Difference between revisions of "Project ideas"

From Protein Prediction 2 Winter Semester 2014
(Force directed network (spring algorithm))
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==Force directed network (spring algorithm)==
 
==Force directed network (spring algorithm)==
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 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.
   
 
Sources:
 
Sources:
 
* [http://sydney.edu.au/engineering/it/~aquigley/3dfade/]
 
* [http://sydney.edu.au/engineering/it/~aquigley/3dfade/]
 
* [http://gephi.github.io/ Gephi]
 
* [http://gephi.github.io/ Gephi]
Mentor: PP2_CS_2014 mentors <br>
+
Mentor: PP2_CS_2014 mentors, Yana Bromberg (Rutgers University) <br>
Students: 3
+
Students: 3-4
   
 
[[File:Netscape tcv call.jpg | 300px | center | Graph]]
 
[[File:Netscape tcv call.jpg | 300px | center | Graph]]
 
   
 
==HSSP curve==
 
==HSSP curve==

Revision as of 17:57, 11 November 2014

Venn Diagram Viewer

Venn diagrams present a very popular method to display list comparisons. [Jvenn] is an interactive Venn diagram viewer written in JavaScript. The objective of this project would be to use the code base of Jvenn to make it compatible with BioJS2.0.
Literature: jvenn: an interactive Venn diagram viewer
Mentor: PP2_CS_2014 mentors
Students: 2

Jvenn example

Genome Browser

Protein Viewer

Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2

Chemical Viewer

Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2

Graph Viewer

Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2

Gene Cluster Viewer

Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2

Dot-Bracket Notation

Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2

Pedigree Chart Visualization

A pedigree chart is a simple and easy to read diagram showing the occurrence and appearance or phenotypes of a particular gene in an organism and its ancestors. Pedigrees use a standardized set of symbols:

  • squares: males
  • circles: females
  • diamonds: the sex of the person is unknown
  • filled-in (darker) symbol: someone with the phenotype in question
  • shaded or half-filled symbol: heterozygotes
  • horizontal and a vertical line: connects parents to their offspring
  • ....

Literature:

Mentor: PP2_CS_2014 mentors
Students: 2

Pedigree chart

Sub-cellular localization in a cell

Archaea, Bacteria and Eukaryota form the three domains of life. Eukaryotic cells contain a nucleus and other membrane-bound organelles. The cells of archaea and bacteria in contrast are formed by a single compartment that is surrounded by the plasma membrane (Gram-negative bacteria have an additional outer membrane). The objective of this project is to visualize biological cells and highlight by a user selected sub-cellular compartments in a way that they stand out from the un-selected ones. Similar idea: The Compartments database
Mentor: PP2_CS_2014 mentors
Students: 2

Pedigree chart

Force directed network (spring algorithm)

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.

Sources:

Mentor: PP2_CS_2014 mentors, Yana Bromberg (Rutgers University)
Students: 3-4

Graph

HSSP curve