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 ...

PictoDS

http://cbds.free.fr/Softwares/PictoDS/?language=en

It didn't run for amd64 so I ripped the swt.jar from Vuse (Azureus) and replaced the one in lib/swt.jar and it worked!
http://www.megaupload.com/?d=PWGU052H

http://ubuntuforums.org/showthread.php?t=154852
Originally Posted by art View Post
apt-get install imagemagick
On the command line type
convert file.pdf file.jpg

Then I did `convert book.pdf book.jpg` and I got all my jpgs w00t. I also needed to create this dir manually ` $ mkdir -p /home/foo/PictoDS_linux_2.1.0/bin/pictodstmp`

Now I can view PDFs in ComicDS


http://www.r4ds-forums.com/viewtopic.php?f=38&t=705
Soft reset on NDS
Where can I find it?

The soft reset is represented by a little R circle (either green or red) at the top right of the bottom screen when you are in the folders.

Green = soft reset function is enabled.
While in a game, press L+R+A+B+X+Y (i.e. the front two shoulder buttons and the four buttons next to the bottom screen of the NDS)

http://www.r4ds.cn/r4ds.html

http://colors.collectingsmiles.com/faq.php#43
Colors! for drawing stuff on a NintendoDS

Homebrew Apps
http://dshb.50webs.com/pages/hb.htm

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

Project JDS -- learning hiragana, katakana
http://dl.qj.net/Homebrew-Applications/pg/12/fid/14919/catid/220

raikachan and other japanese learning tools

Raikachan mozilla jap translation plugin

http://rikaichan.mozdev.org/installation.html

BabelFish Instant Translation 1.84
by NettiCat

https://addons.mozilla.org/en-US/firefox/addon/7004

Learn Japanese with NintendoDS
http://learn-japanese-ds.blogspot.com/2008/06/anpaman-toasobo-i-u-e-o-kyoushitsu.html

Comic DS [convert PDF to JPG] ... slow?
http://cbds.free.fr/Softwares/ComicBookDS/?language=en#download

offline maps
http://sdesmedt.wordpress.com/offline-maps/

japanese nouns

学生寮　がくせいりょう　student dorm
地図　ちず　map

job applicant qualities

We would like to know who you are and how you think. Incorporate the following into your application:

* Your information
o Name, email, and website(optional)
o Brief background: education and relevant work experience
* Your programming interests and strengths
o What are your languages of choice?
o Any prior experience with open source development?
o What do you want to learn this summer?
* Your interest and background in biology or bioinformatics
o Any prior exposure to biology or bioinformatics?
o Any interest in learning a bit of biology this summer?
* Your ideas for a project (an original idea or one expanded from our Ideas Page)
o Provide as much detail as possible
o Strong applicants include an implementation plan and timeline (hint!)
o Refer to and link to other projects or products that illustrate your ideas
o Identify possible hurdles and questions that will require more research/planning
* What can you bring to the team?
o Are you enthusiastic?

eeepc screen brightness

to remember the screen brightness level on every startup

BRIGHTNESS

When the computer gets idle, the screen becomes darker. Unfortunately, when it wakes up, the brightness is restored to 100 %. To suppress this behavior, I went to System > Preferences > Power management and unchecked boxes called "Dim display when Idle", "Reduce backlight brightness" and moved the cursor on the bar called "set display brightness to". This is probably redundant, but this solved my problem.

Do this for both AC and Battery Power. Adjust the brightness level and then check the boxes again if you like.

http://forum.eeebuntu.org/viewtopic.php?f=28&t=2331

japanese phrase book

http://wikitravel.org/en/Japanese_phrasebook

Please speak slowly.
ゆっくり話してください。 Yukkuri hanashite kudasai. (YOO-kuree hanash-teh koo-dah-sah-ee)
Please say it again.
もう一度言ってください。 Mō ichido itte kudasai. (mo EE-chee-doh ee-te koo-dah-sah-ee)
Please help!
助けて！ Tasukete! (tahs-keh-teh!)

いいです。 結構です。
Ii desu. Kekkō desu.
"It's good/excellent." Used when you don't want more beer, don't want your bentō lunch microwaved, and generally are happy to keep things as they are. Accompany with teeth-sucking and handwaving to be sure to get your point across - both of these expressions may be interpreted as positive responses if you don't include enough nonverbal indications to the contrary.

I need a doctor.
医者に見てもらいたいです。 Isha ni mite moraitai desu.

I don't feel well.
気分がわるいです。 Kibun ga warui desu.

I need your help.
たすけてください。 Tasukete kudasai.

... hurts.
… が痛い。... ga itai.

What?
何？ Nani? (nah-nee)
Where?
どこ？ Doko? (doh-koh)
Who?
誰？ Dare? (dah-reh)
When?
いつ？ Itsu? (it-soo)
Which?
どれ？ Dore? (doh-reh)
Why?
どうして Dōshite (doh-sh'teh)
How?
どうやって？ Dōyatte (dohh-yah-teh)
How much?
いくら？ Ikura? (ee-koo-rah)
What type of?
どんな？ Donna? (dohn-nah)

Earthquake
地震 (jishin)

now
今 (ima)
later
後で (atode)
before
前に (mae ni)

six o'clock AM
朝6時 (asa rokuji)

today
今日(kyō)
yesterday
昨日(kinō)
tomorrow
明日(ashita)

Sunday
日曜日 (nichiyōbi)
Monday
月曜日 (getsuyōbi)

January
１月 (ichigatsu)
February
２月 (nigatsu)