From Protein Prediction 2 Winter Semester 2014
(Second Week(28.11.2014 - 4.12.2014))
(First Week(21.11.2014 - 27.11.2014))
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==First Week(21.11.2014 - 27.11.2014)==
==First Week(21.11.2014 - 27.11.2014)==
*Got to know about web workers.
*Got to know what and how force directed graph works
*Deciding on the libraries to be used for the implementation
*Understood Max implementation of web workers.
*Understood how spring layout works.
*Understood how spring layout works.

Revision as of 23:46, 30 December 2014

The objective of this project is to visualize a network (large networks of >2000 nodes) in a way that the distance of a node from the rest of the network is determined by the number of nodes it is connected to => the more neighbors a node has the larger is its distance from the network. The component must allow zooming in/out, selection by the number of neighbors, coloring by various thresholds and other graph-related features.


Force Directed Network is obtained by using the Force-directed graph drawing algorithms(SPRING ALGORITHM). This algorithm is mainly based on the forces assigned among the set of nodes and edges of a graph.The forces can be either atractive which is used to attract pairs of endpoints of the graph's edges towards each other or repulsive which is used to seperate all pairs of nodes.In equilibrium states for this system of forces,the edges tend to have uniform length(using spring forces) and the nodes which are not connected by any edge tend to be drawn further apart(due to electrical repulsion).


mockup 1
mockup 2
mockup 1
mockup 4


  • Zoom in and Zoom out of the graph.
  • Distance of a node from the rest of the network is determined by the number of nodes it is connected to.
  • Selection by the number of neighbors
  • Coloring by various thresholds
  • Dividing the whole network into module based on the modularity.
  • Applying filters.
  • Defining the layout of your choice.
  • Exporting the visualisation as an image.


  • Import from Text format
  • Export to image
  • Visualization Using FORCE DIRECTED NETWORK

Application Design

  • Fancy Libraries
    • d3.js
    • jQuery
    • JavaScript InfoVis Toolkit



The input data should be in json/csv format

E.g: var json = [{

     "adjacencies": [  
           "nodeTo": "graphnode1",  
           "nodeFrom": "graphnode0",  
           "data": {  
             "$color": "#557EAA"  
         }, {  
           "nodeTo": "graphnode13",  
           "nodeFrom": "graphnode0",  
           "data": {  
             "$color": "#909291"  
         }, {  
           "nodeTo": "graphnode14",  
           "nodeFrom": "graphnode0",  
           "data": {  
             "$color": "#557EAA"  



mockup 1

Roadmap for Implementation

Cytoscape Worker API :


First Week(21.11.2014 - 27.11.2014)

  • Got to know what and how force directed graph works
  • Deciding on the libraries to be used for the implementation
  • Understood how spring layout works.

Second Week(28.11.2014 - 4.12.2014)

  • Asked our doubts regarding Max's implementation of web workers in hangout.
  • Prepared the road map for the next weeks.
  • Started working on the force directed graph with 2000 nodes and web workers implementation in parallel

Third Week(28.11.2014 - 4.12.2014)

Goal Understand Max Goals To define this Milestone Plan Decide on the Approach to parallelize code Reading List (BenchmarkJS, ParallelJS, Google Dev Tools) Discuss with Max Debug Tools of Cytoscape

Max Comments & Hints: Separate the Graph into separate components (Subgraph components, Subsets of the Graph (Force-directed Layout)) Normalization, Fitting Step in the End to resolve conflicts if subset has connection / edges between Approach Arbor uses (good example to look at). Own Worker API Lot’s of different ways to parallelize things (depends on the layout) Spread Layout using ParallelJS (convert using Cytoscape Worker API) One thread is offload the computation Always measure performance on the same machine! (console, timer, profiling) It would be great to have a automated benchmarking

Rmaco: https://github.com/cytoscape/cytoscape.js/pull/700

Unexpected difficulties: synchronization between workers (avoid communication between them in the beginning)

Fourth Week(5.12.2014 - 12.12.2014)

Basic Program which is parallelised (Nested in Cytoscape) Please mind the Coding Style of Cytoscape Send Graph Data to the Worker Program and back Benchmark the simple program i.e. BenchmarkJS

Fifth Week(13.12.2014 - 18.12.2014)

Report, work on Spread Layout Algorithm. Some functions parallelized if possible.

Sixth Week(19.12.2014 - 29.12 .2014)

Run the first Layout Algorithm (pick one algorithm) with multiple cores (parallelized) Test and BenchmarkJS

Seventh Week(30.12.2014 - 05.01 .2015)

08.01.2015 Final Presentation

15.01.2015 Submission Deadline

Source Code


  • PP2_CS_2014 mentors, Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
  • Students: Kommanapalli Vasantha Kumari,Anuradha Ganapati,Ahsan ZiaUllah

Additional Links