03/31/2017New We are looking for talented postdoc and software engineer to join the NIH-sponsored project in the field of microbiology and systems biology. Applicants should submit a cover letter, CV and names, e-mail addresses and phone numbers of 3 referees to Dr. Charles DeLisi (DeLisi@bu.edu), Dr. Segre, Daniel (dsegre@bu.edu) and Dr. Zhenjun Hu (zjhu@bu.edu)

Postdoctoral Association
A postdoctoral association position is available for research on a multilab microbiome project supported by National Institutes of Health at BU's Bioinformatics Program. The candidate for this project will be responsible for computational method development and analysis. The ideal candidate should be broadly experienced with analyzing next generation sequencing data and network-based analysis. Prospective applicants should have made significant contributions to their area of study, as evidenced by a strong publication record.
REQUIREMENTS
Qualified candidates should have
  • A Ph.D. in Computer Science, Bioinformatics, Biostatistics, or a related field
  • Proficiency in one or more statistical or scripting languages appropriate for salable data analysis
  • Comfort and experience with programming for biological data analysis
  • Familiarity with functional genetic and/or genomic data, as indicated by publication record
  • Ability to communicate scientific material and collaborate well with lab members
Software engineer
A software engineer position is available for research on a multilab microbiome project supported by National Institutes of Health at BU's Bioinformatics Program. The position will support the labs' needs for developing pipelines, databases and web platforms. The main duties include:
  • Help to design and build new software tools and systems
  • Perform comprehensive unit, integration and scale testing of all software produced
  • Working with the scientists who provide data and analytic capabilities
  • Exploring new techniques and studying related scientific developments
  • Work with existing users to provide education and resolution of issues
  • Work to integrate new technologies and systems into existing infrastructure
REQUIREMENTS
  • Must have experience in Java. Experience with Grails/Groovy strongly preferred
  • Knowledge of web programming technologies such as AJAX, HTML5, JavaScript and jQuery
  • Knowledge of relational databases and SQL queries
  • Knowledge in UNIX/Linux environments, including basic shell scripting
  • Knowledge of REST-based Web Services highly desirable
  • Knowledge of Amazon EC2/Elastic Beanstalk desirable
  • Knowledge of Spring framework, Hibernate and Unit Testing desirable
  • Knowledge of scientific graphics (especially using D3) is desirable
  • Knowledge of using design patterns is desirable
  • Knowledge of VisANT and COMETICS is desirable but not required
  • Knowledge of bid data processing framework such as Hadoop and Spark is desirable but not required
  • Interest in biology, genetics, or drug discovery highly desirable but not required

03/30/2017New Here is our regular maintenance plan on 9 am at following days:

04/26/2016 New VisANT publication on PlOS Computational Biology: Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. The paper may also be downloaded here.

04/21/2016 Release of VisANT 5.50 with following enhancements:

Enhacned error check for Edge List
The Edge List format is the simplest format delimited either by Space or Tab to import/add the network data in VisANT. It has been designed to be simple and flexible. This new release added new functions to check and remind the correct format as indicated below.
  • While the first 2 columns in general can be anything, the 3rd column however must either be method ID available in Method Table or an integer (ranging from -9 to 9 at this moment) indicating the type of interaction. An invalid method ID will trigger the error message as shown below:

    Users have the option to ignore the error, or stop the parsing procedure. If the former is selected, VisANT will try to solve the problem automatically and in the exmaple shown in above image, the default method ID M0099 is used to replace the illegual one MX036. On the other hand, if the user choose to stop the parsing procedure, VisANT will discard the rest lines including the current one.
    Note: The 3rd and 4th columns are exchangeable.
  • The fifth column is used to represented the normalized edge weight and must be between 0-1, otherwise, following error message will appear:

    Similarly if the user chooses to ignore the error, VisANT will set the edge weight to 0 if the value is less than 0, or 1 if the value is larger than 1.
  • The sixth column is used to attach the references to the interaction. These reference must be PubMed IDs delimited by ,. If there is an error in the PubMed IDs, or the total number of columns is bigger than 6, the following message will appear:

    VisANT will rescue as many references as possible if the user chooses to ignore the error. In the example shown above, VisANT ignores the first reference XX because it is not a valid PubMed ID, and then attach the rest 2 to the edge as shown above.
Enhacned navigation of networks embedded in metanodes with COMETS Plugin
  • Hide the embedded networks using a global control, see corresponding section in the manual.
  • Hide the selected nodes, detailed can be found in the updated user manual.
    Note:Except the global control, the hidden nodes can also be recovered by the explortory navigration, just click the nodes that linked with the hidden nodes. You may want to turn off the Database Online option under the menu File to avoid the database query.
    Note:You may need do double-click twice.

03/26/2015 Release of VisANT 5.20 to modify the behavior of Reaction Node: the exploratory navigation is only available when there is no enzyme embedded in Reaction Node, otherwise, it will behave like normal metanode: double-click will show/hide embedded nodes, as illustrated below:

Note: the species information is required to query the enzymes of the reaction

 

 

There are 7 Homo sapiens enzymes for reaction R00623, as shown in the tool-tip in above figure.

Note: The Node(s) menu is always node specific.

 

Note: if the linked metabolites are hidden, it can be shown through the menu Node(s)/Query Interactions of Selected Nodes with corresponding reaction node being selected.

03/13/2015New Both VisANT database server and web server will not be accessible from 11 PM Saturday 3/14 through 8 AM Sunday 3/15, due to the emergency repair of IT devices of Boston University

02/27/2015New Release of VisANT 5.12 to fix several bugs

08/29/2014 Release of VisANT 4.19 .with beta release of MBL plugin available under Layout menu that supports the network layout inside the metanodes.

06/06/2013 New manuscript published on NAR (Nucleotide Acid Research) that systemically described our efforts to forge VisANT as integrative network platform for systems biology, systems pharmacology and translational science:

VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies PDF

The manuscript presents new convenient functions including (i) integrated search and navigation of disease and drug hierarchies; (ii) integrated disease-gene, therapy-drug and drug-target association to aid the network construction and filtering; (iii) annotation of genes/drugs using disease/therapy information; (iv) prediction of associated diseases/therapies for a given set of genes/drugs using enrichment analysis; (v) network transformation to support construction of versatile network of drugs, genes, diseases and therapies; (vi) enhanced user interface using docking windows to allow easy customization of node and edge properties with build-in legend node to distinguish different node type.

05/16/2013

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

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

 

Download this macro

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

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

7/15/2012 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 of 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 metagraph 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.

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:

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.

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

03/19/2009New   Release VisANT 3.55:

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.


 

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.

***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;

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.

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.

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:

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

#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.

11/16/2006 

Release of VisANT V2.54.

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

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

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

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

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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