News

PathPort server down for maitenance (30 May 2007)

PathPort server will be shutdown for installing new hard disk drives from 5:00am to 7:00am US Eastern time on 5/31/2007. PathPort web services will not be available during the shutdown time. PathPort web site will not be affected. We appreciate for your understanding.

ToolBus/PathPort Beta Release has been rebuilt (5 Apr. 2007)

The ToolBus/PathPort Beta Release has been rebuilt for updating the session file to change web services URLs.

myGrid and ToolBus/PathPort Interoperability software demonstration at ISMB 2006

myGrid and ToolBus/PathPort are two complimentary bioinformatics software suites. ToolBus/PathPort focuses on data visualization and exploratory analysis, while myGrid focuses on high-throughput, automated analysis. Both systems are built on Web service standards, allowing them to interoperate at multiple levels. This interoperability was demonstrated at ISMB 2006 by Tom Oinn and Konstantinos Krampis. Additional information about the demo can be found at the following links:

ToolBus/PathPort Beta Release has been rebuilt (11 Sept 2006)

The ToolBus/PathPort Beta Release has been rebuilt for updating the Phylogenetic Tree plugin and web service. ToolBus Tutorial and session file have also been updated.

Two presentations made at BIOCOMP'06 (5 July 2006)

Dr. Boyu Yang attended the BIOCOMP'06 conference from Jun. 26 to 29 held at Las Vegas, USA. BIOCOMP'06 is a subconference of WORLDCOMP'06 - The 2006 World Congress in Computer Science, Computer Engineering, and Applied Computing.
Dr. Boyu Yang attended the conference and made the following two presentations:
Bioinformatics Web Services
Genome Annotation and Comparison System
For people who are interested in the two presentations, they are available online.

ToolBus/PathPort new Beta Release (31 Mar 2006)

VBI is pleased to announce a new Beta Release for ToolBus/PathPort, version 2.1.10.18. The purpose of the refresh is to make publicly available the bug-fixing, performance tuning, and usability work that we've been doing in some of the existing tools over the past several months. The beta does not contain all of the tools that have been previously shipped with ToolBus/PathPort, it is just the ones that have had significant attention, mostly in the genomics space. It will handle larger datasets, perform faster, and be easier to use, and have all known bugs fixed. If you are using a tool that is not in the Beta Release, please note that we have provided the ability to continue downloading and using your current version.

VBI Network maintenance notice (11 Oct 2005)

Due to VBI network maintenance, PathPort web site and all web services deployed on servers within VBI may not be available between 5am and 7am on Thursday(13 Oct. 2005).

Web Services Symposium (4 Apr 2005)

The Virginia Bioinformatics Institute (VBI) at Virginia Tech and Sun Microsystems are working together to offer an "International Symposium on Web Services for Computational Biology and Bioinformatics." The Symposium will be held at VBI on May 26 and 27, 2005. Please visit http://webconference.vbi.vt.edu for registration and additional information.

ToolBus/PathPort Release 2.0 (2 Sep 2004)

We are pleased to announce a new production release of ToolBus (version 2.0) as well as a new production release of the bundled set of corresponding ToolBus/PathPort visualization plugins. This release incorporates many bug fixes and enhancements. The most noticeable and significant enhancement is the inclusion of context sensitive pop-up menus (instead of key modifiers for mouse clicks). This enables new users to more quickly learn and navigate the system, as well as enable occasional users to reacquaint themselves with the system more easily.

PathPort Training On The Road (9 Feb 2004)

The Virginia Bioinformatics Institute (VBI) PathPort team today begins a series of PathPort demonstrations and training sessions that will take them to Maryland, Virginia, and the District of Columbia. These training sessions will give PathPort users the tools to optimize the technology at their own institutions.

Developed by leading bioinformaticians, PathPort (short for Pathogen Portal) combines information about pathogens and their near relatives from around the world with powerful analysis and visualization tools to aid in the rapid detection, identification, and forensic attribution of high-priority pathogens, whether they can cause infectious diseases or potentially be used as a biological weapons. The platform offers a one-stop shop for data analysis and tool interoperation. Unique features include drag and drop data transport tools, saving and sharing analysis work sessions, and data viewers with no command lines.

Day-long workshops will provide hands-on training to use genome analysis tools such as genome comparison, BLAST searches, sequence alignments, gene prediction, phylogenetic trees and other advanced features using VBIs integrated PathPort software system. The team will also be providing researchers with information on how to access VBIs Core Laboratory Facility and Core Computational Facility services.

The workshop series begins Wednesday in Bethesda, MD. The training sessions will then move to Charlottesville, VA (February 13) and Baltimore, MD (February 18 and 19).

PathPort/ToolBus Version 1.1 Released (27 Oct 2003)

VBI at Virginia Tech has released a new, updated version of the groundbreaking PathPort/ToolBus software. Version 1.1 includes new web services and updated visualization plugins. This new version now includes a microarray visualization and analysis suite that provides significant new abilities to PathPort users.

Other new additions include enhanced versions of visualization plugins to examine genomic DNA, multiple sequence alignments, extensive background information on 21 human pathogens, bacterial gene phylogenies, and sequence similarity for BLAST, PCR/Hybridization probe design, and others.

New Analysis Web-services Are Added To The System (16 Jul 2003)

Two new analysis web-services were added to the system for doing large sequence comparisons and parallel Blast and Fasta searches. MUMmer 3.1, from The Institute for Genomics Research (TIGR), compares sequences to find similar subsequences as well as (in)exact repeats and inversions.

The new Condor based version of our Blast and Fasta facility uses the idle compute cycles on our desktop computers. Unlike the parallel Beowulf cluster implementation, the parallel Condor Blast and Fasta searches will be provided free of charge, though with possibly slower response times.

At the same time, the OligoArray service has been removed from production and placed on the development server. Tests showed that it was experiencing memory usage patterns that were interferring with other production services.

Finally, all prodcution services were updated to enable determination of which services are currently in use and to refuse to initiate new service requests. These two capabilities will enable cleaner shutdowns with fewer interruptions to the user community.

ToolBus 1.0 Released (26 Jun 2003)

Virginia Bioinformatics Institute (VBI) Director Dr. Bruno Sobral today announced the release of PathPort 1.0, a global pathogen portal created with the aid of a $4 million federal contract. This unique portal collects and collates genetic information about all known pathogens and their close relatives. PathPort will connect diverse pathogen data and tools, thus aiding researchers in their studies of high-priority pathogens, speeding up development of countermeasures.

The software infrastructure supporting the PathPort project centers around ToolBus, and web services that allow researchers to easily access programs and data from distributed sources. This software architecture allows users to form groupings of related information and to perform comparative analysis. "This type of system also serves as a testbed for what the NSF calls cyberinfrastructure, which will revolutionize the way scientific research is conducted and communicated," explained Dr. Sobral.

New tools on version 1.0 cover such areas as DNA sequence and sequence annotation, gene prediction, phylogenetic analysis, homology search, and others. Background information on most of the pathogens from the CDC's and NIAID's A, B, and C lists of pathogens of concern will be available via these tools in the coming weeks.

Software architecture of this kind will prove essential for protection against infectious diseases and biological weapons. "In times such as these," Sobral said, "we are acutely cognizant of living in a society defined by, and dependent on, science and technology. Bioinformatics tools such as PathPort will continue to forge essential links between research communities."

VBI developed PathPort with the US Department of Defense in order to strengthen the nation's security against pathogens. "This portal will strengthen not only the nation's security, but infectious disease research as well," said head PathPort architect Dr. J Dana Eckart.

PathPort's development is supported by the Department of Defense U.S. Army Soldier and Biological Chemical Command Unit. For more information about the PathPort project, please visit http://pathport.vbi.vt.edu.

Beta 3 Release (28 Feb 2003)

A new look and lots of new features including: multiple session loading, improved group comparison, better model and view management, additional on-line documentation, and a host of new tools have also been added. Numerous bugs in the beta 2 have also been fixed and the installation process has been streamlined using a graphical install program.

Beta 2 Release (12 Dec 2002)

A number of fixes have been implemented, particularly those relating to the loading and saving of configurations. Startup is somewhat faster and the overall size of the distribution has been reduced.

Beta 1 Release (23 Nov 2002)

The first beta release of the ToolBus software is now available, along with improved versions of the PathPort model/views. Some of the many improvements over the alpha release include: saving/loading configuration, GUI preferences, generalized group comparisons via user created Venn diagrams and improved web-service binding support. A first draft of a tutorial for developers wanting to write model/views for ToolBus is also now available.

Public Website Established (30 Aug 2002)

With a non-commercial open-source license in hand, an alpha version of ToolBus along with serveral web-services and LGPL licensed visualization components are made available on the new public portion of the web-site.

Last modified on 04Jul2008