3DScapeCS User Manual Introduction System
Contents
1. node edges whenever there is no node edge selected in Cytoscape If there is node edge selected in Cytoscape only the selected ones will be changed Visualize Expression Data Expression data can be loaded in Cytoscape expression matrix data format http wiki cytoscape org Cytoscape_User_Manual Expression Data Load the data either from File gt Import gt Attribute Expression Matrix or from the ry Hige aggji Import button If data are loaded before the 3D Expression Data Import pes sync conversion use the Sync button to synchronize expression matrix with the 3D network The nodes are rendered according to a gradient color ie schema in which the positive values are Mita ta ree ry rendered in red and negative values are rendered Color schemalsof ls 0 in green The label Timepoint shows the condition in each time point By pressing the Animation speed high low Play Pause button the 3D graph replays through all conditions automaticlly Timepoint Time series Data Import qm Sync Node edge animation Timepaint Node edge can indicate relative values according A ieee eat ae to their size width which is usefully in visualizing time series data such as metabolic Animation speed high low W Loop play W Smooth play flux The data should be prepared as tab delimited format see the following example Each row has the label of the node edge and each column are specified with a condition2. network view However not all the shapes in Cytoscape can be matched in Ubigraph so the node shapes are converted according to the following rules Cytoscape Ubigraph lt gt Diamond 7 V pers hedron Hexagon gt Octagon Parallelogram Rectangle Round Rectangle cube COne Triangle Ellipse The default shape in Ubigraph is cube If all nodes in cytoscape network view are round they are converted to cube automatically after conversion for improving performance search node eage a Hide Node Attributes gt Type node edge label in the search box and it will W Node labels try to auto complete it There is an option to Hode colar specify which term to search beside the box The selected node edge will be highlighted with a label ZZ beside it in the Ubigraph window Pee i Node shape Selection Double click a node in Ubigraph will return the node label in an node attribute browser in the Cytoscape panel below Change the appearance of hode size G the selected node edges or add delete them in Cytoscape will also be reflected in the Ubigraph 3D renderer W edge labels edge color edge width Node Edge Attributes Node Edge attributes such as label color shape size can be set in each panel You can collapse the panel Show Node Edge Attributes and use the buttons and sliders in the panel The Node Edge attributes changes will be applied to all
3. 3DScapeCS User Manual Version 0 7 Aug 31 2013 Introduction Thank you for choosing 3DScapeCS which provides three dimensional multi desktop dynamic network visualization in Cytoscape You can get the latest version from http sourceforge net projects scape3d System Requirements 3DScapeCS runs on any platform with Cytoscape installed However 3DScapeCS requires Ubigraph which can only run on Linux or MacOSX You can download Ubigraph from http www ubietylab net ubigraph Installation Guides Put 3DScapeCS jar into Cytoscape plugin directory Ubigraph needs to be started outside Cytoscape so check Ubigraph requirements for your system Ubuntu sudo apt get install libglut or sudo apt get install glut3 CentOS or Redhat freeglut3 or equivalent Editor 3DScapecs Filters Cerebral see MacOSX nothing required BINDhuman Usage Convert to 3D Ubigraph_server should be started first before you use 3DScapeCS Once Cytoscape finished Search oOo B loading 3DScapeCS will be found in the left tab of Cytoscape panel Try import a network in Cytoscape and select its label in the drop list then use Convert to 3D button to create a three dimensional view in 3DScapeCS The 3D network are rendered in Ubigraph_server window after the conversion is completed Help About Us Tutorial The node edge are converted with styles created according to their shape color size and label in their Cytoscape
4. F THE AGREEMENT BETWEEN US SUPERSEDING ANY PROPOSAL OR PRIOR AGREEMENT ORAL OR WRITTEN AND ANY OTHER COMMUNICATIONS BETWEEN US RELATING TO THE SUBJECT MATTER OF THIS LICENSE 3DScapeCsS is free software you can redistribute it and or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 2 1 of the License or at your option any later version You should have received a copy of the GNU Lesser General Public License The program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details You should have received a copy of the GNU Lesser General Public License along with this library if not you can get a copy from _http www gnu org licenses lgpl html or write to the Free Software Foundation Inc 59 Temple Place Suite 330 Boston MA 02111 1307 USA Contact For more questions or bug report please e mail to gwang big gmail com
5. Pathway 4h 8h 16h GOP pd Glucose 1 2 3 GIP pp G6P 2 1 3 GOP pp F6P gt 2 l Load the data using Import button If data are loaded before the 3D conversion use the Syne button to synchronize data with the 3D network The values relative to the nodes edges are rendered in different node size edge width Multiple network animation 3DScapeCS can join a series of networks into one motion network if the networks share nodes with the same label To create a motion network use the button Order networks in the Network Animation panel In the dialog popped up you can add the networks you would like to use A motion network is created hereafter You can use the Play Pause button to replay each network The animation speed control is available beneath the play button By selecting the Fixed Play 3DScapeCS will only render nodes edges invisible from one motion frame to another instead of adding removing them from the network By selecting the Accumulative Play 3DScapeCS will only add nodes edges from one motion frame to the next frame but do not remove them even they are not presented in the following network The label showing the name of experiment in each time points will be rendered in different colors as well as the node edges appeared with each time points Comparison between fixed and default visualization Time point 1 Time point 2 Time point 3 nodeg nodes nodes noded Default 4a ode node h
6. oded node node vode nodet en godez s nodeg Fixed hid i 0 no g B 1 ai J A o T d node i nodes Hodes Parallel Monitor Support 3DScapeCS use XML RPC protocol to communicate with each ubigraph_server _ Host address 127 0 0 1 Therefore you can open several ubigraph_server on different computers just to make sure the clients are in the same network The default client si is your local host with an IP address 127 0 0 1 You can add another network client using Add button In the dialog popped up you input the IP Latency O Add a Remove Host address 197 168 1 200 address of destinate network client To remove a ae T network client from the panel use press the E A oe E Remove button The Latency slider can be use Ff a Remove for specify different time points for each client whenever playing through multiple time point animation such as expression data Multiple monitor visualizaiton Ubigraph Operations Read the following operation instructions found in Ubigraph document Key s Function ESC Exit full screen mode Tand Zoom in out Zoom way out Zoom way in lt and Start increase stop y axis rotation u d Start increase stop z axis rotation r Reset vertices to random positions Increase decrease time step h Toggle Runge Kutta Euler step p Toggle serial parallel f F Decrease increase friction V Toggle draw vertices S Toggle draw strain S Show performance sta
7. ts Frequently Asked Questions FAQs Q Why Ubigraph freeze when I add lots of nodes edges A It seems to be a problem with the 64 bit release Try 32 bit release instead if you encounter this See this post http stackovertlow com questions 5557100 free alternative to ubigraph for detail Q Why I saw libstdc so0 6 version GLIBCX X_3 4 9 not found when I started Ubigraph A You may need to remake a soft link to libstdc so 6 0 10 using the following command In s urs lib libstdct so 6 0 10 urs lib libstdc so 6 Q Why Ubigraph freezes when I converted a graph drag time point slider change node attributes A Ubigraph sometimes freezes when there is heavy computational load One solution is to terminate it using Ctrl C in the terminal and then start it again Also remind you that Ubigraph window should be kept in background when there is heavy computational load Copyright THE PROGRAM IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT WILL THE AUTHOR or AUTHORS BE LIABLE TO YOU FOR ANY DAMAGES INCLUDING INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THE PROGRAM EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES YOU ACKNOWLEDGE THAT YOU HAVE READ THIS LICENSE UNDERSTAND IT AND AGREE TO BE BOUND BY ITS TERMS AS THE COMPLETE AND EXCLUSIVE STATEMENT O
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