May 5, 2006
CPU quotas
Due to the popularity of MPI-MrBayes, it's necessary to introduce CPU quotas.
Now a user's jobs are only submitted to the computer resource if the user is not already using more than 4 CPUs.
If there are idle nodes on the cluster, jobs are submitted regardless.
You can still create as many jobs as you wish, they will simply not be submitted to the resource right away and
will be listed as “Submitted to the system” in the job admin view.
March 28, 2006
MPI version of MrBayes available
The MPI version of MrBayes is available as a separate application. Apply to hpc-drift@usit.uio.no for access.
March 28, 2006
Submission of jobs is now back up again.
Submission of jobs is now back up again, and the problems at the computing cluster seems to be under
control. However we have lost some jobs in the process. Please check your running jobs, and resubmit
them if appropriate. We are sorry for any delay or inconvenience this may have caused.
March 28, 2006
Submission of jobs has been suspended for the time being, due to problems with the computing cluster.
Submission of jobs has been suspended for the time being, due to problems with the computing cluster. We will try to
have it back up again as soon as possible.
February 23, 2006
MrBayes phylogenic trees available
Phylogenic trees are generated for running and completed MrBayes jobs. Look for the
file MrBayes_tree.txt in the job view. As always, please report any problems
to hpc-drift@usit.uio.no.
February 16, 2006
MrBayes preview plots available
Preview plots will now be generated from MrBayes jobs both during and after a MrBayes job. The PNG
files are available in the job view. For running jobs the plots are updated every night.
February 16, 2006
Phyml and prottest are now available on the bioportal
Phyml and prottest are now available on the bioportal. You can get access
to this by sending us an email at hpc-drift@usit.uio.no.
February 15, 2006
Preview plots being added
We are in the process of adding a preview plot feature to MrBayes jobs. Accidents may happen.
Please report any problems to
hpc-drift.
January 4., 2006
The bioportal back up again.
The bioportal is again back up again. Feel free to submit jobs. Report problems to
hpc-drift. We are sorry about any
inconvenience.
January 4., 2006
The bioportal down again due to problems with the previous upgrade.
The bioportal down again due to problems with the previous upgrade. All web-services will be
available in this time. We hope to have it back up again by tomorrow. We are sorry about the
delay and any inconvenience.
December 20., 2005
The bioportal is back up again.
The bioportal is back up again. Feel free to submit jobs. Report problems to
hpc-drift. We are sorry about the delay and
any inconvenience.
December 16., 2005
The computing resources on the bioportal are still down, and will remain down until tuesday 20. january.
Unfortunately the computing resources on the Bioportal will be down until tuesday 20. january, due to delays. We
apologize for any inconvenience this may cause.
December 15., 2005
The computing resources connected to the Bioportal is now down, due to scheduled maintenance
Plans are that the resource will be back up again some time on friday afternoon/evening. Jobs
will be submitted to the system, but will not start on the resource. All web-services will be
available in this time.
December 9., 2005
Bioportal will be down from wednesday 14. until friday the 16. of december
The computational resources connected to the bioportal will be taken down for upgrades from
wednesday 14. until friday the 16. of december. Jobs will be submitted to the system, but will
not start on the resource. All web-services will be available in this time.
November 22., 2005
Cooling issue resolved
The machine room cooling issued has now been resolved, all operations are back to normal.
November 21., 2005
Technical problems with the bioportal
Some of the compute nodes used by the Bioportal have been shut down due to a machine room cooling issue. Jobs currently
in the system will be re-routed to other compute nodes, and new jobs will start when compute resources are available.
The only application that does not work at the moment is Blast.
October 20., 2005
Bioportal seminar: Structure Presentation and Hands on material
October 17., 2005
Bioportal seminar: Inference of population structure by model based clustering
Genetic mixture analysis aims at finding groups of genetically similar individuals
in a population genetic dataset. Roughly, groups are assembled such as to minimize
deviations from Hardy-Weinberg equilibrium and linkage disequilibrium within groups.
The number of groups can be determined by comparing likelihoods for different
configurations. The program structure is a free software package for using multi-locus
genotype data to investigate population structure. Its uses include inferring the
presence of distinct populations, assigning individuals to populations, studying hybrid
zones, identifying migrants and admixed individuals, and estimating population allele
frequencies in situations where many individuals are migrants or admixed. It can be applied
to most of the commonly-used genetic markers, including microsatellites, AFLPs and SNPs.
During the seminar I will introduce the program structure, show how to use it on bioportalen,
discuss how to interpret the output and in particular how to determine the optimal number of
group, and present some application examples from the literature. Although we will not have
time to run a complete analysis, you are welcome to bring your own dataset to discuss.
Homepage:
http://pritch.bsd.uchicago.edu/structure.html
It could be useful to print the manual and take it to the seminar.
References:
Inference of population structure using multilocus genotype data. J.K. Pritchard, M. Stephens and P. J. Donnelly, 2000.
Genetics 155: 945-959.
Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. D.
Falush, M. Stephens and J.K. Pritchard. 2003. Genetics, 164: 1567-1587.
Evano, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE:
a simulation study. Mol. Ecol. 14: 2611-2620.
Examples of applications:
The genetic structure of human populations. N.A. Rosenberg, J.K. Pritchard, J.L. Weber, H.M. Cann, K.K. Kidd, L.A.
Zhivotovsky and M.W. Feldman, 2002. Science, 298: 2381-2385.
Origin of extant domesticated sunflowers in eastern North America. Harter AV, Gardner KA, Falush D, Lentz DL, Bye RA,
Rieseberg LH. Nature. 2004 430:201-5.
Other programs for genetic mixture analysis:
Corander, J. Waldmann, P. and Sillanp, M.J. (2003). Bayesian analysis of genetic differentiation between populations.
Genetics, 163, 367-374.
Corander, J., Waldmann, P., Marttinen, P. and Sillanp, M.J. (2004). BAPS 2: enhanced possibilities for the analysis
of genetic population structure, Bioinformatics, 20, 2363-2369.
Dawson, KJ and Belkhir, K (2001) A Bayesian approach to the identification of panmictic populations and the assignment
of individuals. Genet. Res. 78: 59-77.
October 10., 2005
The new Bioportal
This is the new Bioportal that is to be launched on Monday October 10th 2005!
At that time we will transfer the name www.bioportal.uio.no to the new server. Files from the old
server is available on request (remember to include you username from the old portal).
The main characteristics of this new Bioportal are:
- 30 times more compute power
- A new security structure
- A more flexible architecture
- More applications
What does this mean for the users (apart for getting a new computational infrastructure)
- As the new Bioportal uses an updated securety structure you will have to fill in the
"Apply for access" form.
- The new Bioportal uses a different scheme for managing fils and submitting jobs, we have written a
short tutorial that will be published shortly.
October 4., 2005
A Bioportal lecture series
Dear colleagues,
The BioPortal is an internet site for computational biology at University
of Oslo (http://www.bioportal.uio.no/). This site offers services in
phylogeny, population genetics and high throughput sequence analyses.
During the last year thousands of analyses were have been done through
these services, and research groups from all life-science research
environments at UiO are using the implemented applications.
One of the main aims this year is to reach out to students and scientists
that are beginners in the field of biocomputing and introduce them to
programs and the underlying theories of the different methods available on
the BioPortal. Therefore, we are now organizing seminars which will include
an introductory lecture about the theory and applications of the programs
and a hands-on-session in a computer lab. The topics of the seminars are as
follows:
Population genetics
Model selection in phylogenetic inferences
Phylogeny
High throughput sequence database search and download of sequences
The seminars are usually divided in two sessions, including an introductory
talk and a hands-on demonstration. These sessions will take place in two
different rooms see the following table for time, speakers and topics:
13/10/05
The bioinformatics team (BIT, UiO)
Presentation of the new Bioportal and demonstration of applications
room 2621: 9:15-10:30
room 1252: 10:45-12:00
20/10/05
Dorothée Ehrich (NCB - National Centre for Biosystematics, UiO)
Inference of population structure by model based clustering
room 2621: 9:15-10:30
room 1252: 10:45-12:00
10/11/05
Geir Storvik (Professor, Department of Mathematics, UiO)
Evaluation of evolutionary models in phylogenetic inferences
room 2621: 9:15-10:30
room 1252: 10:45-12:00
24/11/05
Torgeir Ruden (BIT, UiO)
High throughput analysis of sequences. Quality assessment, BLAST and GO
searches.
room 3313/3315: 9:15-10:30
room 1252: 10:45-12:00
Time and place
The seminars will take place in the Biology building (Kristine Bonnevies
house) at Blindern (University of Oslo).
Registration
In order to have enough computers and hands-on material for the
participants a registration will be required. To register, please send an
e-mail to Beatriz Decenciere (beatriz.decenciere@bio.uio.no).
Contact information
Bioportal organizing committee:
Beatriz Decenciere (beatriz.decenciere@bio.uio.no)
Andreas Botnen (andreas.botnen@usit.uio.no)
Torgeir Ruden (t.a.ruden@usit.uio.no)
Kamran Shalchian-Tabrizi (kamran@bio.uio.no)
Webpage
http://www.bioportal.uio.no
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