text:
\section{Introduction}\label{sec:intro}

Genome sequencing methodologies have led to a significant increase in the amount of data to be processed and analyzed by Bioinformatics experiments.
Consequently, this led to an increase in the demand for their scalable execution.
Most bioinformatics studies aim to extract information from DNA sequences and can be classified as \textit{in silico} experiments.
\textit{In silico} comprise mathematical and computational models that simulate real-world situations;
they depend on the use of computational resources and specialized technologies for their execution.
Simulations often require the composition of several applications, or activities, which have dependencies and manipulate large amounts of data.
These aspects make it difficult to manage and control \textit{in silico} experiments.
Due to the complexity of simulation-based scientific experiments, it is necessary to use approaches that support their design, execution, and analysis, such as scientific workflows \cite{Deelman2009}.
A scientific workflow is an abstraction that formalizes the composition of several activities through data set production and consumption.
Each activity corresponds to a computational application, and the dependencies between them represent the execution data flow, in which the output of one activity is input to another.

Scientific Workflow Management Systems (SWfMS) can be used to manage the various steps of the life-cycle of a scientific workflow, i.e. design, execution, and analysis.
SWfMS can be deployed in high-performance computing (HPC) environments, such as clusters, clouds, or computational grids.
They can also capture and store provenance information.
Provenance records the process of deriving data from the execution of a workflow. For this reason, provenance describes the history of a given experiment, ensuring its reliability, reproducibility, and reuse \cite{Freire2008}.
Provenance may also contain computational and scientific domain data, making it an important resource for the analysis of the computational behavior of an experiment and its scientific results.
By combining computational and domain data, it is possible, for example, to make optimizations in the experiment as well as predictions for execution time and the amount of storage that it will require.

In this work, we present BioWorkbench: a framework that couples scientific workflow management and provenance data analytics for managing bioinformatics experiments in HPC environments.
BioWorkbench integrates a set of tools that cover the process of modeling a bioinformatics experiment, including a provenance data analytics interface, transparently to the user.
For managing scientific workflows, we use SWfMS Swift \cite{Wilde2011}, because of the support that the system provides for executing workflows in different HPC environments transparently and also due to its scalability \cite{Wilde2009}.
Provenance data related to workflow performance and resulting data associated with the application area of the experiment are automatically collected by the framework.
As part of the framework, we have developed a web application where workflow results are presented in a data analytics interface, from the abstraction of a set of queries to the provenance database, supporting the process of analysis by the scientists.
We also demonstrate that it is possible to use machine learning techniques to extract relations from provenance data that are not readily detected, as well as to predict and classify the execution time of workflows.
In this way, BioWorkbench consolidates various activities related to scientific workflow execution analysis in a single tool.

We evaluated the BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow.
Each case study has its own characteristics. However, the three allowed the evaluation of aspects related to performance gains and provenance management covered by our framework.
We show results where we obtained a reduction of up to 98.9\% in the total execution time, in the case of SwiftPhylo, decreasing from $\sim$13.35 hours to $\sim$8 minutes. Also, we demonstrate that with the provenance collected through the framework, we can provide useful results to the user who does not need to inspect files manually to extract this information.

\section{Related Work}\label{sec:related}

In general, our proposal addresses aspects related to the modeling of bioinformatics workflows, their parallel execution in high-performance computing environments, as well as provenance data analytics, including predictions on computational resource usage. Here we compare BioWorkbench to related solutions from these different points of view.

There are a variety of SWfMS for modeling and executing workflows in different application areas. Some of them allow execution in high-performance computing environments. Among them, we highlight Pegasus~\cite{Deelman2015}, which enables the specification of workflows through the XML format. The provenance is managed through the Wings/Pegasus framework \cite{Wings2008}, and can be queried using the SPARQL language.
Askalon \cite{Nadeem2007} allows the definition of the workflow through a graphical interface, using UML diagrams or the XML format. Workflow performance monitoring information is used by a service that supports planning the execution of activities.
Taverna \cite{Wolstencroft2013} is an SWfMS widely used by the bioinformatics community, where workflow activities usually comprise web services. Parallel execution has an optimization engine that identifies and simplifies complex parts of the workflow structure \cite{Cohen2014}.
Provenance is collected and stored in a database and workflows can be shared through the \textit{myExperiment}\footnote {https://www.myexperiment.org/home} platform.
With a focus on cloud environments, SciCumulus \cite{silva2014} is a SWfMS based on relational algebra for workflow definition that uses a provenance database for configuration and monitoring of executions. It is distinct in that it allows provenance queries to be made during the execution of the experiment. Compared with these solutions, we use the Swift SWfMS because it transparently supports the execution of workflows in different HPC environments, it has been shown that it has a high potential for scalability \cite{Wilde2009}, and it supports provenance management \cite{Gadelha2012}. In addition, it supports workflow patterns such as conditional execution and iterations that not supported by similar systems such as Pegasus \cite{Deelman2015}. It also evaluates the workflow dynamically, possibly changing task execution sites for efficiency of reliability.

Juve et al. \cite{Juve2013} present Wfprof, a tool for collecting and summarizing performance metrics of workflow activities. Wfprof was coupled to the Pegasus SWfMS to identify the complexity level of different workflows and how computational and I/O intensive they are.
In \cite{Krol2016}, an approach for analyzing the performance of workflows executed with the Pegasus SWfMS is presented, which also studies the effect of input parameters on task performance.
The PDB \cite{Liew2011} presents an approach that collects and stores computational data in a database for planning the execution of workflows that occur in memory and out-of-core.
ParaTrac \cite{Dun2010} is a data-intensive workflow profiler with an interface that allows its use by different SWfMS. ParaTrac uses the Linux {\em taskstats} interface to collect memory usage, CPU and runtime statistics, and the FUSE file system to record the amount of data that is passed between workflow activities.
In \cite{silvaintegrating}, provenance data is integrated into the TAU code profiling tool, allowing the performance visualization of workflows executed with the Scicumulus SWfMS. This work aims to carry out the monitoring and profiling for the detection of anomalies in the execution of large-scale scientific workflows.
Visionary \cite{Oliveira2017} is a framework for analysis and visualization of provenance data with the support of ontology and complex networks techniques. However, the work is focused on the analysis of the provenance graph and does not include domain data or predictive analysis. Our approach provides profiling analysis of the execution of workflows from the provenance collected by Swift, in addition to being able to aggregate domain data from the experiment. We show that it is possible to combine provenance and domain data for more detailed analysis. Also, we demonstrate that these analyses can benefit from machine learning techniques for extracting relevant information and predicting computational resource consumption that are not readily detected by queries and statistics from the provenance database.

Focusing on bioinformatics workflows, the WEP \cite{Wep2013} tool enables the modularization of the workflow, allowing the user to execute the entire experiment or just the necessary activities. In addition, WEP also allows access to intermediate files and final results through the web interface. It does not provide detailed computational profiling or parallel and distributed execution features as does BioWorkbench.
ADAM \cite{Adam2013} is a scalable API for genome processing workflows that uses Spark \cite{Zaharia2016}, a framework for managing Big Data. Both tools allow for running experiments in HPC environments, but they implement parallelism at a lower level, within the activities. ADAM requires the API functions to be implemented according to Spark's model of computation, using distributed datasets and applying  actions and transformations, such as map and reduce, to these. BioWorkbench allows for the parallel composition of workflow activities that may be implemented using different models of computation. Therefore, BioWorkbench is more flexible in incorporating existing and legacy bioinformatics tools into its workflows.

\section{Materials and Methods}\label{sec:desimpl}

\subsection{Design and implementation}\label{subsec:desimpl}

BioWorkbench
was developed to support users in the specification process of an experiment, the experiment execution in HPC resources, the management of consumed and produced data, and the analysis of its execution results.
BioWorkbench uses a SWfMS for definition and execution of bioinformatics workflows, and a web application for provenance data analytics. Figure \ref{fig:arq_bio} shows the layered conceptual architecture of BioWorkbench.
It should be noted that this architecture is available for demonstration in a Docker \cite{docker} software container\footnote{Available at https://hub.docker.com/r/malumondelli/rasflow/}
that allows one to reproduce the computational environment described and used in this work.
In this way, BioWorkbench supports reproducibility at two levels: the computational environment and the data derivation history (through provenance information).
In the following subsections, we detail the features and functionalities of each layer.

\begin{figure*}[!htb]
	\begin{center}
	    \includegraphics[width=0.8\linewidth]{img/bioWorkbenchArq}
	\end{center}
    \caption{\label{fig:arq_bio}BioWorkbench layered conceptual architecture.}
\end{figure*}

\subsection{Specification and Execution Layer}\label{subsec:management}

This layer uses Swift \cite{Wilde2011}, a SWfMS that allows users to specify workflows through a high-level scripting language and execute them in different HPC environments.
The scripting language follows functional programming principles that allow, for example, all operations to have a well-defined set of inputs and outputs and all the variables to be write-once.
Through the Swift scripting language, datasets are declared as variables of primitive types, such as floats, integers, and strings; mapped types, which associate a variable with persistent files; and collections, which include arrays and structures.
The activities that comprise a workflow are represented as \textit{app functions}, responsible for specifying how applications outside Swift should be executed, their inputs and outputs. \textit{Compound functions} are used to form more complex data flows and can include calls to \textit{app functions}, loops, and conditionals.
All expressions in a Swift script whose data dependencies are met are evaluated in parallel. Through the \textit{foreach} loop instruction, it is possible to process all elements of an array in parallel.
The independence of locality is another essential feature of Swift and allows the same workflow to run on different computing resources without the need to change its specification.
Therefore, Swift supports the management and parallel execution of these workflows in HPC environments.
This layer is then responsible for managing, through Swift, the execution of the workflow in the computational resources to which the user has access and intends to use.

\subsection{Data Layer}\label{subsec:data}

The data layer handles the provenance of workflow executions.
For this, the layer also uses Swift because of its capability of tracking provenance of the workflow execution behavior as well as its activities \cite{Gadelha2011}.
All information regarding the execution of a workflow in Swift, or its provenance, is recorded in a log file. Each of the activities executed by a workflow also has a log file, called {\em wrapper log}. These files contain information such as the computational aspects of activity executions: the number of read and write operations to the file system, CPU and memory utilization, and other details.
Also, the log files keep track of the files consumed and produced by each of the activities, analyzing the data derivation process of the experiment possible.

To provide access to provenance, Swift has a mechanism that processes these log files, filters the entries that contain provenance data, and exports this information to a relational SQL database (SQLite) \cite{Mondelli2016a}.
The main entities of the Swift provenance model are presented in Figure \ref{fig:sqlite}.
The \textit{script\_run} entity contains the description of the execution of a workflow; the \textit{app\_exec} entity describes aspects of the activities associated with a workflow, and \textit{resource\_usage} has the computational information of the executions of those activities. The \textit{file} entity has the record of all the files consumed and generated by the execution of a workflow; \textit{staged\_in} and \textit{staged\_out} entities, in turn, record the process of deriving data, relating the files to the executions of the activities.

Workflow executions may also produce domain provenance data related to the application area of the experiment.
Domain data comprises the results obtained by the execution of computational activities of the workflow or parameters used by them. Usually, these results are stored in files.
In bioinformatics, for example, the domain data from a sequence alignment experiment may consist of rates or scores, indicating to the scientist the accuracy of the alignment. Thus, domain data is data essential for bioinformatics analyses.
In order to store the domain data along with the provenance Swift collects by default, this layer can use a set of extractors developed for collecting domain data, or annotations, from some bioinformatics applications.
Extractors consist of scripts that collect domain data from the files produced by the activities, and that can support the analysis process by the user.
These annotations can be exported to the provenance database and associated with the respective workflow or particular activity execution in the form of key-value pairs.
The provenance database contains a set of annotation entities, which relate to the model presented, giving more flexibility to store information that is not explicitly defined in the schema.
More entities can be added to the database allowing for better management of the results of the workflow execution, depending on the type of annotation to be stored. In the section \ref{sec:evaluation}, we describe some of the entities that have been added to the Swift provenance model in order to provide better domain data management of a case study. Once the provenance data is stored in the database, they can be accessed by the {\em Analytics Layer}, described in the next subsection, in order to facilitate access and visualization of the results.

\begin{figure*}[htb]
	\begin{center}
	    \includegraphics[width=0.6\linewidth]{img/sqlite}
	\end{center}
    \caption{\label{fig:sqlite}Main entities in the conceptual model of the Swift provenance database.}
\end{figure*}

\subsection{Analytics Layer}\label{subsec:vis}

This layer abstracts a set of database queries from the data layer, facilitating the access to the provenance of the workflow.
The main goal is to provide the user with a more intuitive way to understand the computational profile of the experiment and to analyze the domain results.
Without the set of query abstractions that we propose in this layer, the user would have to manipulate both the provenance database and the output files of the experiment.
As part of the query abstraction process, we use R scripts that connect to the provenance database, perform the queries and extract useful statistics for analysis.
The results of the queries retrieve data that are presented to the user through graphs and tables in a web interface.
This interface was developed using the Shiny library\footnote{https://shiny.rstudio.com/}, which allows an analysis implemented in R to be accessed via web applications interactively.
The interface provides a menu so that researchers can carry out their analyses. This menu, shown in Figure \ref{fig:interface1}, allows them to select a workflow execution from the list of executions available for analysis.
The charts and tables are updated according to the chosen options.
Computational analyses present graphs such as the execution time of the activities, the percentage of CPU used by each of them, and the parallelism level of the workflow. Information about the total time of execution of a workflow, the number of executed activities, and whether the workflow ended successfully is also displayed.
Domain analyses provide information about the scientific domain of the workflow.
In the RASflow case study, presented below, this information includes data on the genetic mutations found in patients.

\subsubsection{Machine Learning Techniques in Support of Provenance Analysis}\label{subsubsec:ml}

Provenance data can be a useful resource for a wide variety of machine learning algorithms for data mining.
The application of machine learning algorithms consists in statistical analyses and automatic generation of models.
These models can produce: (i) predictions, allowing scientists to estimate results or behavior based on some previous information; and (ii) learning, related to the discovery of implicit relations that are not always detected by human observations or simple queries.
From a data set of interest, the models take into account a set of attributes that must be passed as input to produce an output, which in this case can be a prediction.
If the output receives values in a continuous numeric range, the models comprise a set of mathematical and logical operators, resulting in a regression problem.
On the other hand, if these outputs can only assume a previously defined set of discrete values, named classes, then the models map the input attributes in classes, resulting in a classification problem.
In bioinformatics workflows, for example, we can have as input to a machine learning algorithm a set of attributes such as genome sequence size, statistics on memory usage and CPU to analyze them. The output of this algorithm may be the prediction of the execution time. In comparative genomics, more specifically, behaviors or relations such as the required computational time, memory or space for comparing an arbitrary number of genomes can also be predicted.

In this work, as part of the analysis process, we combine provenance data and machine learning by using the free software Weka \cite{hall2009weka}.
Weka provides a broad set of machine learning and statistical analysis techniques for data mining tasks.
These techniques include rule- and tree-based algorithms, such as \textit{J48, BFTree, OneR}, in which the values of all input and output attributes are previously known.
To evaluate the performance of a generated model we used metrics related to the differences between the previously known values (which we can call ``real values'') and the predicted values of the output attribute.
Regarding the generalization capacity of the model, whenever possible the algorithms were evaluated using the methodology known as ``cross-validation,'' with 10 folds \cite{arlot2010survey}.

Therefore, we hope to indicate some relevant opportunities that arise from the association between provenance data and machine learning techniques, both in the specific case of SwiftGECKO, presented below, and in the scientific workflows field.
Also, these experiments can contribute to the understanding of workflow behavior, being useful, for instance, in guiding optimization efforts and parameter configurations.
It is worth mentioning that the techniques used in this work were applied using the original algorithm attributes proposed in the software Weka, except for the minimum number of tuples classified at a time by the models.
This attribute provides a minimum amount of tuples that need to be simultaneously classified by a model for each possible input parameters configuration, thus influencing in the model complexity. The values of this parameter were changed to increase the legibility of the obtained results.
A more detailed description of the algorithms included in Weka, together with some statistical information that we did not include in this work for scope reasons, can be found in papers such as \cite{arora2012comparative} and \cite{sharma2013weka}.

\begin{figure*}[!htb]
	\begin{center}
	    \includegraphics[width=1.0\linewidth]{img/interface1}
	\end{center}
    \caption{\label{fig:interface1}BioWorkbench web interface displaying information about a RASopathy analysis workflow (RASflow) execution.}
\end{figure*}

\section{Results and Discussion}\label{sec:evaluation}

We present three case studies to evaluate BioWorkbench: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow.
These workflows are analyzed from both computational and scientific domain points of view using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web interface.
The values and statistics presented in this section were extracted from queries to the Swift provenance database.
In the case of SwiftGECKO and RASflow, in addition to the computational information already collected and stored by Swift, annotations were also gathered from the scientific domain of the experiment, such as the size of the sequences used as input for the workflow execution.
This demonstrates the usefulness of Swift both in supporting the parallel execution of the experiment and in the analysis of those runs through queries to the provenance database. The executions of each of the workflows were performed on a shared memory computer, with a single node with 160 cores and 2~TB of RAM.
It is worth mentioning that the computational resource is shared with other users and was not dedicated to these executions. This can be considered as one of the factors influencing the performance gains.
We highlight that the workflows were executed directly in the aforementioned computational resource, not taking into account the Docker structure presented in the Figure \ref{fig:arq_bio}. The Docker container was built for reuse purposes only, to encapsulate the components that compose the framework.

\subsection{SwiftPhylo: phylogenetic tree assembly}

SwiftPhylo\footnote{Available at https://github.com/mmondelli/swift-phylo} is based on the approach proposed in \cite{Ocana2011}. Its goal is to build phylogenetic trees from a set of multi-FASTA files with biological sequences from various organisms.
The construction of phylogenetic trees allows understanding the evolutionary relationship between organisms, determining the ancestral relationships between known species. Results obtained through phylogenetic experiments contribute, for example, to the development of new drugs \cite{anderson2003process}.
SwiftPhylo is composed of six activities, shown in Figure \ref{fig:diagram_phylo} and described as follows:

\begin{figure*}[htb]
	\begin{center}
	    \includegraphics[width=0.6\linewidth]{img/swiftPhylo}
	\end{center}
    \caption{\label{fig:diagram_phylo}SwiftPhylo workflow modeling.}
\end{figure*}

\begin{enumerate}
\item Sequence numbering: the activity receives multi-FASTA format files as input and uses a Perl script so that each sequence contained in the file receives is numbered.
\item Multiple Sequence Alignment (MSA): the activity receives the result of Activity 1 and produces a MSA as output through the MAFFT \cite{katoh2002mafft} application.
\item Alignment format conversion: this activity converts the format of the file generated by the previous activity to the PHYLIP format using the ReadSeq \cite{Gilbert2003} application.
\item Search for the evolutionary model: this activity tests the output files of Activity 3 to find the best evolutionary model, through the ModelGenerator \cite{keane2006assessment} application.
\item Filtering: this activity uses a Python script to filter the output file from Activity 4.
\item Construction of phylogenetic trees: this activity receives as input the resulting files of Activities 3 and 5, and uses the RAxML \cite{stamatakis2006raxml} application to construct phylogenetic trees.
\end{enumerate}

SwiftPhylo works with a large amount of data and can be run with different parameters. This means that, in practice, managing its execution without the help of a SWfMS becomes a cumbersome task for the scientist.
Taking into account that the workflow modeling specifies independent processing for each input file, with the implementation of SwiftPhylo we have a workflow that allows us to explore the characteristics of Swift's parallelism.

In the SwiftPhylo implementation process, the computational applications that compose the workflow were mapped to the Swift data flow model. In this way, the activities are represented in the Swift script as \textit{app functions}. The app functions determine how the execution of a computational activity external to Swift is performed, including its arguments, parameters, inputs, and outputs.
Once this has been done, activity chaining was defined by indicating that the output of one app function is the input of another. Parallelism has been implemented in a way that the activity flow can be executed independently for each input, as shown in the code in Listing \ref{lst:swift_1} through the \textit{foreach} statement.

\begin{figure}[h]
\begin{lstlisting}[label={lst:swift_1}, style=mystyle, frame=single, language=SwiftK, caption={SwiftPhylo specification sample.}]
app (file o) mafft (file i) {
	mafft filename(i) stdout=filename(o);
}

foreach f, i in fastaFile {
	mafftFile[i] = mafft(fastaFile[i]);
}
\end{lstlisting}
\end{figure}

SwiftPhylo was executed using a set of 200 multi-FASTA files, with the size of each file ranging from 2~KB to 6~KB, resulting in the execution of 1200 activities. The total execution time averages and speedup of the workflow are shown in Figure \ref{fig:time_phylo}. The results indicate a reduction of the execution time of the SwiftPhylo from $\sim$13.35 hours, when executed sequentially, to $\sim$8 minutes, when executed in parallel using 160 cores.
This represents a decrease of 98.9\% in the workflow execution time. Also, the speedup metric was used as a way to evaluate the performance gain between parallel and sequential executions. In this case, SwiftPhylo executed in parallel was $\sim$92 times faster than its sequential execution.

\begin{figure*}[htb]
	\begin{center}
	    \includegraphics[width=0.6\linewidth]{img/phylo_scale.eps}
	\end{center}
    \caption{\label{fig:time_phylo}SwiftPhylo execution time and speedup.}
\end{figure*}

Another important aspect related to the execution of the workflow concerns its level of parallelism, presented through a Gantt graph in Figure \ref{fig:gantt_phylo}. This type of analysis shows the order of execution and the duration of each of the activities that comprise the \textit{workflow}. In the chart, activities are represented by different colors and each activity is displayed as a horizontal bar that indicates when the activity started and when it ended.
The bars are stacked on the vertical axis in order of execution. Thus, by plotting a vertical line at some time $t$ of the workflow execution, we find the parallelism at time $t$ as the number of activities intercepted by the line.
We can observe that the {\em modelgenerator} activity is the one that demands the most execution time and can be considered a candidate for identify parallelism strategies that reduce its duration.

\begin{figure*}[!htb]
	\begin{center}
	    \includegraphics[width=0.8\linewidth]{img/gantt_phylo.eps}
	\end{center}
    \caption{\label{fig:gantt_phylo}SwiftPhylo workflow Gantt chart expressing its parallelism level.}
\end{figure*}

\subsection{SwiftGECKO: comparative genomics}

SwiftGECKO\footnote{Available at https://github.com/mmondelli/swift-gecko} is an implementation of the  comparative genomics workflow proposed in \cite{Torreno2015}. Comparative genomics studies the relationship between genomes of different species, allowing a better understanding of the evolutionary process among them \cite{alfoldi2013comparative}.
SwiftGECKO aims to identify portions of biological sequences of various organisms with a high degree of similarity, or {\em high-scoring segment pairs} (HSP), between them. SwiftGECKO is composed by 10 activities distributed in three modules, which are presented in Figure \ref{fig:diagram_gecko} and described as follows:

\begin{enumerate}
\item Dictionary creation: this corresponds to the creation of dictionaries for each sequence and includes Activities 1 to 4 (blue boxes). For the dictionary creation, the user must indicate the size of the portion of the sequence, or $K$-mers, that will be used for the comparison. The dictionary consists of a table that organizes the $K$-mers and their respective positions, for each of the sequences.
\item HSP identification: this is composed by Activities 5 to 9 (green boxes) and performs the comparison between the sequences, identifying {\em hits} used to find HSPs. {\em Hits} consist of positions where the $K$-mers of the compared sequences are equal.
\item Post-processing: this is Activity 10, where a conversion of the output format of Activity 9 to CSV is done, allowing analysis of the results.
The CSV file contains information such as the size of the sequences, the parameters used in the comparison, and the number of hits found.
\end{enumerate}

\begin{figure*}[htb]
	\begin{center}
	    \includegraphics[width=0.8\linewidth]{img/diagram_gecko}
	\end{center}
    \caption{\label{fig:diagram_gecko}SwiftGECKO workflow modeling.}
\end{figure*}

SwiftGECKO consumes and produces a significant amount of data. A workflow execution with 40 complete bacterial genomes totals 1560 possible comparisons, resulting in the execution of 8080 activities.
The implementation of SwiftGECKO followed the same steps mentioned in the SwiftPhylo implementation process. Parallelism was divided into two \textit{foreach} stages as shown in Listing \ref{lst:swift_2}. In the first one, the activities that belong to Module 1 are executed; they generate the files that will be consumed by the other activities. The second step, referring to Modules 2 and 3, manages the activities responsible for comparing pairs of all genomes given as input.

\begin{figure}[h]
\begin{lstlisting}[label={lst:swift_2}, style=mystyle, frame=single, language=SwiftK, caption={SwiftPhylo specification sample.}]
foreach f,i in fasta {
     wordsUnsort[i] = words(fasta[i]);
}
foreach f,i in fasta {
     foreach g,j in fasta {
       hits[i][j] = hits(d2hW[i], d2hW[j], wl);
     }
}
\end{lstlisting}
\end{figure}

SwiftGECKO was executed with a set of 40 files containing bacterial genome sequences, ranging in size from 1~KB to 8~MB.
The execution time decreased from $\sim$2.1 hours to $\sim$6 minutes, representing a reduction of $\sim$96.6\%.
Also, the workflow was $\sim$30 times faster when executed in parallel, using 160 processors. In a more in-depth analysis, we illustrate in Table \ref{tab:data_gecko} that the {\em hits} activity is also I/O-intensive. This is a factor that limits the scalability of the workflow.

\begin{table}[!htb]
\centering
\caption{Average duration (s) and the amount of data read and written by SwiftGECKO.}
\label{tab:data_gecko}
\begin{tabular}{|l|r|r|r|}
\hline
\multicolumn{1}{|c|}{\textbf{Activity}} & \multicolumn{1}{c|}{\textbf{Duration (s)}} & \multicolumn{1}{c|}{\textbf{GB read}} & \multicolumn{1}{c|}{\textbf{GB written}} \\ \hline
reverseComplement                        & 11.8                                        & 0.15                                 & 0.14
\\ \hline
words                                    & 55.9                                        & 0.29                                 & 7.05
\\ \hline
sortWords                                & 76.6                                        & 7.05                                & 7.05
\\ \hline
w2hd                                     & 425.1                                       & 7.05                                & 11.67
\\ \hline
combineFrags                             & 425.8                                       & 0.32                                 & 0.16
\\ \hline
csvGenerator                             & 697.8                                       & 0.006                                  & 0.004                                      \\ \hline
filterHits                               & 2402                                        & 111.36                              & 83.09
\\ \hline
FragHits                                 & 3793.3                                      & 94.7                               & 0.32
\\ \hline
sortHits                                 & 4457.3                                      & 111.36                              & 111.36
\\ \hline
hits                                     & 60058                                       & 455.24                              & 111.36
\\ \hline
\end{tabular}
\end{table}

For a more detailed analysis of the SwiftGECKO provenance data, we present predictive models automatically generated by machine learning methods.
These models aim at understanding how some variables influence the total execution time of the workflow.
Besides the CPU time, which was selected as the attribute to be predicted, and the total\_fasta\_size, we included the following attributes as input parameters for the models: \textit{length}, \textit{word\_length}, \textit{similarity}, \textit{total\_genomes},  \textit{total\_reads}, and \textit{total\_written}.

The machine learning methods were applied using Weka \cite{hall2009weka}, a software that contains a set of different algorithms for data classification and prediction.
In this case, the regression algorithms obtained especially promising results.
The simple linear regression algorithm achieved a correlation coefficient of 0.9855 and is represented in the Equation \ref{eq:linear_regression_query4},
while the multilayer neural network algorithm
obtained a correlation coefficient equal to 0.9941.
We have not represented this second model due to its high complexity. Commonly, the high complexity of the models obtained by neural network-based algorithms is responsible for the use of the expression ``black box algorithm'', to refer to them.
These results demonstrate that it is quite possible to predict the execution time of the workflow as a whole, on the chosen set of input parameters.

\begin{equation}
\begin{array}{llll}
	CPU\, time=& -931.4025  & \times & \textit{word\_length = 12 $\vee$ word\_length = 10 }\, + \\
			   & -2704.5534 & \times & \textit{word\_length = 10 }\, + \\
    		   & 0       	& \times & \textit{total\_written }\, + \\
    		   & -1006.3049	& \times & \textit{total\_genomes = 20 $\vee$ total\_genomes = 30 $\vee$ total\_genomes = 40 }\, + \\
    		   & -547.6854  & \times & \textit{total\_genomes = 30 $\vee$ total\_genomes = 40 }\, + \\
    		   & 410.1449   & \times & \textit{total\_genomes = 40 }\, + \\
    		   & 876.1037   & &
\end{array}
\label{eq:linear_regression_query4}
\end{equation}

We divided the domain of possible values for \textit{CPU time} in 5 ranges (which are the classes) $\{ \textit{A, B, C, D, E} \}$ of equal size, in which $A$ includes the lowest values and $E$ includes the highest values. This makes it possible to apply classification algorithms using the same data as the previous analysis.
Having a discrete domain, the information gain ratio values for each attribute are listed in the Table \ref{tab:info_gain_query4}.
Cost matrices were used to avoid the overvaluation of class A, which holds 88.46\% of all tuples.
In this case, the tree-based techniques ``J48'' and ``BF Tree'' obtained the best results, correctly classifying  96.79\% and 96.15\%, respectively, of all tuples.

\begin{table}[!h]
\centering
\begin{tabular}{|l|l|}
\hline
\multicolumn{1}{|c|}{\textbf{Information gain ratio}} & \multicolumn{1}{|c|}{\textbf{Attribute}}\\ \hline
1 & total\_read \\ \hline
0.1842 & word\_length \\ \hline
0.1611 & total\_fasta\_size \\ \hline
0.1208 & total\_genomes \\ \hline
0.0421 & length \\ \hline
0.0271 & similarity \\ \hline
\end{tabular}
\caption{Information gain ratio values of the attributes used for the analysis.}
\label{tab:info_gain_query4}
\end{table}

\begin{small}
\begin{algorithm}[h!]
\caption{J48 query4 without constraints}
\label{a:j48-query4-completa}
\If{total\_read $\leq$ 1020229446482}{
	\Return Class A\;
}\Else{
	\If{total\_fasta\_size $\leq$ 113556442}{
    	\If{length = 80}{
        	\If{similarity = 65}{
            	\Return Class C\;
            }\Else{
            	\Return Class B\;
            }
        }\Else{
        	\Return Class C\;
        }
    }\Else{
    	\Return Class E\;
    }
}
\end{algorithm}
\end{small}

\begin{small}
\begin{algorithm}[h!]
\caption{BFTree query4 without constraints}
\label{a:bfTree-query4-completa}
\If{total\_read $<$ 1.768799155948E12}{
	\Return Class A\;
}\Else{
	\If{total\_fasta\_size $<$ 1.314087315E8}{
    	\If{length=100}{
        	\Return Class C\;
        }\Else{
        	\If{similarity $\neq$ 40}{
            	\Return Class C\;
            }\Else{
            	\Return Class B\;
            }
        }
    }\Else{
    	\Return Class E\;
    }
}
\end{algorithm}
\end{small}

The ``OneR'' algorithm obtained the rule given by the Equation \ref{eq:oneR_query4}, correctly classifying 96.79\% of all tuples.
\begin{equation}
\centering
\begin{array}{lll}
	total\_read: & & \\
    	< 1.768799155948E12  & : & Class\, A \\
        < 2.5173879304975E12 & : & Class\, B \\
        < 3.4581148731605E12 & : & Class\, C \\
        \geq 3.4581148731605E12 & : & Class\, D \\
\end{array}
\label{eq:oneR_query4}
\end{equation}

According to the Table \ref{tab:info_gain_query4},
the \textit{CPU time} is most directly influenced by the amount of data read by the workflow.
Together with the third higher information gain ratio value assigned to the attribute \textit{total\_fasta\_size}, we can suggest that the magnitude of the information to be read is the most influential aspect concerning the execution time.
Despite the I/O routines, the attribute \textit{word\_length} receives the second higher information gain ratio value, highlighting its relevance.

In fact, in the absence of data about the number of hits, the attribute \textit{word\_length} assumes the most prominent position to predict the attribute \textit{CPU time}.
For all this, the value of \textit{word\_length} is also a decisive attribute to predict the execution time of the workflow as a whole, due to its importance in the behavior of the most costly component of the workflow.

Reinforcing the relevance of the I/O routines, both Algorithms \ref{a:j48-query4-completa} and \ref{a:bfTree-query4-completa} employ the attributes \textit{total\_read} and \textit{total\_fasta\_size} in their main conditionals.
As in the Equation \ref{eq:oneR_query4}, the greater the \textit{total\_read} value, the greater the computational time demanded.
Also, the attributes \textit{length} and \textit{similarity} are used to classify a minor number of tuples. However, they can indicate the influence of the cost associated with the amount of fragments found (influenced by the attributes \textit{length} and \textit{similarity}).

Beyond all this, these experiments demonstrate that is possible to generate simple models able to efficiently predict the computational time demanded by the workflow execution, both in terms of continuous or discrete times.
The techniques used to build these models also allows us to infer predictions related to other attributes, beyond the execution time. For example, we can focus on the amount of written data by the workflow or the specific domain data stored in the provenance database.
Also, there are a wide variety of machine learning methods that produce symbolic solutions and allow, in addition to the predictions, knowledge extraction about different aspects.
These aspects include, for example, the structure or the importance degree of relations among the various variables or between variables and constants.
Therefore, machine learning methods constitute an essential toolkit to be explored in provenance data analyses concerning SwiftGECKO and other, to provide predictive models and to reveal implicit knowledge.

\subsection{RASflow: RASopathy analysis}

Genetic diseases, such as RASopathies, occur due to changes in the nucleotide sequence of a particular part of the DNA. These changes modify the structure of a protein, which may cause anatomical and physiological anomalies \cite{klug1997}. RASopathies comprise a set of syndromes characterized by heterogeneity of clinical signs and symptoms that limit the prognosis, still in the childhood, of predispositions to certain tumors or neurocognitive delays. RASopathies are characterized by mutations in genes that encode proteins of the RAS/MAPK cell signaling pathway, which is part of the communication system responsible for the coordination of cellular activities and functions. This type of mutation was found in 20-30\% of cancer cases in humans, setting the RASopathies in the group of syndromes that are predisposed to cancer \cite{Lapunzina2014}.

A consortium between Bioinformatics Laboratory of the National Laboratory for Scientific Computing (LABINFO/LNCC) and the Center for Medical Genetics of the Fernandes Figueiras Institute at Fiocruz (IFF/Fiocruz) established an experiment aimed at the molecular study of RASopathies, from the sequencing of the exome of a set of patients. The consortium seeks to investigate genetic aspects of RASopathies by using DNA sequencing technologies, providing support for the treatment of the disease.
For this, a study that counts on the processing of the sequences of patients diagnosed with RASopathies was established. This study comprises the use of a set of bioinformatics applications and, due to the significant amount of data to be processed, demands high-performance computing.

A scientific workflow, called RASflow, was implemented to support the large-scale management of a bioinformatic experiment to analyze diseases associated with RASopathies and allows the identification of mutations in the exome of patients. Once the exomes of the collected patient samples are sequenced, the results are stored in a text file in the FASTQ format, which records the {\em reads} and their quality scores. The {\em reads} consist of sequence fragments generated by the sequencer.
By using the results obtained through RASflow, a researcher can analyze and identify whether or not there is pathogenicity in the mutations present in the exome.
RASflow was implemented in Swift, and the workflow model is shown in Figure \ref{fig:modeling}.

\begin{figure*}[!htb]
	\begin{center}
	    \includegraphics[width=0.6\linewidth]{img/rasflow}
	\end{center}
    \caption{\label{fig:modeling}RASopathy analysis workflow modeling.}
\end{figure*}

Activity 1 receives a reference human genome and indexes it. The results are stored in files in the BT2 format, which records the indexes according to the sequence size. This activity requires large computational time, and its results are used in the analysis of each patient. Therefore, the workflow checks for the existence of BT2 files in the filesystem where it is executed. The activity is only performed when the files are not found.

Activity 2 receives the exome sequence of the patient in the FASTQ format as input, filters the reads with a certain quality, and maintains the result in the same format. The need to perform Activity 2 depends on the type of sequencer used to sequence the exome of the patient. If the Illumina sequence was used, for example, it is not necessary to perform this activity. If the sequencing comes from IonTorrent, the activity is performed in parallel.

Activity 3 receives the result of Activities 1 and 2 to perform the alignment of the exome and the reference genome sequence, resulting in a SAM format file and a log file with alignment statistics. The SAM file, the result of the alignment, is usually large and therefore difficult to analyze and manipulate. Activities 4, 5 and 6 are used to compress, sort and index the SAM file, respectively, generating the BAM and BAI binary files that store the aligned sequences. The resulting files are used by Activity 7, which filters duplicate reads and produces a file in BAM format as well.

From this point on, mutations are identified by comparing the exome sequence of the patient and the reference genome. However, the workflow presents some variability, and the comparison can be made through two approaches: (i)
using {\em samtools} \cite{samtools2011} or (ii) the toolkit provided by \textit{GATK}  \cite{gatk2010}. A more detailed analysis of the differences between the two approaches that take into account biological aspects falls outside the scope of this work. However, it can be said that the GATK toolkit comprises more sophisticated techniques and the results obtained tend to be more accurate.

In the workflow variation that uses \textit{samtools}, the BAM file produced by Activity 7 and the reference genome are consumed by Activity 8, which performs the comparison. The result is used by Activity 9, which converts the file from a binary format to the VCF format, which is responsible for storing the genetic variants found. The workflow variation using the \textit{GATK} approach performs the set of Activities 10a-10f, indicated in the figure, which also produces a VCF file. The VCF file resulting from the execution of one of the variations is consumed by Activity 11 to predict the effects of the mutations found and to determine the pathogenicity, resulting in a set of VCFs. In this work, we also included Activities 12 and 13 to compress and index the files resulting from Activity 11, respectively. The results are consumed by Activity 14, responsible for combining this set of files. Finally, Activity 15 applies a set of filtering activities based, for example, on the quality and quantity of occurrences of a given variant, generating a single final VCF file.

A set of scientific domain annotation extractors was developed for gathering and adding to the provenance database information from the following files: (i) the GFF file, which describes characteristics of the DNA, RNA and protein sequences of the genome used as reference; (ii) the log file resulting from the execution of Activity 3; and (iii) the file in VCF format, which contains the variations found in the exome.
The conceptual schema of the Swift database has been augmented to enable storage of this information. The following tables, as shown in Figure \ref{fig:domainrasflow}, were added: \textit{gff} and \textit{vcf}, for storing the contents of the GFF and VCF files respectively; and the \textit{file\_annot\_numeric} table, which records the contents of the log file in key-value format.

\begin{figure*}[!htb]
	\begin{center}
	    \includegraphics[width=0.5\linewidth]{img/sqlite_domain}
	\end{center}
    \caption{\label{fig:domainrasflow}Database entities for storing scientific domain annotations in RASflow.}
\end{figure*}

Next, we propose a set of queries to the RASflow provenance database to assist the scientist in the analysis of the results of the workflow.
The queries were defined with one of the researchers responsible for the analysis of RASopathies.
They are available for viewing in the BioWorkbench web interface corresponding to the RASflow experiment. That is, the scientist does not need to redefine them to obtain the results.

\textit{Query 1}: ``Retrieve the alignment rate of each patient's exome sequences relative to the reference genome''.
The alignment process allows identifying the similarity between the patient sequence and the sequence used as a reference. The result is obtained by executing Activity 2 of the workflow, which produces a log file. This file records some statistics and among them the rate of alignment between the two sequences. This type of information is useful for the scientist, who is responsible for deciding what rate is sufficient for proceeding with the analysis. The alignment rate is stored in the \textit{file\_annot\_numeric} table of the provenance database and can be retrieved through the query shown in Listing \ref{lst:query_1}. Table \ref{tab:query_1} displays the result of the query, with the alignment rates for each of the patients used in the analysis of RASopathies of a given workflow execution.

\begin{figure}[h]
\begin{lstlisting}[label={lst:query_1}, style=mystyle, frame=single, language=SQL, caption={SQL query to retrieve the alignment rate of each patient's exome sequences.}]
SELECT         file_id, value
FROM           file_annot_numeric
NATURAL JOIN   staged_out
WHERE key LIKE 'overall alignment rate' AND
               app_exec_id LIKE
\end{lstlisting}
\end{figure}

\begin{table}[!htb]
\centering
\begin{tabular}{|l|r|}
\hline
\textbf{Patient} & \textbf{Alignment rate} \\ \hline
P1.log            & 93.95\%                      \\ \hline
P2.log            & 94.52\%                      \\ \hline
P3.log            & 94.41\%                      \\ \hline
P4.log            & 94.48\%                      \\ \hline
P5.log            & 94.62\%                      \\ \hline
P6.log            & 94.58\%                      \\ \hline
\end{tabular}
\caption{Alignment rate resulting from patients analysis in RASflow.}
\label{tab:query_1}
\end{table}

\textit{Query 2}: ``Retrieve the biotype and transcript gene name from the final VCF file''.
This type of result, without BioWorkbench support, was obtained through a manual scan of the GFF file, used as input in the execution of the workflow, and if the VCF file generated as the final result. In RASflow, these two files are imported into the \textit{gff} and \textit{vcf} tables of the provenance database. To retrieve this information, one can use the query presented in Listing \ref{lst:query_2}, which performs the join of the \textit{vcf} and \textit{gff} tables for a given workflow execution. The result is displayed in Table \ref{tab:query_2}. Through the BioWorkbench interface for RASflow, the result is also presented as a table, but iteratively, allowing the scientist to filter the columns or search for names according to their needs.

\begin{figure}[h]
\begin{lstlisting}[label={lst:query_2}, style=mystyle, language=SQL, frame=single, caption={SQL query to retrieve the biotype and transcript gene name from the final VCF file of a patient.}]
SELECT       v.*, g.Name AS nome,
             g.biotype AS biotipo
FROM         vcf v
NATURAL JOIN file f
NATURAL JOIN staged_out o
NATURAL JOIN app_exec a
LEFT JOIN    gff g ON v.trid = g.ID
WHERE        a.script_run_id LIKE 'loss-run006-3737171381';
\end{lstlisting}
\end{figure}

\begin{table*}[!htb]
\centering
\begin{tabular}{|l|l|l|l|l|}
\hline
\textbf{Patient}                          & \textbf{Gene}   & \textbf{Transcript} & \textbf{Name} & \textbf{Biotype} \\ \hline
P1.log & ENSE00001768193 & ENST00000341065     & SAMD11-001    & protein\_coding  \\ \hline
P1.log & ENSE00003734555 & ENST00000617307     & SAMD11-203    & protein\_coding  \\ \hline
P1.log & ENSE00003734555 & ENST00000618779     & SAMD11-206    & protein\_coding  \\ \hline
P1.log & ENSE00001864899 & ENST00000342066     & SAMD11-010    & protein\_coding  \\ \hline
P1.log & ENSE00003734555 & ENST00000622503     & SAMD11-208    & protein\_coding  \\ \hline
\end{tabular}
\caption{Mutation list with the biotype and the name of the transcribed genes in the final VCF file of a patient.}
\label{tab:query_2}
\end{table*}

To evaluate the performance of the workflow, we used exome sequences of 6 patients as input, ranging in size from 8~GB to 11~GB.
It is worth mentioning that a preliminary version of this workflow was developed in Python. In this work, we chose to develop it using Swift to take advantage of the parallelism offered by the system.
By considering the variability of the workflow, executions were made for the two possible approaches: one using the \textit{samtools} tool and the other using the \textit{GATK} toolkit.
In the approach using \textit{samtools}, a reduction of $\sim$77\% of the execution time of the analyses was obtained, representing a gain of $\sim$4 times in the execution with Swift compared to the sequential execution in Python. The approach using \textit{GATK} had a reduction of $\sim$80\% in execution time, for a gain of $\sim$5 times. The parallelism strategy of RASflow explored the simultaneous analysis of patients. Thus, the total time of execution of the workflow is associated with the execution time of the most time-consuming patient analysis.

Because it has been executed with a small set of patients, the workflow has a large run-time variability.
However, genetic variant analysis can be applied to other diseases.
For diseases such as cancer, for example, the volume of sequenced genomes is much larger and therefore, there is an opportunity to obtain higher performance gain through the approach used in RASflow.

\section{Conclusion and Future Work}\label{sec:conclusion}

Large-scale bioinformatics experiments involve the execution of a flow of computational applications and demand HPC. The execution management of these experiments, as well as the analysis of results, requires a lot of effort by the scientist.
In this work, we demonstrate that the use of scientific workflow technologies coupled with provenance data analytics can support this management, allowing for the specification of experiments, parallel execution in HPC environments, and gathering provenance information.

To benefit from the use of scientific workflow technologies and support the whole process of scientific experimentation, we have developed the BioWorkbench framework. It was designed to use the Swift SWfMS for the specification and execution of bioinformatics experiments, and a web application for provenance data analytics.
In this way, through BioWorkbench the user has access to a tool that integrates various features ranging from the high-performance execution of the workflow to profiling, prediction, and domain data analysis.
We can observe that BioWorkbench enables a better scientific data management since the user does not have to directly manipulate the provenance database and the resulting files from the experiment execution. Another important aspect concerns the reproducibility of the experiment, which is facilitated by the provenance and the reproduction of the computational environment through a Docker container.

We used three case studies that model bioinformatic experiments as workflows: SwiftPhylo, SwiftGECKO, and RASflow. In addition to the performance gains achieved by using Swift in BioWorkbench, we have demonstrated how the provenance allows the identification of bottlenecks and possible optimization opportunities in the execution of workflows. Also, we conclude that users can benefit from the application of machine learning techniques in provenance analysis to, for example, predict and classify workflow execution time. It is noteworthy that, during the development of this work, SwiftGECKO was integrated into the Bioinfo-Portal scientific portal\footnote{Available at http://bioinfo.lncc.br/} \cite{Mondelli2016a}. Through the portal, users can execute the workflow through a web interface in a transparent way, using geographically distributed computational resources managed by the Brazilian National System for High-performance Computing (SINAPAD).

\section*{Acknowledgements}

This work was partially supported by Brazilian funding agencies CNPq, CAPES, and FAPERJ. M. Wilde has an employment and ownership interest in the commercial firm Parallel Works Inc.

\bibliographystyle{abbrv}

redpajama_set_name: RedPajamaArXiv


text:
If You'd Like To Achieve Success In Bacterial, Here Are 5 Invaluable Things To Know
The tool works by creating an area backup of your device (so you will want to make sure you will have enough storage house for the backup), after which analyzing that backup. Because of that, I recommend starting the tool and checking on it after a while. While NordVPN has lived on this list for a long time, we moved it to the penalty field in October 2019 to re-evaluate our recommendation after a report emerged that one in all its rented servers was accessed without authorization in 2018. Nord's actions following the invention included — finally — a number of safety audits, a bug bounty program and heavier investments in server security. Last year, Salt Lake County in Utah provided park prescriptions to its employees "to improve or maintain bodily and psychological health whereas constructing sustainable health behaviors," Sarah Kinnison, who oversaw this system, said in an electronic mail. At $10 a month or $80 a yr, IPVanish is clearly trying to maneuver you towards its yearly program. That would mean those that turned totally vaccinated by the middle of January can be eligible for a booster shot this month. Some 90% of Americans have a vaccine site inside 5 miles of where they reside, Zients said, and getting a booster shot might be simply as easy as getting the first shot.
Zients stated 90% of Americans have a vaccine site inside 5 miles of where they reside. Both the Moderna and Pfizer vaccines have confirmed to be greater than 90% efficient towards hospitalizations and dying. More than four hundred faculties and universities are additionally requiring vaccines for college kids who plan to absorb-person classes. White House Press Secretary Jen Psaki said on Aug. 17 that the US could have enough vaccines to each provide boosters for those who're fully vaccinated in the US and meet the global demand. 3, administration health officials warn that the scientists of the FDA and CDC might not have sufficient time to approve boosters from all vaccine manufacturers in time to satisfy Biden's purpose of beginning booster photographs on Sept. The FDA hasn't authorized a second dose of the Johnson & Johnson vaccine for immunocompromised individuals, because of a lack of data. The plan for boosters has resulted in a backlash amongst international locations which might be struggling to deliver first and second pictures to residents.
Health Would not Have to Be Exhausting. Read These 9 Tips Go Get A Head Begin.
Three Quick Ways To Be taught Online Pharmacy
Blood Pressure Awards: Six Explanation Why They Don't Work & What You Can Do About It
How To Seek Out Pain Relief Online
5 Days To A better Asthma
The Last Word Guide To Cardiovascular
7 Strange Information About Infection
6 Ridiculously Simple Ways To Improve Your Hair Loss
Diabetes Creates Specialists
Why Cholesterol Does not Work…For Everybody
How You Can Make Your Allergy Appear Like 1,000,000 Bucks
Nine Life-Saving Tips about Allergy
4 Questions It's Essential Ask About Men's Health

redpajama_set_name: RedPajamaCommonCrawl


text:
Q: Parametrized cancelations in stable Morse theory Let $B$ be a closed manifold. Let $\pi : M\to B$ be a submersion such that each fiber is a manifold without boundary. Let $f : M \to \mathbb{R}$ be a function such that the restrictions $f_x$ to each fiber $\pi^{-1}(x)$ satisfies:
$\bullet$ The critical points and gradient trajectories between them are compact. We say that $f$ has compact fiber-wise flow categories.
This means that the Morse homology of each $f_x$ is well-defined. Also, assume that the global Morse homology is well-defined. In fact, assume that some Lipschitz condition (or similar) is satisfied both for the fibers and the global $f$.
One can also assume that the global Morse homology can be calculated using a Serre type spectral sequence with page 2 given by $H_*(B,MH_*(f_x))$, where the Morse homologies define a local system. I am not sure if this is useful in the following.
Stabilization: We may stabilize by simply crossing $M$ with $\mathbb{R}^n$ and replace $f$ by $f+q$ where $q$ is a non-degenerate quadratic form on $\mathbb{R}^n$. This makes all problems with $\pi_1$ of the fibers go away (but not the base - as is standard in parametrized stable homotopy theory).
Question: Assume that the fiber-wise Morse homology is either $0$ or $\mathbb{Z}$. When can you (are there any good conditions) deform a stabilization of $f$ on a compact set through a family with compact fiber-wise flow categories to an $f'$ which has either no fiber-wise critical points or a single critical point in each fiber (depending on whether it was $0$ or $\mathbb{Z}$)?
Simplification: If nothing is know in this general case. I am also interested in the simpler case where $M=B\times \mathbb{R}^k$ and $f$ is fixed equal to a non-degenerate quadratic form outside a compact set (see edit below).
Reduction: Standard Morse theory proves this for $B$ a point. So doing induction in skeleta could be done by answering the question: what do we need if $B=D^n$ has boundary, but the function is already "fiber trivial" (i.e. has none or a single critical point) over the boundary, and we can may only deform it over the interior of $B$. A nice answer to my question could be a perfect description of the obstruction to extend this.
Note: I believe that the cases where the Fiber-wise Morse homology are non-trivial (not $0$ or $\mathbb{Z}$) are much more intricate, but I am not completely sure - the trouble might lie elsewhere. However, note that if the Morse homology is $\mathbb{Z}$ we essentially have a stable sphere bundle over $B$ and this need not be trivial.
Edit: I did not explain the simplification very well. If it is equal to a quadratic form outside a compact set one can always interpolate directly with this quadratic form and get the result that everything is trivial. However, if one considers the relative case described in the reduction, combined with this simplification - the simplified problem also becomes interesting.

redpajama_set_name: RedPajamaStackExchange


Home › Advice › Is your ride ready for winter?
Is your ride ready for winter?
(ARA) – In many parts of the country, winter can test even the most seasoned driver's skills with sudden road and weather changes. In ideal circumstances you have warning of what Old Man Winter might bring for the day, but many times wet roads can become icy and a few flurries can become a snowstorm without any warning at all.
Check your battery: Instead of landing on your "I Forgot" list, put this one at the top. Make sure your battery posts and connections are free of corrosion and that the battery has the water it needs. If your battery is older than three years, have a certified repair shop test its ability to hold a charge.
Belts and hoses: When you're having your vehicle serviced, make the mechanic checks the belts and hoses for wear and tear, regardless of the age of your car. Cold weather can also affect the belts and hoses of a modern car, so an inspection can't hurt.
Have the right antifreeze mix: You will want to aim for a 50-50 mix of antifreeze (coolant) and water inside your radiator. This prevents the mixture from freezing at extremely cold temperatures. Or try using a coolant additive like Royal Purple's Purple Ice that is a high performance, synthetic, radiator coolant additive. Royal Purple recommends a minimum of 20 percent antifreeze concentration be used in street-driven vehicles because Purple Ice has no effect on the boiling and/or freezing point of water. Learn more at www.coolerradiators.com.
Check your four-wheel drive: If your vehicle has four-wheel drive, you probably haven't used it during the summer, so it's good idea to check the status of your four-wheel drive system. Make sure the system engages and disengages easily and that all the drivers of the vehicle know how and when to use the system.
Get an oil change: When you're getting your vehicle ready for winter, change the oil using the right viscosity for your vehicle for the time of year. Conventional oil tends to thicken as it gets colder, and if too thick, it won't properly lubricate your engine. Check your owner's manual for guidance about which oil to use in different climates and temperatures. Another alternative is to use a synthetic blend or full synthetic motor oil like Royal Purple that will extend the time between oil changes, saving you money and having less impact on the environment.
Emergency preparedness: If you know you're going to be on the road during the winter months, make sure you have an emergency kit in your trunk. Items you should include in your kit are: a blanket, boots, gloves and warm clothes, water and food including hard candy, ice scraper, small shovel, jumper cables, tool kit, tire chains, tire gauge, spare tire (ready to be used), tire changing equipment, first aid kit, paper towels and abrasive material such as non-clumping cat litter or sand to provide traction in the snow.
With a little preparation, you can ensure you vehicle doesn't leave you out in the cold this winter.


Printed promotional mugs are a good choice for any event. They're available in white or colors, and in numerous supplies including durable ceramic and plastic. It is possible to print on the mugs with sturdy, washable inks, including four colour images that wrap all around the mug. There is a good quantity of space for a reputation, logo, or artwork to promote a company, enterprise, store, restaurant, bar, or product.
Change Your Life For example, just look at how quickly Visible Studio variations are released with so many new capabilities. By the point you begin to feel comfy in a single launch, there's already a brand new release announced. Pragmatists: Prime Websites The age of digital printing also implies that you not have to buy folders in bulk. You can order them in any quantity, including single folders. That saves cash and in addition helps to avoid wasting the setting.
Past versatility, the query of how assets or purchasable commendable. The functioning refers to questions in regards to the flexibility of property in question: will I divide this ability active if surfaces change into redundant? The group of bodily flows and allows fluid so obligatory a partition or division of the asset or the location?
To do business from home, you must be able to tell your prospects precisely why they need to (or should) buy your product. So, record down the benefits of your product now! If you do not know what your prospects want or want, or why they should buy the product, too dangerous, you'll not get a purchaser.
The in depth verification checks of pros, binding contracts, and stay human representatives for every project makeBidsList a good and trusted medium for qualified purchasers, minimal verification fees, and affordable commissions utilized only when a job is completed; make BidsList the perfect platform for any nicely respected skilled. BidsList has launched its service in California and is quickly increasing. Presently BidsList can create binding contracts in each state within the United States. They are searching for investor partnerships with open arms to increase their business into other vertical markets, as well as other international locations. BidsList is now out there for cellular units on the Android and I telephone app shops.
One more vital side of starting off a company is picking out the authorized framework of the organization. There are lots of varied alternate options like sole proprietorship, partnership, Restricted Legal responsibility Firm, corporation and S-company. Review the tax implications of each, together with the positive elements every type affords, upfront of picking out one particular. It's essential to additionally choose a enterprise identify and pay money for all of the necessary permits and licenses relevant in your town.
Have you ever had a day while you wasn't certain whether you made the appropriate resolution about something? The eighty-20 rule signifies that in any space of our lives, literally eighty percent of our fruits are derived from only 20 p.c of doing "what matters". In different words, there may be only a very small portion of all that we do each day, whatever the scenario, that brings us the "larger return".
24 yrs old Quality Guarantee Manager Duane Zerbe from Haliburton, usually spends time with pastimes which include r/c boats, . and bee keeping. In recent times has attended Historic City of Meknes.


text:
Don Crawford
CEO & President, Analytics 4 Life
Don Crawford, president and CEO of Analytics 4 Life, is a seasoned medical device executive with a proven track record of excellent results-driven leadership through team efforts and focused execution. Don previously founded and led Sapheon Inc., a cardiovascular-focused medical device company, from inception to $238 million acquisition by Covidien in 2014. His career started with Medtronic and included sales and marketing positions of increasing responsibility with Guidant Corporation, Ventritex, and Intermedics, including an international sales director role in charge of a $100 million cardiovascular business. Don received his BChE in chemical engineering from Georgia Tech and an MBA from Emory University.
Knowledge partner:


First things first: I want to give a shout out to the Little Free Libraries of the world. A few weeks ago I picked this up from one in my neighborhood and it was my first time borrowing anything from one of those tiny bibliotecas. I'd heard of this novel but might not have been prompted to borrow it if I hadn't seen it through the friendly little window. I'm inspired to pay it forward by adding something from my "already read" stack when I return it.
Second, I don't normally read reviews before I write my own, because I want to be honest about what I'm feeling and I don't want to inadvertently borrow someone else's thoughts or jump on a bandwagon. But I'm struggling a bit with this one, mainly because I don't normally read young adult literature. I can enjoy something from that genre, but I will rarely love it. My initial reaction to this novel is it has positive things to say and it's an important story, but it's not terribly subtle. I'm the first to admit that I've become jaded from seeing the same story play out on the news on a weekly (daily?) basis. I don't think it's tremendously insightful to say that an unarmed man shouldn't be pulled over and shot by the police for driving while black, and whether or not he was a drug dealer is an irrelevant discussion. This shouldn't be a revolutionary idea.
Then I read a review like one I saw recently on GoodReads, and I realize my naiveté stems from underestimating what counts as a revolutionary idea.
Then I tried to find a sarcastic meme about racism to go with this point and had to stab my eyes out with an American flag because of the sheer number of truly racist memes there are online. Then I went back and read The Hate You Give again and asked forgiveness for ever doubting its necessity.
So I guess the reviewer's point is that she/he doesn't see color? And anyone who talks about race issues is racist?
So after giving this book much thought, I decided I may not love it in terms of its style and execution, but it wasn't written for me. It's also not written for people who have decided either a) racism doesn't exist or b) white men are persecuted just as much as anyone else. I'd love to see young adults of every race read this novel to help them develop empathy and understanding of another group's challenges. But primarily, I think this was written for the 16-year-old black girl who doesn't see herself and her issues represented often enough in main stream movies and television. Starr is a hero for the 21st century: brave (though she denies it repeatedly), strong, loyal. Of course this doesn't stop parents complaining about the book and getting it banned in some school districts because of either the use of profanity, the references to drugs, or the perceived "anti-police" message.
Don't worry kids, if you can't get this book at school, you can always check it out of a little free library!
Here I am returning it!
And paying it forward with Ready Player One. Good karma, here I come!
Filed Under: Fiction, Young Adult Tagged With: #blacklivesmatter, #CBR10, Angie Thomas, black author, KimMiE"
I love those Little Free Libraries! Interesting selection in there.
Excellent review. I don't usually read stuff that's going to make me sad/mad (because I am a weenie), but I love reading all about books that are taking the world by storm, and this one especially has gotten a lot of CBR attention.
This is a "love/hate" book by bringing up all the "feels" we have on the subject. Great review!


The charge SOUTHWES was first reported Jan 4, 2014.
SOUTHWES charge has been reported as unauthorized by 99 users, 10 users recognized the charge as safe.
Help other potential victims by sharing any available information about SOUTHWES.


text:
Cleared in arrest of Miss Black Texas, police chief quits
MDH: Concerning rise in new STD, hepatitis C cases in 2016
Almost 20 million new sexually transmitted infections occur in the United States every year costing the American healthcare system almost $16 million in direct medical costs alone, says a report by the U.S. Centers for Disease Control and Prevention (CDC).
Minnesota saw significant increases past year in sexually transmitted disease cases, and state health officials are warning of a worsening trend among drug users, particularly those using heroin, prescription opiates and methamphetamine.
Rates of new hepatitis C infections also increased 38 percent in 2016 compared to 2015, and over half of the new cases reported injection drug use, according to a news release. The number of HIV cases stayed the same.
The most recent statistics from the Indiana Department of Health report 108 cases of gonorrhea, 668 cases of chlamydia, and almost 70 people living with HIV/AIDS in the Health Connection service areas of Knox, Daviess and Vigo counties.
Gonorrhea is the second most commonly reported STD in Minnesota with 5,104 cases reported in 2016, a 25 percent increase from past year.
Gonorrhea remained the second most commonly reported STD in Minnesota with 5,104 cases reported in 2016 compared to 4,097 in 2015, a 25 percent increase.
The state's report showed a trend of STDs, HIV and hepatitis C affecting young people and minorities.
Firefighter falls from roof battling apartment building blaze
That was his position as the outside ventilation firefighter, operating around the area where Ladder 135's bucket was located. Firefighter William Tolley died Wednesday while battling a blaze in Queens when he fell off a roof.
Minorities were hit hard by chlamydia and gonorrhea in 2016.
Injected drug users and sexually active people to be tested at least once per year for STDs, HIV and hepatitis C, they said.
"These diseases usually do not show physical symptoms immediately", said Kristen Ehresmann, who directs infectious disease work at the Health Department. STD screening and early diagnoses are essential in preventing transmission and the long term health consequences of STDs.
Syphilis cases reported in 2016 rose 30 percent to 852 from 653 the year before. Effective prevention methods include consistent and correct condom use during sex, limiting the number of sexual partners and not sharing injection drug, tattoo and piercing equipment, health officials say.
Officials also encouraged the use of pre-exposure prophylaxis, a prescription medication that can help reduce the risk of HIV infection.
For more details, read the Health Department's annual STD report.
2 companies ask to join Arkansas execution case
The judge filed her order Thursday after the state complained to the Arkansas Supreme Court that she was taking too much time. A handful of drug companies are telling Arkansas that they don't want their products used to kill inmates.
FBR Capital Gives Peabody Energy Corporation Price Target With Potential 41.61% Upside
The transaction was disclosed in a filing with the Securities & Exchange Commission, which is accessible through this link . Zacks has also assigned Peabody Energy an industry rank of 225 out of 265 based on the ratings given to related companies.
Amid competition, Verizon loses key customers for first time
For its Fios service, Verizon added 35,000 internet subscribers, lost 13,000 cable subscribers and lost 8,000 voice subscribers. Verizon Communications Inc. (VZ) has a mean recommendation of 2.71, according to data compiled by Zacks Investment Research.
Cardell Hayes sentenced to 25 years for Will Smith killing
That was the same request from Hayes' mother, whose uncontrollable sobbing led to a brief recess while she composed herself. For all the expected emotion, legal experts say there is little chance Buras will be influenced by either side.
Pro-Life Group Endorses Karen Handel in Georgia Congressional Runoff
Ossoff's campaign will also launch a series of clips promoting the former congressional aide Thursday, the newspaper reported. The victor replaces Republican Tom Price , who stepped down to serve as Mr Trump's Secretary of Health and Human Services.
Russian Federation assures no more USA strikes on Syrian army
The base is one of two of Russia's primary military installations in Syria, and is the primary base used by Russian air forces. Advanced anti-aircraft missile defense systems have also reportedly been stationed at the base.
Alves told crying Neymar to learn from loss
To put that in perspective, the entire Juventus team completed 12. "I wish them the best and I think they can win the title". Buffon said: "Maybe it's better to meet Monaco or Real, who will spend significant energy in the fight for the league".
Taiwan return of China dissident seen as bid for better ties
Reports suggest that according to a bilateral agreement between Taiwan and China, there is no such thing as "political asylum". Prior to his apprehension, local media had reported that Zhang meant to seek political asylum in Taiwan.
Fox stock gains ground following O'Reilly firing
It is also a significant moment for other television personalities and the degree to which off-screen misbehaviour is tolerated. In the wake of his dismissal, I think I can speak for millions of women: Frankly, we don't give a damn.
Colorado biotech firm is being acquired to create $90M company in Seattle
Sphera Funds Management LTD. acquired a new stake in Nivalis Therapeutics during the third quarter worth approximately $1,664,000. Endurant Capital Management LP boosted its position in shares of Nivalis Therapeutics by 29.8% in the third quarter.
I was doing my bit to smash health stigma - Harry
Mr Lyons, from Edgbaston in Birmingham, said: "I never imagined in a million years I'd still be at it 37 years later". But on April 23 she will be in London to join thousands of people taking part in the 2017 Virgin London Marathon .
FCC Votes to Allow Broadcasters to Buy More TV Stations
The FCC added 50 percent of the buildings in a county are within a half-mile of a location served by a competitive provider. Democrats in Congress have raised their fears with the commission that more consolidation could harm consumers.
United Airlines to testify at hearing after violent video surfaces
Those on the House of Representatives committee were already pressing federal regulators for a thorough investigation last week. He said the airline will have more to say later this month, after it finishes a review of its policies on overbooked flights.
RSA wants 8% rent hike on 2-year leases
The increase would cost a typical tenant an extra $50 per month on a one-year lease and $100 a month on a two-year lease. Landlords from around the city will present their recommendations for rent hikes on rent-stabilized apartments Thursday.
Russia, US in spat over United Nations condemnation of North Korea
Abe said that it was a "matter of paramount importance for us to seek diplomatic efforts as well peaceable settlements of the issue".
The right response: Trump takes appropriate action to thwart atrocities in Syria
Lindsay Graham is calling for as many as 6,000 more US troops to fight the Islamic State group. Secretary of State Rex Tillerson on Tuesday.
PM asks BJP to reach out to poor Muslims
Union Minister Mahesh Sharma said, "After last five victories we will try to prepare for next elections". The policy orientation of the ruling party is thus Antyodaya and socio-economic equality.
Sold out! OR campsites for August eclipse snapped up
All state park sites available by reservation are now taken, though cancellations may return a few sites to the pool. Sites range from basic to full-service, with a three-night minimum for the August 21 eclipse.
Medical Properties Trust, Inc. (NYSE:MPW)
Mitsubishi UFJ Financial Group assumed coverage on Medical Properties Trust in a research note on Sunday, December 18th. Seven research analysts have rated the stock with a hold rating and three have assigned a buy rating to the company.
Bayern Munich trio confronted referee after Madrid loss
Bayern's Arturo Vidal was also shown a red card in the second half for what appeared to be clean tackle on Marco Asensio. But the Madrid talisman insists the Champions League holders deserved to go through.
Mike Pence to visit South Korea on Easter Day as tensions escalate
Along with his visit to Seoul, the vice president's tour will also include stops in Tokyo, Jakarta, Sydney and Hawaii. If North Korea has ICBMs, it could give it the ability to strike targets in the mainland U.S. and Europe.
Facebook killer takes own life as police close in
Another daughter, Debbie Godwin, said that's what made her father so special. "I wouldn't wish that on anybody". According to WKYC's Chris Tye, the manager called Pennsylvania State Police and that Stephens was there.
Mike Pence reassures Japan of USA resolve on North Korea
Abe said he supported Trump's stance that strategic patience with North Korea had run out, and that all options were on the table. Pence's economic discussions in Tokyo will be closely watched to see how hard a line Washington is prepared to take on trade.
FDA further restricts pain medication use in kids
Codeine also is used in cough syrup and cold remedies and sometimes is combined with other medications, such as acetaminophen. In 2013, the agency restricted use of codeine in children to treat pain after surgery to have tonsils and adenoids removed.
Pope Francis among Time Magazine's 100 most influential people
Canadian Prime Minister Justin Trudeau met with the president in February. Trump met with the Mexican President Peña Nieto on January 31.
Dispute emerges over release of ex-NFL star Hernandez's brain
Hernandez was found hanging in his cell in Shirley's Souza-Baranowski Correctional Center early Tuesday morning, authorities said. A judge added four to five years to Hernandez's prison sentence for that charge, separate from his existing life sentence.
LeBron James to sit out regular season finale vs. Raptors
In four games for the Cavaliers' D-League affiliate in Canton, Sanders averaged four points, eight rebounds and 2.5 blocks. The Cavs have downplayed the importance of the top seed in recent weeks, but they are just 20-21 on the road this season.
Acadia Healthcare Company (ACHC) Earns News Impact Rating of 0.31
Texas "bathroom bill" could cost state more than $3 billion
Iran FM criticizes 'worn-out' USA nuclear accusations
American Airlines Group's (AAL) "Market Perform" Rating Reaffirmed at Cowen and Company
Drake's Home Burglarized of $10 in Soft Drinks
USA backtracks on 'armada' sailing towards N. Korea
May wins House of Commons backing for snap general election
A 'trading disaster:' Trump slams NAFTA, repeats attacks on Canada's dairy industry
Turkey election board rejects petitions to annul referendum
Mumbai Indians beat Royal Challengers Bengalore by 4 wickets
Sweat, NYCFC top Red Bulls 2-0 in Hudson River Derby
Man catches girl who fell from NY amusement park ride
Jury deliberations begin in police shooting
Police Remove Disabled Protesters Outside Mitch McConnell's Office
Arrests at Capitol of health bill protesters
Trump cancels Obama's 'one-sided' Cuban deal
How the Heat Can Impact Flights
Gay pride parades sound a note of resistance _ and face some
Obama slams Senate GOP health care bill
Supreme Court gives Trump more time to file travel ban briefs
'A Very Narrow Path' to Repeal Obama's Healthcare Law
Scalise shooter had a list of 6 Congressmen's names in his pocket
US Republicans defy new healthcare bill
Democrats Have No Alternative to Nancy Pelosi
Trump endorses Senate GOP health care plan
GOP is hiding something in Senate health-care bill
Rep. Steve Scalise released from intensive care unit
Utah evacuees watched flames draw closer, smoke get thicker


The Arcade is a well-preserved example of a Victorian shopping arcade, providing a beautiful shopping experience. It runs between Rundle Mall and Grenfell Street.
Adelaide Arcade is home to 70 specialty stores, including renowned South Australian chocolate makers, Haigh's.
Exit the carpark at Wyatt Street and turn right, heading north until you reach Grenfell Street. Cross the road and the Adelaide Arcade is directly in front of you.


Avoid being an aggressive driver: Aggressive driving can lower mileage by as much as 33% on the highways and 5 percent within city.
Check your speed limit: Aerodynamic drag on vehicle increases exponentially with the speed of car exponential. You can typically save 15% fuel just be driving at 62 mph (100 km/h) vs 75 mph (120 km/h). However you are advised to get it validated against model, type and age of the vehicle of youe car.
Fuel weight in trunk: Full trunk brings additional weight and reduces fuel mileage.
Keep vehicle clean: Keep your vehicle washed and if possible waxed as it reduces aerodynamic drag on your vehicle. Mud, dust particles, bug on the vehicle increases the drag and hence increase fuel consumption.
Servicing Regularly: Get your vehicle serviced regularly and keep air filters clean, replace old spark plugs and maintain fluid level.
Keep Windows Closed: Open windows especially on highway increases the drag on vehicle resulting in about 10% more consumption of fuel.
Turn A/C ON when necessary: AC causes about 20% more fuel to be consumed as it puts extra load on the engine. So use it when it is necessary.
Avoid acceleration or Brake hard: Save fuel by about 20% by using simple technique of applying slow steady acceleration and braking.
Keep your boot empty: Remove unnecessary items from you boot and reduce weight that helps reduce fuel consumption.
Extraordinary blog. Very helpful. This content is very informative. Really I will keep in my mind these fuel-saving tips. Thanks for sharing this content.


Phenomenal architect designed home for sale that's situated superbly to take advantage of its spectacular 10.7 acre site along Credit River. With significant southern exposure, the home radiates with natural light. Accented by stone and walls of glass, this is a home you must step inside and see for yourself.


text:
Greater Manchester News
Watch: Salford City unveil plans for new stadium
Bosses want to completely transform the Moor Lane ground as it gears up for the Football League
Todd FitzgeraldNews editor
Sign up to the MySalford newsletter and don't miss a thing happening in and around the city
This striking video shows Salford City FC's ambitious plans for a new 5,000-capacity stadium.
The Class of '92 is pumping cash into the club as it continues its fairytale rise to the professional game.
Bosses want to completely transform the Moor Lane ground as it gears up for the Football League - and put in a 600-capacity supporters' club.
Salford City, part-owned by former United legends Paul Scholes , Ryan Giggs , Nicky Butt, Gary and Phil Neville, now sit just two promotions from League Two after securing their place in the Vanarama National League North last campaign.
Following two promotions in two years following the club's takeover, the United lads are now aiming for another promotion every two years.
The plan is for Salford City to be a Football League side by 2020.
The new stadium will have a capacity of 5,100
See Gary Neville's city centre development plans at consultation event
The Class of 92's debut season as owners of Salford City was documented in a hit BBC show.
The new fly-through footage shows how the ageing home would be transformed.
A planning application is yet to be tabled to Salford council chiefs for the 5,100-capacity stadium, with a 600-capacity supporters' club.
The cost of the project has not yet been revealed.
The club tweeted: "We are delighted to share the proposed designs for our new stadium at Moor Lane, going into planning imminently!"
And ex-United star Gary Neville posted: "Come on @SalfordCityFC!!"
Initial plans for the new stadium were unveiled earlier this year, complete with new stands and terracing.
It is understood a new all-seater stand would run the length of the pitch, with an executive seating and viewing area planned for the centre.
A new all-seater stand would run the length of the pitch, with an executive seating and viewing area
Class of 92 documentary returns to BBC One
Standing terraces would sit at the east and west ends of the ground, behind the goals.
Class of '92 Suite, allowing the club's illustrious owners the best seat in the house, is also believed to be included in the plans - a far cry from the grass mound they currently watch the action from.
The iconic concrete main stand which currently stands at Moor Lane is set to remain, with a view to further renovation, next to the existing clubhouse, tea bar and dressing rooms.
Plans to segregate visiting fans are also understood to be included in the beefed-up blueprints.
Three separate fan zones are understood to have been included in the plans - one for home supporters, one for away and one for families.
A small car park will be added for executives, it is understood.
Gary Neville's plans for Manchester
This St Michael's poetry has to be heard
We're rebuild pub brick by brick
Historic England blast skyscraper plan
Gary Neville on life in 'my Manchester'
ShoppingMum puts school meal parcels to shame with massive Aldi food shop costing just £10The savvy shopper revealed how far the change from a bottle of milk went at the budget supermarket
What's OnA 'groundbreaking' new drama focusing on the AIDS epidemic of the 1980s and mostly filmed in Manchester will air on Channel 4 this month


text:
8mins India in talks to be part of East Asian Observatories Consortium
48mins Delhi Assembly elections: Kejriwal files papers after six hours in queue
59mins Need to have fairer, more equitable terms in trade relations, says Piyush Goyal
59mins Police officer killed, Army jawan injured in encounter in J&K's Pulwama district
1hr Dabholkar killing: Sanatan Sanstha member Vikram Bhave's bail plea rejected
10 new roads on outskirts to ease congestion in Bengaluru
Suchith Kidiyoor
Bengaluru, January 13, 2020 23:42 IST
KRDCL has floated a tender for a detailed feasibility report
With the aim of decongesting Bengaluru, which is choking with vehicular traffic, the Karnataka Road Development Corporation Limited (KRDCL) is developing a network of roads on the outskirts that connect directly to national highways. Once completed, they will negate the need for motorists to enter the city.
After taking up a project to develop roads on the outskirts leading to Kempegowda International Airport (KIA), the KRDCL has now floated a tender for a detailed feasibility report to develop 10 additional roads — with a total distance of 148 km — around Bengaluru.
The longest stretch (43 km) is the one from Bidadi on Mysuru-Bengaluru highway to Nelamangala Chandrappa Circle, Tavarekere and Sondekoppa. This network, said officials, will decongest NICE Road and provide alternative options for motorists travelling from Bidadi to Nelamangala.
In addition, there are plans to develop a 16-km stretch from NICE Road junction to Whitefield via Sarjapur Road. This will help people working in the IT corridor.
The estimated cost for the 10 roads is around ₹1,200 crore though the final figure will depend on the detailed feasibility report.
KRDCL Managing Director B.S. Shivakumar told The Hindu that the proposed roads will have four lanes. "As of now, beyond NICE Road, there is no good infrastructure that connects Mysuru Road with Magadi Road and Tumakuru Road. We want to build a network from Bidadi to Nelamangala. In addition to this, for the benefit of those who are using NICE Road to reach KIA, we are proposing a road network from Makali to Kakolu. This will help passengers to reach KIA faster. Providing an alternative road from NICE Road to the airport will help decongest the existing traffic at Goraguntepalya, Hebbal and other junctions," the official said.
Toll collection on the cards
The network is being developed under Phase II project beyond NICE Road and the proposed Peripheral Ring Road (PRR) project. When asked about whether KRDCL will be building toll roads from Bidadi to Nelamangala, Mr. Shivakumar said, "As per our plan, it is a toll road. However, the State government will take a final decision."
Under Phase I, the KRDCL has taken up construction of roads in the eastern and northern outskirts of Bengaluru. These include Hoskote-Budigere Cross-KIA via Budigere-Singahalli and Mylanahalli. The 20-km road is estimated to cost ₹254 crore, and it will will benefit motorists coming from Electronics City, Whitefield, Sarjapurand Hoskote.
Other roads to be developed in Phase I are the stretch from Nelamangala to Madhure, and Madhure to Devanahalli Road via Rajanukunte and Thimmasandra. The 39.24-km road is estimated to cost ₹548 crore.
KRDCL had proposed that toll be collected on these roads.
Related Topics Bengaluru
Previous Story 600 Bengaluru police personnel in drum jam
Next Story Co-operative bank meeting postponed
Printable version | Jan 21, 2020 7:04:44 PM | https://www.thehindu.com/news/cities/bangalore/10-new-roads-on-outskirts-to-ease-congestion-in-city/article30561778.ece
A warm gift from the police to the homeless
Vidyaranyapura police distribute blankets to people sleeping on footpaths
Next Story » Co-operative bank meeting postponed
The Hindu MetroPlus