Journal of integrative bioinformatics

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The official bioinformatics tool list for the Journal of Integrative Bioinformatics (JIB).

All bioinformatics tools published in JIB are automatically added to with first authors having the ability to edit their entries and directly import the tools information to


Web application 
Plant biology Genomics 
Search engines and retrieval systems are popular tools at a life science desktop. The manual inspection of hundreds of database entries, that reflect a life science concept or fact, is a time intensive daily work. Hereby, not the number of query results matters, but the relevance does. In this paper, we present the LAILAPS search engine for life science databases. The concept is to combine a novel feature model for relevance ranking, a machine learning approach to model user relevance profiles, ranking improvement by user feedback tracking and an intuitive and slim web user interface, that estimates relevance rank by tracking user interactions. Queries are formulated as simple keyword lists and will be expanded by synonyms. Supporting a flexible text index and a simple data import format, LAILAPS can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. With a set of features, extracted from each database hit in combination with user relevance preferences, a neural network predicts user specific relevance scores. Using expert knowledge as training data for a predefined neural network or using users own relevance training sets, a reliable relevance ranking of database hits has been implemented. In this paper, we present the LAILAPS system, the concepts, benchmarks and use cases. LAILAPS is public available for SWISSPROT data at

JIB Publications
  • Lange M, Spies K, Bargsten J, et al. The LAILAPS Search Engine: Relevance Ranking in Life Science Databases. J Integr Bioinform. 2010;7(2):1–11. doi 10.2390/biecoll-jib-2010-110; PubMed 20134080
  • Lange M, Spies K, Colmsee C, Flemming S, Klapperstück M, Scholz U. The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases. J Integr Bioinform. 2010;7(3). doi 10.2390/biecoll-jib-2010-118; PubMed 20375444
  • Esch M, Chen J, Weise S, Hassani-Pak K, Scholz U, Lange M. A query suggestion workflow for life science IR-systems. J Integr Bioinform. 2014;11(2):237. doi 10.2390/biecoll-jib-2014-237; PubMed 24953306