VisANT News Updates

02/06/2013New Release 4.07, add link out information for drugs as shown below

12/31/2012New Release 4.06, added following features:

 

Download this macro

  • Disease Enrichment Analysis (DisEA) to detect the statistically over-represented diseases for a given set of genes represented by the metanode, please reference DisEA manual for detail.

9/18/2012New Add a new section "Filter the Network Based on GO Annotation" in VisANT user manual upon user request.:

8/15/2012New Release 4.03, fix the bug of VisML loading with saved legend node.

7/15/2012New Release 4.0, added following features:

Enhanced user interface (UI)

Docking windows: There are two docking windows in this new release: ToolBox/Hierarchy Explorer, by default is visible; property window---a window that is used to customize the node/edge, as well as global properties, as shown below:

To hide the docking window, click the small button outlined in the small red circle (upper right corner) as shown in above figure. One advantage of the docking windows is that they can provide maximum working space when necessary, as shown below:

To make docking window, either mouse over  or click the button on the side bar, as shown below:

Docking window will become invisible when you leave the window for several seconds, or click on some other components, such as the empty place in the network. You can however the fix the docking window by clicking the small button (red circle) shown in above figure.

 

Node/edge customization. One key purpose to implement the docking window in VisANT is to make the properties customization easier and extensible. As shown in the above figure, the properties window is in the style of spread sheet, with common user convention to make it easier to use. When node(s)/edge(s) are selected, all corresponding properties are editable except those that are grayed. Properties are grouped and these groups can be collapsed/expanded. As shown in the figure below, Edge properties and global properties are collapsed while node properties are expanded in which properties of node label are however collapsed. As also shown in the figure below, the column width can be changed in case the name of property is too long. Clicking on each property row will also display the detailed explanation as shown for node shape in the figure below.

 

Legend Node. It becomes necessary when there are lot of node(s)/edge(s) customization. This release has provided a primary implementation of legend node for this purpose, which can be activated through the menu Network Legend

The legend node is just a metanode and can be collapsed/expanded, and the nodes inside the legend nodes are just common nodes in VisANT and can be customized. The legend node will list all nodes that have been customized, and user can change the label of nodes to explain what such customization means through the property window.

Note: The current implementation is limited and only provides the legend for nodes. There will be more features in the future release of the legend node, including the edge legend and filtering (e.g., clicking a node that has been customized with red color inside a legend node will select nodes in the red color).

 

Navigation of disease/drug hierarchy

One main addition of this release is the support of disease/drug hierarchy. As shown in the figure below, there are four disease hierarchies available in VisANT:

Note: it is recommended that the current species to be set as Homo sapiens so that the number disease associated gene (or therapy associated drugs, e.g., there are total 2529 genes annotated in ICD-10) will be shown correctly.

Note: in the near future, the four disease hierarchies will be integrated into one (ICD-10). Current disease-gene association for ICD-10 is based on KEGG disease database.

Note: functions for disease/drug hierarchy is similar to GO hierarchy

 

Discover the association between disease/gene and drug/therapy

From gene to disease. There is new menu under the menu Nodes that allows query of diseases for a given list of genes, as shown below:

The query results will be shown as part of the node description so that it will be immediately available when mouse-over the node. Moreover, clicking on the node with disease annotation will show the corresponding disease hierarchies as shown in the following figure (given the assumption that Link to Network option is checked, configurable through the button near search as marked using red circle):

 

From disease to gene. The disease can be searched using key words in the Hierarchy Explorer, as shown below (make sure you choose the disease database in the drop down list, the figure sows the results of "lung cancer"):

 

One the disease is shown in the hierarchy structure, it will be immediately visible whether there are known associated genes based on the number near the disease name (as shown in the above figure). To know what genes are associated with the disease, simply drag&drop the disease from Hierarchy Explorer to the network panel, as shown in the following figure:

 

Visual construction of disease/therapy network

Repeat the drag&drop processes mentioned above, disease/therapy network can be easily be build using the built-in function based shared components or interactions, as shown below:

Network transformation

To facilitate the study of the network from different perspective, the new release VisANT provides two function to transform the network represented by metagraph, which are available under the menu Metagraph/Network Transformation. One function transforms the metagraph to bipartite graph between metanodes and the nodes they contained in metagraph. In the case of disease network, it facilitates the study of disease gene from the point view interaction network, as shown below:

 The another functions transforms the metagrap into a co-metanode interaction network, i.e., it it creates an interaction network where components inside a metanode are connected each other. In the case of disease network, it creates an interaction network of co-disease genes where an edge between two genes indicates that they are associated with the same disease, as shown below:

 

12/05/2011New Release 3.93, fixed several bugs and add new support of provenance information for interactions. For each interaction, there are corresponding menus available to link back to its original databases, as shown below:

.

09/06/2011New We are looking for talent research assistants/postdocs/software engineers to join this exciting project of network/systems biology. The ideal candidate shall have at least one of the following background: bioinformatics, algorithm development, computational biology, graph theory, and modeling and simulation. The candidate needs to know the programming. Knowledge of Java and VisANT is a plus. Persons interested shall send their CV to Dr. Charles DeLisi (DeLisi@bu.edu) and Dr. Zhenjun Hu (zjhu@bu.edu).

08/26/2011New We are pleased to announce that VisANT has successfully won the NIH grant again! Many thanks to your continued support of VisANT project, especially those we wrote us the supporting letters/emails. VisANT can not succeed without your support.

08/25/2011New Release 3.91 Enhancement of the KEGG pathway integration.

  • KEGG pathway page in VisANT web site has been updated, pathways shown in pink are not available for the specified organism, they are listed just for your reference:

  • KEGG pathways, including the KGML and pathway-gene mapping, are now being updated monthly, similar to those interaction data.

  •  As a result of this synchronization, there may be significant changes in your old networks:

    • some pathways may no long be available, for an example Urea cycle and metabolism pathway for Homo Sapient (pathway ID: 00220) shown in  10/08/2009 release note is no long available. For backward compatibility, we keep these old KGML files so that the link in our page will not break, but map00220 will NO long be available in VisANT.

    • Some genes may be mapped to much more pathways (e.g. TP53 of Homo Sapient), some may no long mapped to any pathway (e.g., PTP1 in yeast is no long mapped to pathway 00470, and pathway 00470 is no long available for yeast).

    • Some pathways IDs may be changed (e.g. MAPK signaling pathway 04010 for yeast has been changed to 04011)

    • .......

    A new menu named "Update Selected Nodes Name" (corresponding new macro "name_update") is added to facilitate the easy updating of pathway mapping information without query of the interaction (regardless whether the node's name has been resolved before or not), as shown below:

  • To make it more informative, the tooltip of the nodes now shows the pathway title in addition to the pathway ID, which will also be saved as part of VisML file, as shown above.

  • Similarly, the menu "Expand Pathway" will show the pathway title.

  • KGML parser has also been updated to display those nodes that has no links in the pathway, such as TP53 shown below:

03/29/2011New Release 3.9 with enhanced performance of query-related macros, also some bug-fixing.....

06/04/2010  Release VisANT 3.86, with a new filter to remove self-loop as shown below:

and support of new interaction databases IntAct & HPRD (monthly synchronization) so that you may find more interactions, see Interaction Statistics page for detail.

12/09/2009  Add new tutorial Develop VisANT plugin in Eclipse

10/08/2009  Release VisANT 3.68, fix the bug of the visualization of metabolites concentration using node color:

In the above example, KEGG pathway 00220 is loaded from KGML, and then the data of the metabolite concentration (we made it up just to illustrate) is loaded from a local file (can also be copy/paste to Add textbox) in the format of expression data. Click to load the  resulted network.

09/26/2009  Release VisANT 3.67, fix the bug of polygon shape (convex hull) of expanded metanode when zooming or panning. When a metanode position is locked, its expanded shape will also be locked and nodes inside the metanode will not be able to be moved out of the fixed polygon; and once unlocked, the shape will fit the nodes inside, and can be changed by moving the nodes around, as shown below:

Although the locked node can not be moved around, its position can be changed when the whole network is panned, Such behavior of the expanded metanode is designed to allow it to model the cellular compartment, although these functions have not been finalized yet. The information of the cellular compartment may easily be obtained by drag & drop operation from the GO Explorer released since v3.5, and related functions have been detailed in our recently publication: VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology

08/12/2009  Release VisANT 3.66, with new macros to select nodes based on their properties, such as node color, size and shape etc., more ...

05/24/2009  Release VisANT 3.63, fix the bug of text edit and add a new filter to select protein/gene nodes with no GO annotations.

05/07/2009  The first video tutorial, as well as a complete list of file formats supported by VisANT is now available. VisANT 3.62 is released with bug fixing, including the one for PSI-MI 2.5., with primary support of Graph Markup Language (GML). Here is a macro file that animates the network by loop through 5 GML files. Try out!

04/12/2009  Release VisANT 3.60, with two new features being added:

  • Add support of the database of functional linkage networks (FLN) for three species:Escherichia coli K-12, Homo sapiens and Saccharomyces cerevisiae. To query the FLN, change the database to Functional Linkage Network, as shown below:

Note: all FLN are weighted. You can adjust the weight cutoff to filter out the edges

Note: when changing the database to FLN, please clear the network if the current species is not supported by FLN. the default species for FLN is Homo sapiens

Note: FLN data can not be downloaded from statistics page, or the method table in VisANT. Using this page to download the all FLN data.

  • Add support of of visualization of expanded metanode using convex hull, as shown below (load this network in VisANT):

    Note: as usual, the shape of the convex hull can be changed by moving its component nodes. The shape is fixed when the node is locked, such as the metanode shown in the upper-left corner in the above figure. The node can be locked using the menu shown below (once the metanode is locked, its component nodes will NOT be able to be moved beyond the locked shape):

    Note: the default shape of an expanded metanode is still rectangle. To change the shape of expanded metanode, the user will need to select the metanodes to be changed first, and then use the menu shown below:

    Note: although highly optimized, the convex hull still cost more time to draw than the default rectangle.

03/24/2009New   User manual for release 3.55 is updated.

03/19/2009New   Release VisANT 3.55:

  • Add the red cancel button at the right-bottom corner of the status bar to cancel the time-consuming task as shown below:

    Note: the cancel button only cancel the current analysis. In the case of macros, the macros will continue for the next command if there is any. Press Esc key will stop all macros, including the current time-consuming process.

  • Allow the customization of the node color used to indicate the relative contributions of genes to the overall enrichment of a given module (metanode). An example is shown in which a node with greener color indicates more contribution. Try out the quick macros for example shown below. The macro file can be downloaded here.

  • Report of NMEA results, such as:

  • Report of GOTEA results, such as:

For more information, please reference the updated manual for new functions in V3.5.

03/06/2009New   Release VisANT 3.52, with two new plugins:

02/10/2009New   Release VisANT 3.49, with new functions for Gene Ontology visualization, integration and annotation.

  • GO Explorer is provided to visualize the GO hierarchy as shown below.

    • Terms under three different categories are highlighted using different color.

    • Each term is associated with a checkbox to indicate the selection state.

    • Search box is provided to allow user to search the GO term using key words or GO id. When multiple key words are presented, searching will be processed using AND operation

    • When searching is processed, all matched terms are highlighted and all the paths the matched terms  to the root of the ontology will be shown (see figure below)

    • The width of the GO explorer is adjustable.

    • GO database is updated monthly and annotation are updated weekly from Entrez Gene database.


 

Note: Because the search function returns all possible paths of the matched terms to the root and GO terms usually have multiple parents, the number of the paths is often bigger than you expected (e.g. if search  "cell cycle" will results in about 3700 paths). To address this challenge, the searching is processed in another thread and the tree is disabled (meaning you will not be able to click the tree nodes) and the number of the paths being added to the tree is shown in the status bar (bottom of the above figure). At the same time, you can still play with the network. Because of the large number of the paths shown the GO Explorer, VisANT may run out of the memory, especially when VisANT is run as an Applet. Please reference here for the solutions when VisANT is run as a local application.

Note: By default the GO term's child terms will NOT be shown when display the path unless it has been queried before. In order to know all its child nodes, user can first collapse then expand the interested GO term in the GO explorer.

Note: Key word searching in the combination of drag & drop operation shown below provide an alternative way to search genes (and therefore their interactions) using key words in VisANT.

Note: The tree of the GO explorer looks much compact in the Window's Look & Feel (as shown in above figure). A new Look & Feel menu has been added under the View menu to allow user to change different look & feel of VisANT.

  • Integration between GO Explorer and the network:

    • Mouse-clicking to display the hierarchy of the terms annotated for the gene with the terms being highlighted (see figure above). This also applies to the metanode of GO terms as introduced below.

    • Drag & drop the term node from the GO Explorer to the network will create an expanded metanode if the node has child node or has genes annotated under the term base on different options, or collapsed one. There are 4 options for the drag and drop operations, as shown below (for simplicity, we drag the term to an empty network):

    Drag & drop can be used to create the multi-scale network when integrated with interaction network, an example as shown below:

    Note: option 2 in above figure actually gives the user the capability to quickly group genes which have the same GO annotation in an existing network, especially the interaction network, which make it easily to turn an interaction network into a network of GO-defined functional modules.

    • When clicking on the term node in the GO explorer, the corresponding metanode in the network will be selected to let user quickly identify it.

    • The metanode of GO term, such as GO:0030192 shown above, can be expanded by double-clicking, while will always show its child terms and genes directly associated with.

  • Flexible annotation schema: VisANT provides 4 basic options to annotate genes using GO annotations where option 1-3 listed below can also be applied to the selected branches of the GO annotations (indicated by the selection state of the checkbox), resulting in 7 combinatory annotation schemas in total. These options provide users the great flexibility to test different hypotheses under varied circumstance.

    • Option 1: genes are annotated with most specific functional descriptions at the lowest abstract level.

    • Option 2: genes are annotated using informative GO terms under which (i) the total number of genes annotated is bigger than a given cutoff and (ii) the number of genes annotated under child terms is less than the same cutoff (reference).

    • Option 3: genes are annotated using those terms under which the total number of associated genes is bigger than a given cutoff,

    • Option 4: genes are annotated using only the selected GO terms shown in the GO explorer. For an example, if a gene is annotated under term GO:0000082 (G1/S transition of mitotic cell cycle) while only the term GO:0007049 (cell cycle) is selected, then the gene will be annotated using the term GO:0007049 because  GO:0000082 is grandchild of cell cycle.

    Note: for user added data, name resolution will be performed automatically when annotation is processed

    Note: Menus for GO annotation and name resolution are now also available under MetaGraph menu. The functions of these menus will operated on all nodes (including those hidden nodes of the collapsed metanode) instead selected ones, which is very useful for metanetwork.

    Note: results from different options can coexist as node descriptions for comparison purpose.

    Note: Annotation is always queried against database whenever it is processed. The old result will be overwritten to keep the annotation up to date.

***Coming soon: VisANT 3.5 will provide plugins for network-based enrichment analysis to find over-represented GO annotation and network-based enrichment analysis to find over-expressed pathways/network modules.

11/25/2008New  Release of V3.43. This release provides following new/enhanced functions;

  • GO annotation is now available for 12 more species (was only available for Saccharomyces cerevisiae before, through the menu Nodes/GO Annotation once nodes interested are selected, GO annotations will be available as node description if they are available)

Arabidopsis thaliana Bos taurus Caenorhabditis elegans Drosophila melanogaster
Danio rerio Gallus gallus Homo sapiens Magnaporthe grisea
Mus musculus Oryza sativa Plasmodium falciparum Rattus norvegicus

The macros to make above change are listed in the above figure.

  • Primarily support of visualization of GML format: sample file, loading sample file in VisANT.

  • VisML file now save the canvas size of the network, which can also be set through a new command: make it much easier to save network in any size, or export the network as images in any size you prefer.

  • Automate the creation of co-metanode network: each node inside the same metanode will be connected each other, i.e., a clique will be create for each metanode) . The function can be useful, in the cases such as:

    1. Given a meta-network of protein complexes, this function will create a clique for members in the same complex, as shown below (be aware that all duplicated nodes are merged when co-metanode network is created):

    2. given a meta-network of diseases (cancer subset of The Human Disease Network published on PNAS), with each disease as a metanode and corresponding disease genes as its components, the function will create the network of disease genes, as shown below:

    3. similarly, given a meta-network with each metanode representing a scientific publication and its components as the authors, the function will create a so-called coauthor network.

    Note: When there is embedded metanode, there will be no connection between the embedded metanode and other components, as shown here:

  • Automatic login applies to all the running mode. Once you login the system, you will no long need to login again in the macros/commands, and vice versa.

  • Enhanced FitToPage function that takes into the account of exact label size and position for all the nodes.

  • A lot of mini enhancements and bug fixing.

07/12/2008New  We will present at BioPathway SIG meeting at ISMB 2008, Canada, to introduce the concept of metagraph and its application in multi-scale visualization and modeling for biological networks. In addition, we will demonstrate the latest development of VisANT on July 20th, with special focus on visualizing large-scale networks with improved readability and performance.
 

07/11/2008New  Release of VisANT 3.22, which adds following new functions:

07/10/2008New  Five new tutorials have been added:

07/01/2008New  A brief summary of mouse operations in VisANT has been added for your quick references

06/06/2008New  Add new tutorial "How to use VisANT in your own web site".

06/01/2008New  The Laboratory of Cell Systems Analysis in the Biomedical Engineering Department, Boston University, is seeking a self-motivated post-doc to join a dynamic team working on the development of visual data mining software and its application to transcriptional regulation, evolutionary biology, cancer, cardiovascular, and infectious disease. The position requires a strong background in biology, with interest in and some familiarity with software engineering Knowledge of the VisANT system (VisAnt.bu.edu) is desirable. This is a two-year position, renewal pending availability of funds and performance. Persons interested in this position should send their CV to Dr. Charles DeLisi  (DeLisi@bu.edu) and Dr. Zhenjun Hu (zjhu@bu.edu).

03/06/2008New More screenshots of the huge network is listed in sample page.

02/26/2008New  Release of V3.19. We are pleased to announce this new release which provides a new running mode of VisANT: batch mode that will automate the network process quietly in the background. More importantly, the batch mode is highly optimized in memory handling and system performance, make it possible for VisANT to handle networks with millions of nodes and edges. A test case using a network with 15,447 nodes and 1,722,708 edges (from http://www.functionalnet.org/mousenet/) has been carried out on a PC with duocore and 2G memory. The network was first loaded using Edge-List format and then laid out using elegant-->spring-embedded relaxing. A screenshot of the network after layout is shown below (more screenshots are listed in the sample page):

More information about the test case, as well as other information of the batch mode, can be found here. In addition, this release also provides following several new functions.

  • The login dialog now provides an option to remember the login information as shown below. If this option is selected. VisANT will login automatically when it starts. Logout at any moment will cancel this auto-login. This function is only available when VisANT is run as a local/web-start application.

  • There is a new menu named Group Subnetwork as a Metanode under Metagraph menu. As its name stands, the new menu will group the disconnected subnetworks as metanodes. This function is also available as batch commands.

  • Global network statistics, such as degree distribution etc, can not be exported as tab-delimited text files for further processing. Please check out the new menus under Topology/Global Statistics. These new functions are also available as batch commands.

  • The zooming level, regardless whether it is zoom in or out, is now saved in VisML so that the network will be at exactly the same zoom level as it saved when loaded into VisANT.

  • Many bug fixes.

02/21/2008New  The first phase of the database upgrading has been finished: Predictome database now supports 539,961 interactions for 103 species. Please visit Interaction Statistics for more information.

07/11/2007New  Quick release of V3.04 in response to user quests to pan network using right-mouse dragging and zoom in/out the network by mouse wheel scrolling. The old pan/zooming functions still available.

In addition, we had received several error reports of the two recommender system (developed by Stuart Lab) which predict potential genes in the same pathway based on the expression data for a given set of query genes. However, these errors are due to the wrong ID system entered by the user. We have added a warning message in both recommender system, as shown below:

Above figure also shows common error to use unsupported ID as the query input. Follow figure shows the correct steps in the case you are not sure whether the gene ids/names you have are the supported IDs for the recommender system:

 

06/28/2007New  VisANT team is recruiting a Software Engineer

The VisANT team is seeking a self-motivated software engineer to explore this exciting field. The duties of the engineer would include but are not limited to the development of VisANT project, from GUI design, to VisANT server and Predictome database. The engineer will also be required to develop technical documentations. Expert knowledge of Java and J2EE, as well as database development, are required. Knowledge in computational biology, graph theory, bioinformatics and modeling and simulation is a plus. Knowledge in VisANT is also a plus. Persons interested in this position shall send their CV to Dr. Charles DeLisi (DeLisi@bu.edu) and Dr. Zhenjun Hu (zjhu@bu.edu).

 

06/27/2007New  Release V3.03, there are two new features in this release:

  • Visualize the edge weight using the color of the edge. This option is available under Option menu and can be coupled with the option to visualize the edge weight using edge thickness, as shown below:

as usual, this option, as well as customized color for max/min weight, can be saved in VisML, as the attribute of  the <Edges> tag. Following links allow you to try out this new feature in VisANT directly:

Using edge color only       Using both edge color and thickness       Using edge thickness only

  • Enhanced edge-list format for metanode to support automatic duplication in response to the the representation the formation of homodimer, homotetramer etc. For an example, following input:

#complex AAA
Flih Flih Flih

will result in the creation of a complex node shown below:

05/07/2007

New perspective paper appeared in Nature Biology describing the detail of metagraph and its potential applications in biology. Systems biology is seeking to move beyond static pictures of cellular networks to representations that show how networks change over time. the paper describes approaches for achieving this, with an emphasis on hierarchical representation and semantic zooming.

02/05/2007

Release of VisANT V3.0, user manual about new features can be found here.

02/02/2007

Release of VisANT V2.92, detail to follow soon....

01/25/2007

Release of VisANT V2.91, detail to follow soon....

01/12/2007

Release of VisANT V2.61, fixed several bugs reported by users.

01/05/2007 

Release of VisANT V2.60.

Be aware that the matched nodes are selected and notice the difference when mouse over the node and Available Links under Nodes menu, before/after loading the ID-Mapping file. Please reference user manual for the detail about ID-Mapping file.

  • There are now three options when export the network as Tab-delimited file. Please reference user manual for detail.

  • Network can now be saved as visML file when VisANT is running as an Applet, in the similar form when saving as SVG file.

  • Nodes can easily to added to the existing metanode through drag and drop. Please reference user manual for detail

  • Change the menu Metanetwork to Metagraph, add Grouping and Duplication menu under Metagraph. Enable quick group/ungroup using ctrl-g and ctrl-u.

  • Provides a new menu under Duplication to select all duplicated node instances.

  • Fixed several bugs, including ungroup and select/deselect all methods etc.

11/16/2006 

Release of VisANT V2.54.

  • Allows loading network from URL. There is a new menu under "File" menu for corresponding action.
    Note: When VisANT is running as an applet, this function can only load network from the same host where the applet is downloaded.

  • Enhanced SVG exporting. This enhancement makes sure that what shows in the VisANT screen will be what shows in a SVG viewer.
    Note: When you zooming the network, SVG actually saves all part of the network, including those that are current invisible in VisANT.

  • Fixed the bug in changing the label position of the node.

09/15/2006 

Selected nodes will be aligned to the LAST selected node to make it easier to determine which node is aligned to (Drag the mouse to select multiple nodes, then hold CTRL key and click the node you want other nodes to be align to). Please download the new version of VisANT and VisANT version number remain unchanged (V2.52).

08/25/2006

  • Release v2.52 with built-in support of SVG. Please reference updated user manual for detail. A brief comparison of general screenshot and SVG output is shown as following:

  • In addition, Align & Distribute functions have been provided to help user to manage the network under Layout menu.

  • Tooltip over the node has been changed to show both visible and invisible linkages. If the node has not been queried against database, the question mark will be shown for the total number of linkages, as shown below:

  • Edge-weight cutoff (w) has been changed to as the range from min-max, i.e., following example show the range 0<=w<=1:

    if you want show all the edges with w<=1, leave the left column empty, else, leave the right column empty.

  • Provide a new checkbox Database Online under File menu. Deselecting this checkbox will disable all database-query functions. For example, search function will only perform screen search if this option is deselected. This option is saved in visML.

08/10/2006 

Release v2.5 beta with enhanced expression module allows for the expression profile (example network) , See updated user manual for detail.

03/27/2006 

Release v2.46. There are two new improvements in this release which enable hyperlinking the network and converting it to SVG for high resolution images.

HTTP Linking:

When you put your network online, make it more than just a nice picture, make it live! For example, given a network (in VisML format) that resides on a web server, such as: http://prelude.bu.edu/O2/O2_visant.xml. To construct a hyperlink that will open this network directly in VisANT, simply create a URL using the following format:

http://visant.bu.edu:8080/vserver/DAI?command=link&location=http://prelude.bu.edu/O2/O2_visant.xml

By clicking the above link, VisANT will be opened and the network specified by location will be loaded. This new feature makes it convenient to create links to VisANT networks that can be used in web pages (as shown at http://prelude.bu.edu/O2/networks.html ), as well as placed as web references in papers. The only requirement is that the user clicking on the link has java web start installed. And if you have problems to put your network on-line, simply let us know and we can help you put your network in VisANT web page.

Note: The network used in this example is provided by Dr. Daniel Segre' in his most recent paper: The Effect of Oxygen on Biochemical Networks and the Evolution of Complex Life. The VisML file was produced in MatLab, and customized according to VisML specifications such that double clicking on a node will launch a webpage instead of expanding the interactions of the node (VisANT specifications can be found here: http://visant.bu.edu/misi/visML.htm ).

Converting to Scalable Vector Graph (SVG):

Additionally, in response to user requests, we have created a service so that you can convert a VisANT network into a high-resolution, Scalable Vector Graph (SVG) format. Using the SVG format, network pictures in any size can be created. Please visit http://visant.bu.edu/svg/ for more information.

Note: This function is still in beta-version, it will eventually become part of VisANT.

02/24/2006 

Release v2.43. This is a quick release to allow nodes without any edges to be exported in the tab-delimited format.

02/10/2006 

Release v2.42. This release improves the color schema of the general node (not meta-node) so that the node color is closer to the color specified by the user. This new color schema will change the brightness of the color of all existing VisANT network. If you do want to keep your old schema, simply load the network in VisANT with version less than 2.42. If you need a copy of old version, please send email to VisANT@zlab.bu.edu.

12/01/2005 

Release v2.41. This release provides part of ongoing function (Node Name Normalization) per user request, which enables user to label the protein/gene with its official name.  The official names are defined according to corresponding nomenclature databases and are automatically updated. 

Two menus are added. One is under Nodes Menu and is named as Label Protein/Gene with Official Name. This new menu will label the selected nodes using their official names. If the node do not have official name, its label will be turned off. The other one is under Filters menu and is named as Select Nodes DO NOT Have Official Name, which will select those nodes that do not have official names.

Note: You may need to run Name Normalization (which is also under Nodes menu) before label the node with its official name.

Note: When the interaction of a given node is queried (double-mouse-clicking), its name is automatically normalized. However, its linked nodes may not have their names normalized.

To the date of this release, the species and their total number of official proteins/genes are listed below:
 

Rattus norvegicus:17131              Mus musculus:39149              Homo sapiens:  22260

Note: Please feel free to email us if we missed species that have nomenclatures.

11/16/2005New  
Database Synchronization: Predictome database has been synchronized automatically with other interaction databases such as BIND and MIPS etc. so that computationally predicted functional associations can be directly compared with experimentally determined ones. The interactions/associations are integrated through the Name Normalization function that allows identification of genes/proteins from various alias and external database ids (this function will be announced later because it is still in process of similar automation, the function however, already available in VisANT) and are categorized based on interaction detection methods compatible to those defined in the ontology of molecular interaction proposed by Proteomics Standards Initiative (PSI-MI). To the date of this update, VisANT supports searching/query of 98924 experimentally-determined interactions and 307017 computationally-predicted ones in 103 organisms. Detailed description of the number of interactions/associations for each organism can be found in the Statistics page.
Statistics Page: This page is automatically updated whenever the Predictome database is changed. It lists global interaction statistics of Predictome database as well as statistics for individual organism. For each species, only the method that has interactions is listed. Click on the the number of each method will load the all interaction of this method in VisANT applet as shown in following figure:

The function shown in above figure is very similar to the one in of the Method Table in VisANT. However, the page makes much easier for large-scale analysis of the interaction network because it lists those methods that have the interaction only and all 10354 interactions can be directly loaded into VisANT by several mouse-clicking. 

Note: When loading all the interaction of one method in VisANT, the node size is generally set to the minimum automatically and the network is laid out using circular layout. To resume the node size, simply click the Zoom Out button and then click the Reset button and Fit to Page button. Similarly, to set node size to minimum, click Zoom Out button several times and then click Fit to Page button.
VisANT 2.4: In this new release, an interaction's supporting literature is stored as part of its properties. When an edge is selected, a new menu will appear as shown in the following figure:

In the above figure, there are four literature references regarding method M0031 for interaction between P53 and MDM2 in Homo sapiens. Click on the menu will load the PubMed abstract of the four references in the browser. 
Note: The literature reference for large scale method such as M0037 (phylogenetic profiling) may not available for the individual edge, however, it is available for the corresponding method in the Method Table (Ref button), which is merely in the consideration of storage efficiency. The literature references are stored in VisML.

Note: You must requery (forced query in VisANT) the corresponding to make these literature available for existing network that created using early version of VisANT.

10/12/2005New  
New plug-in tutorial create to illustrate how to create/modify nodes and edges in VisANT. The plug-in API is also updated

09/28/2005New  
Release of V2.3. Fixed the KEGG pathway bug and enabled the direct loading of KGML file. You can also append KEGG pathway by copy/paste the KGML to the Add field.

08/19/2005New  
The function to query GO functional annotation is now available. This function is under Nodes Menu

08/09/2005New  
One VisANT server was hacked. The function to query GO functional annotation is not available.

07/01/2005 

New paper published at NAR web-service edition: VisANT: data-integrating visual framework for biological networks and modules. Please site this paper if you use Meta-Network in your research.

06/28/2005 

Presentation at BioPathway Sig:

Networks, Pathways and Modules in VisANT

Live demo at ISMB 2005, Detroit:

VisANT: Integrative Visual Analysis Tool for Biological Networks, Pathways and Modules

Post session at ISMB 2005, Detroit:

Using Meta-Network to Analyze Networks of GO Functional Modules

06/13/2005

Tutorial and Plug-ins pages are updated.

 

05/04/2005 Release v2.1 with critical enhancements of VisANT Application

  • VisANT now starts with a startup network. Users running VisANT as application/web start will be able to use their own startup network. Please note that the startup file may be updated by VisANT server in case there is certain modification of method table. To save your own startup network, simply type CTRL-U or invoke corresponding menu item under File menu. The default startup file is shown as following :. Load startup.

  • Complete off-line when run VisANT as a local application. The startup file enables VisANT to run offline because it contains all necessary information.

  • If for any reason the user can not save the network, we have implement an emergency function that will copy VisML to Add text box (if the network is bigger, the rest part of VisML may be copied to Search box). The user can then copy the VisML from one or two textbox to a local file and email the file to VisANT@zlab.bu.edu, and we will help you to fix the problem and recovered at least, if not whole, most of the network. This function can be invoked by CTRL-Y or corresponding menu as shown above.

  • Users can now add their own methods through the window of Method Table. If a user saves a network having their own methods as the startup network, their own methods will always be available whenever VisANT starts.

  • Easy upgrade of VisANT when run as local application. VisANT is under active development and upgrade is now only one mouse-click away. A new menu has been added under Help menu. When the user query the Predictome database (e.g., search a protein), VisANT checks the update automatically and an icon will be shown near the Help menu if update is available. The user can click the icon to upgrade. (Upgrade is only applicable for users who download and run VisANT locally, other users always run the latest version of VisANT.

  • Enable a list of recent opened network file up to 9 files under File menu. These files can be quickly invoked by key combination CTRL-0-8. . This function is not available when run VisANT as an Applet

  • Auto-updating both Edge & Node Property Window when the node/edge selection has been changed. In other words, any change in the property window will always apply the current node/edge selection, regardless whether the selection has changed or not.

  • Enhanced Edge & Node Property Window to allow long edge/node names

  • VisML parser has been re-engineered, users will experience much better performance when load large VisML network.

  • Re-engineered the drop-down list of species to enable user to see the full name of species.

03/29/2005   Complete tutorial: Create & Filter the Weighted Network.

03/08/2005  Complete documents of plug-in development and corresponding tutorials.

03/02/2005  Invited book chapter (8.8) in Current Protocols in Bioinformatics.

Hu Z., Mellor,J. and DeLisi,C. (2004) Analyzing Networks with VisANT, In Current Protocols in Bioinformatics. John Wiley & Sons, New Jersey, US

02/17/2005  New home page, with Search, Java Web-Start and Application download options.

The Start button has been moved to the right-upper corner of VisANT banner in its home page. To avoid broken links of the page, it is advised not to open links of VisANT site in a new window. The new pages have been carefully designed will open any page in new window if necessary. Please also do not block pop-up page of this site if you have Google/Yahoo etc toolbar installed.

02/14/2005  Official version 2 release. Please wait for the lists of of new features.

11/20/2004  More flexible customization of both node and edge annotation. Screenshot  Sample Network

  • Allow change of Node Color through Node Property Window

  • Allow change Edge Thickness (using weight) and Edge Annotation through Edge Property Window

09/16/2004 Add a status bar, see following image

  • The status bar is used to indicate the number of total nodes (N) and edges (E); total selected nodes (SN) and total selected edges (SE). Please note that the total number of nodes and edges may exceeds the total visible nodes and edges.

  • If you want to know the number of total nodes and edges, simply select all nodes and edges (CTRL-A) and SE and SN are the numbers you want to know.

08/15/2004 Release of version 2.0 beta. Screenshot |Sample Network

2.0 beta requires JDK 1.4 or above. If you can not see the Start button at the center of this page, please download and install the latest JRE. The most sophisticated feature of Version 2.0 is the support of Meta-Network. Try out the new Grouping function in 2.0. Version 1.0 is still available, check out the left link for version 1.0. The user manual will be updated soon with the new feature in v2.0.

8/15/2004

VisANT 1.0 will stop developing after Aug. 2004, all network files saved with version 1.0 should be able to be opened in new release of VisANT. If you have problem to open the file, contact VisANT@zlab.bu.edu. This page will be expired once VisANT 1.0 is no long supported by VisANT application server.

 

08/11/2004

VisANT now supports searching of fruit fly gene/proteins interactions (total 33268 genes and 4780 Y2H interactions). Note: searchable terms for gene/protein of fruit fly is case-sensitive, and VisANT also enables searching with Greek symbols. For example, use &gamma;Snap to search for γSnap, see mapping table for more information. For fastest searching, please use official gene symbol defined by Flybase.

 

06/22/2004

Enhance the visual effect of edge's arrow.

 

06/22/2004 Enhance the visual effect of edge's arrow.

 

03/23/2004 "Add" button is now enabled by default without login based on user request.

 

03/23/2004

Add around 800 (click to load) Human Protein-Protein interactions from BIND database. Registered users before 03/05/2004 have been shared with a VisANT file containing the whole network.

 

03/07/2004

Full integration with Genew database, enables searching human gene using HGNC defined name and aliases, add cross links to OMIM, GeneCard etc, mapping to KEGG human pathways.

 

03/05/2004

Change the name of two menu items under Node Menu. Add a new menu item to query the internal connections between selected nodes.

 

02/25/2004 Added 3627 synthetic genetic interactions [from Tong, et al. Science, Feb 06 2004 ]. Helpful tip on loading whole data sets.

 

02/23/2004 Full text of VisANT paper available at BMC Bioinformatics.

 

01/22/2004 Add anonymous user "visant@bu.edu" with password "visant".

You should create an account if you wish to upload and save your data for later, however.

01/15/2004 Fixed bug related with zoom-out and reset function.

 

01/02/2004

  1. Add the degree distribution statistics for networks.

  2. The pop-out menu is reorganized

  3. Improved performance for the refreshment of control panel when changing from animation state to normal for JRE 1.2 above.

12/15/2003 Release VisANT v1.0.

 

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