x60t and linux update

just a quick update; i've been using my lenovo x60 table with the 2008.1 build of mandriva for several months. in general, it is extremely usable as a laptop and, to a lesser degree, a tablet.

i cannot get the tablet to autorotate and, while krandr worked fine in mandriva 2007 -- it appears to be broken in 2008.1.
[added note: must be x server issue as xrandr crashes x. hmmmm...]
i also cannot get the x server to recognize the eraser or pen-click/switch.

curiouser and curiouser:
the stylus works -- even after suspend to either memory or disk. even more curiouser (sic), the touchscreen also works with my finger (though, better with my fingernail!). i suspect that the stylus is NOT working via the x server, but rather via 'touchscreen' -- i've got to do some poking around in this regard.

below is a hand-drawn picture from gimp (pen width 3 pts) using the stylus. you can see the jitter .. which i have been unable to change using the details from the linuxwacom faq.
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recipe software

i'm a big fan and overuser of accuchef. that may read a bit strange, as i also predominately use linux as an operating system. to reconcile the fact that there are many highly useful windows-based applications that i enjoy using, i've also been a longtime registered user of codeweaver's crossover office (an wine-based project). designed to run, cxoffice is also handy for running programs like quicken ... and small, handy applications like ... accuchef! in fact, the recipes i've posted on gfb.log.alt were compiled and reside in my accuchef recipe database.

accuchef runs perfectly under cxoffice, though a small trick is required to update the windows registry to upgrade to the registered (i.e., paid) version of the software. after downloading and installing the shareware version, you will need to download the avsc.exe registration file (following the link that will be emailed to you).
  • using the cxoffice program, run/install the avsc.exe file.
  • when the winzip self-extractor window pops up, be sure that the "unzip to folder" option is pointing to your linux home directory (contrary to the accuchef directions...).
  • within cxoffice, run the windows command "regedit.exe" which will bring up the registry editor.
  • under the "file" menu, choose the "import registry file" option.
  • navigate to your linux home directory and choose the "avsc.reg" file.
  • close the registry editor; start accuchef; and you're off to the races!!

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2008 NIH funding in danger

from a recent email from ASBMB:

'Alert: The President has threatened to veto the modest increases in NIH funding proposed by Congress.

What We Need From You: Your calls or e-mails to the White House urging the President not to veto the 2008 Labor/HHS/Education appropriations bill.

Background: The FY2008 Labor/HHS/Education Appropriations bill (which allocates funding for the NIH and other federal agencies) has been approved by both houses of Congress and sent to the President for his signature.

The bill allocates $30 billion for NIH, a 3.1% increase over FY 2007, the first increase since 2003 that keeps the agency's budget even with inflation. The President has threatened to veto the bill because (among other reasons) the total spending in the bill is about $10 billion above his budget request.

It is unclear at this point whether there will be enough votes to override a veto in the House or the Senate. Therefore it is crucial that we do our best to discourage the President from casting a veto in the first place. It is critical that we protect the modest increase for NIH in the L/HHS bill because there could be no NIH increase at all this year if the bill is vetoed.

Action: Please contact the White House and urge the President to support biomedical research and sign the 2008 Labor/HHS/Education Appropriations bill.

Please contact the White House at:


Phone: 202-456-1111

Contact us if you have questions:

Peter Farnham, CAE

ASBMB Public Affairs Officer


Angela Hvitved, Ph.D.

ASBMB Science Policy Fellow


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x60 tablet info

some have asked; so, here we go!
[root@localhost gfb1] $ lspci
00:00.0 Host bridge: Intel Corporation Mobile 945GM/PM/GMS, 943/940GML and 945GT Express Memory Controller Hub (rev 03)
00:02.0 VGA compatible controller: Intel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller (rev 03)
00:02.1 Display controller: Intel Corporation Mobile 945GM/GMS/GME, 943/940GML Express Integrated Graphics Controller (rev 03)
00:1b.0 Audio device: Intel Corporation 82801G (ICH7 Family) High Definition Audio Controller (rev 02)
00:1c.0 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 1 (rev 02)
00:1c.1 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 2 (rev 02)
00:1c.2 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 3 (rev 02)
00:1c.3 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 4 (rev 02)
00:1d.0 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controller #1 (rev 02)
00:1d.1 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controller #2 (rev 02)
00:1d.2 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controller #3 (rev 02)
00:1d.3 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controller #4 (rev 02)
00:1d.7 USB Controller: Intel Corporation 82801G (ICH7 Family) USB2 EHCI Controller (rev 02)
00:1e.0 PCI bridge: Intel Corporation 82801 Mobile PCI Bridge (rev e2)
00:1f.0 ISA bridge: Intel Corporation 82801GBM (ICH7-M) LPC Interface Bridge (rev 02)
00:1f.1 IDE interface: Intel Corporation 82801G (ICH7 Family) IDE Controller (rev 02)
00:1f.2 SATA controller: Intel Corporation 82801GBM/GHM (ICH7 Family) SATA AHCI Controller (rev 02)
00:1f.3 SMBus: Intel Corporation 82801G (ICH7 Family) SMBus Controller (rev 02)
02:00.0 Ethernet controller: Intel Corporation 82573L Gigabit Ethernet Controller
03:00.0 Network controller: Intel Corporation PRO/Wireless 3945ABG Network Connection (rev 02)
15:00.0 CardBus bridge: Ricoh Co Ltd RL5c476 II (rev b4)
15:00.1 FireWire (IEEE 1394): Ricoh Co Ltd R5C552 IEEE 1394 Controller (rev 09)
15:00.2 Generic system peripheral [0805]: Ricoh Co Ltd R5C822 SD/SDIO/MMC/MS/MSPro Host Adapter (rev 18)

the wacom tablet is "WACf008" [ /sys/bus/pnp/devices/00:0b/id ]
CPU is "Intel(R) Core(TM) Duo CPU L2400 @ 1.66GHz" [ /proc/cpuinfo ]

since the install of mandriva 2008.0, most things are working very well... with the exception of the periodic loss of the stylus following 'sleep'.
curiously, the "setserial ... " command does not refresh/reload the stylus.


the ongoing saga ... mandriva and lenovo x60 tablet

so... on the advice of some mandriva-gurus, and the promise of increased support for wacom tablets and laptop acpi in 2008.0 -- i downloaded Mandriva 2008.0, popped it into my usb dvd drive, and booted. i chose to install (NOT upgrade) mandriva 2007.1 (spring).

install went smoothly; but no recognition of the wacom tablet. so.. set up software distribution sources (making sure to load both official and distribution sources) -- then load the wacom tablet drivers and control panel.

following all the steps in previous posts on this blog took about 90 minutes (eliminating all the things that did not work...), and pretty much everything works out of the box!
(even an old pc-card iomega clik drive... boy, do i feel old... ).

well.. of course, the stylus wouldn't work for anything.

the problem?
turns out that mandriva.2008.0 inserts a:
Identifier "Mouse1"
statement into the "InputDevice" section of the xorg.conf file.
this is bad.

change it to:
Identifier "Configured Mouse"
and ... all joy!
(remember to also change the InputDevice line in the "ServerLayout" section)


calendar syncing

i've been enamored, of late, of GCALDaemon for syncing multiple calendars across evolution (on my lenovo x60t), ical (on my 12" g4 mac laptop), google and .mac -- whew. this was a bit of a pain, til i discovered GCALD...

in any case, i added a small wrinkle on my linux box. once you have successfully run the .sync_now script

write a small script in the /etc/cron.daily subdirectory, by:
# vi /etc/cron.daily/evo_google_sync
for the script -- type:
don't forget to chmod...
chmod 755 /etc/cron.daily/evo_google_sync

then... you have a script that will automatically sync your evolution calendar with your google calendar(s). i prefer this to the GCALD... notebook configuration, which polls the network every 10 min (or whatever you the setting of your property).

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lenovo x60 and linux: matrix

here's where things stand. a few issues remain, but, with impending knee surgery (another post for another time), i'm sure i'll have lots of time to make this work! (btw, spacing in this post is odd... matrix is down the page a bit).

category item working??
installation external dvd yes,
but see this.
display laptop screen yes

external monitor / projector no

screen rotation yes,
but not automatic

stylus kind
of, no eraser or clicker
power management hibernate yes

sleep yes
audio inc. buttons yes
wireless wifi yes

bluetooth yes
extra keys mute / volume yes,

tablet buttons no

f(n) keys sleep,
but nothing else (yet)
fingerprint scanner
harddisk protection

from install
with modification

so far, so good... :) ...

lenovo x60 and linux: round 3b

on to the fingerprint reader...

these directions are solid:
these are better (or, at least, more general):

and here is the 'source'.

on to the 'key' issues...
according to the lenovo site;
install tpb
this worked like a champ for all 'blue' keys and volume .. nice onscreen msgs too!!
(although its pretty amusing that i have a bluekey for a keyboard light -- just no light...)

working on cisco vpn. the default vpn client (pkgd w/mandriva) does not work with the psu wireless network.
will try the cisco client packed for psu next.


lenovo x60 and linux: round 4

i was just reading a pdf file in tablet mode. i've been a bit annoyed that i haven't been able to map the alternate 'arrow' keys on the tablet face... and i had just set the pen down on the coffee table. since my knee is killing me (another story for another post)... i jabbed at the screen with my finger.

i was quite surprised to find that the pdf reader scrolled to the next page. a bit of experimentation, showed that the multitouch screen indeed worked. it was slow, clunky and unresponsive... i couldn't draw or write a note... BUT; i could tap buttons and scroll through a pdf.
very interesting.... since all the ubuntu forums suggest that the multitouch screen does not work at all...
more on this to come as i experiment...

i have also installed the GCalDaemon to synchronize my evolution calendar with my google calendar (e.g. here). it is a very simple process and works like a charm. i have also installed GCalD on my mac; and it also works very nicely. i am thereby able to take advantage of the google calendar AND use either my mac or linu.x60t for calendaring activities... curiously, since evolution also has an exchange plugin -- i am able to simultaneously manage a college/department calendar using my regular clients.
and i didn't think this would be a possibility!!!

curiouser and curiouser.


lenovo x60 and linux: round 3

this is helpful!

install xinput:
result: useless...

install xbindkeys...
result: also useless...

... there MUST be a better solution -- emperor.linux has a fully functioning version of any flavor of linux on the x60.tablet, which seems to include handwriting recognition. not yet worth the $300...

so.......still working.

(BTW... volume/mute buttons on keyboard work just fine. further, bluetooth works great, just install kde tool + bluez )



having a few computers around the house, and a home network filled with ripped cd's (.ogg -- of course!) and family photo's -- somehow, i allowed my wife's mac to go without a backup for over 6 months. as you may have guessed, a cracked toilet tank and small flood 'fixed' the hard drive.

sad; but, here is a reminder of what we ALL should be doing -- right?
but, if you REALLY need to find some files (once the box has dried out)... i seriously recommend one of the live linux discs/usb -- which even work on mac hardware!
very nice.

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lamarck and lysenko (old post)

Jean-Baptiste Pierre Antoine de Monet Chevalier de Lamarck, (of course) was a french biologist, who championed the idea of the inheritance of acquired characterstics. however, he did this in the early 1800's, with his original publication, Philosophie Zoologique, dated 1809.

read on...

the 'cat' experiment, as discussed in class was originally cited by Mr. St. George Mivart in his book "The Cat" (1881). He mentioned a case where a female cat had her tail badly injured when a cart-wheel ran over it and the owner judged it best to amputate the whole tail. Since then, the female had had two litters of kittens, and in each litter some of the kittens had a stump of tail, while the others had full-length tails.

as far as russia goes: i intended to refer to lysenko, who revived the long-discarded ideas of lamarkism in russia. indeed, genetics had been declared a 'bourgeois pseudoscience' in the Soviet Union in 1948 which persisted though the mid 1960s, lysenkoism was found to have caused mass starvation and serious, long-term harm to Soviet agriculture -- though it appeased the communist rulers of the time.

i won't even go into the manx cat... but, will note that the nytimes has an excellent section on evolution in todays paper!


lenovo x60 and linux: round 2

definitely install mandriva. i've been using this flavor since mandrake 9.0; and just can't get used to ubuntu. further, it seems that several things seem to work flawlessly with mandriva (2007.1).
e.g., wireless, power, sound, sleep/suspend, dynamic cpu, etc.
i also don't hear any of the 'whining' or 'clunking' referred to by others.

install additional software via mandriva software manager:
  • acpi tools
  • setserial pkg
  • configure-thinkpad pkg
  • wacom pkg
install current stable release of wacom drivers
follow instructions... to install in prebuilt subdirectory,

edit /etc/X11/xorg.conf per

edit rc.local per

don't forget to chmod 755 the x60t-swivel* files

add your userid to sudoers file
(this is REALLY important; and a little detail 'missing' from some of the other sites.)

rotate command works from the terminal, but keycodes seem to be incorrect in all those files:
get xev, since acpi_listen doesn't seem to work/compile in mandriva.
[xev does not identify the 'sound' keys or any key on the display..... ]

that works ok for keyboard; but not for other 'switches' on the tablet panel.

ok... try:
tail -f /var/log/messages
then.. press all nonfunctioning keys.
this gives you the rotate/tools/esc key on the panel (but no others).
add to /etc/rc.local file

still no joy... try:
su -c "/home/gfb1/Applications/getscancodes /dev/input/event0"
(sudo -- if you use ubuntu)

FINALLY; here's the problem.
the tablet and the keyboard are 2 different devices. BUT -- the keycodes overlap. so, i suppose i need to reassign different keycodes via "setkeycodes" in rc.local file.

more to come ...

just when you thought it was safe to -omic

there is an interesting set of articles surrounding the individual
genome sequencing of craig.venter and jim.watson!

i really can't decide if this is extreme
; or, just a sophisticated way of mooning
the universe...

either way, it borders on the ... (dare i type it?!?) .. c-omic-al ...


lenovo x60 and linux

my brandy new lenovo.x60 tablet pc was delivered today. it is exactly the size i had in mind, rivaling my 12" powerbook for the 'most useful size' award.

needless to say, the darned thing came with a brand new version of the business edition of vista. so, i immediately had plans to upgrade to one of my favorite flavors of linux. the good news, i suppose, is that my research.aide convinced me that i should keep vista (since i paid for it... ) and should set up a dual-boot system. but, this raised several interesting questions.

1) how to repartition the hard drive?? on principle, i refused to pay for any new i was pleasantly surprised that vista allows you to 'shrink' the hard drive; but, returned to reality, when the disk management utility would only allow me to create a 30Gb partition (of 100Gb).

so... off to the Spring 2007.1 dvd of Mandriva. booting on an external usb dvd drive was painless (remember to hit 'f12'); but, the mandriva disk resizing program failed.

2) now to the Kubuntu 7.04 dvd. again, booting went just fine, and i repartitioned the hd to a 70Gb linux partition and a 30Gb vista partition. the installation was completed without a hitch..

upon rebooting; i was kindly greeted by a nice 'selection' screen asking to choose the operating system. curiously, there were 2 vista choices... the 1st option led me to the lenovo recovery system. the 2nd began by running chkdsk, and rebooted. vista started normally (if you call that normal... it is s...o...o...o s....l....o....w...!).

i have to admit thinking at this point... why am i keeping this system?

finally, i rebooted and chose to start kubuntu. it booted right up. most of the pc-stuff worked... but, as i began to load the new wacom driver, i started to wonder about mandriva again....

so.... back to the mandriva 2007.1 boot dvd. at this point, i decided to remove the ext3 and swap partitions created by kubuntu; then autoallocate a new set of partitions via the custom disk partitioning option in mandriva. i quite like having a separate /home partition, to make upgrades easier!

more to come...


managing references

for years i had used reference.manager, then switched to end.note a few years ago (the same time i started using a 12" powerbook). both are excellent programs, now owned by the same company. however, these days i find myself searching through pubmed and the ncbi molecular biology databases with regularity -- and the web interface modules of the aforementioned software are kludgy (at best)...

somewhere along the line i stumbled upon zotero! what a treat!! a firefox extension (you DO use firefox, right?), it may be one of the best web apps i've seen in a long time. it will integrate sets of references into different folders, even keeping track of attachments (like those long lost pdf files), abstracts and your own notes.

all this and more, howie.
the data are maintained in a sqlite database (though i would have placed the database in an easier-to-backup location) and are exportable into a variety of formats: including endnote and will also easily integrate with openoffice!

now, if 'they' can only make zotero a web2.0 app -- with shareable databases.
i would catch the vapors...


P = G + E

and here i thought i might have a minority point of view!

not according to:

1) Science
The etiology of most chronic human diseases (such as asthma, atherosclerosis, and cancer) is complex, involving a mix of genetic and environmental factors interacting with each other over hours, days, months, or years.



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genes and diets and fat, oh my!

at the same time that Consumer Reports rates Dr. Barbara Rolls' (a fellow faculty member here at Penn State) book "The Volumetrics Eating Plan" the top-rated diet plan. the NYTimes (Genes Take Charge, and Diets Fall by the Wayside - New York Times ) suggests:

... that once a person got fat, the body would adjust, making it hopeless to lose weight and keep it off.

meaning that genes are more important that ANY diet in determining a persons body weight and/or level of obesity.

oh my! what to believe... ?!?

as anyone in my genetics course could tell you, neither argument is really correct. a person's body weight is a function of both genes AND environment (including nutrition, dietary choices and habits). there is NO single diet for every combination of genes (or person); no panacea.

though, it is fairly clear that for most of us: less is more.

oh yeah; try walking around the block now and again.

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just do it

there are many of us working in or with the poultry industry from Va Tech. given the horrific tragedy, some students have come up with a GREAT idea, as a show of support for their fellow students and the university community.

this weekend will be the Penn State Blue&White weekend, a celebration of spring (and spring football) at Penn State. some students have started a facebook group calling for everyone to wear the maroon and orange. other schools are joining in.
even Wilkes University.

this weekend; everybody is a hokie.

[crossposted and]


genomes as commodities

"Nature" has been publishing comments from scientists regarding their "question of the year". what would you do if the price of sequencing fell to $1000? this will, more than likely, occur in the near future.
this reminds me of an old presidential debate, where ross.perot asked which you would rather manufacture -- 'computer chips or potato chips'...

the answer, of course, is ... it depends. both computer chips and potato chips have become commodities of a sort. neither is particularly profitable (that is, each has a low per-unit profit and you need to sell lots to make lots of profit). though, at least some folks are making money by selling $10/lb potato chips!

what would i do?

in a few years, the kilo-buck sequence (sorry, dr.o'brien) will only be a buck.
in a few more years our computers will be able to process the huge amount of data we are discussing. by that time, after all our genomes have been sequenced and terrabases of sequence extracted, we will finally realize what we knew way back when.

that Genotype does not exist independently of Environment and that Phenotype is an emergent property of a system -- not a sequence.


Manager resources

Webwise, there are many resources to find (legitimate) management (re)sources. e.g., Free Management Library .

However, the sine qua non of the managerial lifestyle, is the management text! These books go through surges and resurgences .. usually based on their appearance in assorted M.B.A. programs!

A few of my favorites are (not in order):

... as you can see, I've been highly influenced by eastern philosophies. These are the books I return to time after time. Having said that, I am currently enjoying The No Asshole Rule by Robert Sutton. The sub-title says it all: "Building a civilized workplace and surviving one that isn't".

How about you?? What are your top 5??

[cross-posted at Poultry Management]

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Towards work

this is the start of a new category of notes for me; Tork.

i think i have too many email accounts (7 that i know of, and probably a dead hotmail account or 2); have had more digital devices (from C to Z: Clie to Newton to Palm to Zaurus); and still keep trying different things to be more efficient.

i've been a real fan of the cornell.notetaking.system and have created an openoffice template for printing out your own corny.notes.
there is also a very nice pdf notepage generator!

however, on some days, you just need a PDA (parietal disgorgement aid).
i've even been know to use the PocketMod -- very useful and cool, if difficult to fold.

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discs of the week: 004

ok, i know i've been stuck in the blues for more years than i care to count... so, i suppose that it would be ok for me to admit to buying (finally) the king biscuit flour hour recording of b(lues). b(oy). king (with special guests johnny and edgar winter and george benson). this is a treat, even if the rock licks feel a bit tired.

for some reason, my old lp of the beatles, sargeant peppers lonely hearts club band is back on my horizontal tracking, technics turntable!! it's amazing to think what a few amazingly creative folks can do with some great themes, lyrics and a 4-track recorder (or two)...

[originally posted 2006.02.01]

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disc of the week: 003

"sans vous, je suis rien" -- (sic; not sick) les mccann

perhaps with yesterdays loss of Coretta Scott King, you might try to give a listen to an old jazz standard "compared to what?". the song was written by gene mcdaniel, his inspired response to the assassination of Martin Luther King. i think he left the country shortly thereafter. anyway, i also seem to remember the song was first recorded by della reese (yes, that della reese, as in 'touched by an angel' -- strangely appropriate).

anyway, find the les mccann eddie harris album, 'swiss movement', preferably vinyl, though the cd is nice (if antisceptic -- to my ears)...

"avec vous, je suis tout (toot?!)" -- les, again ...

[originally posted 2006.04.10]

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evolution 2.6 on mac

i was recently asked how to set up this software on the mac -- so, here goes:

the 2.6 mac os.x (10.3.x or 10.4.y) build for evolution is available here. documentation for evolution is very complete and quite nice.

make sure you have a functioning x11 installation; meaning that you can get to xterm. then, just install the osx-evolution-2.6 build.

the tricky thing, of course, is to read the instructions. i realize that this is over-rated, but; you MUST initially launch evolution by using xterm. [cd] into the /opt/gnome-2.14/bin directory ... then using the command [sh ./launch_evolution]; you're on your way!

if you run into problems, more than likely you will need to:

  • chown 777 launch_evolution

  • to repair broken icons, place the command into the file .gtkrc-2.0 in your $HOME directory.

    gtk-icon-theme-name = "gnome"

    • if you don't have such a file, create one,
    • contrary to some posts, you do NOT need to install the hicolor theme.

  • if you need to access a m$.exchange server:
    • create a pop or imap mail account first
    • THEN, activate the exchange plugin.
    • quit/restart evolution (again, use xterm!)
    • now, you can create an exchange account

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