-
The BioInformatics Center Resource Unit staff are assisting Dr Patrick Tan of
the National Cancer Center and his vendors, Retrieva in a National GRID
Office (NGO) project entitled "A Personalised and Adaptive Literature Curation
System for the Biomedical Sciences".
November 2006 -
The BioInformatics Center Resource Unit will be hosting a 1 day workshop on Machine learning for BioMedical Informatics on the 21
st of November 2006
at the NUS Mathematics Department Computer Lab. The workshop examines how to use Machine Learning techniques in the computing sciences and apply and adapt them to the life sciences. Computing techniques regularly used in medical and bioinformatics include Artificial Neural Networks (ANN), Genetic Algorithms (GA), Hidden Markov Models (HMM), Support Vector Machines (SVM).
The workshop is hosted together with Department of Biochemistry, Yong Loo Lin School of Medicine. Detailed information can be found at
http://everest.bic.nus.edu.sg/mediawiki/index.php/ELMworkshop2006
BioSLAX Updates
August 2006 -
The first update to the live CD suite of bioinformtics tools has been released. The update coincides with the release of
the SLAX live CD's 5.1.7 as well and incorporates new changes such as the ability to
boot in LINUX from a single ISO file or expanded ISO files within the Windows environment.
More information will be updated at the BioSLAX official website,
http://www.bioslax.com.
BioSLAX - Bioinformatics Live CD Suite Released!
April 2006 -
A new live CD suite of bioinformatics tools has been released by BIC. Bootable from any PC, this CD runs the
SLACKWARE version of LINUX operating system in a compressed format
also known as
SLAX.
Knoppix based live CDs were previously used by the Life Science Module practicals but the inability to customise the build easily
and sluggishness of this version, made it a less than attractive choice.
SLAX is becoming the live CD of choice because of its ability to modularize almost any application and plug it into the system on the fly.
For those who wish to have the system installed on the hard drive of their PCs or to their USB thumbdrives, a BioSLAX installer is also
provided as one of the applications.
Lead by Mark De Silva, the team has released (in just over 2 weeks since starting), 2 versions, the '
Power User' version
full of popular bioinformatics and life science tools and a '
Power Developer' version
which is essentially the same as the '
Power User' version except that it has programming tools and libraries for developement. The '
Power
Developer' version can only fit on a DVD due to its size and is recommended only serious developers or for those who intend to install the
system to the hard drive.
The official website for BioSLAX is at
http://www.bioslax.com.
HPC Challenge 2005/2006, PC Grid Parallel Speedup Category - 2nd Prize
March 2006 - BIC staff, who formed part of the group that took part in the High Performance Computing Challenge together with LSM
staff, emerged runners up in the PC Grid Parallel Speedup Category. The team consisting of Tan Tin Wee, Mark De Silva, Lim Kuan Siong, Justin
Choo, Ung Choong Yong and Patrick Tan, presented a United Devices BLAST project to support 300 LSM2104 students working on multiple blast
searches on Patrick Tan's Aero-meta-genomics project.
First Prize winner is Bernett Lee, a Biochem Dept grad student also formerly under BIC and now with BII. He was the key person who grid-enabled
his HMMer algo for updating his DEDB Drosophila Alternative Splicing Database.
Awards presentations will be held on the 4th of April.
Tera Campus Grid - BIC Blast Web Portal
March 2006 - BIC is currently working with Computer Center staff and contractors involved in the GRID project under the Tera Campus
Grid (TCG) to produce a web interface to both a GRID version of BLAST and HMMER. The Grid versions of these popular software will increase
efficiency and speed of queries, making what took days, become just mere hours. The Grid BLAST has been completed and is still undergoing
testing at the moment. Users can try it out by following the Resources->Computational link from the menu bar on this website.
The process is still very manual in the sense that users have to submit their query, get a job id and periodically check if the
job is complete before requesting for the results from the system. The Grid HMMER will be started on soon. Plans are in the pipeline to
fully automate both processes in the future such that users need only submit their queries and wait for results to be mailed to them.
BIC Website - Retrofitted!
January 2006 - After nearly three years, the BIC website has been given a facelift. Keeping with the NUS commercial design, the new
website is spiffier, easy to navigate and chock full of information. Articles and news snippets dating back to 1996, when the center was
first formed, are still available as well as lots of new information. Resouces links have been updated and are now syncronized with a back
end database that stores all the resources available - this means you get access to the resource the minute the administrators add it in.
Drop in and take a look!
Invitation from the Center of Bioinformatics and Genomics
October 2005 - BIC senior staff, Mark De Silva and Lim Kuan Siong, have been invited to teach in the
2nd Training Course on Bioinformatics and Functional Genomics Applied to Insect Vector of Human Diseases and
4th Regional Training Course on Bioinformatics Applied to Tropical Diseases in Southeast Asia.
The two TDR-sponsored Training Courses will be held at the Center for Bioinformatics and Applied Genomics (CBAG) at the Faculty of
Science, Mahidol University, Bangkok, Thailand during the weeks of 19th to 30th of September 2005 and 3rd to 14th of October 2005.