Software

Here I have listed programming projects in which I have participated. Most of them originated from bioinformatic research. In the course, various techniques for software development were applied, e.g. Kanban, User Stories, or UML.

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  ModeRNA - RNA 3D structure modeling

  ModeRNA is a software for comparative modeling of RNA 3D structures. It takes a template structure and a sequence alignment, and builds a 3D model from that. ModeRNA contains many functions useful for manipulating and editing RNA as well.
  [ PubMed abstract ]

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  REPAIRtoire

  The REPAIRtoire database contains eight DNA repair pathways for selected organisms. It annotates the pathways in interactive diagrams, and lists many participating proteins, damages, diseases of the DNA repair metabolism etc.
  [ PubMed abstract ]

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  Modomics - Database of modified RNA nucleotides

  Modomics is a comprehensive resource about naturally occuring modified nucleotides in RNA. It contains a catalog of more than 100 modifications, pathways of their synthesis, detailed descriptions of modification enzymes, and modified RNA sequences (tRNA, rRNA, and snRNA).
  [ PubMed abstract ]

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  LaJolla

  LaJolla is a fast algorithm for searching similar RNA substructures. It uses n-gram based indexing and produces a set of 3D superpositions to found substructures.
  [ PubMed abstract ]

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  Knotted2Nested

  The Knotted2Nested web server removes pseudoknots from a list of RNA base pairs, using different algorithms. It produces in pseudoknot-free (dot-bracket) 2D structures.
  [ PubMed abstract ]

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  RNA @ Biopython

  I have added several small branches to the BioPython library. Some are mere bugfixes, others add functionality for working with RNA. They can be found in the public GIT repository.

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  Voronoia

  Voronoia is a softare for analyzing the packing of protein structures. It calculates packing densities and finds cavities in the protein interior. Voronoia is available as a web server, standalone program, and as a PyMOL plugin.
  [ PubMed abstract ]

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  SuperHapten

  Haptens are small molecules that cause an immune response when bound to proteins in the human body. The SuperHapten database contains more than thousand haptens with their 2D and 3D structures.
  [ PubMed abstract ]

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  eMovie PyMOL Plugin

  eMovie provides a toolbox for the PyMOL molecular viewer in which you can edit movie sequences consisting of camera movements and normal PyMOL commands assigned to specified frames.
  [ PubMed abstract ]

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  rTools PyMOL Plugin

  This is an older but frequently used collection of PyMOL plugins. It allows to use the DSSP and HBExplore programs from within PyMOL, to create animations, and call frequently used scripts.

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  Frutris - forget about vegetables

  Frutris is a Tetris-like game, in which the player piles up identical fruit adjacent to each other to make them vanish. The game has been completely written in Python and uses the Pygame library.

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  tilegamelib

  Tilegamelib is a Python library that helps creating 2D games built from square pieces. It contains Pac and Snake, two example games. The library uses Pygame.