BioManager

BioManager is an integrated bioinformatics workspace providing a single, user-friendly, and intuitive web interface to hundreds of powerful bioinformatics tools.

BioManager and ANGIS will be discontinued from November 30, 2009. This section of the Sydney Bioinformatics web site provides detailed information and the answers to frequently asked questions about the closure of BioManager and ANGIS.

The material in this section will be updated regularly as further information becomes available or changes as a result of the process of closing down BioManager and ANGIS. Please check this information regularly for updates.

Any further queries not addressed below can be addressed to Sonia Cattley or Jonathan Arthur (see the Contact Us section of the About tab).

Last updated: October 8, 2009

Use of BioManager has been steadily declining over the last few years, mainly due to:

• the emergence of post-genomic technologies
• the increasing availability and maturing of alternative, freely available, online resources
• life science researchers becoming increasingly capable of identifying and using their own solutions to their bioinformatic needs

As a result of this decline in usage nationally, BioManager is being discontinued.

BioManager will be closed on November 30, 2009. After this date, BioManager will only be available to download data. BioManager will be permanently closed on December 18, 2009.

• Contact all people within your department who are currently using BioManager or who have data stored in BioManager. Inform them of the change and ask them to finalize their usage of the system and download any data they want to keep by November 30, 2009.
• Watch for further correspondence from Sydney Bioinformatics and regularly check this web site for updates regarding the change.
• If you cease to be the contact person before December 18, 2009, please information Sonia Cattley so any further correspondence can be directed to the correct contact person.

Plan to complete your usage of BioManager and download any data you want to keep as soon as possible but, in any case, by November 30, 2009.

Depending on the anniversary date of your subscription, you may have paid in advance for access to BioManager beyond November 30, 2009.

Refunds for these over-payments have been issued to the departments or institutions affected. The refund cheques were processed and mailed by the University of Sydney Financial Shared Services group at the end of September. Sydney Bioinformatics sent a separate letter regarding the refunds on September 30, 2009, to the account contact person as per our records on this date.

If you receive your letter but do not receive your cheque, please contact us so we can put you in contact with the University of Sydney Financial Services team to track down the refund.

Sydney Bioinformatics is actively exploring various options for making BioManager available so individuals or departments could run their own version.

Users should not, however, assume such a scenario will eventuate. All users should plan to complete their usage and download the data they need by November 30, 2009.

Please note BioManager is an enterprise level software application requiring substantial computational infrastructure, very large reference databases, and ongoing maintenance and upgrades. Further, one needs access to individuals with expertise to manually and independently complete the installation process.

It is not possible to simply download and double-click to install BioManager on your own desktop computer.

If you believe your institution has the required hardware and expertise to install your own version of the application, and you wish to explore this option, please contact Jonathan Arthur.

Sydney Bioinformatics is currently seeking organizations or groups interested in hosting the BioManager application after the ANGIS/BioManager service closes on November 30. (See also the item above.) Information on other installations of BioManager can be found here.

BioManager provides a user interface to a wide variety of bioinformatics software packages. Many packages in BioManager are freely available. If you use a particular pacakge e.g. CLUSTALW, try using Google to search for the package name. Often you will find a site from where you can use the package online and/or download a local copy.

Other integrated interfaces similar to BioManager are:

• Galaxy - (main.g2.bx.psu.edu) - a resource that appears to be free provided by the Center for Comparative Genomics and Bioinformatics at Penn State University.
• Geneious - (www.geneious.com) - a commercial product produced by Biomatters Ltd in New Zealand

The Sydney Bioinformatics Chipster service will also be discontinued on November 30, 2009. However, Chipster can still be accessed through the CSC in Finland.

Additionally, other freely available software packages for microarray analysis include:

• CARMAweb
• MeV

We encourage individuals and institutions disadvantaged by the closure of BioManager to work together with existing groups to advocate for increased investment in bioinformatics research and teaching infrastructure.

In this regard, it may be helpful to contact:

• Bioinformatics Australia - the Australian professional society for bioinformatics.
• Bioplatforms Australia - a national body established to support life science research through investment in genomics, proteomics, metabolomics, and bioinformatics.

The following references contain information on the development and use of BioManager and previous versions of the application (BioNavigator, WebANGIS, etc.) and may be cited in papers making use of BioManager.

• Cattley S and Arthur JW, BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training, Briefings in Bioinformatics, 8:457-465, 2007
• Littlejohn TG, Bioinformatics in Australia, Bioinformatics 16:849-850, 2000
• Littlejohn TG, BioNavigator- Real science, Australian Biochemist 31:48-49, 2000
• Littlejohn TG, Bucholtz CA, Campbell RMM, Gaeta BA, Huynh C, and Kim SH, Computing for biotechnology - WebANGIS, Australasian Biotechnology 6:211- 217, 1996
• Littlejohn TG, Bioinformatics: The Essential Ingredient, Todays
  Life Science 8:28-33, 1996
• Littlejohn TG, Biocomputing at ANGIS: a 24 hour a day Dry Lab, Uniserve Science News 4:7-8, 1996