Difference between revisions of "Project ideas"
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==Genome Browser== |
==Genome Browser== |
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+ | @Miguel, Manny: can you please add description here? |
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Relevant sources: |
Relevant sources: |
Revision as of 20:08, 11 November 2014
Contents
- 1 Venn Diagram Viewer
- 2 Genome Browser
- 3 Protein Viewer
- 4 Chemical Viewer
- 5 Graph Viewer
- 6 Gene Cluster Viewer
- 7 Dot-Bracket Notation
- 8 Pedigree Chart Visualization
- 9 Sub-cellular localization in a cell
- 10 Force directed network (spring algorithm)
- 11 HSSP curve
- 12 Graphical Model Editor
- 13 2D Chemical Components Visualizer
- 14 Genome Browser
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
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
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
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
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:
- Mika S and Rost B (2003) UniqueProt: creating representative protein sequence sets. NAR.
- Rost B (1998) Twilight zone of protein sequence alignments. Protein Eng.
Mentors: PP2_CS_2014 mentors
Students: 2
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
Genome Browser
@Miguel, Manny: can you please add description here?
Relevant sources: