Description

Bacterial Artificial Chromosome Data Management (BACMan) is a Microsoft Access based application designed for the management and analysis of hybridization data related to the high throughput screening of large insert genomic libraries associated with physical mapping projects. BACMan integrates information from the entire process involved in BAC based hybridization screening so that final hybridization data are tractable through individual autoradiographs, probe preparation, and gridding of the blots used in the experiment. All BAC library plates and autoradiographs are indexed using a barcode system both to facilitate this data tracking and to ensure quality control. This barcode system also allows for computer-assisted scoring of autoradiographs and therefore increases the potential throughput of an individual user. BACMan also facilitates the design and deconvolution of pooled probe multiplexed experiments to maximize data generation, and allows for interoperability with FPC.

Features

The current features of BACMan v2.1 include:

• Integrated management of BAC based physical mapping hybridization data including:
  • Gridding of library filters
  • Preparation of probes as genomic clones or development as overgos
  • Probe sequence information
  • Experimental data for hybridizations
• Production of 'Code 39' Bar Code labels for autoradiographs
• Creation of scoring grids for printing on transparency film
• An experiment builder for pooled probe multiplex hybridization experiments
• Deconvolution of pooled probe multiplex designs for up to 576 probes with triple redundancy
• Experiment definition tool which allows user to define additional pooled probe multiplex experiment formats
• Overview queries of the database including probe hybridization status and film scoring status
• Multiple data entry interfaces including
  • Bar code assisted manual data entry using a programmable Zebex CCD bar code scanner
  • BACGrid data entry
  • OCR data entry using ABBYY Fine Reader in conjunction with the BACEater data processing application
• Identification of films that possibly contain scoring errors and may need to be error checked
• Printing error checking sheets

Download

The full BACMan suite download includes includes a self installing package that includes the full set of programs that are used by PGML for physical mapping. The individual packages may also be downloaded separately. By downloading this software you agree to abide by the GNU General Public License.

• BACMan - Main BACMan MS Access database. This includes an example dataset and requires a local copy of MS Access to run.
• BACGrid - A MS Word macro for entering scored film data from scoring templates.
• BACEater - Converts scored template data from ABBYY FineReader into the format used for BACMan.
• Barcode Font - The bar-coding capabilities of BACMan rely on a free Code 39 barcode font. This font must be installed in your windows font directory.
• BACMan Web Package - includes the MyBACMan.pl Perl script that creates the tables needed for web publication of BACMan as well as the php pages for presenting data on the web

The use of this full suite of packages is described in the BACMan User Manual.

User Manual - (pdf|MS Word)

An extensive user manual describing the entire BACMan suite is available in both pdf and microsoft word formats. This manual includes an in depth discussion of pooled probe multiplex experiment design and deconvolution. It also includes step by step instructions for using the BACMan film scoring and error checking methods. All tables and forms are extensively documented within the user manual.

Online Database Access

Online database access to BACMan databases is currently supported as a set of PHP scripts that access a MySQL version of the BACMan database. Examples of these scripts in action at PGML are available for our grasses database and for cotton.

Registration

We would like everyone who uses this software to register with us so that we can track the people that are using the  BACMan package. A registration protocol will be established shortly.

Author: James Estill Last Updated: Wednesday, 15 June 2005