Project ideas

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

Protein 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

The viewer is supposed to show the conserved gene order in prokaryotic genomes. The data will be derived from GenBank.

Source: Example for visualization
Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2

Dot-Bracket Notation 1

RNA secondary structure is often defined using Dot-Bracket Notation (DBN). Valid structures in DBN format are well-parenthesized words consisting of dots '.', opening '(' and closing ')' parentheses. Dotted positions are unpaired, whereas matching parenthesized positions represent base-pairing nucleotides. As the number of nucleotides interacting is always even (everyone must have a parter), the brackets must be balanced. Source: [Wikipedia: http://ultrastudio.org/en/Dot-Bracket_Notation]

Sources:

• Wikipedia

Mentors: Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2

Dot-Bracket Notation 2

This project deals with a slightly different representation of the Dot-Bracket Notation.

Sources:

• Antczak M, SzachniukM, et al. (2014) RNApdbee––a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. NAR.

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:

• Wong L. (2000) Visualization and manipulation of pedigree diagrams. Genome Informatics.
• Wikipedia

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

• http://sydney.edu.au/engineering/it/~aquigley/3dfade/
• Gephi

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 projects:

• Poseview
• iMolecule
• JSDraw

Mentors: Julian Heinrich (CSIRO) julian.heinrich. (at) .csiro.au, Björn Grüning (Galaxy) gruening. (at) .informatik.uni-freiburg.de
Students: 2-3

Genome Browser

@Miguel, Manny: can you please add a description here?

Relevant sources:

• Compact genome browser
• UCSC genome browser

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:

• Jimenez R, Corpas M. et al. (2013) iAnn: an event sharing platform for the life sciences. Bioinformatics.
• The iAnn project
• iAnn on ISCB

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

Visualization of events on the GOBLET platform

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

Sources:

• http://mygoblet.org/training-portal
  
• http://mygoblet.org/

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:

• Cock PJS, Rise P et al. (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. NAR.
• http://maq.sourceforge.net/fastq.shtml

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