June 30, 2003
Lively debate at home ... or domestic homicide in the making?
Englishman Mil Millington lives with his German girlfriend, Margret. All quite straightforward, you might think. Ha. Read on ...
Nothing keeps a relationship on its toes so much as lively debate. Fortunate, then, that my girlfriend and I agree on absolutely nothing. At all.
Combine utter, polar disagreement on everything, ever, with the fact that I am a text-book Only Child, and she is a violent psychopath, and we're warming up. Then factor in my being English while she is German, which not only makes each one of us personally and absolutely responsible for the history, and the social and cultural mores of our respective countries, but also opens up a whole field of sub-arguments grounded in grammatical and semantic disputes and, well, just try saying anything and walking away ...
For example (and this made me laugh embarrassingly loudly in the office just now) ...
The sheer volume of food that needs to be crammed into the freezer means it's only possible at all because Margret employs two ruses.
The first is brute force. Basically, she just hammers things into the drawers with the heel of her shoe. Which works, but at the expense of horrifically deforming whatever she's storing. We're all used to this now, naturally. Jonathan [First Born to M and M -- D.] pretty much expects his turkey dinosaurs to be a collection of misshapen body parts: they're turkey dinosaurs, as modelled on the scenes of carnage the day after the comet hit Earth ...
The second point is that she only has any chance whatsoever of jamming all the things in if she throws away the cardboard boxes in which everything's packed. The boxes which, of course, bear the cooking instructions ...
Posted by daen at 06:28 PM
Books in the wild!
The "3 Rs" of BookCrossing...
1. Read a good book (you already know how to do that)
2. Register it on BookCrossing (along with your journal comments), get a unique BCID (BookCrossing ID number), and label the book
3. Release it for someone else to read (give it to a friend, leave it on a park bench, donate it to charity, "forget" it in a coffee shop, etc.), and get notified by email each time someone comes to BookCrossing and records journal entries for that book. And if you make Release Notes on the book, others can Go Hunting for it and try to find it!
It's a great idea, but I'm not sure I like the idea of "losing" my books like this ...! Maybe I'll just have to buy extra copies for "release" into the wild ...
Posted by daen at 01:40 PM
June 28, 2003
All that Jazz
Posted by daen at 10:08 PM
June 26, 2003
A Python course in Bioinformatics
This course is designed for biologists who already have some programming knowledge, in other languages such as perl or C. ... This course can be considered a complement to the Biopython tutorial, and what's more often refers to it, by bringing practical exercises using these components.
Posted by daen at 07:07 PM
EMBOSS (The European Molecular Biology Open Software Suite) fuzznuc application
fuzznuc uses PROSITE style patterns to search nucleotide sequences.
Posted by daen at 12:46 AM
June 25, 2003
Building broadband wireless for communities
Consume is a collaborative strategy for the self provision of a broadband telecommunications infrastructure
FreeNetworks.org is a voluntary cooperative association dedicated to education, collaboration, and advocacy of the creation of free digital network infrastructures.
Posted by daen at 08:57 PM
Tom Lehrer's "Elements" animated with Flash
Brilliant Macromedia Flash animation of Tom Lehrer's elements (words by Tom Lehrer, tune by Sir Arthur Sullivan -- the Major General's song from the Pirates of Penzance, of course)
Posted by daen at 08:10 PM
June 24, 2003
Biological sequence alignment : presentations
Powerpoint presentation, with useful commentary on Needleman-Wunsch and Smith-Waterman alignment algorithms.
Link to .PDF on implementing Smith-Waterman algorithm in Perl.
Posted by daen at 12:30 AM
June 21, 2003
Igor! Bring me an Atari 800!
Slashdot has this story:
As case mods go, this one's not the weirdest, But it has its own retro charm. Musician and geek Andy Hutson slipped a Mini-ITX motherboard into an Atari 800 case... and used an old cartridge as the mouse! Too bad the original keyboard's not functional.
Posted by daen at 12:52 PM
June 18, 2003
DNA sequencer output and sequence file formats
Phred/Phrap and Consed are industrial strength sequence assembly programs that are currently used for LARGE sequencing projects at the genome centers. If you are sequencing a few thousand nucleotides, you don't need this program. Use something like SeqMan, Sequencher, or GCG. If you are assembling genomes or thousands of ESTs, then this is the program for you. However, Phred and Phrap are not for the faint of heart. There is a significant learning curve.
Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Phred can read trace data from SCF files and ABI model 373 and 377 DNA sequencer chromat files, automatically detecting the file format. After calling bases, phred writes the sequences to files in either FASTA format, the format suitable for XBAP, PHD format, or the SCF format. Quality values for the bases are written to FASTA format files or PHD files, which can be used by the phrap sequence assembly program in order to increase the accuracy of the assembled sequence.
Phrap ("phragment assembly program", or "phil's revised assembly program") is a program for assembling shotgun DNA sequence data. Some of its key features are: (1) allows use of entire read, not just highest quality part; (2) uses a combination of user-supplied and internally computed data quality information to improve accuracy of assembly in the presence of repeats; (3) constructs contig sequence as a mosaic of the highest quality parts of reads, rather than a consensus. Phrap does not provide editing or viewing capabilities; these are available with consed or phrapview
Mostly HIV related, but includes some useful examples of sequence file formats: GenBank, FASTA, Nexus (PAUP) and Phylip.
SeqVerter™ - standalone version
SeqVerter™ is a free sequence file format conversion utility by GeneStudio, Inc. SeqVerter encapsulates a small subset of the features offered by the GeneStudio™ Pro suite of programs. While the standalone SeqVerter is a simple dialog-based utility, the free SeqVerter component of the GeneStudio Pro suite adds sophisticated viewers and sequence formatting functions, including a viewer for automatic DNA sequencer chromatogram files (traces).
Raw Data File Formats, and the Digital and Analog Raw Data Streams of the ABI PRISM 377 DNA Sequencer.
Has a link to 35 page .ps file presumably describing the format
(I haven't got Ghostscript or Ghostview installed, so I can't tell at the mo'). Update, 24 June 2003 -- Yes, this is the ABI 377 data file format ... and here is the link to Ghostscript and Ghostview, which you will need to view and print PostScript on Windows ...
Posted by daen at 11:39 PM
June 04, 2003
Samba - the fatal dance of Unix and Windows
Don't forget about smbpasswd!
Posted by daen at 03:17 PM
GPS measures continental drift, predicts weather, raises dead
Dr Bingley said: "Work is still being done in this area... but there are suggestions GPS could be used to better understand the organisation of thunderstorms and perhaps anticipate when they will happen.
"We have already seen that GPS can show the build up of water vapour before cloud formation or a storm."
For this reason, the Met Office has become involved in funding fixed GPS stations.
OK, I was kidding about raising the dead ...
Posted by daen at 03:11 PM
June 03, 2003
Posted by daen at 11:39 PM
Danish bioinformatics tools
Thanks to Søren W Rasmussen for this link.
SEQtools is a comprehensive program package for batch handling and analysis of nucleotide and protein sequences. The program includes a series of trivial functions to help you carry out common operations. In addition SEQtools will assist you with more demanding operations like unattended blast search and result-parsing with hundreds of sequences.
Special functions are included for design of microarray gene expression analysis experiments, for expression analyses with the SAGE procedure and for managing small EST projects. Utilities are included for primer design and ordering, renaming files, creating codon usage tables, building local searchable databases, aligning nucleotide and protein sequences, comparing sequences and a lot more...
Posted by daen at 11:13 PM
June 02, 2003
Computer stuff in Denmark
Posted by daen at 08:28 PM