What kind of experimental inputs can I use in SIMScells?

Once you have chosen an experiment, the wizard will ask you to select the necessary parameters:


Biological Systems: The full human organism or a specific cell type...?

Define which virtual experimental model you want to treat:

  •  You can choose one from the list provided by SIMScells, which includes different cell types and the whole human organism, characterized based on to the publically available scientific information.
  •  You can create a customized system, by modifying the available models according to your specifications (see the Model customization section). You can include:
    •  Features characteristic of your specific system system, e.g. p53–/–, stable cell line over-expression of a protein…
    •  Information about your unpublished results, e.g. protein–protein new interactions, protein activation/inhibition by other proteins, newly reported clinical effects of a drug…
    •  Your non-confirmed hypotheses (pathway activity, interactions, implication in mechanism of action…), if you want to test their effect in the global system.

Stimulus: Drugs, chemical compounds, protein activity modification, gene knockdown…

A stimulus is the "treatment" applied to your biological model. It may include a single element (one drug, one protein activation…) or a set of elements (drugs cotreatment, double gene knockdowns…). SIMScells' wizard will offer you to choose among some of the following options to define the stimulus of your experiment:

    protein
  • Proteins: up-regulation or down-regulation of protein activity, loss of function… You can modify any of the proteins recorded in the SIMScells' protein list, which contains most of the entries of the database, its reference source (only proteins without interactions or very sticky proteins have been necessarily excluded). We continuously add new entries to the list through the annotation of new knowledge and the constant improvement of our technology.
  • gene
  • Genes: you can also modify the expression levels of any gene stored in the SIMScells' gene list. Like SIMScells' protein list, the ever-growing SIMScells' gene list contains most of the entries of the UniProtKB/Swiss-Prot database.
  • drug
  • Drugs: you can either select any protein-targeting drug from the DrugBank database, or create a new one:
    •  Create new compounds: do you want to test your experimental drug? You only need to specify its targets and its effect upon them (activation, inhibition or unknown).
    •  Modify existing drugs: have you discovered a new target for a drug...? Remove or add new targets to the ones associated to existing drugs, adapting them to your updated knowledge.
  • *Note: SIMScells uses the protein targets linked on DrugBank for existing drugs; thus drugs that only target DNA cannot be included on the analysis.


Response: Activation of a pathway, a pathological condition, a change in protein activity…

A response is the biological or clinical effect caused by a stimulus in a biological system, in other words, the biological consequence of a specific stimulus. SIMScells' wizard will offer you to choose among some of the following options to define the stimulus of your experiment:

You will be offered to choose between some of the following options to define the stimulus of your experiment:

    protein
  • Proteins: up-regulation or down-regulation of protein activity, loss of function… You can modify any of the proteins recorded in the SIMScells' protein list, which contains most of the entries of the database, its reference source (only proteins without interactions or very sticky proteins have been necessarily excluded). We continuously add new entries to the list through the annotation of new knowledge and the constant improvement of our technology.
  • drug
  • Drug indication/adverse event: you can choose any drug indication/adverse event from the ever-growing list offered by SIMScells, which contains the most common adverse events and indications reported by the FDA.
  • gene
  • Gene: you can also modify the expression levels of any gene stored in the SIMScells' gene list. Like SIMScells' protein list, the ever-growing SIMScells' gene list contains most of the entries of the UniProtKB/Swiss-Prot database.
  • disease
  • Disease: you can choose any disease from the list offered by SIMScells, which contains the most common pathologies, in a constantly-growing number.

Parameter monitoring: What happens to a protein, pathway, pathological condition…in my experiment?

Parameter monitoring refers to the measuring of selected biomolecules, pathways, clinical effects… through the experimental process, without interfering with the obtained response. For example:

parameter