Fight the Future: The (Re-)Launch of this blog
We started this Blog under the name “xBASE blog” a couple of years ago, with the idea that it allow us to publicise developments with our xBASE genomics facility. However, it is now clear that we need to write on a much broader canvas and tackle all manner of exciting developments that are taking place [...]
Importing Genbank Data, Quickly
NCBI is currently listing a total of 1668 bacterial genome projects, counting both complete and incomplete. With the advent of high-throughput sequencing technologies this number looks set to mushroom even further. This is great news, but for bioinformaticians it provides serious challenges. When it came to updating the xBASE database, we found ourselves in a [...]
My xBASE Announced at Genomes 2008, Paris
Mark Pallen has announced a new service for the users of xBASE entitled ‘My xBASE’. My xBASE is a service to aid researchers exploit the data produced by next-generation bacterial genome sequencers such as 454 (Roche)and Solexa (Illumina). Early applications of my xBASE will include: storage and processing of raw read files mapping (alignment) against [...]
Genomes 2008, Paris #4
Yesterday, George Weinstock treated us to his vision for the Human Microbiome Project and outlined some of the major problems which need to be solved. The approach is quite exhaustive: 100 volunteers have samples collected from many different environments offered by the human body: different sites in the mouth, stomach, small and large bowel, but [...]
Genomes 2008, Paris #3
Yesterday highlights included Julian Parkhill’s highly anticipated reveal of how the Wellcome Trust Sanger Institute are making use of the next-generation sequencing technology. His talk, entitled “Variation detection in highly monomorphic bacteria using new sequencing technologies” demonstrated the use of 454 and Solexa sequencing on Salmonella enterica serovar Typhi. The use of the term “monomorphic” [...]
Genomes 2008, Paris #2
Several stimulating talks so far today. A highlight was the announcement from Erick Denamur of Genoscope that they have finished 6 new E. coli strains. One of the nice findings from the talk was a very nice phylogenetic reconstruction of the E. coli (and Shigella) groups. To the consternation of Mark Pallen he made the [...]
Genomes 2008, Paris
Greetings from the ‘Genomes 2008′ conference, this year being held at the Institut Pasteur, Paris. The conference so far has had an interesting mix of talks, covering a wide range of bugs, from human and plant pathogens to insect endosymbionts, and even a talk on viral photosynthesis! Genomics has been covered in the forms of [...]
xBASE Genome Alignments
We’ve had feedback about the xBASE whole-genome alignment function from some of you and there have been a number of recurring problems: sometimes the genome alignment does not seem to complete processing, and you can only get to the alignment view by clicking the supplied URL. Also a strange error message occur. the drop-down menu [...]
xBASE2 in Nucleic Acids Research Database Issue
A paper describing xBASE2 is available as a pre-print in advance of the publication of Nucleic Acids Research’s 2008 database issue. You can read the full-text article here for an introductory primer to the functions within xBASE.
Further downtime: apologies
We had to take the xBASE servers down last night unexpectedly due to rainwater coming in through the roof in the Centre for Systems Biology where we are based! The downtime lasted from about 3:30pm yesterday (6th Dec) until midday today. Apologies for the loss of service.