Difference between revisions of "Project ideas"

From Protein Prediction 2 Winter Semester 2014
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==Genome Browser==
 
==Genome Browser==
  +
@Miguel, Manny: can you please add description here?
   
 
Relevant sources:
 
Relevant sources:

Revision as of 19:08, 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
Mentors: PP2_CS_2014 mentors
Students: 2

Jvenn example

Genome Browser

Protein Viewer

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

Chemical Viewer

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

Graph Viewer

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

Gene Cluster Viewer

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

Dot-Bracket Notation

Mentors: 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:

Mentors: 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
Mentors: 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.

Relevant sources:

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

Graph

HSSP curve

The HHSP curve at a threshold of interest (HSSP value=0 is default) must be visualized in a 2D graph. Additionally, alignments of protein sequences, provided by the user, must be plotted on the graph.

Literature:

Mentors: PP2_CS_2014 mentors
Students: 2

HSSP curve

Graphical Model Editor

@Juanmi, can you please add a description here? Thanks :)

2D Chemical Components Visualizer

The goal is to automatically create 2D diagrams of chemical complexes with known 3D structure according to chemical drawing conventions.

Similar project: Poseview
Mentor: Julian Heinrich (CSIRO) julian.heinrich. (at) .csiro.au


Poseview

Genome Browser

@Miguel, Manny: can you please add description here?

Relevant sources: