Tutorial Video 1
How to use AMASS application?

How to test AMASS application using hypothetical example data sets provided?
  1. Copy 4 files in the folder ".../AMASS/ExampleDatasets”
  2. Paste 4 files in the folder "../AMASS" (the same folder as the AMASS application)
  3. Double click "AMASS.bat”
  4. Wait for about 1-3 minutes for the AMASS to run
  5. Open and read the "AMR_surveillance_report.pdf" newly generated in the "../AMASS" folder
How to use AMASS application with my hospital data?
  1. Make sure that you are the hospital staff and can analyze hospital data based on your duty and responsibility. If your aim is to generate cumulative AST (antimicrobial susceptibility report) for your hospital for service, no ethical clearance is usually needed. Please consult your line manager if you are uncertain on whether permission to analyze hospital data is granted. 
  2. Export microbiology laboratory data as .csv or .xls. Please refer to Example_Dataset_2 for an example on data format and the list of essential variables. If “no growth” data is not available, AMASS can still generate a basic report for you without the "no growth" data. [Please check the list of essential variables in the user manual]
  3. Export admission data as .csv or .xls. Please refer to Example_Dataset_2 for an example on data format and the list of essential variables. If hospital admission data is not available, AMASS can still generate a basic report for you without this file. [Please check the list of essential variables in the user manual]
  4. Check your variable names and data values in your microbiology_data file, and fill the data_dictionary_for_microbiology_data [Please refer to the user manual for more details]
  5. Check your variable names and data values in your hospital_admission_data file, and fill the data_dictionary_for_hospita_admission_data [Please refer to the user manual for more details]
  6. Put your files in the folder "../AMASS" (the same folder with AMASS application)
  7. Rename your file names as hospital_admission_data and microbiology_data
  8. Double click "AMASS.bat"
  9. Wait for about 1-3 minutes for the AMASS to run
  10. Open and read the "AMR_surveillance_report.pdf" newly generated in the "../AMASS" folder

**Please note that AMASS.bat is case sensitive **

If you experience any problems and cannot solve it, please feel free to email your queries to cherry@tropmedres.ac and direk@tropmedres.ac

 

If you can run AMASS successfully, we recommend that you save your dictionary files to be re-used again in the future. When you have to re-analyze your data and re-export your data from the hospital again, your completed dictionary files can be re-used automatically if it's in the same folder.

 

If you make a completed dictionary based on your hospital data , and you are happy to share the dictionary files, we would be happy to receive your dictionary files and host them for you. We will acknowledge your contribution. The files could be very helpful to many people in low and middle-income countries worldwide.

 

We wish AMASS can be somewhat helpful to you, your patients, your hospitals and your country.

 

Sincerely,

Cherry Lim and Direk Limmathurotsakul