itquery — An interface to query ItemTracker from BioNumerics¶
Version: 2.0.8
About¶
itquery is a graphical interface to display location information of strains, frozen stock’s and DNA’s stored in a LIMS system (ItemTracker) within a strain database maintained in BioNumerics. An “ItemTracker ID” links data related to a strain in both databases.
Features¶
- Display location information of Strains, Frozen stock’s or DNA’s in the freezer.
- Display and set/unset the selection status of Strains, Frozen stock’s or DNA’s in the LIMS database.
- Display additional information related to an item in both databases (Saved between sessions).
- Get all items marked as selected in the LIMS database.
- Cherry picking view displays status of sequencing (Finished, Repeat, Picked). Filter by user or sequencing status.
- Export sequence trace information or DNA information related to a strain as a CSV file.
Citation¶
itquery is discussed in
Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains
O’Farrell B, Haase JK, Velayudhan V, Murphy RA, Achtman M (2012). PLoS ONE 7(10): e48022. doi:10.1371/journal.pone.0048022
Requirements¶
Python 2.6 (tested with 2.6.6)
Download - http://python.org/
PyQt4 32-bit for Python 2.6 (tested with 4.9.1)
Download - http://www.riverbankcomputing.co.uk/software/pyqt/download
Database connectivity requires the pyodbc module (not required for demo)
Download - http://code.google.com/p/pyodbc/
Demo¶
Run file itquery_demo.py
The main program is itquery.py would require modification to handle a
specific data structure. A sample of all data structures used for the demo is
contained in data.json.
