speling correction

communication/Bioinformatics/jflow_BIOINF.tex

@@ -25,18 +25,19 @@ Castanet-Tolosan Cedex, France.}
 
 \section{Summary:}
 Biologists produce large data sets and are in demand of rich and simple
-web portals in which they can upload and analyse their files. Providing such
-tools requires to mask the complexity induced by the needed High Perfomance
+web portals in which they can upload and analyze their files. Providing such
+tools requires to mask the complexity induced by the needed High Performance
 Computing (HPC) environment. The connexion between interface and computing
 infrastructure is usually specific to each portal. With Jflow, we introduce
-a Workflow Management System (WMS), composed of Jquery plugins which can easily be
+a Workflow Management System (WMS), composed of Jquery plug-ins which can easily
+be
 embedded in any web application and a Python library providing all requested
 features to setup, run and monitor workflows.
 
 \section{Availability:}
 Jflow is available under the GNU General Public License (GPL) at
-http://bioinfo.genotoul.fr/jflow. The package is comming with full
-documentation, quickstart and a running test portal.
+http://bioinfo.genotoul.fr/jflow. The package is coming with full
+documentation, quick start and a running test portal.
 
 \section{Contact:}
 \href{support.genopole@toulouse.inra.fr}{support.genopole@toulouse.inra.fr}
@@ -44,7 +45,7 @@ documentation, quickstart and a running test portal.
 
 \section{Introduction}
 
-Building rich web environments aimed at helping scientists analyse their data is
+Building rich web environments aimed at helping scientists analyze their data is
 a common trend in bioinformatics. Specialized web portals such as MG-RAST (Meyer
 et al., 2008), MetaVir (Roux et al., 2011) or NG6 (Mariette et al., 2012) provide
 multiple services and analysis tools in an integrated manner for specific
@@ -65,12 +66,12 @@ definition or check file formats.
 
 To our knowledge, Jflow, presented in this article, is the only WMS designed to
 be embedded in any web application, thanks to its organization as five Jquery
-(http://jquery.com/) plugins.
+(http://jquery.com/) plug-ins.
 
 
 \section{Methods}
 
-Jflow user interface gathers five Jquery plugins providing user oriented views.
+Jflow user interface gathers five Jquery plug-ins providing user oriented views.
 
 \begin{itemize}
   \item \textit{availablewf} lists all runnable workflows accessible to users,
@@ -80,23 +81,23 @@ Jflow user interface gathers five Jquery plugins providing user oriented views.
   \item \textit{wfoutputs} displays all outputs produced by the workflow
   organized per component,
   \item \textit{wfstatus} shows the workflow execution state as a list or an
-  execution graph. The graph visualisation uses the Cytoscape web JavaScript
-  plugin (Lopes et al., 2010).
+  execution graph. The graph visualization uses the Cytoscape web JavaScript
+  plug-in (Lopes et al., 2010).
 \end{itemize}
 
-The plugins give access to multiple communication methods and events. They
+The plug ins give access to multiple communication methods and events. They
 interact with the server side through Jflow's REST API, running under a cherrypy
 (http://www.cherrypy.org/) web server. The included server uses the JSONP
 communication technique enabling cross-domain requests. 
 
-To be available from the different Jquery plugins, the workflows have to be
+To be available from the different Jquery plug-ins, the workflows have to be
 implemented using the Jflow API. A Jflow component is in charge of an execution
 step. Adding a component to the system requires to write a Python
 \textit{Component} subclass. In Jflow, different solutions are available to ease
 component creation. To wrap a single command line, the developer can give a
 position or a flag for each parameter. Jflow also embeds an XML parser which
-allows to run geniune Mobyle (Neron et al., 2009) components. Finally, to
-allow developpers to integrate components from other WMS, Jflow provides a class
+allows to run genuine Mobyle (Neron et al., 2009) components. Finally, to
+allow developers to integrate components from other WMS, Jflow provides a class
 skeleton. This class only requires to implement the parsing step. A workflow
 chains several components. A Jflow workflow is built as a \textit{Workflow}
 subclass. Components are added to the workflow as variables and chained linking
@@ -112,14 +113,14 @@ data type compliance for each parameter. Job submission, status
 checking and error handling, rely on Makeflow (Albrecht et al., 2012) and
 weaver (Bui et al., 2012). Therefore Jflow manages error recovery and supports
 most distributed resource management systems (Condor, SGE, Work Queue or a
-single multicore machine, \ldots). Replacing Makeflow by an other job submiter
+single multi core machine, \ldots). Replacing Makeflow by an other job submitter
 requires to implement a new \textit{Engine} subclass. This class creates and
 execute the workflow directed acyclic graph (DAG).
 
 
 \section{Example}
 
-Jflow user interface has been designed to allow an easy integration in mashup
+Jflow user interface has been designed to allow an easy integration in mash up
 web applications. Hereunder, we present its integration in NG6, which provides a
 user-friendly interface to process, store and download high-throughput
 sequencing data. The environment displays sequencing runs as a table. From
@@ -127,21 +128,22 @@ this view, the user can add new data by running workflows in charge of loading
 the data and checking its quality. Different workflows are available considering
 data type and sequencing technology.
 
-Workflows are listed by the \textit{availablewf} plugin built within a
+Workflows are listed by the \textit{availablewf} plug-in built within a
 NG6 modal box. It requests the server to get the workflows implemented by the
 developer. A \textit{select.availablewf} event thrown by the
-\textit{availablewf} plugin is listened and catched to generate the parameter
-form using the \textit{wfform} plugin. Considering the parameter type, Jflow
+\textit{availablewf} plug-in is listened and caught to generate the parameter
+form using the \textit{wfform} plug-in. Considering the parameter type, Jflow
 adapts its display. For example, a date is displayed as a calendar and a boolean
-as a checkbox.
+as a check box.
 
 Biologists use NG6 to check sequencing reads quality, including experimental
 samples contamination measure (quantification/search). The first input of this
 analysis is the contaminant reference genome fasta file, displayed as a file
 selector. The second input is a parameter set describing the biological samples.
-It includes the read files and metadata such as sample name, tissue and
-developpement stage. To help biologists populate it, Jflow uses a structured
-data input rendered by the \textit{wfform} plugin as a spreadsheet. It allows to
+It includes the read files and meta data such as sample name, tissue and
+development stage. To help biologists populate it, Jflow uses a structured
+data input rendered by the \textit{wfform} plug-in as a spreadsheet. It allows
+to
 copy and paste multiple lines. Jflow iterates then on the table content to
 launch each sample processing.
 
@@ -149,22 +151,25 @@ launch each sample processing.
 	\centering
 	\includegraphics[width=\linewidth]{jflow_example.png}
 	\caption{\textbf{Jflow integration:} (a) A piece of the NG6 HTML code source in
-	which is positioned an empty div to build the \textit{activewf} plugin and a
-	modal box for the \textit{wfstatus} plugin. (b) The Jquery code in charge to
-	build Jflow plugins and manage user action. When the \textit{select.activewf}
+	which is positioned an empty div to build the \textit{activewf} plug-in
+and a
+	modal box for the \textit{wfstatus} plug-in. (b) The Jquery code in
+charge to
+	build Jflow plug-ins and manage user action. When the
+\textit{select.activewf}
 	event is thrown from \textit{activewf-div}, a function is called with two
 	parameters: \textit{event} and \textit{workflow}. The last parameter stores
 	all the workflow's information, such as its name and its id, used in this
 	example to update the modal box title and to build the \textit{wfstatus}
-	plugin. (c) The workflow status displayed as a graph.}
+	plug-in. (c) The workflow status displayed as a graph.}
 	\label{fig::jflow_example}
 \end{figure}
 
 
 To monitor running workflows, NG6 provides a table in a specific page. The
-table is filled by the \textit{activewf} plugin. In the same way as
+table is filled by the \textit{activewf} plug-in. In the same way as
 described above, the \textit{wfstatus} is built on a modal box when a
-\textit{select.activewf} event is thrown by the \textit{activewf} plugin, as
+\textit{select.activewf} event is thrown by the \textit{activewf} plug-in, as
 presented in Figure~\ref{fig::jflow_example}. This view shows the workflow's
 execution graph where nodes represent components and edges links between inputs
 and outputs.