This is a list of projects made by students of the MSc on Bioinformatics for Health Sciences as part of their homework on the subjects Python, Mathematics, Molecular Simulations or Systems Biology. All projects are open source and their authors can be found in the corresponding sites. Worth checking how good many of them are:
- 2011-2012
- IMMUNOSYM: Simulating immune response
- Clustering-Lib: Library of clustering methods
- PreDyJe: Python program that evaluates dehydrons in PDB files.
- NGSDataQEval: NGS data quality evaluation.
- MacroEvolve: Platform to simulate algorithms to maximize/minimize functions using AI techniques.
- CancerDynamics: Website that shows the dynamics of a tumor by solving a system of ordinary differential equations.
The results are two kind of graph images, and a gif file, being all of them available for download as a compressed file. - BindingDB: Join BindingDB and DRugBank databases.
- CancerVaccine: Simplified representation of the main immune system cells and their interactions.
- ClusteM2: MD Trajectory clustering.
- CGScore: Scoring protein-protein interaction poses with coarse grain potentials.
- MetaProt: Quality control in metagenomics.
- MultiStoPy: Stochastic and Deterministic solutions in biochemical kinetics.
- 2010-2011
- SPoRNA: Software package for analyzing statistical potentials of RNA molecules
- PythonGeneticAlgorithm: Genetic Algorithm implementation in Python
- Molecular Superposition MPI: Molecular superposition from MIPGen results
- MIPGen: Molecular Interaction Potential Generator
- Deh’s Pred: Prediction of dehydrons
- PerfectCrossMatch: Emulation of HLAmatchMaker
- Clust’em-D: Clusters results from MD runs
- BUBLES: Takes grids from MIPGen and gives you a pattern for superposition
- BIOPALO: Protein alignment optimizer
- 2009-2010
- PYENSA: PYthonbased-Elastic-Network-Sequence-Aligner
- 2008-2009
- NOTCH-DELTA: Simulating morphogenesis during development
- 2007-2008
- INMUNDO: Python program devoted to study the relationship between cells during inmune response. It is based on a 3D periodic boundary conditions grid where cells see each other and react according to certain movement, growth and interaction rules.