linux disk utilities

been having problems with my ata 4gb siliconmotion ssd that came with my asus eeepc, just missed the 1yr warranty by 2 months so I'm stuck with it ...

some useful info from my google travels

Linux disk utilities
http://felipecruz.com/linux-disk-utilies.php

TestDisk / PhotoRec -- fine data recovery tool
www.cgsecurity.org/wiki/TestDisk_Download

UltimateBoot CD
www.ultimatebootcd.com/

UNetBootin -- bootable usb images
unetbootin.sourceforge.net/

Damn Small Linux (DSL) ~50mb
http://www.damnsmalllinux.org/wiki/index.php/Install_to_USB_From_within_Linux

Natural Language Processing - NLP

Good summary of current NLP tools that are available

http://torg.media.mit.edu/rob/index.php/NLP_Seminar

MKL and Numpy

http://www.shocksolution.com/2008/09/19/installing-numpy-with-the-intel-math-kernel-library-mkl/

Intel MKL (math kernel library) http://software.intel.com/en-us/intel-mkl/ install with Numpy

1. Unpack the tar file with: tar xfvz numpy-1.0.4.tar.gz
2. cd numpy-1.0.4
3. cp site.cfg.example site.cfg
4. vi site.cfg
5. python setup.py install –home=~

[mkl]
library_dirs = /opt/software/intel/mkl/10.0.1.014/lib/em64t
mkl_libs = mkl, guide
lapack_libs = mkl_lapack
include_dirs = /opt/software/intel/mkl/10.0.1.014/include

http://mail.scipy.org/pipermail/numpy-discussion/2007-November/029881.html
http://www.scipy.org/Installing_SciPy/Linux#head-7ce43956a69ec51c6f2cedd894a4715d5bfff974

Norman Borlaug, 1970 Nobel Peace Prize for developing high-yielding crops

http://www.reuters.com/article/scienceNews/idUSTRE58C0KM20090913?feedType=RSS&feedName=scienceNews

WASHINGTON (Reuters) - Norman Borlaug, the U.S. agricultural scientist who received the 1970 Nobel Peace Prize for developing high-yielding crops to prevent famine in the developing world, has died at age 95, Texas A&M University said.

Borlaug, hailed as a central figure in the "green revolution" that made more food available for the world's hungry, died on Saturday night from cancer complications in Dallas, the university said in a statement.

The "green revolution" -- the development of crops such as wheat that delivered better yields than traditional strains -- is credited with helping avert massive famines that had been predicted in the developing world in the last half of the 20th century.

Dr. Richard Bruskiewich - International Rice Research Institute

http://beta.irri.org/index.php/Home/Welcome/Frontpage.html
International Rice Research Institute - IRRI

http://www.sfu.ca/alumni/our_alumni/outstanding/

Dr. Richard Bruskiewich, BA ’87 - Academic Achievement
Senior Scientist, Bioinformatics, International Rice Research Institute – Manila, Philippines

Dr. Richard Bruskiewich is one of the world leaders in Bioinformatics. After completing his degree at SFU with a minor in Computing, Richard trained in Biological Sciences at UBC and became interested in combining computational analysis with biology. As a PhD student he became renowned for being the first person to transfer the genome database, Acedb, to the PC. This led to post-doctoral research at the Sanger Centre in England, one of the most internationally prestigious centers for computational genetic analysis. During this time he made salient contributions to many important genomic analyses, including the analysis of the human chromosome 22. With several world-class opportunities available to him, he took the road less traveled by choosing to carry out his research in a developing country, joining the International Rice Research Institute in the Philippines. At the IRRI, he is responsible for using bioinformatics to decipher the genetic structure of rice, one of the largest and most important food crops in the world. His work develops both understanding and prediction of those genetic features that are critical to crop yield and environmental and disease resistance under various conditions. Since food – particularly rice – is one of the biggest health determinants in the third-world, Richard’s research impacts the developing world in ways often overlooked by the western world.

How To Format a USB Pen Drive in Linux

http://www.cyberciti.biz/faq/howto-format-usb-pen-drive/

Q. How do I format a USB pen drive under Ubuntu Linux for ext3 file system?
A. You can format USB pen drive with the help of following commands:

[a] fdisk : Partition table manipulator for Linux

[b] mkfs.ext3 : Create an ext2/ext3 filesystem by formatting given partition name (/dev/partition)

[c] e2label : Change the label on an ext2/ext3 filesystem

First make sure USB pen is not mounted. Click on Places > Computer > Select USB pen > Right click > Select Unmount Volume.

Let us assume that /dev/sda1 is your partition name for USB pen. To format type the following command (Open X terminal and type the command)
$ sudo mkfs.ext3 /dev/sda1
Caution: Careful while entering device/partition name; wrong name can wipe out entire hard disk!!!
Now use e2label command to change the filesystem label on the ext3 filesystem located on device /dev/sda1:
$ sudo e2label /dev/sda1 usb-pen
You can also create an MS-DOS/Windows XP file system under Linux, enter:
$ sudo mkfs.vfat /dev/sda1

Now you are ready to use USB pen.

TestDisk: File recovery tool

I thought my pictures were a gonner when my digi cam reported that my memory card is corrupted

fortunately, this handly tool allowed me to recover pictures from my SD, it even recovered pictures that I already removed! wow

testdisk-6.11.3/linux$ sudo ./photorec_static

My micro sd camera card is in /dev/sdb1

http://www.cgsecurity.org/wiki/TestDisk_Download
http://www.cgsecurity.org/wiki/PhotoRec_Step_By_Step

graduate school, research topics

About EBI
http://www.ebi.ac.uk/Information/About_EBI/about_ebi.html


http://www.ebi.ac.uk/Thornton/
* Elucidating and evolution enzyme function through structural analysis
* Deriving principles of protein structure
* Functional annotation of genomes, proteins and structures
* Functional genomics analysis of ageing
* Web tool and resource development

http://www.ebi.ac.uk/Rebholz/
The group focuses on extraction of facts from scientific literature in molecular biology. This is mainly based but not limited to matching of language patterns. In addition we do research on the disambiguation of semantic types, e.g. proteins, genes, species, drugs, and on automatic methods to identify language patterns. Both approaches require machine learning expertise and domain knowledge. The group has strong experience in Natural Language Processing methods (NLP) in the biomedical domain, and has applied its methods to different problems, e.g. identification of protein-protein interactions, extraction of acronyms and identification of mutations. All solutions are implemented as stand-alone modules, which can be combined and used to process text data in a pipeline. Existing modules are made available to the public through EBI's central services ('Whatizit', now as SOAP Web Service).

http://www.ebi.ac.uk/luscombe/
The Luscombe group's research focuses on the genomic analysis of regulatory systems.

We study how the biology of an organism is shaped by regulation of gene expression. We investigate this at various levels of complexity, from single-celled bacteria and yeast to complex mammals. Expression of a gene - i.e. production of a protein - is a complex exercise requiring large, gluttonous protein machines which expend the cell's energy reserves. Hence, the organism needs to be judicious in choosing which proteins to produce when and where. Furthermore, the expression of all genes at all times would be detrimental to the organism. Expression must be rigorously regulated so that the right genes are ‘switched on or off’ in response to changes in the internal and external environments of the cell.

http://www.ebi.ac.uk/chembl/
The ChEMBL group's research focuses on mapping the interactions and functional effects of small molecules binding to their macromolecular targets.

The group studies the interactions of pharmacologically active molecules and their receptors. In particular the group builds and maintains a series of drug discovery databases that are components of ChEMBL.

http://www.ebi.ac.uk/goldman/
Our main interests are in methods for the analysis of DNA and amino acid sequences to study evolution. Past work has been on the theoretical basis of phylogenetic analyses of this data, aiming to understand and improve methods, and on the development of statistical methods that test the accuracy of current mathematical models. More recent work has concentrated on devising new, better, mathematical models and the application of these models and methods to comparative genomic data.

http://www.ebi.ac.uk/panda/
The Protein and Nucleotide Database Group (PANDA) is a large group providing all the sequence resources at the EBI, from DNA through to Protein and encompassing the associated databases, such as genome databases (eg, Ensembl), protein families (eg, InterPro), protein function (eg, UniProtKB), proteomics (eg, IntAct) ontologies (eg, GOA), and pathways (eg, Reactome).

http://www.ebi.ac.uk/compneur-srv/
The interests of the group Computational Neurobiology revolve around signal transduction in neurons, ranging from the molecular structure of membrane proteins involved in neurotransmission to modelling signalling pathways. A strong focus is the molecular and cellular basis of neuroadaptation in neurons of the basal ganglia. We also provide services that facilitate our research, including database production and software development.

http://www.ebi.ac.uk/bertone/
The Bertone Group analyses genetic and biochemical mechanisms underlying cellular differentiation events, particularly in human and mouse embryonic stem (ES) cell lines.

SFU Bioinformatics Program
http://compbio.cs.sfu.ca/bio_graduate.htm

UBC Bioinformatics Program
http://www.bioinformatics.ubc.ca/

Bioinformatics at Boston University
http://bioinformatics.bu.edu/

July 15 deadline
http://www.embl.de/training/eipp/application/index.html

research groups
http://www.embl.de/training/eipp/application/recruiting_gl/index.html

research topics
http://www.embl.de/training/eipp/application/research_topics/index.html

Data integration / structural biology
http://www.embl.de/research/units/scb/schneider_reinhard/index.html

********** Data integration - disease mechanism
http://www.embl.de/research/units/scb/schneider_reinhard/index.html

******* Protein interactions and complexes - disease mechanism
http://www.embl.de/research/units/scb/russell/index.html

*** Gavin
http://www.embl.de/research/units/scb/gavin/awards/index.html

shared applicant questionnaire
https://www-db.embl.de/jss/servlet/de.embl.ml.phdProgramme.PhdApplicationExternalViewer?m=handleRequestExtView

Structural and Computational Biology:

Bork Group - Deciphering function and evolution of biological systems
Briggs Group - How proteins manipulate membranes - cryo-electron microscopy and tomography
Russell Group - Structural bioinformatics
Scheffzek Team - Signal transduction – disease proteins
Schneider (Reinhard) Group - Data integration and knowledge management

http://www.icapture.ubc.ca/who/who_mark_wilkinson.shtml
He then worked as a freelance bioinformatics consultant for one year, after which he joined the iCAPTURE Team, and now continues working in the area of bioinformatics, with a particular focus on data integration and machine-readable knowledge representation.

Visit the Wilkinson Lab Homepage (http://wilkinsonlab.ca) for up-to-date information on our research activities. The Wilkinson Laboratory is
interested in the problem of facilitating the interaction between a biologist and the data and analytical tools they require each day to make new discoveries. Our laboratory focuses on four main themes: Annotation, Interrogation, Integration, and Visualization.
http://www.biomoby.org/

CardioSHARE
http://cardioshare.icapture.ubc.ca/
CardioSHARE will use the knowledge of biologists, encoded in "Ontologies" to help interpret these kinds of questions, and automate the discovery and retrieval of the answers. When completed, CardioSHARE will be sufficiently powerful to answer questions for which the answer IS NOT KNOWN - putting it well beyond the power of keyword-style searches like Google and Entrez. CardioSHARE will accomplish this by having sufficient
understanding of biological/bioinformatics analyses that it can automatically construct and execute the pipeline of analytical tools necessary to answer the question being asked, thus finally bringing the power of in silico research into the hands of biomedical bench scientists.
- semantic web


http://www.stat.ubc.ca/~jenny/research.html
* High-throughput phenotypic experiments, genome-wide reverse genetic studies
* Finding informative sets and clusters of genes. Novel forms of meta-analysis. Using concepts from graph theory and survival analysis in the context of cluster analysis.

eeebuntu home key

eeepc eeebuntu keyboard shortcuts is under system/control centre/keyboard shortcuts

super L = home = window key

very helpful tip, can't see the ok or cancel buttons in dialog boxes because they are below the screen?

> If you hold down the alt key and drag (double tap on touchpad) (anywhere in) the window up you should be able to see those buttons.

http://www.sizlopedia.com/2008/10/09/install-ubuntu-on-eee-pc/

what to pack for japan

http://www.realgap.co.uk/What-to-pack-for-Japan

bags, sturdy backpack
documents
warm clothes and rain coats - weather http://www.japan-guide.com/e/e2273.html, june = rain (tsuyu), 31-5 degrees
shoes
towel
camera
toiletries, toilet paper, toothpaste, floss, sunscreen, deodorant,
first aid kit
guide books, phrase book, form book
pen and paper
gift
padlock
alarm clock
money - atm and visa on post offices (http://www.japan-guide.com/e/e2208.html) (yuubinkyoku 郵便局 http://www.yuubinkyoku.com/index.html) and 7-eleven
ear plug
entertainment - ds


http://www.japan-guide.com/e/e2063.html
July
Kyoto Gion Matsuri (more details)
Kyoto
The festival of Yasaka Shrine, Gion Matsuri is ranked as one of Japan's three best festivals, featuring over 20 meter tall festival floats. The highlight of the festival takes place on July 17.

Format USB drive in linux

http://www.cyberciti.biz/faq/howto-format-usb-pen-drive/

$ sudo mkfs.ext3 /dev/sda1

To see the list of mounted drives, do
$ mount | grep /media
/dev/sdb1 on /media/disk type vfat (rw,nosuid,nodev,uhelper=hal,shortname=mixed,uid=1000,utf8,umask=077,flush)

To unmount do
$ umount /dev/sdb1

http://www.pgts.com.au/cgi-bin/psql?blog=0808&ndx=b002

Finally create a folder called "games" in the root of the Micro SD disk. You can copy .NDS games into here. While I was about it I created some additional folders, called "pictures", "music" and documents. This enabled the kids to use the Micro SD as memory stick when it wasn't being used as part of the R4DS. Here is a summary of the commands to use for Linux. Take Note: This example uses the values of /dev/sdb1 and the mount point of /media/disk -- As stated earlier, This may vary according to the version and hardware -- Substitute the appropriate device name and/or mount points, for your system, in the commands below:

1. umount /media/disk
2. sudo mkfs.vfat -I -F 32 -v /dev/sdb1
3. Mount the device again (just unplug it and plug it again -- if you have automount, or use "mount" if you know the command)
4. Change directory to the location where you downloaded the RAR file, and enter this command:
unrar x English-1.18.rar
5. chdir English
6. cp -rp * /media/disk/
7. mkdir /media/disk/games /media/disk/pictures /media/disk/music
8. You can now copy games to the /media/disk/games folder.
9. umount /media/disk
(or use "Safely Remove" option).

If you are a windoze user, (what are you doing reading this blog?), these commands should work:

1. Use WinZip to upack the RAR, make sure that you preserve the Folders. Copy it to a separate folder (eg. C:\FOO)
2. Insert the USB stick (with the Micro SD in it). Determine which drive it has mounted as. (Check with Windoze Explorer). I'll assume that it is drive E:. Substitute the appropriate drive.
3. format e: /fs:fat32
4. e:
5. xcopy /s c:\foo\English\*
6. mkdir games
7. mkdir pictures
8. mkdir music

dbsk-tohoshinki-doshite-kimi-wo-suki-ni-natte-shimattan-daro

http://sapphirebluelove.wordpress.com/2008/06/14/mp3-updates-dbsk-tohoshinki-doshite-kimi-wo-suki-ni-natte-shimattan-daro-cddvds/

passing away

good friend for 2 yrs has passed away, blame it all on the weather and the heater ...