grnsight 4.0.0 → 6.0.0

package/documents/abstracts/SIGGRAPH 2017 Abstract/acmart.ins

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-% Doctrip file for acmart
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-% $Id: acmart.ins,v 1.1 2015/11/23 22:42:55 boris Exp $
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package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bib

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-@article{doi:10.1186/s13742-015-0077-2,
-author = {Pavlopoulos, Georgios A and Malliarakis, Dimitris and Papanikolaou, Nikolas and Theodosiou, Theodosis and Enright, Anton J and Iliopoulos, Ioannis},
-title = {Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future},
-journal = {GigaScience},
-volume = {4},
-number = {1},
-pages = {1},
-year = {2015},
-doi = {10.1186/s13742-015-0077-2},
-URL = { + http://dx.doi.org/10.1186/s13742-015-0077-2}
-}
-
-@article{d3, 
-author={Bostock, Michael and Ogievetsky, Vadim and Heer, Jeffrey},
-journal={IEEE Transactions on Visualization and Computer Graphics}, 
-title={D3; Data-Driven Documents}, 
-year={2011}, 
-volume={17}, 
-number={12}, 
-pages={2301-2309}, 
-doi={10.1109/TVCG.2011.185}, 
-ISSN={1077-2626}, 
-month={Dec}
-}
-
-@book{norman2013design,
-  title={The design of everyday things: Revised and expanded edition},
-  author={Norman, Donald A},
-  year={2013},
-  publisher={Basic books}
-}
-
-@book{shneiderman2010designing,
-  title={Designing the user interface: strategies for effective human-computer interaction},
-  author={Shneiderman, Ben},
-  year={2010},
-  publisher={Pearson Education India}
-}
-
-@book{nielsen1994usability,
-  title={Usability engineering},
-  author={Nielsen, Jakob},
-  year={1994},
-  publisher={Elsevier}
-}
-
-@article{Schade01122004,
-author = {Schade, Babette and Jansen, Gregor and Whiteway, Malcolm and Entian, Karl D and Thomas, David Y},
-title = {Cold Adaptation in Budding Yeast},
-volume = {15}, 
-number = {12}, 
-pages = {5492-5502}, 
-year = {2004}, 
-doi = {10.1091/mbc.E04-03-0167}, 
-abstract ={We have determined the transcriptional response of the budding yeast Saccharomyces cerevisiae to cold. Yeast cells were exposed to 10°C for different lengths of time, and DNA microarrays were used to characterize the changes in transcript abundance. Two distinct groups of transcriptionally modulated genes were identified and defined as the early cold response and the late cold response. A detailed comparison of the cold response with various environmental stress responses revealed a substantial overlap between environmental stress response genes and late cold response genes. In addition, the accumulation of the carbohydrate reserves trehalose and glycogen is induced during late cold response. These observations suggest that the environmental stress response (ESR) occurs during the late cold response. The transcriptional activators Msn2p and Msn4p are involved in the induction of genes common to many stress responses, and we show that they mediate the stress response pattern observed during the late cold response. In contrast, classical markers of the ESR were absent during the early cold response, and the transcriptional response of the early cold response genes was Msn2p/Msn4p independent. This implies that the cold-specific early response is mediated by a different and as yet uncharacterized regulatory mechanism.}, 
-URL = {http://www.molbiolcell.org/content/15/12/5492.abstract}, 
-journal = {Molecular Biology of the Cell} 
-}
-
-@book{Tufte:1986:VDQ:33404,
- author = {Tufte, Edward R},
- title = {The Visual Display of Quantitative Information},
- year = {1986},
- isbn = {0-9613921-0-X},
- publisher = {Graphics Press},
- address = {Cheshire, CT, USA},
-} 
-
-@book{card1999readings,
-  title={Readings in information visualization: using vision to think},
-  author={Card, Stuart K and Mackinlay, Jock D and Shneiderman, Ben},
-  year={1999},
-  publisher={Morgan Kaufmann}
-}
-
-@article{peerj,
-  author = {Dahlquist, Kam D and Dionisio, John David N and Fitzpatrick, Ben G and Anguiano, Nicole A and Varshneya, Anindita and Southwick, Britain J and Samdarshi, Mihir},
-  title = {GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks},
-  volume = {2},
-  pages = {e85},
-  year = {2016},
-  doi = {10.7717/peerj-cs.85},
-  url = {https://peerj.com/articles/cs-85/},
-  journal = {PeerJ Computer Science}
-}

package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.tex

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-\documentclass[sigconf,review]{acmart}
-
-\usepackage{booktabs} % For formal tables
-\usepackage{subfigure}
-\usepackage{url}
-
-% Copyright
-\setcopyright{none}
-%\setcopyright{acmcopyright}
-%\setcopyright{acmlicensed}
-%\setcopyright{rightsretained}
-%\setcopyright{usgov}
-%\setcopyright{usgovmixed}
-%\setcopyright{cagov}
-%\setcopyright{cagovmixed}
-
-
-% DOI
-\acmDOI{10.475/123_4}
-
-% ISBN
-\acmISBN{123-4567-24-567/17/06}
-
-%Conference
-\acmConference[SIGGRAPH 2017 Posters]{SIGGRAPH 2017 Posters}{August 2017}{Los Angeles, CA, USA}
-\acmYear{2017}
-\copyrightyear{2017}
-\acmPrice{15.00}
-
-% use the "authoryear" citation style.
-\citestyle{acmauthoryear}
-\setcitestyle{square}
-
-\begin{document}
-\title{GRNsight v2: a web application and service for visualizing models of small- to 
-medium-scale gene regulatory networks}
-
-\author{Eileen J. Choe}
-\orcid{0002-8116-9224}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Electrical Engineering \& Computer Science}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{echoe@lion.lmu.edu}
-
-\author{Nicole A. Anguiano}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Electrical Engineering \& Computer Science}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{nicole.ang94@gmail.com}
-
-\author{Anindita Varshneya}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Biology}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{anu.varshneya@gmail.com}
-
-\author{Mihir Samdarshi}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Biology}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{msamdars@lion.lmu.edu}
-
-\author{Yeon-Soo Shin}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Electrical Engineering \& Computer Science}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{yshin4@lion.lmu.edu}
-
-\author{Edward B. Bachoura}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Electrical Engineering \& Computer Science}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{ebachour@lion.lmu.edu}
-
-\author{John David N. Dionisio}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Electrical Engineering \& Computer Science}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{dondi@lmu.edu}
-
-
-\author{Kam D. Dahlquist}
-\affiliation{
-  \institution{Loyola Marymount University}
-%  \department{Department of Biology}
-  \streetaddress{1 LMU Drive}
-  \city{Los Angeles}
-  \state{California}
-  \postcode{90045}
-}
-\email{kdahlquist@lmu.edu}
-
-
-% The default list of authors is too long for headers}
-\renewcommand{\shortauthors}{E. Choe et. al.}
-
-\begin{abstract}
-
-We present new features in v2 of GRNsight, a web application and service for interactive visualization of small- to medium-scale gene regulatory networks (GRNs) \cite{peerj}. A GRN consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. GRNsight produces weighted or unweighted network graphs from an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. GRNsight represents genes as nodes and regulatory connections as directed edges with colors, end markers, and thicknesses corresponding to the sign and magnitude of activation or repression of the target gene. For GRNsight v2, the user was given greater control over the network visualization's bounding box and viewport size, as well as the way edges and their weights are displayed. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, and has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. The GRNsight application (\url{http://dondi.github.io/GRNsight/}) and code (\url{https://github.com/dondi/GRNsight}) are available under the open source BSD license.
-
-\end{abstract}
-
-%
-% The code below should be generated by the tool at
-% http://dl.acm.org/ccs.cfm
-% Please copy and paste the code instead of the example below. 
-%
-\begin{CCSXML}
-<ccs2012>
-<concept>
-<concept_id>10003120.10003145.10003147.10010364</concept_id>
-<concept_desc>Human-centered computing~Scientific visualization</concept_desc>
-<concept_significance>500</concept_significance>
-</concept>
-<concept>
-<concept_id>10003120.10003145.10003151.10011771</concept_id>
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-\end{CCSXML}
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-\ccsdesc[500]{Human-centered computing~Scientific visualization}
-\ccsdesc[500]{Human-centered computing~Visualization toolkits}
-
-% We no longer use \terms command
-%\terms{Theory}
-
-\keywords{Scientific Visualization, Software Engineering, Bioinformatics}
-
-\begin{teaserfigure}
-    \centering
-    \subfigure[Screenshot of GRNsight]
-    {
-        \includegraphics[height=1.5in]{screenshot-auto.png}
-        \label{fig:full-screenshot}
-    }
-    \subfigure[Weighted graph after manual manipulation.]
-    {
-        \includegraphics[height=1.5in]{never-weights.png}
-        \label{fig:no-weights}
-    }
-    \subfigure[Weighted graph with edge weights displayed.]
-    {
-        \includegraphics[height=1.5in]{always-weights.png}	
-        \label{fig:with-weights}
-    }
-    \caption{GRNsight v2's automatic graph layout of a 21-gene, 31-edge demo file within an adaptive bounding box (a) allows the gene regulatory network graph to fully relax. Zooming and scrolling options allow the user to see the entire graph when it extends beyond the viewport; (b) the user can manipulate the display of the graph through manual node dragging, and can either hide (b), or show (c) all the weight values, which display on the edges.
-    }
-    \label{fig:screenshots}
-\end{teaserfigure}
-
-\maketitle
-
-\section{Graph Customizations for GRNs}
-
-GRNsight is a web application and service for the interactive visualization of small- to medium-scale gene regulatory networks (GRNs), optimized for use by novice and experienced biologists alike to quickly and easily view unweighted and weighted network graphs \cite{peerj}. Graph visualization in GRNsight is facilitated by the Data-Driven Documents JavaScript library \cite{d3}. D3.js provides data mapping and layout routines, which we heavily customized to produce a graph as a Scalable Vector Graphics (SVG) drawing from the gene object JSON representation provided by the GRNsight web API. Genes are mapped onto labeled rectangles, and directed edges are mapped into Bezier curves. The resulting graph is interactive, initially using D3.js's force graph layout algorithm to automatically determine the positions of the gene rectangles, but also allowing the user to manually manipulate the graph by node dragging. Since the release of GRNsight v1, feedback from peer review and the related GRNmap software modeling team (\url{http://kdahlquist.github.io/GRNmap/}) have motivated the following improvements in GRNsight v2.
-
-\subsection{Separation of Viewport from Graph Bounding Box}
-The default behavior of D3.js's force graph layout algorithm is to give the graph an \emph{a priori} bounding box, which was initially set to fit to a single viewport size. However, the fixed size did not allow for graphs above a relatively small number of nodes to fully come to rest. Nodes would instead bump up against the edge of the bounding box. Thus, we revised the algorithm to provide an option for an adaptive bounding box that could expand beyond the viewport. This allows the graph to expand as far as required for it to converge to a steady state, allowing the force graph parameters to be fully applied. Because of this change, the ability for the user to zoom and scroll the graph within the viewport was also added. The option to utilize the default behavior of a bounding box fixed to the viewport was also retained.
-
-There are three size options for the viewport: small, medium and large. Initially upon loading GRNsight, the best of these preset viewport sizes is chosen using the current size of the browser window. The viewport (and bounding box, if fixed to viewport) can also be custom-fit to the maximize the available space in the browser, beyond these three presets. These settings can be changed at any time. 
-
-\subsection{Edge Weight Value Display Options}
-In GRNsight v1, edge weight values were only displayed upon mouse-over of the edge, one value at a time, making it difficult to compare weight values between two edges. In GRNsight v2, the option now exists for users to always show or always hide weights, as well as the default option of viewing weight values only upon mouse-over (Figure~\ref{fig:screenshots}). Edge Options are selected in the sidebar menu, and under the Format dropdown in the menu bar.
-
-\subsection{Graph Normalization}
-
-To allow for the comparison of weighted network graphs, GRNsight v2 adds the option to customize the normalization factor applied to edge thicknesses. By default, GRNsight detects the maximum and minimum edge weight values of a network, and normalizes the data to fit within 12 distinct preset edge thicknesses corresponding to the strength of the regulatory relationship. This ensures that the edges of a weighted graph are visually distinguishable regardless of the absolute values of the weights. However, with this model, a graph with weights in the range \(-1\) to \(1\) could appear the same as a graph with weights in the range \(-10\) to \(10\). By adding the option for user-specified minimum and maximum values, the edge thicknesses can be normalized to consistent values, so the user can compare different graphs on the same scale.
-
-\begin{figure}[h]
-    \centering
-    \subfigure[Network A]
-    {
-        \includegraphics[height=.5in]{networkA.png}
-        \label{fig:networkA}
-    }
-    \subfigure[Network B without Normalization]
-    {
-        \includegraphics[height=.5in]{networkB.png}
-        \label{fig:networkB}
-    }
-    \subfigure[Network B with Normalization]
-    {
-        \includegraphics[height=.5in]{networkB-normalized.png}	
-        \label{fig:networkB-normalized}
-    }
-    \caption{GRNsight automatically detects the minimum and maximum weights in (a) and (b) to normalize and set edge thicknesses. By overriding the maximum and minimum values of Network B and setting them to \(-3, 3\) in (c), Network B is now normalized to match the scale of Network A.}
-    \label{fig:network-screenshots}
-\end{figure}
-
-\section{Conclusion and Future Work}
-We have successfully built upon GRNsight in v2 to expand its visualization and layout capabilities, giving the user more control over the visual display of the network graph. GRNsight's visualization and automatic layout of unweighted and weighted network graphs enables the interpretation of weight parameters more easily than one could from an adjacency matrix alone.
-
-GRNsight is in active development, closely interacting with the GRNmap modeling group. We plan to add features to compute and display graph statistics, such as betweenness centrality, and provide different graph layout options, such as a hierarchical or block layout, as well as explore the effectiveness of alternate visualization paradigms for biologist users who are seeking visual insight into GRNs.
-
-\bibliographystyle{ACM-Reference-Format}
-\bibliography{siggraph-abstract-review}
-
-\end{document}

package/documents/abstracts/SWE Collegiate Competition 2017.md

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-Abstract (500 words)
-
-**GRNsight v2: a web application for visualizing models of small gene regulatory networks**
-
-Authors - Eileen J. Choe, Nicole A. Anguiano, Anindita Varshneya, Mihir Samdarshi, Yeon-Soo Shin, Edward B. Bachoura, John David N. Dionisio, and Kam D. Dahlquist
-
-In systems biology, an effective network visualization of gene regulatory networks (GRNs) allows users to derive insights from the data that model these networks. A GRN consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. Although many software applications exist for network visualization, most require installation of stand-alone software, have a complex feature set that novice users find difficult to learn, or are specialized for large networks.  To address this, we have developed GRNsight, a web application and service that fills a niche for visualizing small- to medium-scale GRNs in a way that is simple and intuitive to use, and adds value to the interpretation of GRN modeling results. GRNsight automatically lays out weighted or unweighted network graphs from an Excel workbook containing an adjacency matrix, a Simple Interaction Format (SIF) text file, or a GraphML (XML) file. GRNsight represents genes as nodes and regulatory connections as directed edges with colors, end markers, and thicknesses corresponding to weight values that represent the sign and magnitude of activation or repression of the target gene. GRNsight is written in JavaScript, and builds upon the D3.js visualization library to generate a force-directed graph that responds to changes in force graph parameter sliders. Manual node dragging can be used to refine the visualization. Since the release of GRNsight v1, feedback from peer review and the related GRNmap software modeling team has motivated improvements and new features. In GRNsight v2, the graph bounding box is separated from the viewport and is allowed to expand as far as required for the graph to converge to a steady-state, allowing the force graph parameters to be fully applied.  Because of this change, the ability for the user to zoom and scroll the graph within the viewport was added. The option to restrict the graph to the viewport was also retained. New analysis features include the ability to always or never show edge weight values, the ability to customize the edge thickness normalization factor, and set the threshold for coloring the edges gray. These features facilitate comparison of multiple graphs so that the thicknesses of the edges will be on the same scale and allows the user to gauge the importance of particular regulatory relationships by "graying out" weak connections. Based on feedback from initial usability testing by the GRNmap modeling group and undergraduates in the Biomathematical Modeling course at Loyola Marymount University, GRNsight's visualization features enable the interpretation of weight values more easily than one could from the numerical data alone. GRNsight follows open and test-driven development software engineering best practices, with an exhaustive testing framework consisting of over 230 unit tests for quality control. Future plans include providing different graph layout options, computing and displaying graph statistics, and coloring the nodes to represent each gene's expression over time. The GRNsight application http://dondi.github.io/GRNsight/ and code https://github.com/dondi/GRNsight are available under the open source BSD license.
-
-(490 words)