information for drugs
as shown below
Release 4.06, added following features:
Add a new section "Filter
the Network Based on GO Annotation" in VisANT user manual upon user request.:
Release 4.03, fix the bug of VisML loading with saved legend node.
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
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.
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
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
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:
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:
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:
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:
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 (firstname.lastname@example.org).
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.
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
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
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
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:
Release 3.9 with enhanced performance of query-related macros, also some
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
Add new tutorial Develop VisANT
plugin in Eclipse
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
Click to load the resulted network.
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
VisANT 3.5: multi-scale network visualization, analysis and inference based
on the gene ontology
Release VisANT 3.66, with new macros
to select nodes based on their properties, such as node color, size and shape
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
04/12/2009 Release VisANT 3.60, with two new features
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
Note: FLN data can not be downloaded from
statistics page, or the method table
in VisANT. Using this page to download the all
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
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
Note: although highly optimized, the convex
hull still cost more time to draw than the default rectangle.
User manual for
release 3.55 is updated.
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
Report of NMEA results, such as:
For more information, please reference the updated
manual for new functions in V3.5.
Release VisANT 3.52, with two new plugins:
Release VisANT 3.49, with new functions for Gene Ontology visualization,
integration and annotation.
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
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
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
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.
Release of V3.43. This release provides following
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)
Command-file can be directly loaded into VisANT as
macro file given that the file starts with the line "#!batch commands",
just like any files supported by VisANT. The commands (macros) can
also be add directly to VisANT as shown below:
of the macro file can be found here, which illustrates some of the new
commands that can be used to change the visual properties of the network. You
try out the macro file by clicking here. Here is
another file with macros to automatically query the interactions of the
In general, macros allows users to combine tedious
or repetitive tasks/analysis into one single action, make it much easier to
define your own work flow, do live demo,
pretty network with simple edge-list etc. In the near future, you will be
able to save macros as menus and have a version of VisANT for your own.
Note: You can always stop the macros by press
the ESC key.
Many new commands to
support simple loop, loading network from URL, and setting
nodes/edges properties etc., some
of the functions are only supported by the commands so far, such as
changing of the edge transparency,
font style and
node shape etc, as shown below:
Above network can be loaded by
Here is another example to illustrate the usage of
changing the edge transparency and font style so that the node label can be seen
clearly (detailed explanation of the
commands can be found here):
The macros to make above change are listed in the
Primarily support of visualization of GML format:
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:
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):
a meta-network of diseases (cancer subset of
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.
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
Release of VisANT 3.22, which adds following
new tutorials have been added:
brief summary of mouse operations in VisANT has been added for your quick
Add new tutorial "How
to use VisANT in your own web site".
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
screenshots of the huge network is listed in sample page.
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
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
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
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
Many bug fixes.
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.
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:
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
Release V3.03, there are two new features in
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
Flih Flih Flih
will result in the creation of a complex node
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.
Release of VisANT V3.0,
manual about new features can be found
Release of VisANT V2.92, detail to follow
Release of VisANT V2.91, detail to follow
Release of VisANT V2.61, fixed several bugs
reported by users.
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.
for the detail about ID-Mapping file.
There are now three options when export the
network as Tab-delimited file. Please reference
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
Provides a new menu under Duplication
to select all duplicated node instances.
Fixed several bugs, including ungroup and
select/deselect all methods etc.
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
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.
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).
Align & Distribute
functions have been provided to help user to manage the network under
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.
Release v2.5 beta with enhanced expression module
allows for the expression profile (example
network) , See updated
user manual for detail.
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.
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
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
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
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
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
Note: This function is still in
beta-version, it will eventually become part of VisANT.
Release v2.43. This is a quick release to allow
nodes without any edges to be exported in the tab-delimited format.
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
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:
Homo sapiens: 22260
Note: Please feel free to email us
if we missed species that have nomenclatures.
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
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.
tutorial create to illustrate how to create/modify nodes and edges in
VisANT. The plug-in API
is also updated
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
The function to query GO functional annotation
is now available. This function is under Nodes Menu
One VisANT server was hacked. The function to
query GO functional annotation is not available.
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
Presentation at BioPathway Sig:
Networks, Pathways and Modules in VisANT
Live demo at ISMB 2005, Detroit:
Integrative Visual Analysis Tool for Biological Networks, Pathways and
Post session at ISMB 2005, Detroit:
Meta-Network to Analyze Networks of GO Functional Modules
Tutorial and Plug-ins
pages are updated.
v2.1 with critical enhancements of
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
Complete off-line when run VisANT as a
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
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
Easy upgrade of VisANT when run as
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
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.
Create & Filter the Weighted
Complete documents of plug-in development and
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
New home page, with Search, Java Web-Start and Application download options.
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.
More flexible customization of both node and edge annotation.
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
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
The most sophisticated feature of Version 2.0 is the support of
Try out the new
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
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
VisANT now supports searching of
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 γSnap to search for γSnap, see
mapping table for more information. For
fastest searching, please use official gene symbol defined by
Enhance the visual effect of edge's arrow.
Enhance the visual effect of edge's arrow.
"Add" button is now enabled by default without login
based on user request.
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
Full integration with
Genew database, enables searching human gene using
HGNC defined name
and aliases, add cross links to OMIM, GeneCard etc,
KEGG human pathways.
Change the name of
two menu items under Node Menu. Add a
new menu item to query the internal
connections between selected nodes.
synthetic genetic interactions [from Tong, et al. Science, Feb 06 2004 ].
Helpful tip on loading whole data sets.
Full text of VisANT paper available at BMC
Add anonymous user "email@example.com" with password "visant".
You should create an account if you wish to upload and save your data
for later, however.
Fixed bug related with zoom-out and reset function.
distribution statistics for networks.
menu is reorganized
for the refreshment of control panel when changing from animation state
to normal for JRE 1.2 above.
Release VisANT v1.0.