDF offers. For larger
systems, it is unclear whtether complete RDF solutions (e.g. Virtuoso) systems, it is unclear whether complete RDF solutions (e.g. Virtuoso)
will be satisfactory or whether a hybrid system will be satisfactory or whether a hybrid system
based on name-value pairs (e.g. CouchDB, MongoDB) will be sufficient. based on name-value pairs (e.g. CouchDB, MongoDB) will be sufficient.


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2 changes: 1 addition & 1 deletion websites.bib
Expand Up @@ -104,7 +104,7 @@ @webpage{WebOpenData
url = {http://www.opendefinition.org/licenses/#Data} url = {http://www.opendefinition.org/licenses/#Data}
} }
@webpage{WebCrystalEye, @webpage{WebCrystalEye,
title = {Crystal Eye}, title = {CrystalEye},
url = {http://wwmm.ch.cam.ac.uk/crystaleye/} url = {http://wwmm.ch.cam.ac.uk/crystaleye/}
} }
@webpage{WebPubChemStandardizer, @webpage{WebPubChemStandardizer,
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