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Frequently Asked Questions
What is Cell-in-Silico?
Cell-in-Silico is a comprehensive Systems Biology suite aimed at addressing the need of Experimental Biologists and Bioinformaticians for studying biological systems in (w)holistic fashion. The software offers an intuitive solution through simple and uncluttered GUI front-end to construct, visualize and evaluate biological networks in the context of gene expression analysis which is critical for studying the effects of systemic perturbations at single cell and multicellular levels.
How is Cell-in-Silico licensed?
See license agreement for Cell-in-Silico verion 1.0.00-beta
How do I download and install Cell-in-Silico?
To install Cell-in-Silico application along with its prerequisites on your machine, please download zip file containing the installer and the prerequisite available at www.cellinsilico.com/Download.aspx and follow the steps given below:
  1. Unzip the downloaded cellinsilico-setup.zip file.
  2. Double click on Cell-in-Silico-Installer.exe file present in the extracted folder to trigger the installation process. Follow the onscreen instructions to complete the installation. More details on the installation process can be found in the user’s guide. It is available at www.cellinsilico.com/Download.aspx
  3. If a gene has been replaced/modified in NCBI database, the application will not able to fetch the annotation.
  • Note: Administrator privileges are required for installing the software. You may need to confirm that you want to proceed with installing a program from an ‘unknown’ or ‘unidentified’ publisher.
How do I start using Cell-in-Silico?
Double-click on the Cell-in-Silico icon to launch the application. A Getting Started page opens after the application is launched. It provides introduction to the product and shortcuts to start using the application.
I closed the Getting Started page. How do I re-open it?
To re-open this page, click on Getting Started under View >Show/Hide menu.
What is a kinetic model and how do I construct it using Cell-in-Silico?
A kinetic model of a biochemical network is an abstraction to represent the mechanisms of the interactions between biomolecules. A reaction in a kinetic model represents a state transition of the connected species. For e.g. a biochemical reaction, an interaction between proteins, or a regulatory relation between genes. The biochemical and genetic meanings of species and reactions are distinguished by their symbols in Cell-in-Silico. To construct a kinetic model in Cell-in-Silico, choose the option “Kinetic Model” under Model Type in New Model dialog box.
What is a logical model?
A logical model of a biochemical network is a qualitative abstraction wherein the biomolecules are represented with discrete levels of activities and their interactions as transitions between different states. A transition in a logical model is equivalent to a reaction in a kinetic model, and represents a way in which level of QualitativeSpecies involved in a model is altered depending on the level of some other QualitativeSpecies. To construct a logical model in Cell-in-Silico, choose the option “Logical Model” under Model Type in New Model dialog box.
Why do I need to specify organism while constructing or importing a model in Cell-in-Silico?
If organism is specified for a model in Cell-in-Silico, it allows fetching of biological annotations of the genes/proteins in the model. Please note that the genes/proteins should be named with their official NCBI gene symbols for fetching biological annotations.
Where can I find some example models for Cell-in-Silico?
After the launch of Cell-in-Silico, its sample files can be found under: File >Sample Models >CiS Models, or, on the Getting Started page under Samples. The sample models can also be downloaded from following link: www.cellinsilico.com/Download.aspx.
How do I disable continuous construction mode while constructing a model in Cell-in-Silico?
Continuous construction mode facilitates construction of several species/reactions of the same type without the need to click on Construction Toolbar every time. In case you want to disable it, following are the ways: (1) press “Esc” button on the keyboard, (2) click on the Continuous Construction Mode button under Selection Toolbar to deselect it, or (3) click on any other icon on the Selection Toolbar.
I have constructed a model using another tool. Can I import this model in Cell-in-Silico?
Yes, Cell-in-Silico offers import functionality for opening models constructed using other tools. To do so, go to: File >Import.
In my imported model, all the species and reactions are changed to a default type. How can I change this default type to suit my need?
Go to: Edit >Preferences >Model and use the drop down menus to change the default species, reaction and compartment type while importing a model.
I have constructed a model in Cell-in-Silico and have also categorized components into pathways and processes. Is there a way to remove a reaction or a pathway from a process but keep its participants in the process?
For conserving the participants of a reaction in the process while removing the reaction, use context menu options by right clicking on the reaction/transition in the network. Participants of a reaction can be conserved in a process while removing a reaction through Edit Process dialog box. Currently, while removing a pathway, its participants cannot be retained in the process.
I notice an additional XML file getting created whenever I create and save a model using Cell-in-Silico. What is the role of this file?
The additional file which gets created at the save of a model in Cell-in-Silico is a Model Extension File. Its filename is of the form: __< System Time>.xml, stores all the manually curated properties added by you. Please note that the model extension file should be conserved if you want to conserve the manually curated properties on the associated model.
I have set up a MySQL database on a remote machine. Can I configure it to fetch biological properties of genes/proteins?
Yes, it is possible to configure a MySQL database on a remote machine to fetch biological properties of genes/proteins. To do so, go to: Edit >Preferences >Database and edit the relevant details.
Can I integrate multiple models and use the integrated model for analysis?
Yes, Cell-in-Silico offers functionality for merging two models at a time. You can use this function iteratively to merge multiple models to create an integrated model. To merge models, on the menu bar, go to: Model >Merge.
I have opened a large network model in Cell-in-Silico. Is there a way to selectively see some part or module of the network?
Yes, you can customize the view of network by using Filter button on the Filter toolbar.
I have normalized gene expression data with me. How can I overlay this on a network using Cell-in-Silico?
You can overlay gene expression data on a network opened in Cell-in-Silico by going to: Gene Expression Analysis >Overlay on Network. Please note that the gene expression data file must be in CSV format. The data file must have Gene Symbol as the first column, Gene Expression Value as the second column, and p-value as the third column. The p-value column is optional. If the p-values are not available, the third column must be kept blank. The gene expression value for the next experimental condition should begin from the fourth column. If the p-values are not available, every alternate column should be kept blank.
How can I change the default fold-change values used in Cell-in-Silico to classify a gene as up/down-regulated?
You can use Configure button on the Gene Expression Visualizer window to change the default fold-change values.
How can I change the default colors used for displaying up/down-regulated and unaffected genes?
You can use Configure button on the Gene Expression Visualizer window to change the default colors of up/down-regulated and unaffected genes.
All the genes in my network appear unaffected in the Gene Expression Visualizer window. What do I do?
You can try decreasing/increasing the default fold-change values for up/down-regulated genes respectively. To do this, use Configure button on the Gene Expression Visualizer window.
Can I save the analysis results for future reference?
Yes, Cell-in-Silico allows export of model, its image and analysis reports in various formats such as PNG, PDF and HTML. You can go to: File >Export, or, File >Generate Reports on main window, or, use Export and Reports button on the Gene Expression Visualizer window for this.
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