Kevin
Kevin is an Olympia based musician and software developer, when not writting code, he is often having his spelling corrected by Sara, other than that he can usually be found on the road touring with his band.
Sara
Sara is a Seattle-based software developer. Before transitioning into software, Sara worked in Museum education where she managed recruitment, registration, staffing, budgets, and events for museum Education programs. Sara enjoys running, baking, looking at cat memes on the internet, and finding spelling errors in other peoples' code.
Michael
Michael is a high ranked software developer. Currently due to the escape room's popularity, a sought after voice actor. He holds two gold medals in dad of the year award. When not being compared to Michael Jordan and Oprah Winfrey, you can find him jogging, paddle-boarding, canoeing, hiking and of course coding.
Keith
Keith is a software developer based in Tacoma. He has a background in visual arts and performs jazz guitar around the greater Seattle area. He first met Kevin, Sara, and Michael while waiting in line at 7-11 and they all decided to form a band. At band practice one day they discovered software development and the rest is history.


I have a background in healthcare and quality improvement
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum.


Michael Flynn attends a dinner honoring the Kremlin-aligned English language media company RT, where he sits near Putin. Flynn made a paid appearance on the network. Green Party presidential nominee Jill Stein attended the dinner as well and sat three seats to Putin’s left.
Source: Washington Post


Final Fantasy 8 Characters
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- Adel [VILLAIN]
- A very not nice lady who kind of had this little reign
of terror going on in Esthar in the past. She was sealed
away by Laguna and a few other revolutionaries and sent
into outer space. Ultimecia uses Rinoa to unseal her.
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- Aki, Instructor
- A very strict instructor in Balamb Garden who
apparently gives hard tests. You can see him in a
one-time-only scene in Disc 3 in Balamb Garden, floor two,
when he berates Squall if he uses magic in the hall.
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- Biggs
- Major Biggs of Galbadia reporting! This guy offers some
nice comic relief, but he tends to send massive mechanical
things after you once he's done.
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- Boco
- A fighting Chocobo and also the star of Chocobo World
(the PocketStation minigame). (See also Character:FF5, Character:FF9, Character:Tactics)
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- Caraway, General Fury
- Rinoa's stern father who's all but disowned her. He's a
top brass in the Galbadian army and she's a dissenter. Go
figure.
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- Card Queen
- A gameplay element who flits from place to place, often
not telling you where she's going, and forcing you to
follow her doggedly to pick up a few almost-not-worth-it
cards.
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- Chocoboy
- A little kid who runs the Chocobo Forest puzzles.
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- Cid Kramer
- He looks too nice to head a military academy, but there
he is. He can be quite forceful when push comes to shove,
but he's a bit of a coward. He started the orphanage with
his wife Edea, but was forced to transform it into Garden
when she was possessed by Ultimecia. Having to live with
the fact that he might have to order his wife's death is
not a nice feeling. When danger from Galbadia threatens, he
runs.
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- Deling, President Vinzer
- The dictator President of Galbadia, who got his way
there very cunningly, had a city named after him, then
invited a sorceress in who promptly got rid of him.
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- Dobe, Mayor
- The pacifist mayor of Fisherman's Horizon wants no
violence at any cost. This changes a little when a
rampaging Galbadia invades, looking for Ellone.
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- Edea Kramer [VILLAIN/GUEST]Show
Images
- Edea's original motives were all for the best. A very
high-class woman, she started an orphanage with her
husband, Cid. However, that all changed when she inherited
the powers of Sorceress Ultimecia (via a bend in time) and
became a sorceress herself. She realized the problems this
could cause. She and Cid started Garden and SeeD, in case
she should ever need to be stopped before destroying the
world. All the children from her orphanage call her Matron,
and have very fond memories of her, which make it all the
harder to be forced to fight her. After she comes to, she
joins up with the youths in the fight against Ultimecia.
(See also Jobs:Edea)
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- Ellone
- Her parents were killed in an Esthar attack, and she
was adopted and raised by Raine and Laguna. She started off
as the cutest little girl, and grows into a graceful young
lady. She has the unique ability to send someone's mind
back in time, which is how Laguna and Squall became so
closely connected. She's continually getting captured and
rescued because of her abilities. Ellone also eventually
ended up in the Kramers' orphanage, and being the oldest
there, everyone looked up to her and called her "Sis".
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- Flo
- Mayor Dobe's devoted wife who's decent at cards.
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- Francesca DiMarco
- The owner of the Timber pub has known Rinoa since she
was a child.
-
-
- Fujin
- A very creepy gal. She has silver hair and an eye
patch. She has a tendency to speak in CAPITAL, ONE WORD
SENTENCES (in JP version, she speaks in Kanji). She can
speak normally, but she doesn't like to. And she packs a
mean kick, usually to Raijin. She, Raijin, and Seifer make
up the Disciplinary Committee of Balamb Garden, for a
little while at least. (See also External Crossovers:Kingdom Hearts
2)
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- Gilgamesh
- Gilgamesh takes a much different role here as a
Guardian Force, looking like a hybrid of his two forms from
FF5. If you gain Odin before the final fight with Seifer,
he will attempt to attack Seifer but become destroyed, his
sword flying towards the heavens. At the end of the fight,
Gilgamesh comes down, brandishing Odin's sword and three
others, and cuts Seifer down. He takes the place of Odin
for the rest of the game at that point. He has four arms
holding a different sword for four different attacks -
Zantetsuken works the same as Odin's attack, Excalibur does
medium damage to enemies, Masamune does high damage to
enemies, and Excalipur does 1 HP of damage (he used this
sword in FF5, thinking it was the real thing, with
hilarious results). Unlike other GF's, Gilgamesh's
appearances can't be controlled; he appears randomly at the
beginning of battles (including boss fights!) and uses one
of the four attacks. (See also Summon:Gilgamesh)
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- Griever
- One of the major symbols of the story. Griever looks
like a silver lion head and appears on Squall's gunblade,
on a plaque in his room, on the ring he gives to Rinoa, and
as the final boss (the "Ultimate GF"). Nancy Lavigne gives an
interesting connection: "Ultimecia searches Squall's mind
for the strongest monster he could imagine, and it was of
course Griever. So Griever was a creature that Squall
imagined, and Ultimecia brought it to life."
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- Hyne
- The Great Wizard Hyne was supposedly the ancestor of
mankind and who gave part of his power to the sorceresses.
It's a great honor to call a Sorceress a "daughter of
Hyne".
- Irvine Kinneas [HERO]
- There's always one. Irvine is the ladies' man of 8;
he's even got the cowboy hat and ponytail, and his dead-on
sharpshooting aim, to try to make their knees weak. It's
very rare that he gets any sort of positive reaction,
though. He tends to put people off by his uncaring
attitude, but it's really just a cover. The real him comes
out sometimes when he gets caught up in things. He also
attended the Kramers' orphanage as a child. (See also
Jobs:Gunner)
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- Julia Heartilly
- The beautiful piano player at the Galbadia Hotel is the
distant object of affection of Laguna, who just falls over
himself and gets embarrassing cramps whenever he tries to
talk to her. He becomes her inspiration for finally writing
her hit song, "Eyes On Me". She eventually marries General
Caraway and becomes Rinoa's mother. She dies in a car crash
at age twenty-eight, when Rinoa is only five. (The song
"Eyes On Me" by Faye Wong is played in one of the nicest
scenes in the game, a conversation between Squall and
Rinoa: Laguna's and Julia's children.)
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- Kadowaki, Dr.
- The resident medical specialist in Balamb Garden used
to be so good at cards she was named the Card King. She has
no patience for Seifer's shenanigans, but she's good in a
crisis.
 He can quietly
dash Laguna's bumbling antics with one short comment. But
their friendship spans countless decades. Kiros is thin,
wiry, and deadly with two blades called Katal which are
more like extensions of his hands than weapons. (See also
Jobs:Kiros)
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- Laguna Loire [GUEST]Show
Images
- Not what you'd really think of being hero type,
actually. His bungles and cock-ups are legendary. Laguna's
more bent on journalism, telling the world about the
horrors of violence, war, and alcoholism. Although he did a
stint for the Galbadian army, he spent the rest of his life
righting wrongs in his own shy way, and eventually landed a
slave job in Esthar. He tricks the Sorceress and seals her
away, ending her years of tyranny. The people rewarded him
by making him President of Esthar, and his first job is to
close the borders and protect its xenophobic people. He
doesn't like getting too close to battle; his gun does all
the damage he needs. The game holds much evidence that
point to him being the father of Squall. (See also
Jobs:Laguna)
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- Lank
- One half of the Trabia Tech Squad, with Port.

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- Martine
- The head of Galbadia Garden was unceremoniously dumped
when Edea took over. He retired and moved to Fisherman's
Horizon, where he's known to play a brutal game of cards
with the ones he confiscated from the Garden.
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- Matron
- Alias of Edea Kramer.
- Nida
- The only other person besides Squall, Zell and Selphie
who managed to pass the SeeD field test. Nida takes control
of the Balamb Garden rudder after its flight capabilities
are discovered.
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- NORG
- A fat and rich Shumi reminiscent of Jabba the Hutt, he
was the one who financed SeeD. However, his cowardice
caused him to want to do anything to appease the new
sorceress, so he decided to give her Cid's head on a
platter. Squall didn't like that idea too much.
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- Odine, Dr.
- An extremely idiosyncratic personage, he has a
scientific mind like a broken mirror - brilliant, but
fractured. He tends to have absolutely no feelings for
anything besides his research. His dress is ridiculous,
looking sort of like a clown with that huge striped collar.
He is a famous researcher of magical artifacts, and has
taken a special interest in the sorceresses. He was the one
who invented Junctioning and discovered GFs, and who
extracted Ellone's powers into a machine. His lab is in
Esthar City.
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- Piet
- The bald director of the Lunar Base. He oversees the
Adel project.
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- Port
- One half of the Trabia Tech Squad, with Lank.
-
-
- PuPu
- A cute widdle alien what has lost his way and got stuck
on earth. The end result of a convoluted UFO quest which
results in either you giving him Elixirs and him giving you
his PuPu Card, or you killing him and getting a neat item
instead.
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- Quistis Trepe [HERO]
- Precocious is the word that comes to mind when dealing
with this tall blonde. Quistis rose quickly in the ranks of
SeeD to become an instructor, but was demoted from her
status after allegations of being lacking leadership
qualities - basically, she couldn't control Seifer. She's
still just as determined as ever. And that whip of her's
packs a nice punch. She also grew up in the Kramers'
orphanage with the rest of the gang. She was adopted, but
had problems with her new home, and ended up in Balamb
Garden at the age of 10. (See also Jobs:Blue Mage)
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- Raijin
- Honest, you almost feel horrible fighting this guy! The
fact that he can kick your butt with his staff doesn't
matter. This dark-skinned, feel-good posse member hangs
around with Fujin and Seifer; they make up the Balamb
Garden Disciplinary Committee. He has a tendency to talk
cool, ya know? And be nice to people. But his friends don't
like that too much, so he gets kicked in the shins a lot.
But he follows them 'cause they're a posse, ya know? (See
also External
Crossovers:Kingdom Hearts 2)
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- Raine Loire
- Laguna's secret love, he seldom revealed the fact that
she married him once she passed away. A very conscientious
woman and an ideal mother, her loss affected both Laguna
and Ellone profoundly. Evidence points to her being
Squall's mother.
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- Rinoa Heartilly [HERO]
- A vivacious, rebellious young girl whose luxuriant
looks and defiant attitude eventually attract Squall to
her. Her parents are General Caraway of Galbadia and Julia
Heartilly, a piano player, who dies before the game is set.
Her faithful dog, Angelo, takes better care of her than
most pets do. Her life gets even more complicated when she
becomes a sorceress and vulnerable to Ultimecia's mind
manipulation. She wears a blue dress with two stylized
angel's wings drawn on the back. (See also Jobs:Black Mage)
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- Seifer Almasy [VILLAIN/GUEST]
- The unruly and unpredictable antagonist of Squall.
Seifer sports a long trench coat, very short orange hair, a
scar from a training battle with Squall, and a chip on his
shoulder a mile wide. He has a tendency to do whatever he
wants, despite any illogic it entails. He also has a
propensity towards violence, which might be why he's head
of the Balamb Garden Disciplinary Committe, with Fujin and
Raijin. He's the only other person in the world of 8 who
wields a gunblade. He attended the Kramers' orphanage as a
child as well. (See also External Crossovers:Kingdom Hearts
2, Jobs:Seifer)
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- Selphie Tilmitt [HERO]
- A spunky girl who never seems to run out of cutsey
things to say at any given time, and who has an
overbearingly naive view of the world, Selphie's always
there when people need cheering up, even if they don't want
it. A transfer student from Trabia Garden who found her
niche in the Garden Festival committee. She doesn't look
it, but she's deadly with nunchaku. She attended the
Kramers' orphanage as a child. (See also External Crossovers:Kingdom
Hearts, Jobs:Gambler)
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- Squall Leonhart [HERO]
- The reclusive, antisocial hero of FF8. Squall sports
brown hair and a facial scar from a tussle with Seifer. An
orphan, we later find out that he attended the Kramer
orphanage. His parents, it is vaguely alluded to, are
Laguna and Raine, which would make Ellone his adopted
sister. (He called her "Sis" in the orphanage either way).
During his escapades as a SeeD, he slowly falls for his
first employer, Rinoa. His weapon of choice is a gunblade -
not the most realistic of weapons, but definitely one of
the coolest. He was supposedly called Squall because he was
supposed to remind you of a passing storm, something that
doesn't get very close up. "Leonhart" is supposedly reused
from Leon, one of the heros from 2, although it's also a
reference to his symbol, Griever. (See also External Crossovers:Kingdom
Hearts, (See also Jobs:Fighter)
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- Ultimecia [VILLAIN]
- We don't hear much about this very evil person except
the fact that she wants to destroy the universe. Truth is,
she was kind of tacked on as an afterthought - we don't
even get to meet her until it's time to kill her. She does
have a weird accent. She takes over Edea and Rinoa in the
course of the game while trying to accomplish her
goals.
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- Ward Zabac [GUEST]
- The third member of Laguna's group, Ward walks heavily
and speaks very little - in fact, nothing at all, after he
loses his voice in a battle with Esthar soldiers. However,
you can always tell what he's thinking by the expression on
his face. He can still do heavy damage with his anchor-like
spear, though. (See also Jobs:Ward)
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- Watts
- Kind of a cheesy gopher working for Rinoa, his job is
gathering information and getting chased by people.
-
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- Wedge
- Private Wedge of Galbadia at your service. A loserly
little dude who always follows instructions and is just
there for comic relief.
-
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- Xu
- Xu's Quistis's friend and another SeeD instructor.
She's also great at the Triple Triad card game. She's
always there for ya in a crisis. (If we're following the
Chinese pronunciation, it should be pronounced "shoe".)
 So full of energy he's sometimes slightly crazed,
this youthful martial arts master somehow fails to endear
himself to anyone around him besides for an unnamed
pigtailed girl. His enormous affinity for the Balamb Garden
hot dogs is only coupled with the complete inability to get
any due to their demand. A resident of Balamb (he lives
there with his mother, who actually adopted him), he joined
the Garden at 13 but still, it seems, hasn't attained
maturity. He attended the Kramers' orphanage as a child.
(See also Jobs:Monk)
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- Zone
- The third piece of Rinoa's rebel faction, the Forest
Owls, who tends to get major stomachaches whenever real
action has to happen. He also has an affinity for girlie
mags.
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Final Fantasy, all games and animation bearing the Final Fantasy name, and all characters in said games or animation are copyright their respective creators, including but not limited to Squaresoft, Square Enix, Square EA, Tokyo TV, and ADV Films.


class: center, middle, inverse, title-slide # Introduction to Linux for Bioinformatics ##
Talk is cheap. Show me the code.
### Lijia Yu @ NCCL in China ### 2019/06/17
(updated: 2020-10-03) --- # Agenda 1. Login to RStudio Server 2. UNIX file system 3. Command line + operations on files 4. FASTA and FASTQ --- # Login to RStudio Server 1. open broswer link: <IP_ADDRESS>:8787 ![](./2019-06-17-Introduction_to_Linux_for_Bioinformatics_files/figure/RStudio.png) --- | RStudio Windows / Tabs | Location | Description | |---------------------------|-------------|--------------------------------------------------------------| | **Console & Terminal Window** | lower-left | location were commands are entered and the output is printed | | **Source Tabs** | upper-left | built-in text editor | | Environment Tab | upper-right | interactive list of loaded R objects | | History Tab | upper-right | list of key strokes entered into the Console | | **Files Tab** | lower-right | file explorer to navigate C drive folders | | Plots Tab | lower-right | output location for plots | | Packages Tab | lower-right | list of installed packages | | Help Tab | lower-right | output location for help commands and help search window | | Viewer Tab | lower-right | advanced tab for local web content | --- # UNIX file system ![](./2019-06-17-Introduction_to_Linux_for_Bioinformatics_files/figure/UnixFileSystem.png) .footnote[ [1] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # UNIX file system ## ls `ls` is a command to list computer files in Unix and Unix-like operating systems. ```bash ls /home/admin ``` ![](./2019-06-17-Introduction_to_Linux_for_Bioinformatics_files/figure/ls.png) --- # UNIX file system: files and extensions - For some operating systems, file extensions are important and define the file type. In e.g. Windows files have a three/four letter extension(e.g. .jpg, .exe, .docx, …) -- - In UNIX file extensions are arbitrary (no particular sense), at least for the operating system. A file can have several extensions and will be recognized by the file permissions and content. -- - Popular file extensions in bioinformatics: - scripts - .sh (shell/bash) - .pl (perl) - .py (python) - .r (R) - data - .txt (text) - .csv/.tsv (tabular) - .fasta/.fastq (sequence files) .footnote[ [1] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # UNIX file system: users and access rights Every file and directory is protected. A set of permissions determines who can access a certain file and what kind of access is allowed. - User: the user who owns the file - Group: other users from the same group - Others: all others in the system - Read: display the file - Write: display and modify the content of the file - Execute: run a file ( only for scripts and compiled programs) .footnote[ [1] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # UNIX file system: users and groups ```bash ls -a ``` print a list of all files and directories (incl. hidden files). Hidden files can be recognized by ‘.’ at the start of the name, ‘..’ is the parent directory ``` [root@nccl /home/lirui]$ ls -a . .. .bash_logout .bash_profile .bashrc ``` ![](./2019-06-17-Introduction_to_Linux_for_Bioinformatics_files/figure/ls-a.png) .footnote[ [1] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # UNIX file system: users and groups ```bash ls -l /usr/bin/gpg ``` ``` lrwxrwxrwx 1 root root 4 Feb 18 11:03 /usr/bin/gpg -> gpg2 ``` - file permissions, - number of hard links, - owner name, - owner group, - file size, - time of last modification, and file/directory name .footnote[ [1] [What do the fields in ls -al output mean? ](https://unix.stackexchange.com/questions/103114/what-do-the-fields-in-ls-al-output-mean) ] --- # UNIX file system: users and groups File permissions is displayed as following; ![](./2019-06-17-Introduction_to_Linux_for_Bioinformatics_files/figure/access_right.png) - r = readable - w = writable - x = executable .footnote[ [1] [What do the fields in ls -al output mean? ](https://unix.stackexchange.com/questions/103114/what-do-the-fields-in-ls-al-output-mean) [2] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # UNIX file system: file permission An example -rwxrw-r--, this means the line displayed is: -- - a regular file (displayed as -) -- - readable, writable and executable by owner (rwx) -- - readable, writable, but not executable by group (rw-) -- - readable but not writable or executable by other (r--) .footnote[ [1] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # UNIX file system When entering a command you can use a wildcard character, this is used a substitute for one or many other characters. They are often used with file and directory name and filesystem commands. - `*` Match any number of characters - `?` Match one character - `[]` specify a range of characters on that position - `{}` specify a list of terms - separated by commas - `!` Exclude this range of characters .footnote[ [1] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # UNIX file system How many files will you find using the following command: - `ls -l *.c` - `ls -l bam*` - `ls -l samtools.?` - `ls -l *.*[!a]` - `ls -l {*.c,*.h}` - `ls -l version.[a-z]h` .footnote[ [1] [Linux for bioinformatics ](https://data.bits.vib.be/pub/trainingen/Linux/Linux_01_2018.pdf) ] --- # Command line + operations on files ## command pattern ```bash ls --help ``` ``` Usage: ls [OPTION]... [FILE]... ``` ```bash R --help ``` ``` Usage: R [options] [< infile] [> outfile] or: R CMD command [arguments] Start R, a system for statistical computation and graphics, with the specified options, or invoke an R tool via the 'R CMD' interface. Options: -h, --help Print short help message and exit --version Print version info and exit --encoding=ENC Specify encoding to be used for stdin --encoding ENC ``` --- # Command line: pwd, cd - ```bash pwd ``` print working directory ``` [root@nccl /home/lirui]$ pwd /home/lirui ``` - ```bash cd ``` change directory ```bash cd /tmp cd ./tmp cd ../tmp cd ~ ``` --- # Command line: cp, rm - ```bash cp /tmp/abc.txt /tmp/yulijia.txt cp -r /tmp/yulijia /tmp/yourname ``` Copy one file or all files in a directory - ```bash rm /tmp/yulijia.txt rm -r /tmp/yulijia ``` To remove objects such as files, directories, device nodes, symbolic links, and so on from the filesystem. --- # Command line: rm .center[![](https://i.pinimg.com/236x/99/32/b1/9932b1cebca00d51d1b6474215252bf5.jpg)] -- .center[**NERVER use `rm -f` !**] --- # Command line: less, cat, head, tail - ```bash less /home/admin/database/reference/human/hg19/chr1.fa ``` View the contents of a text file one screen at a time. It is similar to `more`, but has the extended capability of allowing both forward and backward navigation through the file. - ```bash cat /home/admin/database/reference/human/hg19/chr1.fa ``` Writing context to standard output. - ```bash head /home/admin/database/reference/human/hg19/chr1.fa ``` Display the beginning of a text file or piped data. - ```bash tail /home/admin/database/reference/human/hg19/chr1.fa ``` Display the tail end of a text file or piped data. ---   <!-- less /home/yulijia/.bashrc --> <!-- ``` -->      <!-- vim --> <!-- ``` -->   <!-- vim /home/yulijia/.bashrc --> <!-- ``` -->               <!-- vim /home/yulijia/.bashrc --> <!-- ``` -->    <!-- alias rm='trash-put' --> <!-- ```` -->   --- # Command line: chmod - ```bash chmod ``` modify access rights ```bash chmod 755 /tmp/zyx.txt chmod 600 /tmp/zyx.txt ``` | # | Permission | rwx | Binary | |---|-------------------------|-----|--------| | 7 | read, write and execute | rwx | 111 | | 6 | read and write | rw- | 110 | | 5 | read and execute | r-x | 101 | | 4 | read only | r-- | 100 | | 3 | write and execute | -wx | 011 | | 2 | write only | -w- | 010 | | 1 | execute only | --x | 001 | | 0 | none | --- | 000 | --- # Command line: mkdir, mv - ```bash mkdir /home/yulijia/project1 ``` make a new directory - ```bash #cp /tmp/abc.fasta /home/yulijia/project1 #cd /home/yulijia/project1/ #ls mv /tmp/yourname.txt /home/yourname/yourname.txt mv abc.fasta <Gene Official Symbol>.fasta ``` moves one or more files or directories from one place to another. --- # FASTA format In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. ```bash >SEQUENCE_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL >SEQUENCE_2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH >P01013 GENE X PROTEIN (OVALBUMIN-RELATED) QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP FLFLIKHNPTNTIVYFGRYWSP ``` .footnote[ [1] [FASTA format used in blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp) ] --- # FASTQ format A FASTQ file normally uses four lines per sequence. - Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line). - Line 2 is the raw sequence letters. A,T,C,G,N. - Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again. - Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence. A FASTQ file containing a single sequence might look like this: ```bash @SEQ_ID GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT + !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 ``` --- # FASTQ format ## Illumina sequence identifiers **@HWUSI-EAS100R:6:73:941:1973#0/1** | Name | Meaning| |---------------|---------------------------------------------------------------------| | HWUSI-EAS100R | the unique instrument name | | 6 | flowcell lane | | 73 | tile number within the flowcell lane | | 941 | 'x'-coordinate of the cluster within the tile | | 1973 | 'y'-coordinate of the cluster within the tile | | #0 | index number for a multiplexed sample (0 for no indexing) | | /1 | the member of a pair, /1 or /2 (paired-end or mate-pair reads only) | --- # Quality A quality value `Q` is an integer mapping of `P` (i.e., the probability that the corresponding base call is <u>incorrect</u>). Two different equations have been in use. The first is the standard Sanger variant to assess reliability of a base call, otherwise known as Phred quality score: `$$Q_{sanger}=-10log_{10}P$$` `$$Q_{solexa}=-10log_{10}\frac{P}{1-P}$$` --- # Phred Quality Score | Phred Quality Score | Probability of incorrect base call | Base call accuracy | |---------------------|------------------------------------|--------------------| | 10 | 1 in 10 | 90% | | 20 | 1 in 100 | 99% | | 30 | 1 in 1000 | 99.9% | | 40 | 1 in 10,000 | 99.99% | | 50 | 1 in 100,000 | 99.999% | | 60 | 1 in 1,000,000 | 99.9999% | --- # Encoding ![](./2019-06-17-Introduction_to_Linux_for_Bioinformatics_files/figure/Phred.png) --- # Command line: passwd ## Change your password ```bash passwd ``` ``` [yulijia@nccl ~/]$ passwd Changing password for user yulijia. Changing password for yulijia. (current) UNIX password: New password: Retype new password: password updated successfully ``` --- # Quitz 1.What is the meaning of these command? ```bash ls -lh ls -lt ls -R ``` --- # Quiz 2.Try to edit your fasta file, change the sequence name from `>X54156|Homo sapiens p53` to `>TP53|tumor protein p53` --- # Resource [1] [Introduction to Linux for bioinformatics](https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/124-linux-for-bioinformatics) [2] [An introduction to Linux for bioinformatics](https://sites.ualberta.ca/~stothard/downloads/linux_for_bioinformatics.pdf) .footnote[ * All pictures without footnote are getting from Wikipedia or browser snapshots. ]


LIFE IS BEAUTIFUL (LA VITA E BELLA) A movie review by Joe Barlow (c) Copyright 1999
STARRING: Roberto Benigni, Nicoletta Braschi, Giorgio Cantarini, Horst Buchholz, Sergio Bustric DIRECTOR: Roberto Benigni WRITERS: Roberto Benigni and Vincenzo Cerami RATED: PG-13 RELEASED: 1997 (1988 in the USA, subtitled)
RATING: **** (out of a possible ****)
Roberto Benigni's "Life is Beautiful" is the sort of film which exemplifies the power of cinema: it's art without pretension, hope without fear, dreams without restrictions. Although it has been criticized as a sanitization of the Holocaust, the movie pulls no emotional punches; by sharing the hardships and joy of the characters, we are reminded just how precious and remarkable the human spirit is.
It's 1939 Italy, and Guido Orefice (Benigni) is a pleasant, amiable waiter who works in a restaurant owned by his uncle. Clever and impulsive, Guido uses humor as an ally while serving his customers, making him well-liked, especially by Dr. Lessing (Horst Buchholz), a German who shares Guido's fondness for puns and riddles. Their relationship is particularly intriguing, as Guido is Jewish.
When a chance meeting with the lovely Dora (Nicoletta Braschi, Benigni's real-life spouse) sets his heart aflutter, Guido goes to great lengths to win her love, despite her engagement to a snooty government official. Their mutual affection gradually deepens into something more, culminating in a wonderful scene in which Guido disrupts Dora's engagement party to whisk her away on horseback. It's here that a more conventional film would end... but there's nothing conventional about "Life is Beautiful," and this scene occurs less than halfway through the story.
Flash forward six years to 1945: Guido and Dora are happily married, and are now parents to a five-year old son named Giosue' (Giorgio Cantarini). Fortune has been good to them: Guido even owns the bookstore he's always wanted! But Guido's Jewish heritage is discovered by a facist-filled government, and he and his son are sent to an unidentified concentration camp. Dora, a Gentile, is not required to attend the camp, but she demands to go with her family; her devotion to her husband and child is that selfless.
Young Giosue' is frightened, but it's here that Guido gives his greatest performance, convincing his son that they are embarking on a grand adventure, an epic game that will be exciting and fun. (The prize for winning the game? A full-size tank!) Guido knows that the Nazi officers who run the camp are looking for reasons to dispose of the prisoners, so he tells Giosue' that he (Giosue') can win extra points for hiding, remaining silent for long periods of time, etc. These are poignant scenes, as father and son rekindle each other's enthusiasm and optimism (Dora is in a different part of the segregated camp). Although the other children in the camp are gradually disappearing into the camp's gas chambers, Guido uses humor to keep his son oblivious to their fate, sparing Giosue' from the emotional agony and sense of helplessness that he himself is feeling.
The structure of "Life is Beautiful" is somewhat like Robert Rodriguez's "From Dusk Til Dawn," in the sense that each half of the film has a completely different tone, joined together by a startlingly abrupt transition. It's ingenious and effective: both halves of the movie are masterfully constructed, but as different as night and day. The warm, sunny first half establishes these wonderful characters and their relationships; we see Guido's remarkable personality in full-swing, and witness the passion and joy he derives from simple, ordinary activities. These early moments also set up his fairy-tale love affair with Dora (Guido refers to her as his "princess" throughout the story), and their devotion to each other is made clear-- we understand why she is willing to follow Guido to a concentration camp. The story's second half, by contrast, uses their love as a foundation on which to build triumph and tragedy. The construction is as elegant as any I've encoutered.
It's impossible not to like Benigni's warm portrayl of Guido, the sort of clown who inspires laughter as much by accident as deliberate effort; his mannerisms are so broad and cartoonish that comparisons with Chaplin are justified. Benigni, who not only starred but also directed and co-wrote the screenplay, has a masterful sense of comedic timing. The material flows effortlessly through him, lending both spontaneity to the gags and power to the drama.
Benigni doesn't skimp on the humor, despite the subject matter; even during the horrific scenes inside the camp, Guido is full of life and optimism-- a veritable beacon of hope and sunshine for his fellow prisoners and, most importantly, his son. There are those who have called the film "offensive" because of the way it handles its Holocaust-related material. They are mistaken: this movie isn't *about* the Holocaust; it's about humanity, love, and the desperate facade one man must invent to spare mental anguish for his son while suffering *through* the Holocaust.
There are perhaps ten genuine laugh-out-loud moments in "Life is Beautiful," sprinkled in among the tragedy; like the characters in the film, Guido's antics make the despair bearable for us, right up to the movie's final moments, which involve the triumph of the human spirit over the unimaginable forces of adversity. The film soars, heartens, saddens, uplifts, rejoices... and, like life, is beautiful indeed.
(NOTE: I have updated my "Best of '98" list to include this film. -J.)
E-Mail<EMAIL_ADDRESS>Joe Barlow on Film: http://www.ipass.net/~jbarlow/film.htm
If you'd like to receive new film reviews by e-mail, please write to the above address and ask to be put on my mailing list. Or, you can subscribe directly from my web page.
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Google Earth Enterprise Documentation Home | Google Earth Enterprise client
Clearing the Google Earth EC cache
If you have signed in to a database on GEE Server with Google Earth EC previously, you may be unable to sign in again to the same database. An effective way of resolving this issue is to sign out of your server, clear your cache, and log back in.
To clear your cache (On Windows and Linux):
- Select File > Server Sign Out.
- Select Tools > Options > Cache.
- Select Delete cache file (only when logged out).
To clear your cache (On Mac OS X):
- Select File > Server Sign Out.
- Select Google Earth EC > Preferences > Cache.
- Select Delete cache file (only when logged out).


About Me
Devolper & Designer
Hello,My name is KHOI. I am a Devolper and also a Designer.If you have any Project or if you want make a software for your business conatact me.I make as soon as possible.You really like my work, if you don’t i change until you like I give you seticfaction result.
I’m a Devolper and also a Designer.If you have any Project or if you want make a software for your bussniess conatact me.I make your project as soon as possible.


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Select your profession
Type in the names of your party:
Amount
Item
Cost
Total
Pounds of tendies
0.20 bitcoin
Ethereum
0.10 bitcoin
$0
You must 500x to reach your goal.
Click 'continue' to try to 10x per day.
Click 'rest' to heal your paid group members.
Click 'airdrop' to gather more tendies.
All actions spend one day, and each group member eats 5 tendies per day.
You must 500x to reach your goal.
Click 'continue' to try to 10x per day.
Click 'rest' to heal your paid group members.
Click 'airdrop' to gather more tendies.
All actions spend one day, and each group member eats 5 tendies per day.
Portfolio progress:
Days elapsed: 0
Distance traveled: 0
Tendies left
Ethereum left
Bitcoin left


One day I was waiting for my friends to get home from school cuz I stayed home, so I was looking around the house for money or anything that will help we buy some drugs. When I looked in the medicine drawer I found wellbutrin pills. I have never seen or done these before that day so I decided to look them up on the internet to see if you can get high off them.
I checked that out and I found out that you can get high off them but I didn't know how much to take, so I started out taking four 300 mg pills. I met up with my friends and nothing happened, besides the weed we smoked I didn't feel anything off the pills. Later that night I got into bed. I laid there looking at the wall in the dark and I started to see shadows that looked like little outlines of people dancing. I thought really nothing of it and I closed my eyes and tryed to sleep. When I opened them again I still saw little shadows moving across my wall, so I looked around my dark room and I see shadows all around....at first I thought it was messed up so I fell to sleep.
When I woke up the next morning I decided I wanted to try those again but earlier so I could feel them in the day time. So when I got to school I took four more 300 mg pills in homeroom. All through the day I was really jittery like I took too much adderall or something. My vision was increased and I felt as if I saw everything going around me 100% clearly. As the day went on I noticed that my hearing also increased and all the colors got brighter. I thought I was pretty sweet actually so I was excited for me to start seeing things again.
When I got to my last class I started to twitch and my hands couldn't stop shaking, so I decided to leave class and walk around. Right when I started to walk around, I knew it was about to kick in. I felt alert and worried as if someone was trying to find me (like hide-n-seek). So I got back home and went with my brothers to go smoke.
When we were done smoking at my friends house I started to hear people talking but I couldn't make out what they were saying so I walked to were I thought I could hear them the best, which was the bathroom. When I got in the voices were gone, but I caught a glimpse of something in the mirror (with lights off/in total darkness) I saw someone sitting on the toilet right behind me, I was freaked out so I turned on the lights and he was gone.
I told my friend and my brother what I saw and I told them to come in the bathroom and I’d tell them what I saw. So we got in and turned off the lights the first time and I saw myself in the mirror and I thought nothing of it, until my face started to shrink inward. I raised my hand to touch my face and I noticed that when I moved my hand to touch my face that my hand didn't move but another hand came out of it, so I had three arms now. The arm that wasn't mine had static (like the static you get from your t.v.) dripping off of it.
I was looking at myself in the mirror for a good hour till we left. The whole day felt like my feet were hanging off a cliff and I was in a really upbeat mood. After like 4 hours I start to feel shity when I was coming off, I puked only once and it wasn't really bad but I just felt like really uncomfortable. We drove home and I thought it was pretty much all worn off by now since the only thing that was wierd was every song I listened to sounded faster then it normaly should have, but I didn't really mind that cuz it sounded pretty tight.
 I layed down and I started to see those dancing shaddow people again so I layed there and watched them dance, but all of a sudden they all formed into one big shaddow that was a guy standing over my bed.  But when I looked in my door way I saw three people standing there so I kept looking around trying to avoid looking at them, so I shut my eyes and tryed to sleep but all I heard was people walking in and out of my room so I decided that I was gunna have to deal with this all night so I started to get used to it.
When I looked in my door way again I saw what I thought was my girlfriend cuz it looked just like her but she would just peer around the corner and then go back behind the wall. It would do that over and over and over....all I saw was her head peering around the corner so I didn't care about that too much, until I saw three people hanging from my ceiling...that pretty much fucked up the whole night. I just layed there looking at the thing peering around the corner and the dancing shaddows for the rest of the night until I fell asleep.
For the past week I was really shakey and jittery, but nothing too bad.
Experience Reports are the writings and opinions of the individual authors who submit them.
Some of the activities described are dangerous and/or illegal and none are recommended by Erowid.


| Name | CRN | Type | Status |
| X Pvt Limited | PV1234 | Private | Active |
| XY Pvt Limited | PV1234 | Private | Liquidated |
| Detected Word | Suggessions |
| Lanka | Need to provide G letter requesting to use restricted words |
| Detected Word | Suggessions |
| Bank |
| Violation Type | Supporting documents | Availablitiy |
| Restricted words | Consent letter to proceed | |
| Special Approval | CBSL approval letter |


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| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
| SUMMARY: FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
Object | +--MLA.<events>
Events are captured in the Word application and information is passed to MarkLogicContentControlSupport.js. To insure framework code is not tightly coupled with application code, developers should define their custom content control event handler functions in a separate .js file and call from MarkLogicContentControlSupport.js.
Following events captured:
contentControlAfterAdd()
contentControlBeforeContentUpdate()
contentControlBeforeDelete()
contentControlBeforeStoreUpdate()
contentControlOnEnter()
contentControlOnExit()
| Event Detail |
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| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
| SUMMARY: FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |


at the Mariners Museum Park & Noland Trail
The Mariners' Museum Park is 550 acres of privately maintained, naturally wooded property that offers visitors a quiet and serene place to walk, run, or picnic. Within the park is the 167 acre Lake Maury, named for the famed 19th century oceanographer and native Virginia, Matthew Fontaine Maury. Following the shoreline of Lake Maury is the five mile Noland Trail. Dedicated as a gift from the Noland family in 1991 and with significant ongoing financial support from the Noland family. The trail has fourteen bridges, picnic areas, benches, handicap access, and mile markers. The Mariners' Museum Park is open daily to the public. Benches at approximately every half-mile offer places of rest along the trail, and views of Lake Maury can be found around every corner.


{% include 'header.html' %}
{% include 'nav.html' %}
Upload Manifest
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skip to main content
Test case: DefinitionLists-invalid.html
Definition Lists Tests
- Test #1 - Invalid definition list - no "dd" elements
- Test #2 - Invalid definition list - no "dt" elements
- Test #3 - Invalid definition list - no "dl" elements
- Test #4 - Invalid definition list - no "dl" or "dd" elements
- Test #5 - Invalid definition list - no "dl" or "dt" elements
- Person 1
- Person 2
- father
- coach
- Person 1
- test team lead
Person 1
test team lead
Person 2
test team member
- Person 1
- test team lead
Person 1
Person 2
- Person 1
- test team lead
test team lead
test team member


Manage your home finances with an easy web app.
Wealthy Laughing Duck is a simple logic model that can be adapted by various applications and platforms. It's supposed to be a personal finance managing system. All duck components are just implementations of this model, e.g. web interface implemented with JavaScript, Java Thrift server / PHP Thrift client, python RESTful API (consumed by JavaScript interface) and so on.
Most of duck components are in early development phase so far, but the aim is to make them mature, stable systems that would rely on different technologies used. Developers would clone and easily deploy github repositories and examine the implementation to learn the technologies.
This is more than welcome :) The more contributions and group members there are, the more the duck project will improve. If you wish to make some commits to existing repositories - or even create your own repository that illustrates a technology that's not present in the duck project yet - just contact the @wealthy-laughing-duck.
wealthy laughing duck (original project):
As each duck component relies on the same logic model, different systems should be able to access the same resources, such as: databases, files, file formats, api designs, etc. To ease components communication with each other, some standards were introduced:
mysql
localhost
3306
duck_user
duck_database
wXyqhWzlF0uO20j8
Duck components will connect the database according to above parameters by default.
Those will include: database schema, thrift definitions, JSON api design, file formats.


--- layout: post title: Magic screen and input sharing date: '2010-01-18T00:00:00+01:00' tags: - software ---
I happen to sometimes use more than one computer terminal at once. While I am compiling something on my Linux box I can be playing World of Warcraft on my Mac.
You can actually setup your multi-computer environment without a hardware KVM.
The software allowing you to do that is called Synergy and is available for Windows, Linux and Mac.


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Throw it to the recycle bin?
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Class: ActionCommand::Executable
- Inherits:
-
Object
- Object
- ActionCommand::Executable
- Defined in:
- lib/action_command/executable.rb
Overview
Root class for action commands that can be executed by this library. Override execute_internal to implement one, call one of the variants of ActionCommand.execute_… to execute one.
Direct Known Subclasses
Instance Attribute Summary (collapse)
-
- (Object) parent
Returns the value of attribute parent.
-
- (Object) test
Returns the value of attribute test.
Instance Method Summary (collapse)
-
- (Boolean) api_context?
True if this command was executed using ActionCommand.execute_api.
-
- (Boolean) child_context?
True if this command is a child of another command.
-
- (ActionCommand::Result) execute(result)
Execute the logic of a command.
-
- (Object) execute_internal(result)
Override this method to implement the logic of your command.
-
- (Executable) initialize(args)
constructor
Do not call new directly, instead use ActionCommand#execute_…
-
- (Boolean) rails_context?
True if this command was executed using ActionCommand.execute_rails.
-
- (Boolean) rake_context?
True if this command was executed using ActionCommand.execute_rake.
-
- (Symbol) root_context
action was executed in, see the ActionCommand::CONTEXT_ constants.
-
- (Boolean) test_context?
True if this command was executed using ActionCommand.execute_test.
-
- (Object) testing {|context| ... }
Call this within a commands execution if you'd like to perform validations within the testing context.
Constructor Details
- (Executable) initialize(args)
Do not call new directly, instead use ActionCommand#execute_… variants.
11 12 13 |
# File 'lib/action_command/executable.rb', line 11 def initialize(args) self.class.describe_io.process_input(self, args) end |
Instance Attribute Details
- (Object) parent
Returns the value of attribute parent
8 9 10 |
# File 'lib/action_command/executable.rb', line 8 def parent @parent end |
- (Object) test
Returns the value of attribute test
8 9 10 |
# File 'lib/action_command/executable.rb', line 8 def test @test end |
Instance Method Details
- (Boolean) api_context?
Returns true if this command was executed using ActionCommand.execute_api
39 40 41 |
# File 'lib/action_command/executable.rb', line 39 def api_context? return root_context == ActionCommand::CONTEXT_API end |
- (Boolean) child_context?
Returns true if this command is a child of another command
45 46 47 |
# File 'lib/action_command/executable.rb', line 45 def child_context? return !parent.is_a?(Symbol) end |
- (ActionCommand::Result) execute(result)
Execute the logic of a command. Should not usually be called directly. Command executors should call one of the ActionCommand.execute_… variants. Command implementors should override execute_internal.
54 55 56 57 58 |
# File 'lib/action_command/executable.rb', line 54 def execute(result) execute_internal(result) self.class.describe_io.process_output(self, result) return result end |
- (Object) execute_internal(result)
Override this method to implement the logic of your command
75 76 77 |
# File 'lib/action_command/executable.rb', line 75 def execute_internal(result) end |
- (Boolean) rails_context?
Returns true if this command was executed using ActionCommand.execute_rails
29 30 31 |
# File 'lib/action_command/executable.rb', line 29 def rails_context? return root_context == ActionCommand::CONTEXT_RAILS end |
- (Boolean) rake_context?
Returns true if this command was executed using ActionCommand.execute_rake
34 35 36 |
# File 'lib/action_command/executable.rb', line 34 def rake_context? return root_context == ActionCommand::CONTEXT_RAKE end |
- (Symbol) root_context
action was executed in, see the ActionCommand::CONTEXT_ constants.
17 18 19 20 21 |
# File 'lib/action_command/executable.rb', line 17 def root_context context = parent context = context.parent until context.is_a? Symbol return context end |
- (Boolean) test_context?
Returns true if this command was executed using ActionCommand.execute_test
24 25 26 |
# File 'lib/action_command/executable.rb', line 24 def test_context? return root_context == ActionCommand::CONTEXT_TEST end |
- (Object) testing {|context| ... }
Call this within a commands execution if you'd like to perform validations within the testing context.
64 65 66 |
# File 'lib/action_command/executable.rb', line 64 def testing yield @test if @test end |


Hackathon teams can register here .Please go through the Hackathon Rules before you register. Individual Entries are not accepted.register
Navigate to the Catalog and select your preferred language from the available Runtimes. Give the app a unique host to serve as it's URL. Deploy. Just want a service? Skip this step and just create the service from the catalog.
Select ADD A SERVICE to add one of the services from the Catalog. When the app asks for a RESTAGE, accept the restage. Select the service's tile and then Service Credentials to view API connection information.
Got a question? These are the people to ask.


Environmental groups have warned that the first step by the Obama administration to curb rapidly rising carbon pollution from airplanes, expected as early as Friday, may amount to little more than greenwashing.
The announcement from the Environmental Protection Agency is eight years in the making and
comes in response to lawsuits from environmental groups, and a
failed effort by the European Union to tackle greenhouse gas emissions from aircraft,
one of the fastest growing sources of carbon emissions.
With Friday’s expected announcement, the EPA will extend regulation of carbon pollution from
power plants, cars and trucks, to air planes.
The move puts the EPA on pace with the International Civil Aviation Organisation in setting
global rules for carbon pollution. But those rules, due to be adopted in February 2016, are
unlikely to deliver any significant reductions in carbon pollution, environmental groups
said.
“It’s not a particularly ambitious action,” said Sarah Burt, a lawyer for Earthjustice which first sued the
EPA in 2007 on behalf of the Center for Biological Diversity, Friends of the Earth, and the
Natural Resources Defense Council and other groups. “You will get a standard that is not at
all ambitious at best and at worst is essentially greenwashing.”
The EPA and the White House would not comment on the announcement in advance.
The first step of the EPA process begins unfolding on Friday when the agency will formally
declare its intent to begin regulating greenhouse gas emissions from airplane
pollution.
The airline industry had fought for years to delay just such a measure – and in 2012
forced the EU to back down on its plans of cutting greenhouse gas emissions on international
flights.
Obama at the time had sided
with the airline industry in its refusal to fall into line with the EU plan.
The new ICAO targets in some ways represent a victory for that stonewalling – buying the
airlines time and weakening the rules. The international air authority had struggled for 20
years to deal with climate change.
“The EPA has dragged its heels and delayed with its eyes on the international negotiations,”
Burt said. “The EPA does not want to go out ahead of the international community.”
The international rules are expected to be exceedingly weak, with virtually all of the
airplanes flying today making the grade, which means ICAO is unlikely to deliver any real
reductions on greenhouse gas emissions.
“It is a CO2 standard but everyone already meets the standard so it results not only in no
decrease, but also in a net increase when you see how emissions stand,” Burt said.
Carbon pollution from airplanes is expected to double by 2020. US airline carriers on their own account for about a quarter of global aviation emissions. A number of developing countries, such as India, are expected to see big increases in air travel over the coming decades.


The Great Outdoors
Sleep
Blast off into a world of dreams
Paw Trails
A podcast about animal health & pet ownership.
New Episodes Every Tuesday


Select this option to convert any Java code to Kotlin on paste. IntelliJ IDEA displays the Convert Code from Java dialog. If you don't want IntelliJ IDEA to show the dialog, select the Don't show Java to Kotlin conversion dialog on paste option.


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JS Documentation
Introduction
What you should already know
JavaScript and Java
Hello world
Variables
Declaring variables
Variable scope
Global variables
Constants
Data types
if...else statement
while statement
Function declarations
Reference


{% comment %} TODO This entire file is currently commented out. The content below is the snippet from the designer. With the exception of the "search within results" form, we have all the functionality in some form in the site right now, mostly in openemory.accounts.views.tagged_items() . For this to work in a dashboard tab, though, the functionality is going to need to be AJAXified. So this tab has been commented out until we get around to making that work.
Items 1-5 of 10000
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads
Version: Post-Print
Type: PDF
Status: In Repository & Public Domain
JOURNAL OF CIVIL RIGHTS ADMINISTRATION | Volume 118, Issue 9, July 17, 2003, Pages 454-999.
10,123 Item Views | 5,456 Downloads


Query Execution
Clicking the Go button on the Routes form triggers the execution of the routeGoButton_Click event handler. This event handler performs the following actions:
- Extracts the required parameter values from the Windows Form controls.
- Initializes the DataGridView control that will receive the query results.
- Binds the DataSet to the DataGridView.
- Executes the SELECT query that populates the DataSet.
The results of the query are bound to the DataGridView, and then displayed.
More Information:
SELECT Statement
© 2006 Actian Corporation.
All rights reserved.


public class SimpleBreadthFirstSearchManager extends TokenSearchManager
recognize
until Result.isFinal() returns true. Once a final result has
been obtained, terminate
should be called.
All scores and probabilities are maintained in the log math log domain.
For information about breadth first search please refer to "Spoken Language Processing", X. Huang, PTR
| Modifier and Type | Field and Description |
|---|---|
protected ActiveList |
activeList |
protected ActiveListFactory |
activeListFactory |
protected java.util.Map<SearchState,Token> |
bestTokenMap |
protected long |
currentCollectTime |
protected int |
currentFrameNumber |
protected Timer |
growTimer |
protected Linguist |
linguist |
protected LogMath |
logMath |
static java.lang.String |
PROP_ACTIVE_LIST_FACTORY
The property that defines the name of the active list factory to be used by this search manager.
|
static java.lang.String |
PROP_GROW_SKIP_INTERVAL
The property that controls the number of frames processed for every time the decode growth step is skipped.
|
static java.lang.String |
PROP_LINGUIST
The property that defines the name of the linguist to be used by this search manager.
|
static java.lang.String |
PROP_PRUNER
The property that defines the name of the linguist to be used by this search manager.
|
static java.lang.String |
PROP_RELATIVE_WORD_BEAM_WIDTH
The property that sets the minimum score relative to the maximum score in the word list for pruning.
|
static java.lang.String |
PROP_SCORER
The property that defines the name of the scorer to be used by this search manager.
|
static java.lang.String |
PROP_SHOW_TOKEN_COUNT
The property that when set to
true will cause the recognizer to count up all the tokens in the
active list after every frame. |
static java.lang.String |
PROP_WANT_ENTRY_PRUNING
The property that controls whether or not relative beam pruning will be performed on the entry into a
state.
|
protected java.util.List<Token> |
resultList |
protected boolean |
showTokenCount |
protected boolean |
streamEnd |
buildWordLattice, keepAllTokens, PROP_BUILD_WORD_LATTICE, PROP_KEEP_ALL_TOKENS
| Constructor and Description |
|---|
SimpleBreadthFirstSearchManager() |
SimpleBreadthFirstSearchManager(Linguist linguist,
Pruner pruner,
AcousticScorer scorer,
ActiveListFactory activeListFactory,
boolean showTokenCount,
double relativeWordBeamWidth,
int growSkipInterval,
boolean wantEntryPruning)
Creates a manager for simple search
|
| Modifier and Type | Method and Description |
|---|---|
void |
allocate()
Allocates the resources necessary for this search.
|
protected void |
collectSuccessorTokens(Token token)
Collects the next set of emitting tokens from a token and accumulates them in the active or result lists
|
void |
deallocate()
Deallocates resources necessary for this search.
|
ActiveList |
getActiveList() |
protected Token |
getBestToken(SearchState state)
Gets the best token for this state
|
protected java.util.Map<SearchState,Token> |
getBestTokenMap()
Returns the best token map.
|
int |
getCurrentFrameNumber()
Returns the current frame number.
|
Timer |
getGrowTimer()
Returns the Timer for growing.
|
java.util.List<Token> |
getResultList()
Returns the result list.
|
StatisticsVariable |
getTokensCreated()
Returns the tokensCreated StatisticsVariable.
|
protected void |
growBranches()
Goes through the active list of tokens and expands each token, finding the set of successor tokens until all the
successor tokens are emitting tokens.
|
protected void |
localStart()
Gets the initial grammar node from the linguist and creates a GrammarNodeToken
|
protected void |
localStop()
Local cleanup for this search manager
|
void |
newProperties(PropertySheet ps)
This method is called when this configurable component needs to be reconfigured.
|
protected void |
pruneBranches()
Removes unpromising branches from the active list
|
protected boolean |
recognize()
Performs recognition for one frame.
|
Result |
recognize(int nFrames)
Performs the recognition for the given number of frames.
|
protected boolean |
scoreTokens()
Calculate the acoustic scores for the active list.
|
protected Token |
setBestToken(Token token,
SearchState state)
Sets the best token for a given state
|
protected void |
setBestTokenMap(java.util.Map<SearchState,Token> bestTokenMap)
Sets the best token Map.
|
protected void |
showTokenCount()
Counts all the tokens in the active list (and displays them).
|
void |
startRecognition()
Called at the start of recognition.
|
void |
stopRecognition()
Terminates a recognition
|
java.lang.String |
toString() |
protected ActiveList |
undoLastGrowStep()
Because the growBranches() is called although no data is left after the last speech frame, the ordering of the
active-list might depend on the transition probabilities and (penalty-scores) only.
|
getResultListPredecessor
@S4Component(type=Linguist.class) public static final java.lang.String PROP_LINGUIST
@S4Component(type=Pruner.class) public static final java.lang.String PROP_PRUNER
@S4Component(type=AcousticScorer.class) public static final java.lang.String PROP_SCORER
@S4Component(type=ActiveListFactory.class) public static final java.lang.String PROP_ACTIVE_LIST_FACTORY
@S4Boolean(defaultValue=false) public static final java.lang.String PROP_SHOW_TOKEN_COUNT
true
will cause the recognizer to count up all the tokens in the
active list after every frame.@S4Double(defaultValue=0.0) public static final java.lang.String PROP_RELATIVE_WORD_BEAM_WIDTH
@S4Boolean(defaultValue=false) public static final java.lang.String PROP_WANT_ENTRY_PRUNING
@S4Integer(defaultValue=0) public static final java.lang.String PROP_GROW_SKIP_INTERVAL
protected Linguist linguist
protected int currentFrameNumber
protected long currentCollectTime
protected ActiveList activeList
protected java.util.List<Token> resultList
protected LogMath logMath
protected Timer growTimer
protected boolean showTokenCount
protected java.util.Map<SearchState,Token> bestTokenMap
protected ActiveListFactory activeListFactory
protected boolean streamEnd
public SimpleBreadthFirstSearchManager()
public SimpleBreadthFirstSearchManager(Linguist linguist, Pruner pruner, AcousticScorer scorer, ActiveListFactory activeListFactory, boolean showTokenCount, double relativeWordBeamWidth, int growSkipInterval, boolean wantEntryPruning)
linguist
- linguist to configure search spacepruner
- pruner to prune extra pathsscorer
- scorer to estimate token probabilityactiveListFactory
- factory for list of tokensshowTokenCount
- show count of the tokens during decodingrelativeWordBeamWidth
- relative pruning beam for lookaheadgrowSkipInterval
- interval to skip growth stepwantEntryPruning
- entry pruningpublic void newProperties(PropertySheet ps) throws PropertyException
Configurable
newProperties
in interface Configurable
newProperties
in class TokenSearchManager
ps
- a property sheet holding the new dataPropertyException
- if there is a problem with the properties.public void startRecognition()
public Result recognize(int nFrames)
nFrames
- the number of frames to recognizeprotected ActiveList undoLastGrowStep()
public void stopRecognition()
protected boolean recognize()
true
if recognition is completed.protected void localStart()
protected void localStop()
protected void growBranches()
protected boolean scoreTokens()
true
if there are more frames to score, otherwise, falseprotected void pruneBranches()
protected Token getBestToken(SearchState state)
state
- the state of interestprotected Token setBestToken(Token token, SearchState state)
token
- the best tokenstate
- the statepublic ActiveList getActiveList()
protected void collectSuccessorTokens(Token token)
token
- the token to collect successors fromprotected void showTokenCount()
protected java.util.Map<SearchState,Token> getBestTokenMap()
protected void setBestTokenMap(java.util.Map<SearchState,Token> bestTokenMap)
bestTokenMap
- the new best token Mappublic java.util.List<Token> getResultList()
public int getCurrentFrameNumber()
public Timer getGrowTimer()
public StatisticsVariable getTokensCreated()
public void allocate()
SearchManager
public void deallocate()
SearchManager
public java.lang.String toString()
toString
in class java.lang.Object


Package algorithms.graphs
Class Modularity
- java.lang.Object
-
- algorithms.graphs.Modularity
-
public class Modularity extends java.lang.Object
Newman 2006, "Modularity and community structure in networks" https://arxiv.org/pdf/physics/0602124.pdf modularity is a graph quality function over possible divisions of a network. ... The modularity is, up to a multiplicative constant, the number of edges falling within groups minus the expected number in an equivalent network with edges placed at random. (A precise mathematical formulation is given below.) The modularity can be either positive or negative, with positive values indicating the possible presence of community structure. Thus, one can search for community structure precisely by looking for the divisions of a network that have positive, and preferably large, values of the modularity. on a spectral approximation: maximizing the term involving the leading eigenvalue and completely ignoring all the others turns out to be effective here... ignoring the inconvenient fact that it is not possible to make s perfectly parallel to u1 and go ahead and maximize the term in β1 anyway. Given that we are free to choose the sizes of our two groups of vertices, the greatest value of the coefficient NOTE: a paper with tables summarizing different modularity algorithms for different definitions of communities as disjoint or sharing members is Table 2 on page 5 of https://arxiv.org/pdf/1708.00977.pdfNewman 2006: defines modularity using eignevectors of a characteritic matrix modularity Q = Duch and Arenas 2005 "Community detection in complex networks using extremal optimization" Q = Clauset, Newman, Moore, 2004 Q = Nadakudiki and Newman 2012, "Graph spectra and the detectability of community structure in networks" https://arxiv.org/pdf/1205.1813.pdf
J. Duch and A. Arenas, Community detection in complex networks using extremal optimization. Phys. Rev. E 72, 027104 (2005). A. Clauset, M. E. J. Newman, and C. Moore, Finding community structure in very large networks. Phys. Rev. E 70, 066111 (2004). NOTE: Newman generates random graphs for testing too: https://arxiv.org/pdf/cond-mat/0209450.pdf https://arxiv.org/pdf/cond-mat/0210146.pdf- Author:
- nichole
-
-
Constructor Summary
Constructors Constructor Description Modularity()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
girvanNewman2002(Dendogram.DendogramLayer layer, SimpleLinkedListNode[] originalAdjacencyList, double nEdges)
given the original graph adjacency list, compute the modularity of the graph using the connected components from an iteration of the girvan-newman algorithm for edge betweenness scores.
-
-
-
Method Detail
-
girvanNewman2002
public double girvanNewman2002(Dendogram.DendogramLayer layer, SimpleLinkedListNode[] originalAdjacencyList, double nEdges)
given the original graph adjacency list, compute the modularity of the graph using the connected components from an iteration of the girvan-newman algorithm for edge betweenness scores. Reference: Newman and Girvan 2004, PHYSICAL REVIEW E 69, 026113, "Finding and evaluating community structure in networks" NOTE: If the number of within-community edges is no better than random, we will get Q = 0. value approaching the maximum, Q = 1, indicate strong community structure [50]. values tend to be 0.3 to 0.7 and higher values are rare. NOTE: communities are disjoint sets for Girvan-Newman 2002 and 2004- Parameters:
originalAdjacencyList
-layer
- the results of an iteration of the girvan-newman algorithm followed by use of DisjointForest.connectedComponents to find the disjoint sets of connected nodes.nEdges
- the number of edges in the original graph. presumably the code using this method has calculated it once for the original graph already, to pass in to this method over repeated uses.- Returns:
- the modularity as defined by girvan and newman 2002 and Newman and Girvan 2004.
-
-


My name is Abdulrahman Elsharqawi. Currently, I work as a Software Engineer II at Mozn, a Saudi FinTech company.
I have a strong understanding of HTML, CSS, JavaScript (ES6+), and React. I am also proficient in other web technologies/languages, such as Python, NodeJS, Typescript, Cypress, Jest, WebPack, Tailwind, and React Native. I have a proven track record of delivering high-quality code on time and within budget. I am also a strong advocate for user experience (UX) design principles. I believe that a well-designed user interface can make a significant difference in the success of a web application.
View ResumeFOCAL by Mozn is a suite of products that leverage our powerful AI and machine learning technology to answer the challenges of AML compliance and Fraud Prevention in Emerging Markets.
AlinmaPay is an e-wallet application that allows users to pay for their purchases using their mobile phones. It also allows users to transfer money to other users and pay their bills.
Nana Baqala Helper is an IoT solution that aims to increase the availability of items in the store. It is cheap, compact, and easy to deliver.
Baqala Helper Mobile App React Native application that uses hardware-serial protocol to connect to and control baqala helper devices
AZM is a real-time system that help farmers monitor biometrics for their agriculture products. It also can detect future diseases and soil fertility levels. Proudly, it won the third place in Al-Qasim Hackathon for agricultural technologies
Clima is a weather app written in Swift that uses OpenWeather API to fetch and view weather data for the user
Nana BLE Scanner is a React Native mobile application that uses Bluetooth Low-Energy protocol to connect to Baqala Helper devices and configure them and read their data.
Item Catalog is a blog-like website, where users can add items, modify them, and delete them (All CRUD operations). In this project, I applied all principles I learned in the Full-Stack Nanodegree from Udacity. The project has user authentication, email verification, third-party login, JSON endpoints. The project also was deployed on an Apache server hosted on GCP.
Let's Build Something
Send Email


| {{_enttdetails.psngrtype}} Name | Class | Father Name | Father Mobile | Father Email | Mother Name | Mother Mobile | Mother Email | ||
|---|---|---|---|---|---|---|---|---|---|
| {{row.psngrname}} | {{row.classname}} | {{row.fathername}} | {{row.mobileno1}} | {{row.email1}} | {{row.mothername}} | {{row.mobileno2}} | {{row.email2}} |


About
Come to talk about Code, Tools and Science in a social environment. If you have a problem in one of those areas: bring it along and get help. We also plan to make hands-on sessions where we learn and apply new techniques or tools. You can also find companions to join a professional or fun project.
When and Where
We started this monthly meeting in Würzburg, Germany in 2015. If you have a similar meeting and want to be listed here, or if you want to start a new one at your location just open an issue. Locations:
- Würzburg
- Göttingen
- Griffith University, Brisbane
- Cologne
- Aberystwyth University, Wales, UK
- Potsdam
- Bielefeld
- Hacky hours in Australia
- Tucson, AZ, USA
- DPG-Frühjahrstagungen
- Giessen
Inspiration
This project is inspired by HACKYHOUR@AUCKLAND and the R Study Group.
License
The content of this website is available under CC0. This website uses the hacker template which is also available under CC0.


---
layout: page
title: About code
category: code
---
Code, programming and nerd stuff
I write code all day and have to estimate the effort in projects. My history with economy help me a lot every time I have to set the resources and the plan for the app.


BackupAgent |
class BackupAgent : BackupAgent |
DatabaseHelper |
class DatabaseHelper : SQLiteOpenHelper |
NoteActionManager |
This class parses some of actions that can be done with Notes Such as: ADD, REMOVE, SHOW class NoteActionManager : NoteActionObserverManager |
NoteManager |
Manages Notes and NoteObservers class NoteManager : NoteObserverManager, NoteActionObserver |


Retrieve the dataset service description. This contains information regarding the type of dataset, the services available, and the download options.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | rgis, epscor, elseweb |
| uuid | Dataset identifier | uuid |
None
View the service description for the 2013 Tres Lagunas Post Fire, 10 dataset:
/apps/rgis/datasets/43db7a5d-67ec-4635-aef6-97131bf390cb/services.json
"geoimage" refers to a raster dataset.
The keys referenced by {format} are the list of supported data formats for this dataset.
The keys referenced by {service} are the list of supported OGC services for this dataset (wms, wcs, or wfs).
The keys referenced by {format} are the list of supported documentation formats for the standard.
The keys referenced by {standard} are the list of supported documentation standards for this dataset.
The keys referenced by {standard} are the list of supported documentation standards for this dataset. In most cases, this key will be "all" to indicate that the modifications made to the source documentation are reflected in all documentation representations.
Unless otherwise noted, vector datasets generated by the GSToRE platform are in WGS84 (EPSG:4326). The EPSG code referenced here refers only to the source data (the ZIP format).
This service will be deprecated shortly.
Response for a raster dataset:
{ "downloads": [{"tif": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/treslagunasfire2013_1.original.tif"}], "lastupdate": "20140325", "uuid": "233adca8-5131-4ca1-aac1-669f6be4c530", "taxonomy": "geoimage", "description": "2013 Tres Lagunas Post Fire, 1", "metadata": [ {"FGDC-STD-012-2002": { "xml": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/metadata/FGDC-STD-012-2002.xml", "html": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/metadata/FGDC-STD-012-2002.html" }}, {"ISO-19115:2003": { "xml": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/metadata/ISO-19115:2003.xml", "html": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/metadata/ISO-19115:2003.html" }}, { "ISO-19119:WMS": {"xml": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/metadata/ISO-19119:WMS.xml"}, "ISO-19119:WCS": {"xml": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/metadata/ISO-19119:WCS.xml"} } ], "metadata-modified": {"all": "2014-03-26T03:56:16Z"}, "spatial": { "epsg": 26913, "bbox": [ -105.719133333, 35.7587972222, -105.697138889, 35.7738111111 ] }, "services": [ {"wms": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/services/ogc/wms?SERVICE=wms&REQUEST=GetCapabilities&VERSION=1.1.1"}, {"wcs": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/services/ogc/wcs?SERVICE=wcs&REQUEST=GetCapabilities&VERSION=1.1.2"} ], "preview": "http://gstore.unm.edu/apps/epscor/datasets/233adca8-5131-4ca1-aac1-669f6be4c530/mapper", "type": "dataset", "id": 367375, "categories": [{ "subtheme": "2013 Wildfire Data", "theme": "Digital Orthophotography", "groupname": "Tres Lagunas - Post Fire" }], "name": "treslagunasfire2013_1" }
This request is only available for vector and table datasets and is limited to text-based outputs, for example CSV or KML.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | rgis, epscor, elseweb |
| uuid | Dataset identifier | uuid | |
| ext | Data format | string | CSV, JSON, GeoJSON, KML, GML |
Coming soon.
Stream the RGIS dataset SCAN Alcalde, NM (Mar, 2014) as a KML file:
/apps/rgis/datasets/b6b22969-dfa9-41e5-a836-c483b099c8f7/dataset.kml
The structure of the response depends on the format requested, the filters of the request and the structure of the dataset.
Some datasets are hosted on external sites or, if the format is "html", are external sites. In those instances, the request redirects you to the external location. The options available through the query parameters are not available for those datasets, nor are any GSToRE-generated documentation files included with the response.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | rgis, epscor, elseweb |
| uuid | Dataset identifier | uuid | |
| basename | Dataset name | string | |
| set | string | original or derived | |
| ext | Data format | string | any supported format for the dataset |
| Parameter | Description | Type | Options | Required |
|---|---|---|---|---|
| ignore-cache | Generate a new download | boolean | F (defaults to False) | |
| standard | Specify a specific documentation standard to be included in the zip file. | string | F (defaults to the preferred metadata standard of the application specified) |
Download the zip file for the GeoTIFF for AZ Barth Well, US Topo 2011 dataset:
/apps/rgis/datasets/bb5350f9-64ba-4198-8274-eb11f3813955/AZ_Barth_Well_20111125_TM_geo.original.tif
Download the zip file for the GSToRE-generated KML for NM Gross Receipts January - June 2011 dataset:
/apps/rgis/datasets/0acbf4fd-d2ab-4216-9c48-803418166003/nmgrossreceipts_jan_jun2011.derived.kml
The structure of the response depends on the format requested, the filters of the request and the structure of the dataset.
Download the documentation for the specified dataset.
GSTORE includes support for FGDC-STD-001-1998 (file or vector) or FGDC-STD-012-2002 (raster), ISO-19115:2003, ISO-19119, and ISO-19110 standards. ISO-19119 is only available for those datasets with web services; ISO-19110 only for vector or tabular datasets. Check the dataset service description for the complete listing of metadata options for a dataset.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | rgis, epscor, elseweb |
| uuid | Dataset identifier | uuid | |
| standard | Documentation standard | string | any supported documentation standard |
| ext | Documentation format | string | xml or html (not all formats available for all standards) |
None
Download the zip file for the GeoTIFF for AZ Barth Well, US Topo 2011 dataset:
/apps/rgis/datasets/bb5350f9-64ba-4198-8274-eb11f3813955/AZ_Barth_Well_20111125_TM_geo.original.tif
Download the zip file for the GSToRE-generated KML for NM Gross Receipts January - June 2011 dataset:
/apps/rgis/datasets/0acbf4fd-d2ab-4216-9c48-803418166003/nmgrossreceipts_jan_jun2011.derived.kml
The structure of the response varies by standard and format.
Basic data preview HTML.
Note: this functionality will be deprecated soon. Please take advantage of the OGC Services and other streaming data services in any future development.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | rgis, epscor, elseweb |
| uuid | Dataset identifier | uuid |
None
View the HTML response for the 2013 Jaroso Post Fire Imagery, 32 raster dataset:
/apps/rgis/datasets/43db7a5d-67ec-4635-aef6-97131bf390cb/mapper
The request returns an HTML page containing a basic map preview and dataset information.
Get the attribute definitions for a vector or tabular dataset.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | rgis, epscor, elseweb |
| uuid | Dataset identifier | uuid | |
| ext | format | string | json, kml |
None
View the JSON response for the SNOTEL Chamita, NM (Mar, 2014) vector dataset:
/apps/rgis/datasets/2730123d-070c-45ee-8d8d-b5e4df135faf/attributes.json
{ "total": 19, "results": [ { "datatype": "int", "description": "NRCS Internal Site Number", "original_name": "Site Id", "uuid": "aeb97c0a-3c43-4abb-8837-c8f7e1a6f3a8", "name": "site_id" }, { "datatype": "string", "description": "Date", "original_name": "Date", "uuid": "c9746566-2942-4357-9b34-a1891eb7eff3", "name": "date" }, { "datatype": "double", "description": "Snow Water Equivalent", "original_name": "WTEQ.I-1 (in)", "uuid": "e5a53571-b025-4781-b42e-68a391ac6d4e", "name": "wteqi_1" } ] }
Refer to the KML Documentation for more information.
<Schema name="2730123d-070c-45ee-8d8d-b5e4df135faf" id="2730123d-070c-45ee-8d8d-b5e4df135faf"> <SimpleField type="int" name="site_id"> <displayName>site_id</displayName> </SimpleField> <SimpleField type="string" name="date"> <displayName>date</displayName> </SimpleField> <SimpleField type="string" name="time"> <displayName>time</displayName> </SimpleField> <SimpleField type="double" name="wteqi_1"> <displayName>wteqi_1</displayName> </SimpleField> </Schema>
Allows uploading of model data to the Virual Watershed filesystem.
None.
name: Name of model
modelid: Model Run UUID
payload = {"name": "isnobal","modelid": "1dacc407-6488-42c1-a4de-0b6de97b46c1"} r = requests.post(<IP_ADDRESS>/apps/my_app/data, files=in.0000, data=payload, auth=(u, p))
Coming soon.
Allows uploading of model data to the Virual Watershed filesystem using swift client intermediary.
None.
filename: Name of file
modelid: Model Run UUID (name of container in swift)
preauthurl: Url (provided by gettoken for swift request
preauthtoken: Token (provided by gettoken for swift request
Use case for creating a new model run in VWP, obtaining a swift token and uploading data to that model run using Python
import requests import os import subprocess import json import uuid url = 'https://vwp-dev.unm.edu/' newmodelurl = url + 'apps/vwp/newmodelrun' apiloginurl = url + 'apilogin' gettokenurl = url + 'gettoken' swiftuploadurl = url + 'apps/vwp/swiftdata' s = requests.Session() user = 'yourusername' password = 'yourpassword' login = s.get(apiloginurl, auth=(user,password), verify=False) if login.status_code == 200: # Create Model newuuid=str(uuid.uuid1()) modeldata = json.dumps({"description": "Swift Upload Example","model_run_name":"$model_run_name" ,"model_keywords":"your keywords here"}) newmodelname = "swift upload example " + newuuid data = modeldata.replace('$model_run_name', newmodelname) result = s.post(newmodelurl, data=data) model_run_uuid = result.text # Request Token token = json.loads(s.get(gettokenurl).text) preauthurl = token['preauthurl'] preauthtoken = token['preauthtoken'] # Upload to Swift using token containername = model_run_uuid filename = 'sample_inputs.nc' segmentsize =<PHONE_NUMBER> # 1 Gig command = ['swift'] command.append('upload') command.append(containername) command.append('-S') command.append(str(segmentsize)) command.append(filename) command.append('--os-storage-url='+preauthurl) command.append('--os-auth-token='+preauthtoken) print "Uploading..." print command ls_output = subprocess.check_output(command) print ls_output print "Telling VWP to download..." params = {'modelid':model_run_uuid,'filename':filename,'preauthurl':preauthurl,'preauthtoken':preauthtoken} r = s.get(swiftuploadurl, params=params) if r.status_code == 200: print "VWP has successfully downloaded data file!" else: print "Download failure" print r.text else: print "Login failure" print login.text
Coming soon.
Uploads information about data that has been inserted in to the database.
Payload for this method is a formatted JSON with the following required structure:
{ "formats": [], "description": "$description", "externaluserid": "$valid_UUID", "sources": [ { "mimetype":"$mimetype", "files": [ "$inputFilePath" ], "set":"$set", "external":"$external", "extension":"$extension" } ], "taxonomy":"$taxonomy", "basename":"$basename", "parent_model_run_uuid":"$parent_model_run_uuid", "apps":[ ], "model_set_taxonomy":"$model_set_taxonomy", "model_run_uuid":"$model_run_uuid", "records":"$records", "model_set":"$model_set", "spatial":{ "geomtype":"$geomtype", "records":"$spatial_records", "features":"$features", "bbox":"$bbox", "epsg":"$epsg" }, "services":[ "$service1",... ], "model_set_type":"$model_set_type", "standards":[ "$standard1",... ], "active":"$active", "model_vars":"$model_vars", "categories":[ { "state":"$state", "modelname":"$modelname", "location":"$location" } ], "metadata":{ "xml":"$xml" "upgrade":"$upgrade", "standard":"$xmlstandard" } }
The above is a reasonable baseline template for both raster and vector inserts. However, while filling in the above information is sufficient for raster inserts, vector inserts require additional steps, detailed below.
None.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | vwp |
| Parameter | Description | Type | Options |
|---|---|---|---|
| formats | The file formats that are intended to be offered as downloads | list of strings | |
| description | Description of this dataset | string | |
| sources | Dictionary detailing file information | dictionary | |
| mimetype | Internet Media Type of transmitted data | string | (attribute of sources) |
| files | List of full paths to the uploaded file on the Virtual Watershed | list of strings | (attribute of sources) |
| set | 'original' or 'derived', should be 'original for purposes of insert | string | (attribute of sources) |
| external | If file whose associated data is located on another server | string | true, false(attribute of sources) |
| extension | extension of original file | string | (attribute of sources) |
| taxonomy | Taxonomy of data for purposes of processing | string | file, vector, geoimage, table, service, netcdf_[model] |
| basename | Name used for all download paths when building URLs | string | |
| parent_model_run_uuid | Parent Model Run UUID for this model run | uuid | |
| apps | Application alia | string | vwp |
| model_set_taxonomy | Defines the taxonomy of data for searches within a model set | string | grid, vector, file |
| model_run_uuid | Model Run UUID specific to all datasets in this model run | uuid | |
| records | Number of records in this dataset; should equal records number in spacial information | integer | |
| model_set | Defines the set of data to assign this data to | string | |
| spatial | Dictionary of spatial information regarding the dataset | dictionary | |
| geomtype | Geometry type (required for Vector only) | string | POINT, LINESTRING, POLYGON (attribute of spatial) |
| records | Number of records associated to features (usually same as number of features | int | (attribute of spatial) |
| features | Number of features represented by this dataset, usually 1 for rasters and many for vectors | int | (attribute of spatial) |
| bbox | Bounding box coordinates as a comma-delimited list | string | (attribute of spatial) |
| epsg | EPSG code of the provided BOX geometry | int | (attribute of spatial) |
| services | List of services that are requested to be supported | sring | wms, wcd, wfs |
| model_set_type | Defines type of data within the model set | sring | |
| standards | GIS metadata standards to support | list of strings | |
| active | Whether this dataset is visible to users to start | string | true, false |
| model_vars | Comma delimited string of variables represented by inputs and outputs | string | |
| categories | A triplet enforced by our database as a means of dividing data in to categories and subcategories | dictionary | |
| modelname | Top level category, name of model type being run | string | (attribute of categories) |
| state | Mid level category, name of the state that the model was run in | string | (attribute of categories) |
| location | Bottom level category, name of the watershed that hte model was run in | string | (attribute of categories) |
| metadata | Attached metadata for this file | dictionary | |
| xml | Original Metadata XML. Please use correct and verified metadata as per FGDC standards | string | See Examples below for XML template(attribute of metadata) |
| standard | Standard that this metadata is in (should be in supported metadata list) | string | (attribute of metadata) |
| upgrade | Whether to upgrade metadata to gstore | string | true, false(attribute of metadata) |
XML Metadata Template
Replace any Unknowns with information about your data that is known
All tags within this template are required; if you do not have this information leave it as unknown.
Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown -106.375 -106.3125 36.1875 36.125 Unknown Unknown Unknown Unknown Unknown Unknown Unknown None Unknown Unknown Unknown Unknown Unknown UnknownUnknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown 0.0 Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown UnknownUnknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Raster Pixel 1 1 1 Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown UnknownUnknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown 1 Unknown Unknown Unknown 20130116 Unknown Unknown Unknown Unknown Unknown UnknownUnknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown local time Unknown Unknown Unknown
modelrun UUID
Updates information about a dataset that has been inserted in to the database.
Payload for this method is a formatted JSON with the same structure as Dataset Information Upload
The above is a reasonable baseline template for both raster and vector inserts. However, while filling in the above information is sufficient for raster inserts, vector inserts require additional steps, detailed below.
None.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | vwp |
| dataset_uuid | Dataset identifier | uuid |
See Dataset Information Upload
modelrun UUID
Uploads attribute information about an existing vector dataset.
Payload for this method is a formatted JSON with the following structure:
{ "dataset": "$dataset_uuid", "fields": [ #list of entries with the following form: { "name": "$name", "description": "$description", "orig_name": "$orig_name", "ogr_type": "$ogr_type", "nodata": "$nodataval" "ogr_precision": "$ogr_precision" "ogr_width": "$ogr_width" "ogr_justify": "$ogr_justify" }# ,... ] }
None.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | rgis, epscor, elseweb |
| dataset_uuid | Dataset identifier | uuid |
| Parameter | Description | Type | Options |
|---|---|---|---|
| dataset | The UUID of the dataset | uuid | |
| fields | List of dictionaries representing attribute | list of dictionaries | |
| name | Name pulled the layer field definition | string | (attribute of fields) |
| description | Description of this layer | string | (attribute of fields) |
| orig_name | Name pulled the layer field definition | string | (attribute of fields) |
| ogr_type | OGR Data type from the layer field definition | string | (attribute of fields) |
| nodata | Value used to represent no data | int,float | (attribute of fields) |
| ogr_precision | Precision of data from the layer field definition | int,float | (attribute of fields) |
| ogr_width | Width of data from the layer field definition | int,float | (attribute of fields) |
| ogr_justify | Justify from the layer field definition | int,float | (attribute of fields) |
modelrun UUID
Uploads geometry information about an existing vector dataset.
Payload for this method is a formatted JSON with the following structure:
{ "gid": "$gid", "geom": "$geom" }
None.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | vwp |
| dataset_uuid | Dataset identifier | uuid |
| Parameter | Description | Type | Options |
|---|---|---|---|
| gid | The feature id of the geometry/feature. | string | |
| geom | Well-Known Binary representation of geometry from the feature, encoded to a hex string | hex string |
modelrun UUID
Uploads attribute feature information about an existing vector dataset.
Payload for this method is a formatted JSON with the following structure:
{ "fids": [], # list of feature ids, "records": [ # list of records { "fid": "$fid", "uuid": "$uuid", "observed": "$observed", "atts": [ # list of attributes { #attribute features "name": "$att_name", "u": "$att_uuid", "val": "$att_val", "qual": "$att_ } ] } ] }
None.
| Parameter | Description | Type | Options |
|---|---|---|---|
| app | Application alias | string | vwp |
| dataset_uuid | Dataset identifier | uuid |
| Parameter | Description | Type | Options |
|---|---|---|---|
| fids | List of feature IDs | list of string | |
| records | A list of features | list of dictionaries | |
| fid | Feature id of this attribute feature | string | (attribute of records) |
| uuid | UUID of associated geometry | uuid | (attribute of records) |
| observed | Datetime observed | datetime | (attribute of records) |
| atts | List of attributes | list of dictionaries | (attribute of records) |
| name | Name of this attribute feature | string | (attribute of atts) |
| u | UUID of this attribute feature | uuid | (attribute of atts) |
| val | Value of this attribute feature | (varies) | (attribute of atts) |
| qual | (optional) | (varies) | (attribute of atts) |
modelrun UUID
Creates a database record of the new model run and a landing point for files to be uploaded.
None.
{app}
description: isnobal experimental run.
modelid: Model Run UUID
{"description": "inital insert"}
modelrun UUID
Verifies if a model run UUID already exists.
{app}
modelid:
{"modelid": "1dacc407-6488-42c1-a4de-0b6de97b46c1"}
True or False
Get basic statistics for a dataset. This includes descriptive statistics such as mean, minimum and maximum for numeric fields for tabular of vector data or histograms for raster data.
Coming soon.
Coming soon.
Coming soon.
Coming soon.