Cocktail program version 2.3.4 10/27/2022 Installation notes ------------------ Unpack the Cocktail Setup.exe and Readme.txt files in the Zip folder to your computer, run the Cocktail Setup program, and follow the instructions. The program and the files below will be installed to your C:\Program (x86) folder. OR Just unpack the complete content of the Zip folder into a new folder, place it where you want it, and name it "Cocktail". To establish the link between .ctl data files and the program: 1. Run the program once. 2. Double click a .ctl file. 3. In the “How do you want to open this file?” dialog mark the Cocktail program, check the “Always use this app to open .ctl files” boxand press OK. The program and the associated file type .ctl are now added to the Windows registry. The folder should contain: Cocktail Setup.exe, standalone installer. Coctail.exe, a Windows 64-bit executable file. Readme.txt, this file License.txt Cocktail.pdf, information file Four Cocktail data example files: Bohannan_Lenski_1997_Fig 3B.ctl, Lenski_1988_Fig_2a.ctl, Lenski_1988_Fig_2b.ctl and Fig_2_demo.ctl The program ----------- The Cocktail program models the dynamics of one or two bacteriophages infecting bacteria in a chemostat. The program can be runned with on-screen user input or by loading a data file. The Cocktail 2.3.4 is a beta version. Please let me know if there are issues or bugs. Although I have done my best to assure that it works, it may contain errors. If you think you have spotted an error, send me an email at: anders.s.nilsson@su.se, and include the .ctl file causing the crash / unwanted / erroneous behaviour of the program. Full contact details can be found by left double-clicking somewhere else than in input boxes in the program input window. The program runs on Windows 64-bit systems. It is in English, but some instructions may turn up in the language set on your computer when Windows DLLs are called (file dialogs). It was developed with Object Pascal from the Free Pascal Team (Free Pascal: A 32, 64 and 16 bit professional Pascal compiler. Version 3.2.0. URL https://www.freepascal.org. RRID:SCR_014360), using the Lazarus IDE and libraries developed by the Lazarus Team, (Lazarus: The professional Free Pascal RAD IDE. Version 2.0.10. URL http://www.lazarus-ide.org. RRID:SCR_014362). The IDE, compiler and program libraries can be downloaded from: https://www.lazarus-ide.org/index.php?page=downloads. Developing programs with Lazarus is quick and easy. Lazarus is an Object Pascal extension of Borland's Delphi (presently distributed by Embarcadero Technologies). Cocktail source codes can be downloaded from GitHub: https://github.com/ASNilsson/Cocktail-phage-infection-kinetics The .ctl file ------------- The results of the program can be saved as charts, in PNG or SVG graphics file formats, or as a .ctl data file. The items in the .ctl file constitute the complete settings for running the program. The format is a plain .txt file but note that the format is fixed. Moving items to another position in the file will inevitably result in a file error. A comma (,) is used as a delimiter when more than one item is to be found on a line, with the exeption of the Output list where each item should be surrounded by a blank. Omitting the comma, using another delimiter or the blanks in the Output list, will also result in a file error. Editing a .ctl file that works as a template, and save it under a new name, is a good idea. Advice on use ------------- Infection dynamics is complex. The results are often difficult, and sometimes counterintuitive, to explain. When running a case, try not to change variables randomly but in a systematic way and not all variables at the same time, e.g. keep all but one parameter constant and change just one variable at a time. Also, start simple with known parameter settings and one bacteriophage only. Licence information ------------------- The Cocktail program is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. Feel free to modify the program adding / modifying functions. Commercialisation is not allowed. The source code for the Cocktail program is available from me on request by email or from the journal website where the article decribing the program is published. If you benefit from the program, a donation to Médecins Sans Frontières would be appreciated: https://www.msf.org/donate Disclaimer ---------- The Cocktail program is based on established mathematical models and extension thereof but, as with all models, it only represents a fraction of reality. Users of the program should be aware of that the program results are approximations and are asked to check results by means of own calculations.The main purpose of the program is to generate hypotheses about bacteriophage infection dynamics that can be experimentally tested. I disclaim any responsibility for results generated for other purposes. Stockholm 9/20/2022 Anders.S.Nilsson, anders.s.nilsson@su.se.
ASNilsson/Cocktail-phage-infection-kinetics
Cocktail is a program for mathematical modelling of bacteriophage (phage) infection kinetics. Cocktail is a Windows 64-bit program and the source code can be developed in the directions that users see fit. This will be updated soon with a link to the scientific publication describing the program.