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User Manual
    Explore NeuroDNet


Q. What is NeuroDNet?

NeuroDNet is an open source project meant for constructing and analyzing Neurodegenerative disorders. The database has a user friendly interface and provides the user with tools to construct a biological network. The database contains twelve neurodegenerative disorders and more than 300 genes associated with disease. The database was created by integrating data from reported literature and HPRD, BioGrid, DIP, BIND, Prolinks, KEGG and Gene Ontology. The interface offers different options to learn about the disease causing molecular factors and the related disease models given in literature. The database tool werer developed using a systems approach to understanding diseases. The goal of system level analysis is to identify the most important components associated with a disease quickly and accurately. It enables the user to understand the interactions among implicated genes (network) and study of dynamic behavior of each of the components in order to provide an understanding of behavior of the system. NeuroDNet enables the user to obtain interacting genes that are causing a disease, then analyze and visualize the flow of information among the gene for the disease(s) being studied.

Q. What are the requirements to run NeuroDNet?
The following hardware and software is required to run this database.

  • At least 64 MB of available random-access memory (RAM) (256 MB recommended)
  • An Internet Explorer 7.0 or higher (IE8.0 or higher recommended), Firefox 3.x, Chrome 9, 10
  • JavaScript and cookies enabled, Recommend ActiveX enabled for Internet Explorer
  • Flash player installed

Q. How NeuroDNet is designed?

NeuroDNet is developed as an open source software system using Mysql - 5.0.18 - Win32 and PHP - 5.2.0. The database uses the relational data model. Data from literature published in peer reviewed scientific journals and public databases were used for populating gene, SNP, protein, pathway information in database. Disease model information for neurodegenerative diseases was obtained from established and certified sites.

Q. How do I use NeuroDNet?
The homepage of NeuroDNet has all the query related links. We have provided a user manual to help the user to startup quickly and easily. If you wish to download database information, please send us an email with accepting terms of usage.

Q. Should we send curated signaling pathway information and build own network?
Yes, you can send signaling pathway information that can be used to build your own network. We would like to incorporate your curated pathways and disease models.

Q. What will be in next version of NeuroDNet?
Currently, NeuroDNet can build and helps to analyze neurodegenerative disease related network qualitatively and quantitatively. For quantitative analysis, the user will have to provide the necessary parameters; the default kinetics for is assumed to be first order but the user can specify higher order kinetics. We are trying to develop dynamic pathway visualization and analysis tool. If you would like to collaborate or be part of NeuroDNet, we encourage you to write to us.

Q. Other Tools
Links are provided for exploration of related information and database. Among these, Cytoscape has an excellent set of plugins which allows users to visualize and analyze different networks. The other software one may consider are: Celldesigner (uses SBML Systems Biology Markup Language) and SBGN (Graphical Notation) for network visualization and quantitative analysis environment for Systems Biology.

Systems Biology Group, Indian Institute of Technology Delhi, India.
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