grnsight 5.0.0 → 5.1.0

package/documents/SDF/CMSI_402/spring_2018/402SRS_GRNSightFeedback01.txt

@@ -1,28 +0,0 @@
-GRNSight Project SRS Evaluation
-===============================
-
-Nice job on this, a very good document.
-
-Just a couple of suggestions.
-
-When thinking of requirements, try to be even more specific about what 
-you are specifying.  For example, in requirement 5.2.2.1.7, what do you
-mean by "move in the normal way afterward"?  What is the "normal" way?
-"Afterward" meaning after what, exactly?
-
-These are "philosophy of requirements" issues that you can apply in a
-*general* way to nearly all the requirements in the document.  However,
-in the essence of time remaining, I'm assigning full credit to this
-deliverable, for both the initial and the final submissions.
-
-Be sure to check your spelling...  "examen" in the paragraph for section
-5.2.2 for example...
-
-You don't have to do anything further with this document if you don't
-feel the need to do so.
-
-Deliverable D-02: 15% out of 15% = 100% which is an A-plus
-Deliverable D-05:  5% out of  5% = 100% which is an A-plus
-
-Keep up the good work!
-

package/documents/SDF/CMSI_402/spring_2018/402_SPD.md

@@ -1,223 +0,0 @@
-# 4.0 Software Development Plan
-
-## 4.1 Plan Introduction
-
-This Software Development Plan provides the details of the planned development for the GRNsight version 3.0.0. which provides a web application and service for users to upload, view, and edit graphs of gene regulatory networks.
-
-Existing applications that perform similar tasks are difficult to use for small GRNs with only a few genes represented, and often have very high learning curves. Additionally, they may require standalone download that may not be compatible with every user’s computer. GRNsight aims to provide users with a simple, clean, and easy to use application for visualizing small- to medium-scale gene regulatory networks.
-
-As a part of development, a series of deliverables will be created. 
-
-* Project Proposal Presentations and Project Proposal Paragraph Document was submitted January 22nd 2018.
-* Requirements Document was submitted February 5th 2018.
-* Software Development Plan will be submitted by March 5th 2018.
-* Software Development Plan resubmit will be submitted by March 19th 2018.
-* Requirements Document resubmit will be submitted by April 2nd 2018.
-* Preliminary Version of Poster will be submitted by April 9th 2018.
-* Final Presentation / Demonstration will be April 30th 2018.
-
-
-
-### 4.1.1 Project Deliverables
-
-This section will explain in detail the project deliverables that will be completed and submitted throughout the production of the GRNsight software.
-
-* 4.1.1.1 Project Proposal Document
-  * The project proposal document was submitted on January 22nd. It contained initial information about the scope of the project, the features that are intended to be complete, and an initial set of information about the project itself. It also detailed the rational behind the project. The proposal was presented as a document as well as a presentation given to the class on January 22rd.
-* 4.1.1.2 Requirements Specification Document
-  * The requirements specification document was submitted February 5th. This document contains the information about the requirements of the project, including required features, performance goals, and hardware and software. It also contained projected goals that may be completed over the course of the 402 class. A resubmit of this document will be completed by April 2nd, containing improvements and changes requested by the primary user, Kam Dahlquist, as well as the professor, B.J. Johnson.
-* 4.1.1.3 Software Development Plan
-  * This document is the software development plan. It is to be submitted by March 5th.  This document contains the information about the projected plan of development for the GRNsight software as it currently stands. It contains information about the schedule of the development tasks, as well as the deliverables to be given to the customer. A resubmit of this document containing improvements and changes will be completed by March 19th.
-* 4.1.1.4 Oral Status Reports
-  * Throughout the entire time of development, oral status reports will be given each week. These status reports will contain information on the current task or tasks being completed, what tasks have been completed since the previous status report, and what challenges are currently being faced in completing the current task, if any. 
-* 4.1.1.5 Written Status Reports
-  * These written status reports are very similar in content to the oral status reports. They will contain accomplishments since the last status report, tasks that are to be completed before the next week, and any predicted or current challenges that are faced. 
-* 4.1.1.6 Poster
-  * Preliminary version of poster is to be submitted by April 9th. The poster will provide a summary of the new features of GRNsight version 3.0.0. in a visually appealing way. The poster contains information about the project description, development concerns, citations, and graphics that explain the new features. The final version of the poster will be submitted by April 30th.
-* 4.1.1.7 Final Presentation / Demonstration
-  * The final product presentation will be made on April 30th, time TBD, to give an overview of the project. In addition, demonstration will be held to show the users a live GRNsight and give the opportunity for the users to use the new features.
-
-
-
-## 4.2 Project Resources
-
-The following sections will detail the project resources necessary for the completion of the project. 
-
-* 4.2.1 Hardware Resources
-
-  Development:
-  * Macbook Air, macOS Sierra v10.12.3, 1.4GHz IntelCore i5 Processor, 4GB 1600 MHz DDR3 RAM.
-
-  Deployment:
-  * Server hosted on AWS 
-  * Ubuntu 14.04.2 LTS, 7.74 GB RAM
-
-* 4.2.2 Software Resources
-
-  * Operating System: macOS Sierra v10.12.6 && Windows 10
-  * Editor: Atom v 1.24.0 x64
-    * Packages:
-      * Stylus v3.1.0
-      * Atom-jade v0.3.0
-      * Language-git v0.19.0
-      * Git-diff v1.2.0
-  * Project Software Requirements:
-      * Node v9.5.0
-      * npm v5.6.0
-        * NPM Packages:
-        * Chai v1.10.0
-        * Cors v2.8.1
-        * Cytoscape v2.7.14
-        * Express v4.16.0
-        * Googleapis v1.1.5
-        * Istanbul v0.4.5
-        * Jade v1.11.0
-        * Jquery-Extend v2.0.3
-        * Mocha v2.5.3
-        * Moment v2.17.1
-        * Multiparty v4.1.3
-        * Node-xlsx v0.7.2
-        * Nodemon v1.11.0
-        * Parallelshell v3.0.1
-        * Should v11.2.0
-        * Stylus v0.54.5
-        * Supertest v3.0.0
-        * Xml2js v0.4.17
-        * Xmlbuilder v8.2.2
-        * body-parser: ^1.18.2,
-        * errorhandler: ^1.5.0,
-        * method-override: ^2.3.10,
-        * morgan: ^1.9.0,
-        * serve-static: ^1.13.1, 
-        * coveralls: ^2.13.1,
-        * eslint: ^3.19.0,
-        * markdown-pdf: ^8.0.0,
-        * mocha-lcov-reporter: ^1.3.0
-        * Google Chrome v56.0.2924.87 (64-bit)
-        * Mozilla Firefox v51.0.1 (64-bit)
-        * Libraries:
-          * Bootstrap v3.2.0
-          * D3.js v3.4.4
-          * Bootstrap CSS v3.1.1
-          * Bootstrap File Input 
-          * jQuery v1.11.0
-
-
-
-## 4.3 Project Organization / Human Resources
-
-This section contains the information on the project organization. GRNsight is a team project currently comprised of 3 undergraduates: Eileen Choe (Computer Science), Jen Shin (Computer Science), and Mihir Samdarshi (Biology), and 2 faculty advisors: Dr. John Dionisio (Computer Science) and Dr. Kam Dahlquist (Biology).
-
-For the CMSI402 Senior Project, Eileen and Jen will be completing four majors feature additions to GRNsight. The table below outlines the project member responsible for each feature: 
-
-| Task                              | Developer |
-| --------------------------------- | --------- |
-| Updated GRNmap Spreadsheet Parser | Eileen    |
-| Node Coloring Framework           | Eileen    |
-| Block Layout                      | Jen       |
-| Alternative Layouts               | Jen       |
-
-### 4.3.1 Updated GRNmap Spreadsheet Parser
-
-GRNsight is designed to accept Excel workbooks from GRNmap, a MATLAB GRN modeling program, and lay out the network graph specified by an adjacency matrix contained within one of the worksheets. However, the GRNmap output contains additional worksheets which store data about the GRN and results of the GRNmap simulations that have not been displayed or visualized by GRNsight. To address this, the Excel spreadsheet importer will be redesigned to parse and store data from the entire GRNmap output workbook in a standardized JavaScript Object Notation (JSON) data structure. The complete data extraction from the GRNsight output includes experimental and simulated temporal expression data for each gene in the network.
-
-1. Investigate current spreadsheet controller
-2. Research the GRNmap input and output workbook formatting standards
-3. Design a data model and implement a parser for GRNmap "expression" type sheets
-4. Design a data model and implement a parser for GRNmap "2 column" type sheets
-5. Design a data model and implement a parser for GRNmap "meta data" type sheets
-6. Write unit tests to ensure software quality
-
-
-
-### 4.3.2 Node Coloring Framework
-
-A coloring framework will be developed to visualize expression data in the form of a stacked heat map overlay of the nodes which compares the experimental and simulated gene expression levels. Node coloring allows GRNsight users to better derive insights from the data that model these networks.
-
-1. Perform user interviews to better understand use cases for node coloring
-2. Decide on a color scheme that is color-blind friendly
-3. Review D3 visualization library and complete relevant tutorials
-4. Create a first draft of the node coloring framework
-5. Develop UI menu for node coloring customization
-6. Integrate user feedback for final draft of node coloring framework
-7. Write unit tests to ensure software quality
-
-
-
-### 4.3.3 Block Layout
-
-The block layout alphabetically organizes the nodes in a grid pattern. Users can use a button to apply the layout to the graph and the nodes will be organized alphabetically left to right, then top to bottom. This will make it easier and faster for the users to analyze the data. 
-
-The main developing goals to implement block layout includes:
-
-1. Grid layout button
-2. Applying d3-v4 grid layout.
-3. Including webpack in order to use webpack to import.
-4. Viewport size adaptive grid layout
-5. Alphabetizing the nodes.
-6. Centering the grid layout graph
-7. Toggle to disable/enable force graph with the grid layout button
-
-
-
-### 4.3.4 Alternate Layouts
-
-Once the block layout is finished, alternate layouts will be developed in addition. Currently hierarchical layout and snap to grid feature are highest priority to implement next. The alternate graph layout provides the users an option to organize the nodes on the graph.
-
-If time allows:
-
-1. hierarchical layout
-2. snap to grid feature
-
-
-
-## 4.4 Schedule
-
-### 4.4.1 [GANTT Chart](https://docs.google.com/spreadsheets/d/1FSXKUKDkfHP9eXH_88yZcgP6hzxQvJ-2ait0InETpas/edit?ts=5a8e3963#gid=1115838130)
-
-![gantt chart](https://github.com/dondi/GRNsight/blob/master/documents/SDF/CMSI_402/spring_2018/402-gantt.png)
-
-### 4.4.2 Task / Resource Table
-
-4.4.2.1 Updated GRNmap Spreadsheet Parser
-
-| Task                                     | Hardware                                 | Software                                 |
-| ---------------------------------------- | ---------------------------------------- | ---------------------------------------- |
-| Investigate current spreadsheet controller | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Research the GRNmap input and output workbook formatting standards | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Design a data model and implement a parser for GRNmap "expression" type sheets | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Design a data model and implement a parser for GRNmap "2 column" type sheets | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Design a data model and implement a parser for GRNmap "meta data" type sheets | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Write unit tests to ensure software quality | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-
-4.4.2.2 Node Coloring Framework
-
-| Task                                     | Hardware                                 | Software                                 |
-| ---------------------------------------- | ---------------------------------------- | ---------------------------------------- |
-| Perform user interviews to better understand use cases for node coloring | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Decide on a color scheme that is color-blind friendly | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Review D3 visualization library and complete relevant tutorials | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Create a first draft of the node coloring framework | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Develop UI menu for node coloring customization | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Integrate user feedback for final draft of node coloring framework | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Write unit tests to ensure software quality | MacBook Pro (Retina, 13-inch, Mid 2014)  2.6 GHz Intel Core i5 | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-
-4.4.2.3
-
-| Task                                                         | Hardware                              | Software                                              |
-| ------------------------------------------------------------ | ------------------------------------- | ----------------------------------------------------- |
-| Grid layout button                                           | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Applying d3-v4 grid layout                                   | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Including webpack in order to use webpack to import          | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Viewport size adaptive grid layout                           | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Alphabetizing the nodes                                      | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Centering the grid layout graph                              | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| Toggle to disable/enable force graph with the grid layout button | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-
-4.4.2.4
-
-| Task                 | Hardware                              | Software                                              |
-| -------------------- | ------------------------------------- | ----------------------------------------------------- |
-| hierarchical layout  | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-| snap to grid feature | Windows 10 x64 Dell intel i7 2.40 GHz | Atom, Node, Bootstrap, jQuery, D3.js, Chrome, Firefox |
-

package/documents/SDF/CMSI_402/spring_2018/ProjectProposal.md

@@ -1,22 +0,0 @@
-# Project Proposal
-- Eileen Choe & Jen Shin
-- January 22, 2018
-
-## Description
-GRNsight is a web application and service for visualizing small- to medium-scale gene regulatory networks (GRNs). 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 by representing genes as nodes and regulatory connections as edges, with colors, end markers, and thicknesses corresponding to the sign and magnitude of activation or repression.
-
-We will develop two major features for our 402 project: node coloring and block layout.
-
-### Node Coloring
-GRNsight was originally designed to accept Excel workbooks seamlessly from GRNmap, a MATLAB GRN modeling program, and lay out the network graph specified by an adjacency matrix contained within a worksheet named “network” or “network_optimized_weights.” However, the GRNmap output contains additional worksheets, which include temporal gene expression data and the results of the GRNmap forward simulation. In GRNsight v3, the Excel spreadsheet importer will be redesigned to read and store data from the entire GRNmap output workbook as a first step towards extending the visualization capabilities of GRNsight. Using the extended capabilities of the importer, a framework will be developed to visualize the gene expression over time, through coloring the nodes in the network graph. The node coloring feature provides a more complete visual representation of the GRN, allowing GRNsight users to better derive insights from the data that model these networks.
-
-### Block layout
-In addition, GRNsight v3 will allow the users to display the graph in block layout. Currently GRNsight does not have any options to organize the genes. Users have to manually move the nodes one by one which costs time and effort. There is no way of saving the current position or the layout that the users created manually. This requires the users to repeatedly do the same action even for the same datasheet that they already manually created a layout for. The block layout functionality will lay the nodes in alphabetical order, left to right first, then top to bottom and better display the genes in organized manner. Users can toggle the block layout option by using the menu item on the left. The nodes will be laid out in a grid pattern with even spaces between them. There will be no forces applied, but the nodes can be moved in the normal way afterward. 
-
-GRNsight has been in active development since 2016, and is an ongoing undergraduate research project advised by Dr. Kam Dahlquist (Biology) and Dr. John Dionisio (Computer Science). The end users of GRNsight are biologists seeeking insight into their GRN data.
-The GRNsight application http://dondi.github.io/GRNsight/ and code https://github.com/dondi/GRNsight are available under the open source BSD license.
-
-## Justification
-We have both been working on GRNsight as undergraduate researchers for over a year, and this project gives us an opportunity to fully develop two major features for GRNsight that will enhance the feature set and user experience of the application. This project will allow us to apply the knowledge we've gained from courses in the LMU Computer Science curriculum such as Interaction Design, Programming Languages, Data Structures, and Computer Graphics. We believe that the scope of the two features we will develop are appropriate for the duration of the semester, and will be challenging as well as interesting.
-
-Block layout is a good feature to develop because it solves the problem that the users are currently having. It helps the users to test and analyze the graph more easily. If the functionality is finished before the semester, other layouts such as hierarchical layout, will be implemented in addition.

package/documents/SDF/CMSI_402/spring_2018/SoftwareRequirementsSpecification.md

@@ -1,88 +0,0 @@
-# 5.0 Software Requirements Specification
-
-## 5.1 Introduction
-GRNsight is a web application and service for visualizing gene regulatory networks. It consists of two parts: a web client and a server. The web client displays the web page that the user interacts with and allows the user to upload the data. Uploaded data is sent to the server, where it is formatted and processed before being returned to the web client. The web client then draws the data as a graph.
-
-Section 5.2 contains the functional requirements GRNsight should be expected to have. Section 5.3 contains the performance requirements expected of GRNsight. Section 5.4 contains the environment requirements necessary for GRNsight to run.
-
-## 5.2 Functional Requirements
-Two new features will be added to GRNsight: Node coloring and alternate graph layout.
-
-### 5.2.1 Node Coloring
-As a first step towards node coloring, the Excel spreadsheet importer will be redesigned to parse and store data from the entire GRNmap output workbook in a standardized JavaScript Object Notation (JSON) data structure. The complete data extraction from the GRNsight output includes experimental and simulated temporal expression data for each gene in the network. A node coloring framework will be developed to visualize this expression data in the form of a stacked heat map overlay which compares the experimental and simulated gene expression levels over time. 
-
-5.2.1.1 GRNsight Data Structure Redesign.
-
-  - 5.2.1.1.1 The GRNsight Excel spreadsheet parser shall perform a JSON extraction of all sheets detected in the Microsoft Excel workbook.
-  - 5.2.1.1.2 The GRNsight Excel spreadsheet parser shall inform the user if syntactic errors are detected.
-  - 5.2.1.1.3 The GRNsight Excel spreadsheet parser shall inform the user if semantic errors are detected.
-  
-5.2.1.2 Node Coloring
-  - 5.2.1.2.1 Nodes shall be colored in the network graph in the heatmap style if expression data sheets are detected in the input.
-  - 5.2.1.2.2 Node coloring slices shall be subdivided based on the number of experimental timepoints detected.
-  - 5.2.1.2.3 Expression data shall be averaged, if multiple data points exist for a gene at a given timepoint.
-  - 5.2.1.2.4 The user shall have the option to subdivide the node coloring visualization to display optimized expression data.
-  - 5.2.1.2.5 The GRNsight user interface shall provide a node coloring legend to explain the color encoding.
-
-### 5.2.2 Alternate Graph Layout
-The alternate graph layout provides the users an option to organize the nodes on the graph, thus making it easier and faster for the users to examen and analyze the data. Snap to grid would be an additional feature if time allows. Hierarcharl Layout will also be implemented if block layout is finished by time.
-
-5.2.2.1 Block Layout
-  - 5.2.2.1.1 Block layout shall allow the users to toggle between the force graph and block layouts with an option in the left menu bar.
-  - 5.2.2.1.2 Nodes shall be laid out in a grid pattern.
-  - 5.2.2.1.3 Nodes shall be equally distribute the nodes with even space to fill the area of the viewport.
-  - 5.2.2.1.4 Nodes shall not float or move like with the force graph layout once laid out.
-  - 5.2.2.1.5 Nodes shall be laid out in alphabetical order, left to right first, then top to bottom.
-  - 5.2.2.1.6 Toggling back and forth shall trigger a graph reload.
-  - 5.2.2.1.7 Nodes shall be able to move in the normal way afterward.
-  
-5.2.2.2 Hieararchal Layout
-  - 5.2.2.2.1 Hierararchal layout shall display a structured graph once triggered.
-
-
-## 5.3 Performance Requirements
-### 5.3.1 Processing Return Time
-
-5.3.1.1 The server controller shall take no more than 10 seconds to return processed data.
-
-5.3.1.2 The web client shall take no more than 10 seconds to draw the processed data.
-
-5.3.1.3 The alternate graph layouts shall take no more than 0.5 seconds to rearrange the graph.
-
-## 5.4 Environment Requirements
-### 5.4.1 Development
-
-The following chart shows the hardware requirements for GRNsight during development.
-
-|Category|Requirement|
-|--------|-----------|
-|Processor|Intel Pentium 4 Processor or Later|
-|RAM|1 GB|
-|Hard Drive Space|2 GB|
-|Display|Any|
-
-The following chart shows the software requirements for GRNsight during development.
-
-|Category|Requirement|
-|--------|-----------|
-|Browser| Chrome 56.0.2924.87 (64-bit) or later; Mozilla Firefox 51.0 (64-bit) or later |
-|Operating System|Windows 7 or later; Mac OSX 10.8 or later|
-|IDE|Atom, Sublime|
-
-### 5.4.2 Deployment
-The following chart shows the hardware requirements for GRNsight during deployment.
-
-|Category|Requirement|
-|--------|-----------|
-|Processor|Intel Pentium 4 Processor or Later|
-|RAM|1 GB|
-|Hard Drive Space|2 GB|
-|Display|Any|
-
-The following chart shows the software requirements for GRNsight during deployment.
-
-|Category|Requirement|
-|--------|-----------|
-|Browser| Chrome 56.0.2924.87 (64-bit) or later; Mozilla Firefox 51.0 (64-bit) or later |
-|Operating System|Windows 7 or later; Mac OSX 10.8 or later|
-|Server Operating System|Ubuntu 14.0.4|