It’s been quite a bit of time since I last updated this, but here I am again.

Lately I’ve decided to simplify my life. After all only once I am organized and regulated can I then allow spontaneity. So in order to do that I’ve gone through all the things I’ve wanted to do, planing to do, and doing, and written a large list. Going through this list I’ve noticed a lot of projects that I no longer have any interest in, namely using PICAXE chips. I’ve moved on to Arduino and the more complex opportunities it provides. I’ve also been able to cull some travel plans that simply couldn’t completed because of changing commitments, and, more importantly, a lack of money! Also listing these tasks has made it a lot easier to see what things can be done quickly and simply (throw out old war gaming stuff) and what will take more time ( control an Arduino through a La Fonera with Open WRT using the SCL, SDA, GND lines). Definitely worth the time spent on writing it. And as I keep the list as a notepad file on my 2Gb USB Memory stick, I can easily update it when I think of a new, or remember an old, project.

Another way of simplifying things is to reduce things, in my case, throw out anything I’m not using, or planning to use in the immediate future. As a result I’ve got rid of most of my old PC , modeling and war gaming magazines, freeing up 2 shelves. I’ve also sorted through my books, removing those that I don’t read anymore and consigning them to a charity shop. I’ve also thrown out all the junk I’ve collected with the hope of being able to fix it or make something from it.

There is another reason for this simplification as well. On the 15/16th of August I shall be moving. This is when I move into my new halls of residence when I start university. I will be moving into a smaller room, so to help with the move, and to make it as pain free as possible I want to have to move as little stuff as possible. To save on money I’ll be moving out of my room during the holidays, I’m only there for the semesters, so having less stuff to move will definately be a bonus. This won’t be too much of a hassle as I’m going to a local university, it’s only about an hour away.

One project I’m tryign to finish off at the moment is to get Linux onto my laptop, a R1F-K008e. However this seems to fail a lot. The main sticking point is, I can’t connect to WPA WiFi networks. This is REALLY annoying because I bought to laptop specifically to be mobile, and I’d need to access more secure, therefore more popular, WPA networks. At home I connect to the internet through a WPA WiFi network, but with Linux I can’t, I’ve tried Ubuntu 6.06 and 7.04 and Xubuntu 6.10 and 7.04. But the included “just works” Network mangers, quite simply, don’t. So I need to download something, but I can’t, because I cannot connect to the internet. D’oh!! However Windows does just work, strange that… Another problem is the tablet, the R1F is a tablet PC, but Tablets have very flaky support, but I do remember reading how someone’s managed to get their tablet working in Ubuntu 7.04 which has prompted me to try just a bit more before consigning Linux as a whole to the “it’s a was of time” bin.

My other foray into the land of Linux was getting DD-WRT on to a pair of La Foneras. I’ve managed it with one, which had the earlier, easily crackable, firmware but the second is proving difficult as it has the later 1.7.2 firmware, which is a lot harder to crack. Once I’ve done that I’m hoping to turn it into a simple wireless embedded server which can connect to an Arduino.

It’s been quite a bit of time since I last updated this, but here I am again.

Lately I’ve decided to simplify my life. After all only once I am organized and regulated can I then allow spontaneity. So in order to do that I’ve gone through all the things I’ve wanted to do, planing to do, and doing, and written a large list. Going through this list I’ve noticed a lot of projects that I no longer have any interest in, namely using PICAXE chips. I’ve moved on to Arduino and the more complex opportunities it provides. I’ve also been able to cull some travel plans that simply couldn’t completed because of changing commitments, and, more importantly, a lack of money! Also listing these tasks has made it a lot easier to see what things can be done quickly and simply (throw out old war gaming stuff) and what will take more time ( control an Arduino through a La Fonera with Open WRT using the SCL, SDA, GND lines). Definitely worth the time spent on writing it. And as I keep the list as a notepad file on my 2Gb USB Memory stick, I can easily update it when I think of a new, or remember an old, project.

Another way of simplifying things is to reduce things, in my case, throw out anything I’m not using, or planning to use in the immediate future. As a result I’ve got rid of most of my old PC , modeling and war gaming magazines, freeing up 2 shelves. I’ve also sorted through my books, removing those that I don’t read anymore and consigning them to a charity shop. I’ve also thrown out all the junk I’ve collected with the hope of being able to fix it or make something from it.

There is another reason for this simplification as well. On the 15/16th of August I shall be moving. This is when I move into my new halls of residence when I start university. I will be moving into a smaller room, so to help with the move, and to make it as pain free as possible I want to have to move as little stuff as possible. To save on money I’ll be moving out of my room during the holidays, I’m only there for the semesters, so having less stuff to move will definately be a bonus. This won’t be too much of a hassle as I’m going to a local university, it’s only about an hour away.

One project I’m tryign to finish off at the moment is to get Linux onto my laptop, a R1F-K008e. However this seems to fail a lot. The main sticking point is, I can’t connect to WPA WiFi networks. This is REALLY annoying because I bought to laptop specifically to be mobile, and I’d need to access more secure, therefore more popular, WPA networks. At home I connect to the internet through a WPA WiFi network, but with Linux I can’t, I’ve tried Ubuntu 6.06 and 7.04 and Xubuntu 6.10 and 7.04. But the included “just works” Network mangers, quite simply, don’t. So I need to download something, but I can’t, because I cannot connect to the internet. D’oh!! However Windows does just work, strange that… Another problem is the tablet, the R1F is a tablet PC, but Tablets have very flaky support, but I do remember reading how someone’s managed to get their tablet working in Ubuntu 7.04 which has prompted me to try just a bit more before consigning Linux as a whole to the “it’s a was of time” bin.

My other foray into the land of Linux was getting DD-WRT on to a pair of La Foneras. I’ve managed it with one, which had the earlier, easily crackable, firmware but the second is proving difficult as it has the later 1.7.2 firmware, which is a lot harder to crack. Once I’ve done that I’m hoping to turn it into a simple wireless embedded server which can connect to an Arduino.

I bought an Arduino some time ago, but now I just received an ATMega168 from Daniel Jouiffe in Canada. He’s doing a trust scheme where he burns the boot loader onto an ATMega168, and then posts that and a 16MHz crystal to you, where ever you are. Then you pay him back however much you want. I just put into my Arduino NG board, and it works really nice. I’ve just doubled most specifications of my ATMega8. The forum post is here.

I’ve also gone and bought a Asustek R1F-K008E Tablet Laptop from here. It’s very nice, I like how it looks, comes with lots of extras, there are a few niggles with it, such as the way the pen gets scratched in the holder, or that Vista comes pre-loaded. I’ve spent the last couple of weeks sampling Vista, and this past week I’ve been trying to get it off. No easy task. There are many reasons for removing Vista, but the best are, many programs I live on, just don’t work, I don’t exactly blame Windows for this, but it’s highly annoying. Arduino doesn’t work, iTunes crashes no end, it keeps giving me pop-ups. I mean, honestly pop-ups, you have pop-up blockers on pretty much ALL web browsers, what made Microsoft think people like pop-ups?

Another reason to remove Vista is quite simply, the hardware cannot handle it. I have a laptop, a very nice laptop, Pentium 1.83Ghz Core 2 Duo , 1024Mb of DRR RAM, 120Gb hard disk, and it ran slowly, like a dog, with 2 legs… I put standard windows XP Professional on there, and it was lightning fast, things opened up instantly where as in Vista I’d have to wait 3 seconds, not much, but highly annoying. And lets not forget the BSOD every now and again. Oh sure, there are some features I miss, like the pretty UI and general streamlining, but XP is what I’m used to.

So I formatted the disk, and tried and install XP Tablet Edition, except my copy of XP Tablet Edition is odd. It’s been locked down in particular areas. So I scrub that, and install my copy of XP Professional, this goes fine, but no tablet drivers, nor any other drivers for that matter, so onto the Asustek website to download them. Ah, problem, Asustek have shit servers. I’m getting about 5kb/s on a 50Mb download, where as I have in the past got up to 300kb/s download speeds. 2 hours, 2 WHOLE hours for the drivers for the WiFi. I was not happy. So a day later, after download the drivers, and installing them, I think, great, I’ve basically got a normal laptop. So I went and re-installed my XP Tablet Edition over the top of Professional. So all the drivers are working, the tablet works, but a few things don’t, such as the AVG, and a few of the function buttons. I wonder where I can get another copy of the XP Tablet edition?

I bought an Arduino some time ago, but now I just received an ATMega168 from Daniel Jouiffe in Canada. He’s doing a trust scheme where he burns the boot loader onto an ATMega168, and then posts that and a 16MHz crystal to you, where ever you are. Then you pay him back however much you want. I just put into my Arduino NG board, and it works really nice. I’ve just doubled most specifications of my ATMega8. The forum post is here.

I’ve also gone and bought a Asustek R1F-K008E Tablet Laptop from here. It’s very nice, I like how it looks, comes with lots of extras, there are a few niggles with it, such as the way the pen gets scratched in the holder, or that Vista comes pre-loaded. I’ve spent the last couple of weeks sampling Vista, and this past week I’ve been trying to get it off. No easy task. There are many reasons for removing Vista, but the best are, many programs I live on, just don’t work, I don’t exactly blame Windows for this, but it’s highly annoying. Arduino doesn’t work, iTunes crashes no end, it keeps giving me pop-ups. I mean, honestly pop-ups, you have pop-up blockers on pretty much ALL web browsers, what made Microsoft think people like pop-ups?

Another reason to remove Vista is quite simply, the hardware cannot handle it. I have a laptop, a very nice laptop, Pentium 1.83Ghz Core 2 Duo , 1024Mb of DRR RAM, 120Gb hard disk, and it ran slowly, like a dog, with 2 legs… I put standard windows XP Professional on there, and it was lightning fast, things opened up instantly where as in Vista I’d have to wait 3 seconds, not much, but highly annoying. And lets not forget the BSOD every now and again. Oh sure, there are some features I miss, like the pretty UI and general streamlining, but XP is what I’m used to.

So I formatted the disk, and tried and install XP Tablet Edition, except my copy of XP Tablet Edition is odd. It’s been locked down in particular areas. So I scrub that, and install my copy of XP Professional, this goes fine, but no tablet drivers, nor any other drivers for that matter, so onto the Asustek website to download them. Ah, problem, Asustek have shit servers. I’m getting about 5kb/s on a 50Mb download, where as I have in the past got up to 300kb/s download speeds. 2 hours, 2 WHOLE hours for the drivers for the WiFi. I was not happy. So a day later, after download the drivers, and installing them, I think, great, I’ve basically got a normal laptop. So I went and re-installed my XP Tablet Edition over the top of Professional. So all the drivers are working, the tablet works, but a few things don’t, such as the AVG, and a few of the function buttons. I wonder where I can get another copy of the XP Tablet edition?

Here’s for the first post, I’m rather active in electronics, lately I bought an Arduino (http://www.arduino.cc) and an Infra-Red range finder from http://www.sparkfun.com/commerce/categories.php

The IR range finder is for the mini-bots I’m planning on making, these are small, about 4″ cubed, cheap, less than £20, robots. The idea is to make a swarm of them, so maybe 5 at most. I’ve already designed the PCB which allows the use of either IR or Sonar range finder, they have LDRs for light level sensing, and movement is controlled by two Servos converted for continuous rotation. It is controlled by a 08M PIC really basic, but VERY cheap, £1.79, the PCB will cost more say £2.00 and the Servos will cost the most £5 each.

Arduino is an open source micro-controller based on AMTEL chips, my board has a ATMEGA8 28-pin chip, gives me 3 PWM (Pulse Width Modulated) outputs which are simply analogue outputs, 6 analogue inputs, and 11 digital inputs/outputs, the PWMs can also be configured as digital outputs. I figured, as PICAXE is a bit Secondary School, even Primary school, I should probably find something more complex, but more flexible, and this is what I’ve decided upon. Reading on the site, you see it has a provision made for things called Shields, basically another PCB that is designed to slot into the top of the Arduino board, and provide extra functionality, such as blue tooth and accelerometers, can you say DIY PC Wii-mote ?

Right, that’s the electronics over with. Now onto the rest, Last night was the 9th of December, and on the 9th of December, Placebo (http://www.placeboworld.co.uk/) played a gig at Wembley Arena, North London. And because I love them, I went along. It was ABSOLUTELY FUCKING AMAZING!!!!!! They had 11 large projection screens, numerous lights and LOTS of speakers, the lights and the projections were really good, very Placebo-like. The music, well, I’ve listened to placebo religiously for about 3 or so years now, and I can truly say, they’re much better Live. As for the Arena, It’s quite odd, the set up, I can’t really describe it, because I was kinda sitting at 90 degrees to the band and so forth. Why didn’t I get a standing tickets you ask ? I was meant to go with friends, and they went and lost their tickets, so I figured, ah fuck em, I’ll go alone, so I did. I think I’ll stick to standing tickets, I spent most of the time standing anyway!

Here’s for the first post, I’m rather active in electronics, lately I bought an Arduino (http://www.arduino.cc) and an Infra-Red range finder from http://www.sparkfun.com/commerce/categories.php

The IR range finder is for the mini-bots I’m planning on making, these are small, about 4″ cubed, cheap, less than £20, robots. The idea is to make a swarm of them, so maybe 5 at most. I’ve already designed the PCB which allows the use of either IR or Sonar range finder, they have LDRs for light level sensing, and movement is controlled by two Servos converted for continuous rotation. It is controlled by a 08M PIC really basic, but VERY cheap, £1.79, the PCB will cost more say £2.00 and the Servos will cost the most £5 each.

Arduino is an open source micro-controller based on AMTEL chips, my board has a ATMEGA8 28-pin chip, gives me 3 PWM (Pulse Width Modulated) outputs which are simply analogue outputs, 6 analogue inputs, and 11 digital inputs/outputs, the PWMs can also be configured as digital outputs. I figured, as PICAXE is a bit Secondary School, even Primary school, I should probably find something more complex, but more flexible, and this is what I’ve decided upon. Reading on the site, you see it has a provision made for things called Shields, basically another PCB that is designed to slot into the top of the Arduino board, and provide extra functionality, such as blue tooth and accelerometers, can you say DIY PC Wii-mote ?

Right, that’s the electronics over with. Now onto the rest, Last night was the 9th of December, and on the 9th of December, Placebo (http://www.placeboworld.co.uk/) played a gig at Wembley Arena, North London. And because I love them, I went along. It was ABSOLUTELY FUCKING AMAZING!!!!!! They had 11 large projection screens, numerous lights and LOTS of speakers, the lights and the projections were really good, very Placebo-like. The music, well, I’ve listened to placebo religiously for about 3 or so years now, and I can truly say, they’re much better Live. As for the Arena, It’s quite odd, the set up, I can’t really describe it, because I was kinda sitting at 90 degrees to the band and so forth. Why didn’t I get a standing tickets you ask ? I was meant to go with friends, and they went and lost their tickets, so I figured, ah fuck em, I’ll go alone, so I did. I think I’ll stick to standing tickets, I spent most of the time standing anyway!

It turns out that I won’t be teaching an introduction to programming for biologists, as I announced in February.  Funding was found for that class to be taught by the instructor who has been teaching it, freeing me up to take on a different class as overload.  (I already pretty much committed myself to teaching an overload this year.)

I decided that the most pressing need was for an applied electronic circuits course for our bioengineering majors (the current EE circuits class is way too theoretical).  The School of Engineering’s best EE instructor (Steve P.) and I had discussed doing such a course before I went on sabbatical, and our respective department chairs were enthusiastic, but funding was not found for it.  Everyone was even more enthusiastic this time around, so Steve and I are going to design the course this summer and try teaching it together in Winter (at least, if all the enthusiasm converts into a secure position for him—otherwise he’s going to have to pick up another couple of courses from a different department and not teach the new one).  We probably won’t know for sure about the funding until November, so we’re going to go ahead and design the course on spec, hoping that we get to teach it.

If Steve becomes unavailable, I don’t think I have the confidence to teach circuits by myself, since I’ve never taken a circuits course, being almost entirely self taught (my Dad taught me a little, including a German joke about a Wien bridge, when I was in high school).  After we co-teach it once, I think either of us could do the course alone, though co-teaching with a master teacher like Steve is fun.  (If the applied circuits course falls through for this year, I’ll probably try to cobble together a graduate genome assembly and annotation course, based in part on the Banana Slug Genomics class but adding a bunch of new material, so I’ll end up with a teaching overload and working on a new course this year no matter what happens.)

I’m looking forward to designing a course with Steve. We’ve both designed many courses before, and co-taught senior design project courses, but we’ve not designed a course together before. I’ve lost track of how many I’ve designed—something like 15–20, depending how you count the courses that someone else started but I extensively modified.

The approach that Steve and I are taking to the course design is to start by looking for lab projects for the students to do.  We need 10 labs (one a week for 10 weeks) ranging from very basic getting-to-know-the-equipment labs up to real (but small) design challenges.  We will try out the labs ourselves separately, then compare notes on how things went before writing up the lab handouts.  After we have the labs figured out, we’ll make sure that we cover the theory needed to understand the labs and do the designs, pacing the lectures to stay just a little ahead of the labs.  At least, that is how we both envision the process currently.

Here are a few labs that I’ve been thinking about—I’d appreciate a lot more suggestions.

• Skin conductance meter.  There are a lot of do-it-yourself lie detector circuits for measuring skin resistance (“electrodermal response” if you want to sound medical).  I like the “Lego” sensor that just uses the inputs of a Lego RCX brick to read the resistance between two fingers. But getting RCX bricks for the lab just to measure resistance is silly.
  I wonder if we should give them something that reads and records voltage (like an Arduino or other microprocessor with an A/D converter) and have them make a voltage divider to read resistance.  This could be a good first lab, with them making a single measurement with a multimeter, choosing an appropriate resistor for the voltage divider, then recording a few minutes of skin resistance, perhaps on the inside of the wrist.  We could have them use fancy silver chloride gel electrodes at 500/$80, rather than Al foil and velcro—it’d probably end up cheaper.
• When I told my son that we wanted to design the labs so that they could be done by the students without hand holding, he suggested the experiment where you pass a (small) current through a chain of people holding hands.  This might not be a bad idea also for a lecture demo.
• Electrical field measurements in an electrophoresis gel.  The students would cast a gel (possibly agarose, but maybe just agar, to make it cheaper) with a standard buffer, apply a small voltage (much less than usually used in electrophoresis, since we’ll be working without the safety shield of a closed electrophoresis box), then use a handheld voltmeter to measure the voltage at different points in the gel.  We would also have them measure voltage and current.  We might even have them time the movement of a loading dye at different voltages, but I think that would take too long.
  One problem with this lab is that it requires using the wet lab, and neither Steve nor I are really wet-lab people.  I wonder if we could borrow a TA for a week from another course.  Perhaps a bioengineering senior undergrad could be hired, as many of them have some experience at casting gels.
• Conductivity of saline solutions.  It is standard to measure the ionic content of fresh water and even sea water by measuring its conductivity—Wikipedia has a decent article on the theory of electrolyte conductivity.  A conductivity calculator gives an equivalence of 1 ppm total dissolved solids as 1.56 µS/cm, though they don’t specify the temperature or include a temperature correction.  The City of Santa Cruz 2011 Consumer Confidence Report lists the drinking water in town as 280–760 µS/cm (though they use the charming older name: µmhos/cm), while a 2004 San Lorenzo River Watershed Management Plan gives the conductivity in the estuary as 260–44,860 µS/cm, depending when and where the sample is taken (though they label their table wrong)
  The tricky part here is that the conductivity testing has to be done with an AC signal, not a DC one, to avoid problems at the electrodes. If we trust the students not to spill salt water into the equipment, we could probably do this lab in the electronics lab, and use the bench oscillator and meters.  Later in the quarter we might have them design their own rectifier circuit to communicate with a microprocessor, but I suspect that doing an oscillator may be beyond the scope of the class.
  We may also want to get silver/silver chloride electrodes (or fine silver wire at $0.90/foot and soak it in bleach).    Using thin wires as the electrodes may cause problems with the resistance being very high.  I wonder if we should try doing something cheaper first, like using a pair of pennies cleaned in vinegar and rinsed.  They wouldn’t last long in salt water, but even demonstrating the problem might be instructive.
• A good project for late in the quarter would be a do-it-yourself EKG, which requires a simple amplifier (and gets another use for the silver/silver-chloride gel electrodes).
• We could also do an optical pulse detector, using an LED and a light sensor, though we’d probably end up making our own, rather than buying one for $20.
• Breathalyzer.  A resistance-output sensor for alcohol on the breath looks like it only costs about $5.  This may be too simple.

Several of these labs look like they would be most interesting if they involved hooking up to an Arduino or other cheap microprocessor that can record time-course data.  Since programming is outside the scope of the circuits course, we could have the students buy an Arduino for about $20–30 online and give them a simple recording program (perhaps I can get my son to write them a versatile one, based on the one he wrote for our super pulley recording).  The students could sell the Arduino used if they weren’t interested in doing anything with it (the Digital Arts and New Media students use them and probably would be glad of cheap ones).

Obviously, we’re going to need more lab ideas.  Does anyone have any?