The server has been upgraded. This should reduce the queueing times of the Dali server. There is a new release of the Dali Database. The database will be updated twice a year. Protein structure superimpositions generated by Dali (Dali server, pairwise Dali, Dali database) are interactively visualised using Jmol. The current DaliLite standalone version is 3.1

There is a new release of the DaliLite standalone, version 2.4.4, incorporating a number of parameter increases to deal with segfaults on a few large PDB files. Follow the above link to go to the download page.

Shop Mallick has left our group to work at MIT, Boston, USA. He takes with him his wife Kathy and two children, River and Pearl, and leaves behind a big empty hole where his energy, enthusiasm, and contagious sense of mischief once were! We wish him well in his new position.

Knowledge through Collaboration
There is a strong need in the bioinformatics community for valuable and useful collaborations with research groups working in biological fields - an integrated approach towards problem-solving must only increase the efficiency of scientific knowledge dissemination. It also solves two common problems in computational biology: that wet-lab biologists can struggle for weeks with unfamiliar computational tasks and problems that would take a bioinformatician minutes to resolve; and that bioinformaticians can often lose sight of the biological goal of their research activities.

To this end, we at the Bioinformatics and Structural Genomics group are planning to hold mini-symposia and seminars in which we will present our research themes, applications and expertise to other research groups and scientists, and in which we will invite them to present their research projects and themes so that we can explore potential areas of collaboration. These will be informal and friendly, and open to all with an interest in computational biological techniques.

We plan to hold the first seminar in November 2006 (more information to follow), and we eagerly look forward to hearing from interested parties. Please contact either Petri or Ashwin if you would like more information or would be interested in presenting your work.

Over the summer, we had to place bandwidth restrictions on our largest download files due to excessive requests - our poor server just couldn't cope! This means it will now take longer to download our database flatfiles, as transfer is limited to 512KB/sec. Our largest files are in excess of 600MB, and will take at least 20minutes to download. Please be patient.

It is over a year since the last Dali Database update. We have been experiencing excessive problems with the update procedure, and the ever-increasing demands on our limited computing resources (due to the ever-increasing size of the PDB) have also slowed things down dramatically. We are currently in the process of debugging, and shifting the entire update procedure to the distributed computing facilities provided by the CSC. We do not anticipate a new release this year. We would recommend you use the Dali Server at the EBI if you need to calculate Dali structural alignments. We are sorry for the inconvenience, and will endeavour to fix things as soon as we can.

We had to shut down our webserver today for about an hour after excessive requests from a user in China. Unfortunately, we don't have a very powerful public server, and multiple requests for all of our largest database flatfiles was freezing our server. So please, if you wish to download our database files, click the link once and then wait - the largest Dali DB files are over 300MB and download may take a few seconds to begin. Please do not write scripts to automatically download these database files. We would also greatly appreciate you letting us know in advance if you are going to be heavily using our services, eg: for a course, or for a project involving script-automated downloads, so that we can make allowances. Many thanks.
The Webmaster.

Our webpages are undergoing a facelift. Goodbye javascript menu! The new pages are pure css and should appear exactly as intended in all modern browsers, including IE5+, Firefox/Mozilla, Netscape6, Safari, Konqueror, Opera7+ and any other browser that can cope with xhtml1.1 and css-2. They should be fully validating xhtml and css. Please let me know if you discover something broken or oddly rendered, and I will investigate.

The latest Dali Database update is underway. We have had considerable problems with our production server, which is why the current version is a year old; we are now using computing resources at the CSC. We should have the new update available by May.

Also a new, fast GTG Server is in production and should be ready for public release around the beginning of April. The Global Trace Graph (GTG) is a suite of applications for remote homology and fold recognition. It is competitive with the current best methods for remote homology detection but it needs no structural information, only sequence data. A publication is in submission - more details to follow.

Due to a power failure throughout the entire Biocenter this lunchtime, our pages and services were offline for an hour - sorry for any inconvenience caused. We rebooted as soon as possible, and there seems to be no damage to our hardware or to our databases, but please contact us if you do experience anything strange while accessing our services.

We welcome two new members to the group! Dr Päivi Onkamo, lecturer in bioinformatics, joins us from the Department of Computer Science. Her areas of research and expertise include data mining and pattern discovery, linkage and association analyses, SNPs, microsatellites and gene epidemiology. Dr Petri Toronen joins us from the University of Kuopio. His past research has included hierarchical clustering methods, the use of SOMs, Sammon's Mapping and fuzzy logic in the analysis of gene expression data.

Our group gains two new members and says “Nähdään!” to an old friend. A warm welcome to Dr Alain Schenkel and Dr Nathalie Artemenko, who join us from the Department of Mathematics (University of Helsinki) and the Department of Chemistry at Moscow State University, respectively. And farewell Dr Andreas Heger, long-standing member of the group who leaves us to join Prof Christopher Ponting’s Comparative Genomics Group at the University of Oxford, England. We wish him well.

Our group moved from the EBI to the Institute of Biotechnology in September 2002. This website will be a comprehensive source of services and tools offered by us to the Biosciences Community. Please contact us if you encounter any problems with, or have any comments about, our website and its contents. We will be happy to hear from you!

In addition to the services we offer via the EBI, our local web services include the Dali Database, ADDA (Automatic Domain Decomposition Algorithm), POBO (promoter search and verification algorithm with bootstrapping) and the SOLVX Server (Solvation Preference data for protein structures). Please visit our “Services and Tools” page for a list of all available tools.