SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks

نویسندگان

  • Jie Zheng
  • David Zhang
  • Pawel F. Przytycki
  • Rafal Zielinski
  • Jacek Capala
  • Teresa M. Przytycka
چکیده

SUMMARY SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network. It can be used to generate hypotheses and facilitate experimental studies about causal relations and crosstalk among cellular signaling pathways. AVAILABILITY SimBoolNet package (with manual) is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

CytoCom : a Cytoscape plugin to visualise , query and analyse disease - disease dynamic networks

CytoCom: a Cytoscape plugin to visualise, query and analyse disease-disease dynamic networks

متن کامل

BiNoM: a Cytoscape plugin for using and analyzing biological networks

BiNoM (BIological NetwOrk Manager) is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment. BiNoM plugin with documentation, API and source code is avai...

متن کامل

NOA: a cytoscape plugin for network ontology analysis

SUMMARY The Network Ontology Analysis (NOA) plugin for Cytoscape implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges. The plugin facilitates the annotation and analysis of one or more networks in Cytoscape according to user-defined parameters. In addition to tables, the NOA plugin also presents results in the for...

متن کامل

Cytoscape ESP: simple search of complex biological networks

SUMMARY Cytoscape enhanced search plugin (ESP) enables searching complex biological networks on multiple attribute fields using logical operators and wildcards. Queries use an intuitive syntax and simple search line interface. ESP is implemented as a Cytoscape plugin and complements existing search functions in the Cytoscape network visualization and analysis software, allowing users to easily ...

متن کامل

CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages

SUMMARY CytoscapeRPC is a plugin for Cytoscape which allows users to create, query and modify Cytoscape networks from any programming language which supports XML-RPC. This enables them to access Cytoscape functionality and visualize their data interactively without leaving the programming environment with which they are familiar. AVAILABILITY Install through the Cytoscape plugin manager or vi...

متن کامل

ذخیره در منابع من

ذخیره در منابع من قبلا به منابع من ذحیره شده

{@ msg_add @}


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره 26  شماره 

صفحات  -

تاریخ انتشار 2010