Available positions will be posted here. Thank you for your interest in our group.
(Currently there are no open positions in our group.
But if you think that your talent is exclusive, feel free to contact us.)
The Dali server will migrate from this server (ekhidna.biocenter.helsinki.fi/dali_server) to a new server
(ekhidna2.biocenter.helsinki.fi/dali/). The old server will retire by the end of this year. The new server
is in operation.
There were irregularities in the operation of the Dali server due to a disk mishap. Normal service resumed at 11 pm EET.
All 64-bit Linux computers at the university, including the Dali server, were shut down due to a security scare in the IT department.
Friday 28th November 2008
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
Monday 15th January 2007
There is a new release of the DaliLite standalone,
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.
Friday 1st December 2006
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.
Thursday 5th October 2006
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
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
if you would like
more information or would be interested in presenting your work.
Monday 11th September 2006
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.
Tuesday 04th April 2006
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.
Friday 10th March 2006
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
. 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.
Thursday 21st April 2005
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.