Older blog entries for nutella (starting at number 17)

Thos morning was taken up by a trip to the opticians (or optometrists if you prefer) and since I knew I would be treated with a mydriatic I walked rather than risking the lives of all road users. After the checkup (all healthy) I wandered home by way of Geary, walking on the shaded side of the street to save my poor retinas (retinae?) as the sun had decided to smile brightly on the city. I should say that Dr. Chong had in fact issued me with some "X-ray specs" style eye protectors to help me out but it took me a good while to pluck up the courage (okay, actually it just took long enough for me to start to get a headache from squinting) to slap them on - yeah, I had serious worries that I might run into the lady of my dreams only to have her repelled by my strange eyewear. Anyway, rather than heading straight down to the Great Highway I made a detour to the small park containing the old Sutro House (up on the cliff above the Cliff House) which is something I've always meant to do. I was not disappointed as the view was quite stunning looking south over the end of Golden Gate Park and the ocean towards home. I'll definitely be back there with my camera in the near future. Entertainment while walking beside the ocean was provided by; i) a large group of people demonstrating oriental sword manouevres, and ii) a kite flier who was amused by a dog repeatedly leaping up to try and catch his kite as he buzzed it low across the sand.... only to stop being amused when, through some supercanine effort, the pooch managed to leap high enough to bite on to it and drag it down.

sneakums I was [a|be]mused by your piece on Dark Angel. I've seen the trailers for it over here but haven't bothered watching it, mainly because the main character looks too much like Janeane Garofalo so I have visions of some woman wandering around and solving crime rendering villains helpless through depression.

Yesterday evening I was talking to our lab volunteer who originally hails from El Salvador. She had only this week been able to make contact with her relatives there and thankfully they had all survived the recent earthquake. One interesting thing she mentioned is that when El Salvador sent out pleas for help the first nation to respond was Cuba who immediately sent two transport planes packed with supplies. Alas, thanks to the strange politics of the region the planes were not allowed to unload and were sent straight back to Cuba (I wonder why there was no mention of this in the media in this country). She also mentioned that she was not surprised by this as Cuba had in the past responded in a similar manner to local disasters but had met with the same response.

I attended a couple of interesting inter-departmental talks yeterday evening, both of which used the theme of Perl in bioinformatics. The first was notable in that the speaker overheard a comment from someone in the audience concerning the way in which the Bush campaign site could be accessed through google. He promptly paused his PowerPoint presentation, fired up his browser and tested it out. Concerning the other talk, I thought I was going to be lost very quickly as I am a *very* amateur programmer and the presenter had written a very slick web-accessible way to query sequence information. I was less awed when he described the complicated machinations used (JavaScript - Perl - More JavaScript - More Perl - HTML) and the fact that he used flat text files to store all the information. I immediately asked "Have you tried this with PHP?" to be met by "What's PHP?". Then, "Have you tried using a database for the information, maybe something simple like DBM or a little more fancy like PostgreSQL or MySQL?", "No, I hadn't thought of that". Both he and the other presenter considered that Excel had all the database functionality that they'd need. Of course, they had the big advantage that they were only dealing with yeast sequences (so about 6000 ORFs) and I am sure (prom personal experience) that there would be problems if they tried to scale up much further. Maybe I will make use of the delay in my moving to Chicago to spend some time playing with the PHP/PostgreSQL SwissProt database programs I have been dabbling with before.

"ar dhroim na muice..."
I am having difficulty getting used to this. I was telephoned this morning by my "relocation consultant" who filled me in on all the help the new company will be giving me to move me from San Francisco to Chicago and to assist me in settling. As someone who has been in academia for a good while it sounds completely unreal. When I moved from the Washington DC area to San Francisco I hired a truck and a tow dolly for my car (about $1000 in fees), packed my belongings, loaded the truck and (alone) drove the 3000 miles in three days getting about 10 miles per gallon. I had no reimbursement at all for this. Thankfully some friends in this city were able to store my things in part of their garage and allowed me to stay in their spare room until I found somewhere to live (Thanks, you two!). I am now being told that I should not pack my belongings as the trucking company prefers to do this. I will be paid to drive my car between the cities (if I choose) and there's all sorts of mysterious relocation and accomodation bonuses (some tax free) which will be mine when I arrive. Anyone reading this who has been in a commercial environment for any length of time is probably amused at my naivete, especially as I have heard of people who have fought hard for more and more generous relocation bonuses, but after fending for myself for so long the whole process seems unbelievable.

So, I'd just about resigned myself to the current level of chaos as I juggled timelines for my boss-to-be, my current boss, my rental agency, my car insurance agency, my health insurance agency and my relocation consultant. I was supposed to be stepping into the new job on the morning of February 12th after a 2000 mile emigration eastward. Today I received a telephone call along the lines of "Ummmm... it will take us longer than we thought to process your paperwork - at least another month.". So the adrenaline level is somewhat back to normal. I may now be able to grab a small period of holiday time in between jobs and the climate in Chicago should be a little more suited to the big move. My habit of procrastination means I hadn't yet given notice at the rental agency so I will not have to move across the street to Golden Gate Park. However, my procrastination is not an attribute that should receive any kind of positive reinforcement.

I've been stuffing heaps of paperwork into envelopes to send to various legal departments. As a visitor to this country my passport becomes heavier year by year as I aquire more and more supplementary documentation none of which can be thrown away, ever. Being government issue the forms are poorly typed on tissue paper rendering clear photocopying extremely difficult and some of these forms are now over eight years old. If I stay much longer I foresee being swamped in the manner of Henry Tuttle.

Harry Tuttle: Bloody paperwork. Huh!
Sam Lowry: I suppose one has to expect a certain amount.
Harry Tuttle: Why? I came into this game for the action, the excitement. Go anywhere, travel light, get in, get out, wherever there's trouble, a man alone. Now they got the whole country sectioned off, you can't make a move without a form.

GAR! crackmonkey is a Bad man. In the past he managed to suck away an entire summer of my time through the use of the ZorkCit web-based BBS. He has now spawned the evil Badvogato which is already taking on the feel of the BBS but has the potential to be more addictive. If he is particularly evil he might merge past ZorkCit BBS threads with Badvogato. Legends were created in those times.

Run for your lives!

[Updated 3/31/01]
No, Badvogato has become a complete pile of manure and apart from the consistently dull content it now permits advertising. I warned crackmonkey that this might happen but he decided to just let it develop. Ah well it could have been very sweet. This is not the fault of the code but just the eejits that use it.

So, I appear to have made it through yet another year pretty much intact. The next twelve months should prove quite interesting as I change accomodation, job, timezone and (presumably) lifestyle. I have yet to have any period in my life where I've really settled down so I don't have any feel for a baseline from which to determine what middle-age dissatisfaction with life is supposed to feel like. Maybe you need some form of disposable income before that can happen.

Since there are actually four of us with January birthdays at work we had cake yesterday and beer'n'pizza (note the order) last night (apparently this also doubled as my job success celebration - because all my colleagues are skinflints [not really]) so today has been very low key. I did have a fun phone call from my brother this morning but part of that was taken up with a rant over the fact that my website will not allow you to read it if you are using MSIE (and have JavaScript enabled). He has evolved from being a complete computer newbie a couple of years ago to the point where he should be educated on the subject of software ethics.

elise! Call it! Call it!
My departure time will probably be in mid-February so I'll organise some Crackmonkey madness before then. In the meantime if you are dying for some decent tea and fancy sandwiches and/or some Guinness then call it/them! I'll even brave the horrors of the partial J-Church for some char and antiques - I also need to stock up on face-to-face time with S.F. people before being consigned to the horrors of the mid-west :(

Skud substitute "San Francisco" for "Sydney" in your city description and you'll not go too far wrong (apart from the humidity perhaps). However, most of the problems you see in Sydney are considered "features" in S.F.

I spent a short while last night testing out Becker's ether-wake program to see if I could trigger wake-on-LAN in a sleeping computer. I have the WOL cables in place and the BIOS activated. I am trying to wake from sleep rather than a cold start (so the NIC should be listening). I can see network activity by the LED on the target card and the debug option shows that the information has been sent. I have double checked the MAC addresses. Still the beasties sleep on. Becker indicates that the program is intended for some Intel cards so my SMC cards may need the password option. At least one of the cards comes with a DOS utility to send a suitable wake-up signal so it may be possible to modify Becker's program after monitoring packets while running this utility. I have no idea how to do this but I am sure it would be fun finding out.

Boredom and search engines can be a wasteful combination. I have been running through my various motherboards' capabilities looking to see if there are suitable utilities for addressing them in Linux. It would appear that it should be possible to monitor hardware information such as CPU temperature and fan speed etc. from Winbond-like chips with the lm-sensors module (I'll look into this when I next compile the kernel). Similarly it may be possible to look at S.M.A.R.T. hard drive information. I may even be able to activate the Highpoint HPT370 RAID controller (in non-RAID mode) I have on the Abit motherboard. Why would I want to be able to do all this. Because it's there dammit!

Woohoo! They finally called me with the official job offer. It feels like a big weight has been taken from me. I had no idea just how much I was being dominated by the uncertainty (although this has been dragging on for months). Now I can move to anticipation, flavoured by stress over the paperwork and the move, and coloured by regrets at having to leave people and places in this area. I will definitely have to sponsor a TNICNAZ before I go (or maybe another Crackmonkey High Tea at Lovejoys).

Let the insanity begin!

Not much real news. I have my "spare parts" box up and running now (Debian Potato of course) and the ethernet card is behaving itself admirably (although I have not measured the throughput) thereby allaying previous fears about the cheapie SMC cards. I played around configuring samba, something I've not really used so much in the past, so I can move all the fairly static data (protein and nucleic acid sequences, protein structures, images, sounds etc.) from the Wintel machine and keep them in common on this one (ready for samba or nfs serves).

I was reading a short article by Ronald Rolheiser in which he addresses the problem in society today where people appear to believe that their personal happiness is a legal entitlement. He puts forward the notion that this is a product of people being given the idea that they can (and should) protest genuine injustice but has been twisted to fulfil personal wishes at the expense of others. Such concepts are obviously nothing new but Fr. Rolheiser suggests that a key to avoiding the problem is that people should learn to discern the difference between situations where "to rage" is constructive while in others it is better "to mourn" rather than lashing out at the nearest target or bottling up the frustration within.

Surf's up!
When I leave this city I will really miss the (oblique) view of the ocean from my bedroom window, especially on days like this when the surf is really crashing on to the beach. As has been pointed out many times "Pacific" is not the best name for this body of water. The rain and wind gusts certainly add to the atmosphere so it looks as if winter is edging its way into the bay area. The abrupt change seems to bring out the child in (supposed) adults as when I arrive at work with water dripping from me I am inevitably greeted by a big grin and "Is it *raining* out there?". The correct answer is of course "Not so you'd notice.".

Bench work is going quite well (although not speedily enough for some people). I need to take a break now and again to look at the latest data in depth to help refine my approach. The boss is not pleased to see me "playing with the computer" for hours but I managed to come up with a much cleaner way of attacking the problem so thankfully I managed to justify the time spent (phew!).

I haven't had much free time for Linux exploration but since I was checking the configuration on my Sparc box, prior to having another go at network-wide exim, I was reminded that I'd never managed to configure XFree86 on this machine. The Debian Potato configuration for this is pretty awful as the defaults left are those for an x86 setup. I managed to fix the section for the mouse but the correct keyboard configuration had eluded me as it defaulted to that for a pc and the Sun options are not (to me) intuitive. I hunted for clues with google and quickly came across a mailing list post answering exactly this question. The bizarre thing is that the kind soul who had furnished that information was someone I actually knew from my time at Liverpool University and who I had not seen for over 15 years (although we had touched base by e-mail some years ago). Either the world is smaller than I imagined or maybe I made friends who maintain similar interests independently while contintents apart.