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 are now closed. 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.
Last updated: December 8, 2009
Why were BioManager and ANGIS discontinued?
Use of BioManager had 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 was discontinued.
When did BioManager close?
BioManager closed on November 30, 2009 at 11:59 pm.
How do I access my data now BioManager is closed?
A data download facility is available here. This facility will be maintained until 7:00 am on December 14, 2009. All users should download their data by this time.
A DVD or CD of all data from all users in each department or organisation with a BioManager subscription has been sent to the contact person for that department or organisation. After December 14, 2009, you will have to contact your local contact person to retrieve your data from the DVD or CD.
I am a contact person for our department. What do I need to do?
You should have already informed all users within your department of the changes so they were able to finalize their BioManager usage. At this time you should:
- Remind all users in your department to download their data from the data download facility by 7:00 am on December 14, 2009.
- Make arrangements for the appropriate storage of the DVD or CD containing the data of all users in your department, such that users can access it easily if required.
- Continue to check this web site for any further updates regarding the closure of BioManager and ANGIS.
I am a BioManager user. What do I need to do?
Download all your data from the data download facility by 7:00 am on December 14, 2009. Make sure you are aware of who your local contact person is and the arrangements for storage of and access to the the data DVD or CD in case you need it in the future.
My department paid for access until sometime in 2010! Will I get a refund?
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.
Is BioManager available anywhere else?
A copy of BioManager with minimal support is being maintained by Professor Peter Reeves at the University of Sydney. It is available here. Sydney Bioinformatics is not involved in the provision, maintenance, or support of this copy of BioManager. All queries regarding this copy of BioManager should be directed as per the information on the site above.
Can I get a copy so I can run my own version?
All such queries should be directed to Professor Peter Reeves via the information provided on site for the copy of BioManager given above.
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 Professor Peter Reeves.
Is there a similar piece of software I can use?
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
What about Chipster?
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:
What about 2D ANGIS and other ANGIS related services?
2D ANGIS and all other ANGIS related services will also be closed on November 30, 2009.
Who can I write to about this?
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.
References
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