The quality of blogging is not strained
28Feb 2002
Science gone mad
13:19 New - The Journal of Unethical Sciences and Techniques - Online. Enjoy.
27Feb 2002
All goon
11:12 Spike Milligna dies. I have no heroes left.
I'm sure this would have made him laugh, though; His agent said he died of liver failure surrounded by his family.
27Feb 2002
I heard it on the grapevine
10:10 Interested in protein chip technology? A little bird tells me that LumiCyte may be worth watching.
27Feb 2002
Litigate? License!
10:10 The news that Amersham and ABI are cross-licensing instead of litigating is good for science. I think.
26Feb 2002
Copy, copy, copy me do.
21:31 Now this is cool: CopyPath. Just drag the .plugin to (~)/Library/Contextual Menu Items and BANG! It works. Brilliant.
26Feb 2002
Broadband schmoardband
11:28 Broadband wholesale prices to be cut. Well, it's a start. maybe the Govt has finally realized that broadband takeup in .uk has been so slow because it's too damned expensive.
26Feb 2002
Zzzzzz
11:02 Poorly children = sleepy parents. They're OK, but have picked up middle-ear infections. Both being quite brave about it but Sophie obviously doesn't understand why it hurts, dammit. The amoxycillin should kick in today. #include .nhsrant : waiting forty minutes to see the doc after arriving five minutes early for the appointment, with two sick children. And don't say that's what you get for a free health service; it's not free, I pay my sodding taxes.
24Feb 2002
Wheels
15:01 Rachel, learning to ride her bike: Dad! The wheels keep turning!
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Is this a blog I see before me?
21Feb 2002
Pwetty
12:29 Composite of Big Blue. Handle with care.
21 Feb 2002
Consluting
12:20 I'm telling you, consulting opportunities would seem to abound; whip up a CV with suitable crud on it, and you could be giving lectures to idiots at megabucks a head.... Thanks for that suggestion, John. Shame about my incredibly strong sense of decency . . .
19 Feb 2002
OS X - fit the fifth
21:10 Short update. The iMac is a teensy bit slow to run Aqua, but manages quite well once in the applications themselves. The iBook (500 MHz vs 400) whizzes along nicely, although it would benefit from more RAM. The iMac still suffers from a little flakiness when PPP doesn't work smoothly under X, and I've had to drop ChuToy from the error beeps as that was definitely screwing things around, sound outputwise.
19 Feb 2002
Spooky . . .
21:00 Through one thing and another, the iMac was in 9.2.2 when I awoke her this evening. So I decide to change the front matter of my personal web sites, and in doing so, choose 'Preview' in the BBEdit HTML Palette. It's a mess, but I choose Mozilla 0.9.8. Fine, looks OK, quit out, do some email business, then launch Mozilla from the Finder. And Mozilla 0.9.5 launches. I know this, because this version does not remember where I put the sidebar. Hunh? I then spend about ten minutes trying to trace every copy of Mozilla I have. I can find two - both 0.9.5, one on Thing 1 (9.2.2 boot partition) and the other on Green Eggs - the backup disk. Oh, and there's Mozilla.app on Thing 2 - the OS X partition. But when I try and click that, I get the standard error dialogue which means it's a X application, not a Classic one. After scratching my head a bit, I launch Mozilla 0.9.8 from the BBEdit menu, pull down Recent Applications and try to find the original of the Mozilla alias. Tells me I can't reveal it, because it's in a package. OK, so ctrl-click on the .app, and view the package contents. Navigate my way down and find the application proper. Which launches in OS 9.2.2. And I *can* make aliases to that, so I'm happy again.
19 Feb 2002
Don't give up the day job
13:45 Apparently, Geneforge is an epic adventure in which you play a Shaper, a member of a secretive and powerful magical sect with the ability to create and mold life to do your bidding. You have been kidnapped by a sinister outsider who will do anything to get you to share your secrets with him. It is up to you to fight him. Or, if you want, join him. And that's different to my life, how, exactly?
19 Feb 2002
Knees
12:28 Healing prayer. I make no comments, but pass this on for your perusal. I will not host a debate here.
18 Feb 2002
Nerding
20:30 Keep my promise time. First off, these are the network settings for the iBook under 'Built-in Ethernet':
IP address 192.168.0.2 DNS (optional) Subnet mask 255.255.255.0 192.168.0.1 Router 192.168.0.1
Not sure whether the DNS info is strictly required, but hey, it's not hurting. Much. On the iMac I have the internal modem set up to my ISP, with automagic IP assignment. Both network ports are active, and the 'Built-in Ethernet' part has
IP address 0.0.0.0 DNS (optional) Subnet mask 255.255.255.0 Router
i.e. NOTHING in any of the other fields. Finally, IPNetShareX is set up as follows:
Subnet mask: 255.255.255.0 Router address: 192.168.0.1
The obvious selections for the internal/external interfaces are made, with the following boxes (top to bottom)
yes yes no yes no yes yes yes
This flies with a x-over cable, although kicking the 'Start/stop internet sharing' button each time I make a connection seems to help - which seems to preclude the iBook initiating a dial-up. I can live with that. Now all I have to do is save my pennies for a couple of AirPort cards (and set up the iMac as a software base station. Enjoy. Oh, and I'd *really* like to know what are the commands this thing is using so that I can make my own start-up script. . .
18 Feb 2002
Oooh shiny
14:06 I haven't tried it yet, but this little doohickey should make changing creator types a blast in MacOS both 9 and X.
And no, I haven't forgotten my promise about IPNetShareX; I'll try and report back tonight. Briefly, it works, but is very particular about which IP numbers go where.
18 Feb 2002
Pointy balls
14:01 Robert Kitson - is the man a poet or what? I'm a tad narked - the best game England have had in ages and I didn't get to see it 'cos it was on satellite. Grrrrrrr . . .
18 Feb 2002
Open access
13:55 Let's hear it for George Soros and get those papers into the hands of the people - or at least the people who need it for their research. The whole scientific journal system is utterly corrupt now anyway.
18 Feb 2002
Last man standing
13:53 Australia's first gold at the Winter Olympics. I found this very funny, and a big 'good on yer, MAAAAAAATE!!' to Mr Bradbury.
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A blog! A blog! My kingdom for a blog!
13 Feb 2002
mmmmmBeermmmmm
Marston's Owd Rodger. Stonking.
13 Feb 2002
BLAST this!
20:38 A shout out to Edinburgh Biocomputing systems for providing free downloads (to academics) of their MPSRCH implementation. Now I wouldn't normally give space to a commercial organization, but seeing as I raved about BLAST on the Mac last week, and BLAST has severe deficiencies compared with the Smith & Waterman algorithm, I thought I should give them a go. The striking thing about S&W versus BLAST is the number of hits that BLAST misses. Give it a go - and tell them I sent you. MPSRCH runs on Alpha and Intel Linux architecture - a MacOS X might be in the pipeline if enough people promised to buy it ;)
13 Feb 2002
OS X - fit the fourth
20:30 More of a 'toys for boys' update this, but MT-Newswatcher is now OS X native. Its preferences live in ~/Library/Preferences/MT-NewsWatcher Prefs ƒ, but an alias to my Classic prefs works well - and shoving my Classic groups file in the dock I can launch from there. Cool.
I've also snarfed the beta of IPNetShareX to see if I can share the iMac's 'net connection over a x-over cable with the iBook. Will let you know how I get on.
13 Feb 2002
Bang! Byng!
20:15 Quite what this has to do with anything is beyond me, but while we're on a historical bent I came across this while googling to solve the crossword today. The origin of the phrase pour encourager les autres, no less.
12 Feb 2002
-c0.87
22:20 Even us Limeys should find this version of the Gettysburg address funny.
12 Feb 2002
Mooof!
20:20 CK pointed me at this site, and it is, indeed, a must-have. True MacGeeks (sounds like an honorable, ancient Scottish clan) will need no further explanation. For knowlessmen, try this explanation. If anyone is still worried, the entire thing is sanctioned (FSVO) by Apple. Apparently, the really sad will have this page bookmarked, but that really is pushing the limit.
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New kid on the blog
07 Feb 2002
OS X - fit the third
22:00 Of course, the 'bah' didn't last long. In the absence of a /Library/Sounds (by analogy with the thousands of Fonts folders) I got to play a little:
[localhost:Shared/path/to/file] root# mv ChuToy.aiff /System/Library/Sounds/
- cool.
(Aside - it was good to be able to watch Kate add RAM to her iBook - thanks Charles - and not do anything except say 'no, those two screws there')
I had more fun with root. My hosting is playing up - although it's serving pages fine, ftp has been more dead than not just recently. These pages contain a fair amount of server-side include code, primarily the content itself but also a natty bit of browser detection to determine which stylesheet to serve. Checking such pages had always been a bind under MacOS 9, but I found myself reasoning thusly:
This is unix, right?
We have Apache, right?
Apache does SSI . . . Right!
So after a bit of rooting (har har) around I found where the httpd.conf lives. Right so . . . sudo emacs /private/etc/httpd/httpd.conf but that gives me a locked file. Ah, so only root can play with files that begin '.' . . . no worries, I'm l33t, d00d. That keeps me happy for a while, I check all the files, then find the ftp server is active, so up they go, and drop the connection. Just for fun, let's have a look at /private/var/log/httpd/access_log.
Oh, my. What's all this?
213.122.219.164 - - [04/Feb/2002:21:11:02 +0000] "GET /scripts/root.exe?/c+dir HTTP/1.0" 404 276 213.122.219.164 - - [04/Feb/2002:21:11:10 +0000] "GET /MSADC/root.exe?/c+dir HTTP/1.0" 404 274 213.122.219.164 - - [04/Feb/2002:21:11:19 +0000] "GET /c/winnt/system32/cmd.exe?/c+dir HTTP/1.0" 404 284
etc, etc. Some **** trying to hack in? No, it's 'only' CodeRed/Nimda. Makes me glad - again - I'm a MacHead.
One last thing tonight. Switch my location to ethernet, turn on websharing, and http://127.0.0.1/www.rg-d.com/BioLOG/ means I don't even have to dial in to get that crunchy Apache goodness.
07 Feb 2002
BLAST-a-Mac
21:25 Wow. BLAST on your Mac. Mac OS X, natch.
Apple/Genentech BLAST provides improved accuracy and speed over the standard NCBI BLAST, depending on search parameters such as the nucleotide match-length. For certain common searches this version enables a dual 1-GHz Power Mac(TM) G4 computer to deliver more than five times the performance of a comparable 2-GHz Pentium 4-based system running the standard NCBI BLAST.
07 Feb 2002
Max Perutz
21:20 Accessible and detailed obituary.
06 Feb 2002
Passing of genius
15:31 - updated Sad news for us here at the LMB - Max Perutz died this morning. There is an obituary at the LMB web site.
06 Feb 2002
Where babies come from
11:50 St John's Wort can make you pregnant. Quote: In a separate case, a woman became pregnant while taking St John's Wort. Thank you for that mental polaroid.
06 Feb 2002
Ooh shiny
10:07 From the 'Must try this at home' department. DesktopConsole essentially allows the viewing of files directly on the desktop. Could be useful if you want to keep track of a log file while doing other things I guess. Thanks to CK for the heads up.
05 Feb 2002
OS X - fit the second
19:58 Having installed the 10.1.2 update, we connected the iBook via a cross-over cable to the iMac to grab it, and some other files. Ea-sy ea-sy. Whipping the FW cable out of the iMac and into the iBook gave the expected result, but the real surprise came when I took the USB cable from the Epson Stylus 760 out of the hub and plugged that into the iBook. Kate hit 'print', the Print Centre whizzed into life and we had printing. Her comment was along the lines of 'It works how a computer is supposed to' and mine was 'It's still a Mac!'. This went a long way to allaying some of the fears we had about this new beast.
Now it may 'still be a Mac', but there's much more than previously. My first inkling of this came when iCab and Mozilla kept giving error 500s while trying to download the Norton Utilities beta. I thought 'This is unix, right? There's a command line FTP tool, right?' And so there is. What more can I say? It works. So while I was ftp-ing that, I checked Software Update and found a ton of printer drivers - don't need those so let's inactivate them - and a DVD player update. 15 Meg. Hmmm this is why we signed up to the unmetered scheme. As that's doing, the connection drops, and I discover that downloads through Software Update can be resumed.
So far so good. Then the crap hits the carpet as I try to run Norton. Catalog [sic] errors? Hsm. Boot into single-user mode and run fsck. Clean. But I'm getting random freezes - each application in turn decides to stop responding, sometimes yielding to a kill -9 but more often than not just sitting there until finally the Finder dies too. This happened about 3 or 4 times before I decide 'enough is enough' and de-install Norton. But there's a strange message from the installer about not all files going and the Process Viewer can still see Nortony things.
In the meantime I have discovered that the Disk Utility with X can format 3rd party disks - including my 40 gig FW. So that gets partitioned - 6 gigs (Ham) for a X boot partition and the rest (Green Eggs) for my 9.2.2 backup, iTunes collection, disk images, other backups etc., etc. I reinstall X on a wiped Thing 2, do the update shuffle, set all my prefs and I'm all set. Damn you, Norton.
The next exciting thing is trying to set up my environment how I like it. This includes having ChuToy for my system beep. Gotta love that stereo effect. It doesn't take long to figure out that the system sounds are .aiff format, but I can't alter /System. Bah.
05 Feb 2002
OS X - fit the first
19:44 January 25th. New operating system in the household. Just like having a new baby around, I was prepared for my time to be eaten up, my nights to be sleepless and to find crap all over the carpet. But first I cleared the decks - booted from the install CD and copied all 3 of the iMac partitions onto the external 40 gig FW drive, then reformatted the iMac HD into two, equal size partitions. Not really necessary, but made me feel happier that if one system crashed and burned I'd have a better chance of starting up from the other partition. Then I tried reinstalling OS 9 on Thing 1. Started off with the 9.04 install CD, and worked my way up to 9.1, 9.21, 9.2 . . . but bugger that, all my custom extensions and prefs are lost . . . nuts. I ended up copying the old OS 9 partition straight back onto Thing 1. Booted from the X CD again and set the installer going while I went to eat haggis and drink whisky. Came back, filled in all the details, da dee da, set up a username, I hate choosing passwords so I'll stick to the Multiple Users one, dum te dum reboot.
Well. This is pretty. Had a play, set up some preferences, checked that I could get a connection and went to bed. Next day - Saturday, woohoo! Downloaded the Security Update, the installer Update, and baulked at the System 10.1.2 update. 35 Megs over a 56k modem? Never mind, here's one I prepared earlier - the update on a CD, downloaded courtesy of JANET.
Uh oh. There is no valid disk image. Damn. Nothing for it - install Mozilla from CD, get a connection, and connect to www.apple.com and download it the hard way . . . 30 meg through the download, BTInternet boots me off (SOP after 2 hr connect) and I realize that this version of Mozilla does not have the ability to resume interrupted downloads argh! Argh! Argh! Fire up iCab, check that its download manager functions and try again. This time when the connection drops, I'm able to get connected and resume. One 35 meg update nestling on my HD.
02 Feb 2002
Meta
Welcome to the new look BioLOG. This replaces the news and wibbles page that lived at my MRC pages NO DON'T click on that link. Thank you.
As with all good weblogs this will be brash, arrogant and opinionated - I hope you like it.
Updates will probably be irregular, but at least being on my own server I'll be able to update at weekends in the evenings too. I will archive all blogs for posterity - the title (under the date, over on the right) each update will link to a permanent archive file.
The first real blog will be describing some of my experiences with Mac OSX (that's ten, not ex). As ever, any comments should be directed to biolog at rg-d.com. I reserve the right to publish any comments, so if you're rude, we'll all mock you mercilessly. <span class="merciless">Mock, mock.</span>