Difference between revisions of "Project ideas"

From Protein Prediction 2 Winter Semester 2014
(HSSP curve)
Line 3: Line 3:
 
Venn diagrams present a very popular method to display list comparisons. [[http://bioinfo.genotoul.fr/jvenn/index.html 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. <br>
 
Venn diagrams present a very popular method to display list comparisons. [[http://bioinfo.genotoul.fr/jvenn/index.html 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. <br>
 
Literature: [http://www.ncbi.nlm.nih.gov/pubmed/?term=jvenn%3A+an+interactive+Venn+diagram+viewer jvenn: an interactive Venn diagram viewer] <br>
 
Literature: [http://www.ncbi.nlm.nih.gov/pubmed/?term=jvenn%3A+an+interactive+Venn+diagram+viewer jvenn: an interactive Venn diagram viewer] <br>
Mentor: PP2_CS_2014 mentors <br>
+
Mentors: PP2_CS_2014 mentors <br>
 
Students: 2
 
Students: 2
 
[[File:Jvenn.png | 500px | center | Jvenn example]]
 
[[File:Jvenn.png | 500px | center | Jvenn example]]
Line 12: Line 12:
 
==Protein Viewer==
 
==Protein Viewer==
   
Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
+
Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
 
Students: 2
 
Students: 2
   
 
==Chemical Viewer==
 
==Chemical Viewer==
   
Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
+
Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
 
Students: 2
 
Students: 2
   
 
==Graph Viewer==
 
==Graph Viewer==
   
Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
+
Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
 
Students: 2
 
Students: 2
   
 
==Gene Cluster Viewer==
 
==Gene Cluster Viewer==
   
Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
+
Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
 
Students: 2
 
Students: 2
   
 
==Dot-Bracket Notation==
 
==Dot-Bracket Notation==
   
Mentor: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
+
Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br>
 
Students: 2
 
Students: 2
   
Line 47: Line 47:
 
* [https://www.jsbi.org/pdfs/journal1/GIW00/GIW00F07.pdf Wong L. (2000) Visualization and manipulation of pedigree diagrams. Genome Informatics.]
 
* [https://www.jsbi.org/pdfs/journal1/GIW00/GIW00F07.pdf Wong L. (2000) Visualization and manipulation of pedigree diagrams. Genome Informatics.]
 
* [http://en.wikipedia.org/wiki/Pedigree_chart Wikipedia]
 
* [http://en.wikipedia.org/wiki/Pedigree_chart Wikipedia]
Mentor: PP2_CS_2014 mentors <br>
+
Mentors: PP2_CS_2014 mentors <br>
 
Students: 2
 
Students: 2
   
Line 55: Line 55:
 
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.
 
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: [http://compartments.jensenlab.org/Search The Compartments database] <br>
 
Similar idea: [http://compartments.jensenlab.org/Search The Compartments database] <br>
Mentor: PP2_CS_2014 mentors <br>
+
Mentors: PP2_CS_2014 mentors <br>
 
Students: 2
 
Students: 2
   
Line 66: Line 66:
 
* [http://sydney.edu.au/engineering/it/~aquigley/3dfade/ http://sydney.edu.au/engineering/it/~aquigley/3dfade/]
 
* [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, Yana Bromberg (Rutgers University) <br>
+
Mentors: PP2_CS_2014 mentors, Yana Bromberg (Rutgers University) <br>
 
Students: 3-4
 
Students: 3-4
   

Revision as of 18:08, 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:

  • 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

HSSP curve