Software Downloads/Resources

Several tools that we developed at our institute for scientific purposes are presented here to the scientific community. A laboratory information and management system for mouse research and a software for modelling somitogenesis are available as free downloads.

 

 

MausDB

MausDB is a laboratory mouse information and management system (LMIMS). MausDB has been custom developed for the needs and requirements of the German Mouse Clinic. But it has been made available for the scientific community as well.
Its purpose is to facilitate all aspects of handling laboratory mice

  • by storing all relevant data of a mouse facility including animal data in one central database.
  • by providing this data to all users simultaneously on a multi-user access platform.
  • by ensuring that information is up-to-date and all users have access to the same information (in contrast to working with distributed spreadsheet files).
  • by providing useful overviews and search functions

Its intended use is to comprehensively manage mouse houses ranging from one rack only up to large mouse facilites hosting tens of thousands of mice.

Further information as well as the MausDB program itself you can find here. 

If you have questions concerning the downloads or the programs, please contact
.

Publication:
Maier, H., Lengger, C., Simic, B., Fuchs, H., Gailus-Durner, V., Hrabé de Angelis, M. (2008) MausDB: an open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projectsBMC Bioinformatics 2008, 9: 169

 

 

Gene- and Cell-based simulation of dynamic expression patterns and structure formation in the presomitic mesoderm and pancreatic duct development

Somitogenesis is a process in embryonic development establishing the segmentation of the vertebrate body by the periodic separation of small balls of epithelialized cells called somites from a growing mesenchymal tissue, the presomitic mesoderm (PSM). The Delta/Notch signal transduction pathway seems to be important for boundary formation between forming somites and the remaining PSM by inducing Mesp2 expression just behind a future somitic boundary. We developed a cell- and gene-based computer model for mammalian somitogenesis, simulating a gene regulatory network combining clock (Hes1/7) and gradient (Tbx6, Fgf8, Wnt3a) with Delta/Notch signaling resulting in dynamic gene expression patterns as observed in vivo finally leading to boundary formation.

The Delta/Notch signaling pathway is also important in structuring the the growing pancreatic ducts in embryonic development. Its down-stream target Hes1 is involved in restricting Ngn3 expression to a few cells of the pancreatic duct. These Ngn3 positive cells later form the pancreatic Islets of Langerhans - the sites of insulin production regulating blood sugar concentration.

Publications (manual, supplementary info, and demo videos can be found here as well):

  • Tiedemann, H.B., Schneltzer, E., Beckers, J., Przemeck, G.K.H., Hrabě de Angelis, M.: Modeling coexistence of oscillation and Delta/Notch-mediated lateral inhibition in pancreas development and neurogenesis. J. Theor. Biol. 430, 32-44 (2017)
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  • Tiedemann, H.B., Schneltzer, E., Zeiser, S.*, Wurst, W., Beckers, J., Przemeck, G.K.H., Hrabě de Angelis, M.: Fast synchronization of ultradian oscillators controlled by Delta-Notch signaling with Cis-inhibition. PLoS Comput. Biol. 10:e1003843 (2014)
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  • Tiedemann HB, Schneltzer E, Zeiser S, Hoesel B, Beckers J, Przemeck GKH, Hrabě de Angelis M.  From dynamic Expression patterns to Boundary Formation in the Presomitic mesoderm  PLoS Comput Biol 8(6): e1002586. doi:10.1371/journal.pcbi.1002586 (2012)
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 The Java source code for different operating systems can be downloaded here.

If you have questions concerning the downloads or the programs, please contact

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