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Dictyostelium discoideum
Tools



Open-LIMS, ein Projekt des Instituts für Biochemie I (2010)


Figure 1: The main page of Open-LIMS.

Open-LIMS (Laboratory Information Management System) is an organism independent project management suite for biological projects. It is being developed for the Dictyostelium discoideum functional analysis project at the Institute for Biochemistry I of the University of Cologne.
It allows you to create an unlimited number of projects and subprojects, without resctrictions in the number of levels. You can make your own project frame with an individual XML based template (LIMSML). Moreover, Open-LIMS includes a complete file management function for every project. Furthermore, Open-LIMS allows the group leader to control the projects of his/her organisation unit (e.g. a group or a institute).
If a function is not included in Open-LIMS, adaption to your sepecific needs ca be realised with aditional modules.

March 03, 2010
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Compare 1.1 (2005)
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Contact:
Ludwig Eichinger
Institut für Biochemie Köln, Zentrum Biochemie
University of Cologne
http://www.uni-koeln.de/med-fak/biochemie/transcriptomics/
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Compare 1.1 works with ArrayTools output data or manually created gene lists. It compares the "Significant Gene List" in worksheet "SAM Output" from different experiment workbooks created by ArrayTools or any list of genes created. The input formats supported:
  • Experiment workbooks (SignificantGeneLists) created by Array Tools.
  • Manually created gene lists: copy your list of clones to the first column of an empty excel workbook (to first worksheet).
Open the program, mark type of comparison (SGLs or manually created lists) and select any number of (experiment) workbooks (created with ArrayTools or manually) by double-clicks. Be sure not to mix types; choose any number of ArrayTools experiment files OR manually created lists. Files to be compared are shown in the right window of Compare. Press 'Start' and save output file.
Three worksheets are creates in the output file: The first two (one in the case you compared manually created lists) list all genes with corresponding file-names, worksheet 'Compare' gives detailed information about the distribution of genes among all experiment files (this feature only works with up to 4 experiment files to compare).
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Download Compare (Exe file, 92 KB)

Array Tools 3.3 (2004)
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Contact:
Ludwig Eichinger
Institut für Biochemie Köln, Zentrum Biochemie
University of Cologne
http://www.uni-koeln.de/med-fak/biochemie/transcriptomics/
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Array Tools is an Add-In for Microsoft Excel, which is designed to handle the import and export of Dictyostelium discoideum microarray data. It can be used to:
  • Import ScanArray Express CSV to Excel.
  • Export the data to R by creating Data.spot, R Commands. R and Arrays.txt files.
  • Re-importing data from R to Excel.
  • Exporting data to SAM
More ... about ArrayTools
Download ArrayTools (Excel file, 722 KB)

Microarray-SNAKES (2003)
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Contact:
Ludwig Eichinger
Institut für Biochemie Köln, Zentrum Biochemie
University of Cologne
http://home.vrweb.de/~libotte/
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The need to precisely locate and quantify the tens of thousands of spots of microarray images in an automated way led to the development of Microarray-SNAKES (M-SNAKES) a new method using the model of a virtual, contractive and elastic closed chain for spot location and quantification. This method is based upon the active contour models (snakes; Koss et al. 1987, Int. J. Comput. Vision, 1, 321-331) and was recently used to detect cell edges in Dictyostelium discoideum (Dormann et al. 2002, Cell Motil. Cytoskeleton, 52, 221-230).
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More ... about M-SNAKES Tools
Download M-SNAKES (Zip file, 333 KB)

March 20, 2017
Institute of Biochemistry I, Cologne
Suggestions and wishes: Gudrun Konertz
Voice: +49 221 4786930
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