Project ideas

From Protein Prediction 2 Winter Semester 2014
Revision as of 20:00, 11 November 2014 by Goldberg (talk | contribs)

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, Manuel Corpas (TGAC) mc. (at) .manuelcorpas.com
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:

BigWig and BigBed File Viewers

The idea came from Saket, but Ricardo might be working on it already. Wrote these guys on email/Skype and awaiting reply.

Visualization of iAnn events

The iAnn calendar is one of the most used tools to annotate and curate scientific announcements. The idea of this project is to visualize iAnn announcements in the following ways:

  • as an interactive map
  • a table
  • and e.g. a pie chart or histograms showing statistics by various keywords (dates, country, field, etc.)

Relevant sources:

Mentor: Manuel Corpas (TGAC) mc. (at) .manuelcorpas.com
Students: 2-3

Poseview

Visualization of events on the GOBLET platform

Similar idea as for iAnn events -> visualization of events based on keywords

Sources:

Mentor: Manuel Corpas (TGAC) mc. (at) .manuelcorpas.com
Students: 2-3

Visualization of FastQ formats

FASTQis a common file format storing sequencing read data together with its associated per base quality score. The objective of this project to visualize file in the fastQ format in an attractive ans easily interprtetable way. An example of a fastQ file is given below.

Sources:

Mentor: Manuel Corpas (TGAC) mc. (at) .manuelcorpas.com
Students: 2