dpkg

// list installed packages
$ dpkg -l

// install package, calendar desktop - rainlendar
$ sudo dpkg -i rainlendar2-lite_2.6.b82-1_amd64.deb

http://www.rainlendar.net/cms/index.php?option=com_rny_download&Itemid=32

// remove package
$ sudo dpkg -r xchat

$ sudo apt-get install -f

wallpaper-tray, drapes

nitrogen

random wallpaper background

wallpaper-tray http://ubuntuforums.org/showthread.php?t=534455
drapes http://ubuntuforums.org/showthread.php?t=1470139&page=2

images are in /usr/share/backgrounds

edit  ~/.config/autostart/drapes.desktop
and add
Type=Application

Statistical methods in bioinformatics : an introduction / Warren J. Ewens, Gregory R.

Author Ewens, W. J. (Warren John), 1937-
Title Statistical methods in bioinformatics : an introduction / Warren J. Ewens, Gregory R. Grant.
Published New York : Springer, c2001.
Rating [No one has rated this material]
Permanent link to this record http://troy.lib.sfu.ca/record=b2703803~S1a

LOCATION (click for map) CALL # STATUS
Bennett Library QH 324.2 E97 2001 IN LIBRARY
Descript. xix, 476 p. ; 24 cm.
Series Statistics for biology and health.
Note Includes bibliographical references (p. [449]-461) and index.
Contents 1. Probability Theory (i): One Random Variable -- 2. Probability Theory (ii): Many Random Variables -- 3. Statistics (i): An Introduction to Statistical Inference -- 4. Stochastic Processes (i): Poisson Processes and Markov Chains -- 5. The Analysis of One DNA Sequence -- 6. The Analysis of Multiple DNA or Protein Sequences -- 7. Stochastic Processes (ii): Random Walks -- 8. Statistics (ii): Classical Estimation and Hypothesis Testing -- 9. BLAST -- 10. Stochastic Processes (iii): Markov Chains -- 11. Hidden Markov Models -- 12. Computationally Intensive Methods -- 13. Evolutionary Models -- 14. Phylogenetic Tree Estimation -- C. Computational Aspects of the Binomial and Generalized Geometric Distribution Functions -- D. BLAST: Sums of Normalized Scores.
Call # QH 324.2 E97 2001
Subject Bioinformatics.
Bioinformatics -- Statistical methods.
Add Author Grant, Gregory, R., 1965-
ISBN 0387952292 (alk. paper)

Computing with R
http://www.stat.sfu.ca/~jgraham/Teaching/S890_04/R

gtkpod, ipod errors iTunesDB' does not match checksum

iTunesDB '/mnt/ipod/iPod_Control/iTunes/iTunesDB' does not match checksum in extended information file

// view system, mount points
$ df

/dev/sdc2 1907988 1887456 20532 99% /media/IPOD

$ /sbin/fsck.vfat -a /dev/sdc2

http://forums.fedoraforum.org/archive/index.php/t-120906.html

// view log
tail -f /var/log/syslog


--------------

Get rid of 'Please specify the command to be called on the 'Tools' section of the preferences dialog.' by:

- Preferences > Tools
- Calendar/Contacts/Notes > Set options for Calendar/Contacts/Notes
- uncheck 'Call automatically when synchronizing iTunesDB'

Presentation: GROUP 3 - Genetic Engineering of Fruit Ripening to Prevent Spoilage

http://www.biotopics.co.uk/edexcel/biotechnol/frurip.html

Researchers have managed to modify tomato plants by inserting a gene which prevents one of the plant's 'ripening' genes from working at the usual rate. The tomatoes may then be left on the plant until red to develop a full flavour. They soften more slowly, suffer less damage in transit and have a much longer shelf life, cutting out waste.

ethene gas = promotes fruit ripening
in the USA, whole tomatoes (marketed as Flavr SavrTM are produced in this way

Zeneca in the UK, a gene for stage Y (pectinase enzyme) is inhibited., probably better because it's lower down the pathway so less lethal mutations

http://books.google.ca/books?id=1AvyrJOYStkC&pg=PA340&lpg=PA340&dq=Genetic+Engineering+of+Fruit+Ripening+to+Prevent+Spoilage&source=bl&ots=xzIp_wsEdt&sig=0_hsDveavc-HJwQJ2HsN7mYYpYM&hl=en&ei=66p1S-G3BpCcswO0tYnMCA&sa=X&oi=book_result&ct=result&resnum=2&ved=0CAoQ6AEwAQ#v=onepage&q=Genetic%20Engineering%20of%20Fruit%20Ripening%20to%20Prevent%20Spoilage&f=false
So tomatos have been engineered not to produce ethylene, and so it won't ripe, then during the transport process, tomatos are sprayed with ethylene gas to promote artificial ripening.

This was done by creating an antisense mRNA for the ACC synthase gene (the precursor of ethylene) 'Endless summer variety'

gene subtraction - polygalacturonase

http://answers.yahoo.com/question/index?qid=20090315040540AALXSNU
Most fruit first become ripened because of the release of a hormone within the fruit and the plant called ethylene (H2C=CH2). Ethylene causes the breakdown which in itself causes a production of enzymes that break down the structures of the fruit (eg.: amylase, pictenase).The eyhylene gas also destroys the green pigment of the fruit chlorophyll. But for any fruit to become ripened there needs to be a high enough concentration of ethylene around the fruit to even begin to ripen.

The amylase acts on the starches, which are made of amylose, which is just a long chain of glucose molecule. And what the amylase does is it cuts the bonds of the starch chain, so then the glucose molecules are free; and now the fruit tastes sweet.
The other enzyme pectinase does almost the exact same thing as amylase, it cuts away the bonds of the pectin molecule so now we have a bunch of pectinic acid, and now the fruit is soft enough to eat. Pectin is extremely important for a fruits/plants because it hold the cells together.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705034/?tool=pmcentrez&report=abstract
Ripening-Regulated Susceptibility of Tomato Fruit to Botrytis cinerea Requires NOR But Not RIN or Ethylene1[W][OA]
Dario Cantu, Barbara Blanco-Ulate, Liya Yang, John M. Labavitch, Alan B. Bennett, and Ann L.T. Powell*

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=DetailsSearch&Term=(%22fruit%22[MeSH+Terms]+OR+fruit[Acknowledgments]+OR+fruit[Figure%2FTable+Caption]+OR+fruit[Section+Title]+OR+fruit[Body+-+All+Words]+OR+fruit[Title]+OR+fruit[Abstract]+OR+fruit[Author])+AND+ripening[All+Fields]

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2671613&tool=pmcentrez&rendertype=abstract

http://jxb.oxfordjournals.org/cgi/content/abstract/53/377/2039
Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening
Received 11 April 2002; Accepted 2 July 2002
Lucille Alexander and Don Grierson1

http://jxb.oxfordjournals.org/cgi/content/abstract/53/377/1995
P. J. White
Recent advances in fruit development and ripening: an overview
J. Exp. Bot., October 1, 2002; 53(377): 1995 - 2000.

A word about pre-fetching

http://en.wikipedia.org/wiki/Prefetching

Prefetching generally means loading something ahead of time and could refer to any one of the following topics:

* Instruction prefetch, in computer architecture, a microprocessor speedup technique
* Prefetch input queue (PIQ), in computer architecture, pre-loading machine code from memory
* Link prefetching, a web mechanism for prefetching links
* The Prefetcher technology in modern releases of Microsoft Windows
* PREFETCH an X86 instruction in computing
* Prefetch buffer, a feature of DDR SDRAM memory
* Swap prefetch, in computer operating systems, anticipatory paging

About MPI (message passing interface)
* http://www.cilk.com/multicore-blog/?Tag=MPI
* works well for distributed computing (private memory), but not for multi-cores (shared memory, maybe ok for NUMA - non-uniformed memory access)
* Indeed, MPI represents to distributed-memory multiprocessors what Pthreads and WinAPI threads represent to shared-memory multicore systems: an assembly language for programming concurrent programs. (Thus, some might argue whether message-passing actually merits the designation “concurrency platform.”)
* The MPI_Send()function blocks (does not return) until after the message has been received. The MPI_Recv() function blocks until a message arrives.
* The 12-argument library function MPI_Sendrecv() allows the programmer to both send a message and receive a message as a single operation,
* sends data in between threads to later aggregate data

Disable Firefox' session restor at startup

http://kb.mozillazine.org/Session_Restore

browser.sessionstore.enabled = false
browser.sessionstore.max_tabs_undo
browser.sessionstore.max_windows_undo to 0.

PDF Merge in Ubunti using gs

merge in1.pdf, in2.pdf, in3.pdf to out.pdf

gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=out.pdf in1.pdf in2.pdf in3.pdf ...

http://ubuntuforums.org/showthread.php?t=262411

Bioinformatics interview

http://www.bioteach.ubc.ca/Bioinformatics/interviews/

The Genes series by Benjamin Lewin and Introduction to Genetic Analysis by Anthony Griffiths are good places to start,

VanWoRM

http://www.sfu.ca/~leroux/BCe_VanWoRM_home.htm

# Bora Uyar - Genome Annotation Improvement of Four Caenorhabditis Species: C. briggsae, C. remanei, C. brenneri, and C. japonica

how to judge and oncoming car, turning into traffic

http://wiki.answers.com/Q/When_turning_left_at_a_green_light_and_an_oncoming_car_hits_you_because_they_were_going_to_fast_for_one_to_accurately_judge_how_fast_the_vehicle_was_going_who_is_at_fault

http://everything2.com/title/Turning+into+traffic

In fact, not only is it safer to complete the steering manoeuvre in one go, you will also avoid "dry steering". That is when you twist the tyres round when they are not rolling, which wears tyres and strains the steering, too.

Basically only turn when you are absolutely sure the traffic is clear from any cars at intersections. You have to judge the speed and distance of the vehicles coming across you,

Merging traffic

http://www.monkeymeter.com/drivetips/merge.php

Love's NP-Complete ...

Love's NP-Complete ...

Niji

コブクロ／虹 【PV】　歌詞付き
Niji by Kobukuro

http://www.youtube.com/watch?v=owQFLAkGsRc
Yell - by Ikimono Gakari (blackboard monitor)