You can reference Wolfram SystemModeler in your published work just as you would reference a book or any other publication.

The standard citation elements are:

SystemModeler 5.1

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 5.1
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2018

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 5.1, Champaign, IL (2018).

SystemModeler 5.0

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 5.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2017

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 5.0, Champaign, IL (2017).

SystemModeler 4.3

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 4.3
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2016

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 4.3, Champaign, IL (2016).

SystemModeler 4.2

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 4.2
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2015

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 4.2, Champaign, IL (2015).

SystemModeler 4.0

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 4.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2014

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 4.0, Champaign, IL (2014).

SystemModeler 3.0

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 3.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2012

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 3.0, Champaign, IL (2012).