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donnenberg

Software download address:

Download Mplex 4.20 here

 

Donnenberg License:  download here

Place licence file in the same directory as you placed main program. It is advisable to allow system to use its own addresses unless you want this to be in a special directory.

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Sample DB files for Legendplex examples     -----   RAT

                                                                          -----   HUMAN(download these to your desired directory)

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Cytokine Multiplexing Sample data sets:

Rat: - zipped directory of some of our data - download entire directory

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Video Tutorials

Part 1: General overview  - (MP4)

Part 2: Explanation of the Cytokine measurement charts  (MP4)

Part 3:  How does AutoGate work and assay assignment  (MP4)

Part 4:  Reading files and data management   (MP4)

 

PlateAnalyzer tutorials - general

Some of the Tutorials use older versions so icons may have changed, but functionality remains the same.

1. An Introduction (coming from Youtube)to PlateAnalyzer (3 min) This is a 3.5 minute outline of what Plate Analyzer can do (off our server) This shows the general operating features. It's a good place to start. (44meg)

2. Some general videos on PlateAnalyzer (37 sec) comprehensive data management and analysis tool. This is mostly related to drug screening.

3.  Some nice features - Create a new Parameter  (75 Sec)

4. Save graphics from PlateAnalyzer to Word or PPT (33 Sec)

5. So how fast is PlateAnalyzer? Open it, close it, analyze it! (60 sec)

6. New features March 2012 - tracing the analysis pathway

8. SMILES codes read for drugs see YOUTUBE

9.  New DRUGBOX Controls features YOUTUBE

10. Export CSV data files YOUTUBE

11. Dealing with Empty Wells YOUTUBE

12. 40 PLUS parameter data CyTOF analysis YOUTUBE

13. Autowell finder-extracting single wells from large files YOUTUBE

 

March 2013- Auto Well finder - Accuri, CyAN flow data

There is a new feature in PlateAnalyzer. You can now take native files collected on the Accuri or CyAN via the Hypercyt and separate the files based on time/well number into separate list mode files for each well. The AutoWellfinder has some nice features for cleaning up data, and can read sets of files such as created by Accuri or the single time-based files from CyAn. There is no size limit. Here is the MP4 tutorial (13 megs) to explain how to use this feature or you can go to YouTube.

 

SMILES - addition of link to PUBCHEM and reading CSV files

You can read SMILES codes for drugs with PlateAnalyzer. You must create a CSV file in the exact format as the one HERE. Don't change the number of columns. Just replace the names and add the smiles code. You can create your own CSV sets and load them from the OPTIONS, SMILES dripdowns.

 

Cytof Examples:

Some Demonstration TUTORIALS for PlateAnalyzer

General page for Tutorials

 

New Tutorial for LSRII Data

1. PI Positive VS PI negative (right click to download 7 meg)

Go to Tutorials

 

Full Plate Examples for Drug Dose Responses

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

Vertical Drug Concs. CSV file

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

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 for Cytof users)

1. Initial Ideas (Sept 26, 2010)

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

 

(There are additional CYTOF files available)

 

Data Files

CyTOF only:

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