The Bielefeld University Bioinformatics Server

Bioinformatics Tools
A web service like BiBiServ allows to distribute current bioinformatics tools to the public, independent of the operating system and the (software-technical) experience of the user. The user needs a browser and Internet access. Interaction with the tools is moderated by a web interface, providing user guidance and requiring only a minimum of special skills (e.g. knowledge of input formats, parameters, etc.). The BiBiServ tool section currently contains bioinformatics tools from five different areas:

• Genome Comparison:
  • REPuter: efficient and complete detection of various types of repeats
  • MGA: Multiple Genome Aligner
  • AGenDA: Alignment-based Gene Detection Algorithm
• Alignments:
  • DIALIGN: segment-based multiple sequence alignments
  • DCA: Divide-and-Conquer Multiple Sequence Alignment
  • JALI: Jumping Alignments
  • AltAVisT: Alternative Alignment Visualization Tool
  • TSDA: Pairwise alignment of recombinant DNA sequences
• Primer Design:
  • GeneFisher:Design of degenerate PCR primers for known or unknown targets
• RNA Studio:
  • paRNAss: Prediction of Alternating RNA Secondary Structures
  • RNA Movies: Animated visualization of a series of RNA secondary structures
  • RNA Forester: RNA structure alignment and motif discovery
  • pknotsRG: RNA folding and thermodynamic matching, including (some) pseudoknots
• Evolutionary Relationships:
  • ROSE: Sequence data generator under a random model of sequence evolution
  • SplitsTree: Distance-based phylogeny reconstruction based on split-decomposition

Educational Media
Bioinformatics is a fast and dynamic field. While methods and resources agglomerate, a continuous stream of newcomers is entering the field. Most academic bioinformatics curricula have started only recently. The integration of knowledge from biology and computer science requires a significant educational effort. The BiBiServ Media & Distance-Education section supports teaching in bioinformatics with internet-based multimedia courses. Currently there are four online courses and tutorials available on BiBiServ:

• The ADP pages: Interactive pages that allows to study and experiment with classical dynamic programming algorithms, formulated in the framework of Algebraic Dynamic Programming
• Systematic Dynamic Programming: Notes from a tutorial given at ISMB 2000.
• SADR - Sequence analysis with distributed resources: A newcomer's course teaching how to use standard bioinformatics tools. The course material includes URLs, references, and illustrative animations. It was taught frequently from various sites, and was presented as a tutorial at ISMB 1998.
• BCD archive: The complete documentation of two internet-based, interactive courses on bioinformatics taught in 1996 and 1997 (hypertext lecture notes, session protocols, evaluation, etc.)