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Pratip Chattopadhyay

Last Updated: 16 Feb 2013 (Check what has been updated)

 

Please do not distribute any files. The software and data are provided under confidentiality between PUCL and you. Please respect this. Email JPR if you have problems (jpr@flowcyt.cyto.purdue.edu)

 

Please download the following files.

I suggest you play the tutorials while playing with the files. This way you can follow along with the tutorial. There are more basic tutorials at our EDUCATION page, Tutorials. They may be helpful.

PlateAnalyzer Programs - there are three files - the main file is platAn.exe, there is an INI file which records your file history, and your license file. All three files must be in the same directory. These are coded for your use only. You may use as many copies as you want for your lab use, on as many computers as you want, but they will all be coded with your name. If you want a collaborator to have a copy please send JPR an email.

 

Download the parameters and plate layout files and I suggest you create a directory to identify them as such.

Special Issues for CyTOF data

 


 

Full Plate Examples for Drug Screening - Dose Response

Parameter & Plate Layout

Example drug concentration CSV file (use for plates 58 & 65)

Example PAP file for Plate 58 (simple layout)

Example PAP file for Plate 58 (advanced layout)

Drug Concentration File (CSV) for 58 and 65

Example PAP file for Plate 65 (advanced layout)

Example PAP file for Plate 65 (Very advanced layout) this layout shows how you can create an entire report in a single protocol to produce all 96 graphs.This is pretty cool!

 

Parameter & Plate Layout for Cytof Data Evaluating Dose Response

Vertical Drug Concs. CSV file

Vertical Drug Concs (reversed!!) checking if this is correct!!

Some examples of barcoded data sets.

Example complex layout for Sunitinib data set (works for others)

More compelex file as on 11/29 call - Sunitinib data set (ditto)

Sunitinib data file DE-BARCODED (418meg zip)

New Logic Map Protocol for March 8 2-12 with New DRUGBOXES

 

Tutorials (mainly Cytof)

1. Initial Ideas (Sept 26)

2. Here are the general  tutorials

3. Specific tutorial for Bodenmiller data only (37 meg)

4. Decoding Tutorial is here (4.6 meg)

5. My Video of Checker (2 dec) (5meg)

6. My Video of Starsnstripes (2 dec - low audio sorry!) (7meg)

7. March 8, 2012 - New Drugbox controls

 

 

Example Data Files (Barcoded data)

StarsStripesConcatv7.fcs_subtracted_StarsStripesConcatv7.fcs_subtracted.fcs_Ungated

(This is a 36 meg zip file with all the 96 wells separated for readingin PlateAn and includes the barcoded data)

Cheker_Concatv7.fcs_subtracted_Cheker_Concatv7.fcs_subtracted.fcs_Ungated

(this is a 47 meg file separted into 96 files and includes barcoded data)

 

Staurosporin data set de-barcoded (without barcodes) (320meg zip file)

PAP file for this dataset: For Staurosporin

Concentration file: Conc file

 

Program Download

32 bit:

  • PlatAn.exe   (the latest version of the main program)
  • PlatAn.ini   (can be deleted any time but it remembers what you have done - if you have major problems and the program seems possessed, just deleted this file and start again). The main program installation is in c:/program files (x86)/PUCL/Plate Analyzer (x86 for 64 bit) and c/:program files/PUCL/Plate Analyzer (for 32bit computers). The download is to your /users/name directory (windows 7 does not allow editing files in main program directory) but the program is run from the c:/program files  directory and this is where you MUST place your LIC file.

Special Program for De-Barcoding (see tutorial) (modified Dec 2, 2011 - you can now leave in the barcoded data (check) or leave it out.

64 bit version PlateAnalyzer:

Here is the 64 bit version. This is an automatic download

1. 64 bit version: Download

 

 

 

Platan.lic  (your license) MUST BE IN THE SAME DIRECTORY AS THE PLATAN.EXE file