Difference between revisions of "Project ideas"

From Protein Prediction 2 Winter Semester 2014
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==Sub-cellular localization in a cell==
 
==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.
 
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]
+
Similar idea: [http://compartments.jensenlab.org/Search The Compartments database] <br>
 
Mentor: PP2_CS_2014 mentors <br>
 
Mentor: PP2_CS_2014 mentors <br>
 
Students: 2
 
Students: 2

Revision as of 14:00, 11 November 2014

Sequence Logo 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


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