Difference between revisions of "Project ideas"
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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> |
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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> |
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| − | + | Mentors: PP2_CS_2014 mentors <br> |
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Students: 2 |
Students: 2 |
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[[File:Jvenn.png | 500px | center | Jvenn example]] |
[[File:Jvenn.png | 500px | center | Jvenn example]] |
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==Protein Viewer== |
==Protein Viewer== |
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| − | + | Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br> |
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Students: 2 |
Students: 2 |
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==Chemical Viewer== |
==Chemical Viewer== |
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| − | + | Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br> |
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Students: 2 |
Students: 2 |
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==Graph Viewer== |
==Graph Viewer== |
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| − | + | Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br> |
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Students: 2 |
Students: 2 |
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==Gene Cluster Viewer== |
==Gene Cluster Viewer== |
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| − | + | Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br> |
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Students: 2 |
Students: 2 |
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==Dot-Bracket Notation== |
==Dot-Bracket Notation== |
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| − | + | Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de<br> |
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Students: 2 |
Students: 2 |
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* [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.] |
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* [http://en.wikipedia.org/wiki/Pedigree_chart Wikipedia] |
* [http://en.wikipedia.org/wiki/Pedigree_chart Wikipedia] |
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| − | + | Mentors: PP2_CS_2014 mentors <br> |
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Students: 2 |
Students: 2 |
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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. |
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Similar idea: [http://compartments.jensenlab.org/Search The Compartments database] <br> |
Similar idea: [http://compartments.jensenlab.org/Search The Compartments database] <br> |
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| − | + | Mentors: PP2_CS_2014 mentors <br> |
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Students: 2 |
Students: 2 |
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* [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/] |
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* [http://gephi.github.io/ Gephi] |
* [http://gephi.github.io/ Gephi] |
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| − | + | Mentors: PP2_CS_2014 mentors, Yana Bromberg (Rutgers University) <br> |
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Students: 3-4 |
Students: 3-4 |
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Revision as of 19:08, 11 November 2014
Contents
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
