DON QUIXOTE OF ORSON WELLES A film review by Raymond Johnston Copyright 1994 Raymond Johnston
DON QUIJOTE DE ORSON WELLES (DON QUIXOTE OF ORSON WELLES) Produced, written, directed by Orson Welles Cast: Francisco Perez, Akim Tamiroff, Orson Welles, Editor and head of post production: Jess Franco Mexico/Italy/ Spain 1955-1969, Post Production Spain 1992
When Orson Welles died almost ten years ago he left several nearly finished but unreleased films. Most Famous of these is THE OTHER SIDE OF THE WIND, tied up in a legal dispute with Iranian financiers. Other projects included the fragments of IT'S ALL TRUE, his aborted documentary on Brazil; and a film called THE DEEP, apparently similar to the recent DEAD CALM. Most legendary and speculatively exiting of the projects is DON QUIXOTE. Over the years this unseen project has gained a reputation as one of his best films, because the match of Welles and the character of Cervantes' novel seemed perfect. Welles used his own money, completely, and between 1955 and 1969 filmed enough footage to make at least three films, changing his concept constantly. If any of these films would have been a masterpiece, it is impossible to say. The project currently being screened by his former long time companion Oja Kaddar, who has the rights to his unfinished projects, is an insult to the memory of a sometimes brilliant director.
Technical considerations make this film close to unwatchable. A film consists of nothing more than a visual or image track, and a sound track. The visual track of this film is incredibly poor. It seems as if, and this is a guess, an early rough cut of film was transferred to primitive home video some time in the sixties. This poorly focused and washed out video then was retransferred to film. The result is something not as good as the "Lost Episodes" of the Honeymooners TV show. Cut into this are a few better quality close-ups. An occasional original quality shot sneaks in, reminding one of the great visual quality of other Welles films. This poor footage makes up most of the film. About three quarters of the way through, there is a very good twenty minutes of high quality footage of the running of the bulls in Spain. Welles appears in this, making a film called DON QUIXOTE. Henry Fonda can also be seen briefly. The film the returns to poor quality images as the editors struggle to make an ending out of the available footage. The running of the bulls section seems to be edited by Welles, or at least a professional. The rest, the mixture of poor quality footage, lacks any sense of pacing or focus. The cut in close ups are obviously left over scraps used to stretch out the scenes to accommodate the narration.
The audio track of the film is even worse. Bad sound plagued Welles later works. Why a film maker who got his start in radio and made sound innovations on his early Hollywood films used such poor sound technique in later life is a subject of speculation among film scholars. Many film makers shooting in Spain and Italy in the sixties did not use direct sound, since the films would be dubbed for different markets. As a result, Welles shot most of this film silent, hoping to use his own voice for the English language version. He recorded about ten minutes. The rest of the sound was created in post production. It is an incredibly poor dubbing job that would not pass muster in a kung-fu film. The head of modern post production was Jess Franco. His own films include the women's prison film 99 WOMEN and horror opus NIGHT OF THE BLOOD MONSTER. His team added a flat and hollow track of bored actors trudging through the dialogue, making no effort to match the lips of characters. It is difficult to tell if some lines are supposed to be narration or dialogue. This is accompanied by stock sound effects and almost no music. It is like watching the 'Here's Harold' television versions of Harold Lloyd shorts.
The climactic scene of the film, jousting the windmills, is created by matting a long shot of the actors on their burros over stills, similar to some of the "restoration" Georgio Moroder did on METROPOLIS.
I doubt that this version will get any distribution in the US. For Welles fans I will recount the basic storyline. The story of the film, as it is in this version, has Don Quixote and Sancho Panza in armor wandering through the landscape until all of a sudden they encounter a woman, (Oja Kaddar) on a motorcycle. It is Franco-era Spain. They encounter several modern people, mistake sheep for an army, joust windmills, etc. Don Quixote and Sancho Panza then split up. Sancho Panza hears that Orson Welles is making a film about Don Quixote. Panza wanders through the running of the bulls looking for Orson Welles, who might know where Don Quixote is, or have a use for him in his film. After encountering Welles, Sancho Panza finds Don Quixote. People recognize him Don Quixote as the guy from the book. He passes a Don Quixote restaurant and a Don Quixote Beer sign. They wander off again into the distance.
If the images can be digitally cleaned up, and the sound recorded by true professionals, with a solid score and convincing sound effects, this film would make an interesting footnote to Welles career. As it is, this version should be avoided by all but serious film scholars that need to see what Welles possibly had in mind. Compared to the brilliant OTHELLO; recently cleaned up and restored; DON QUIJOTE DE ORSON WELLES looks like PLAN NINE FROM OUTER SPACE.
.
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In this assignment you will begin developing your backend server and complete the implementation of your frontend web application. Your frontend webapp from this assignment will be reviewed by your peers to provide you user feedback.
Separations of concerns instructs us to divide our application into separate front and back end processes. In this way our application is modular, can be selectively scaled, and we have indepdence to change each at their own pace. In this assignment we will separately host our frontend and backend applications on Heroku.
The remaining implementations missing from our frontend web app are the ability to upload an image with a post, register new users, edit a user's profile including uploading a new profile picture, the listing of followed users with their status headlines and profiles pictures, adding a new followed users, and removing followed users. For our first implementation of the backend server we will implement the status and post endpoints, and provide stubs for the others.
In the previous assignment we implemented the ability for users to login to our webapp, and pulled from the dummy server the user's status message, their profile picture, and their feed of posts. Now we add the missing functionality to create a fully functioning social networking web application frontend.
Continue to use $resource
to communicate with the dummy server. See this section of the API page for help in implementing the picture uploads from your frontend.
For this assignment we will use Protractor and write end-to-end tests to validate the full functioning of our web app. So you can still do test driven development (TDD) by writing the Protractor end-to-end tests first and then implement the missing functionality. During your development, use the python SimpleHTTPServer / http.server to host your web page locally and have Protractor run against it. The required tasks for your end-to-end tests are listed in the requirements section below.
We will have separate frontend and backend applications. Your frontend app is currently talking to my dummy server, and eventually we want it talking to your server. But there's a lot of work to get that done!
Getting started you should do your development for your backend in it's own directory separate from your frontend and separate from your hw submission directory, i.e., just like how we separated hw#-frontend
from the frontend
directory, create a new backend
directory to use for development. Therefore in this assignment we will work in the frontend
directory for completing the frontend webapp and deploying to Heroku, the backend
directory for our implementation of the backend server and deploying to Heroku, and the hw{{vm.hwid}}-{{vm.assignmentId}}
directory that contains our files to submit to turnin.
Let's get our backend setup. If you have not already done so you need to install NodeJS and then get your backend server running. For the "npm init" call below, the defaults are in general fine, i.e., just press enter a lot. Again if you already completed the inclass exercise and have a working Node server, you can skip these steps.
cd backend npm init npm install express body-parser --save wget https://www.clear.rice.edu/comp431/sample/RiceBookServer/index.jsThe "init" call will create for us a
package.json
file which will be the
configuration for our NodeJS application. Given that we want a
MEAN application,
we install express and we'll use the body-parse middleware to make things easier for us.
The --save flag in npm install
adds these dependencies to our package.json
file so when Heroku builds our app it will grab these dependencies for us.
The final step above is to pull the example index.js
from the class website.
We can now run our Node application
node index.js
Test it out by navigating to http://localhost:3000 it should say "Hello World!". In the sample from the course site there is also the POST /post
endpoint. To test this you can either use a browser extension such as Advanced REST Client or Postman, or use curl on the commandline:
curl -H 'Content-Type: application/json' -d '{"Hello": "World" }' http://localhost:3000/post
The -H flag of curl sets a header field which tells the server we are going to send a JSON payload. The -d flag is the payload: Notice that we have formatted it as JSON because that's what we told the server we were going to do. If you don't do this correctly then it won't work correctly! If you look at index.js
you'll notice we use the middleware bodyParser.json()
which parses the JSON input and places the payload in the body
attribute of the request object (normally called req
).
Stubs are "pieces of code used to stand in for some other programming functionality." For this assignment we will create stubs for all of the desired endpoints of our API. After the stubs are created, then we will implement selected functionality in this assignment.
Here is the recommended breakout by endpoint for each source file in your backend server
| endpoint | verbs | source file |
|---|---|---|
| /login | POST | auth.js |
| /logout | PUT | auth.js |
| /register | POST | auth.js |
| /password | PUT | auth.js |
| /posts | GET, PUT | posts.js |
| /post | POST | posts.js |
| /status | GET, PUT | profile.js |
| /statuses | GET | profile.js |
| GET, PUT | profile.js | |
| /zipcode | GET, PUT | profile.js |
| /pictures | GET | profile.js |
| /picture | PUT | profile.js |
| /following | GET, PUT, DELETE | following.js |
// this is profile.js which contains all user profile // information except passwords which is in auth.js exports.setup = function(app) { app.get('/statuses/:users*?', getStatuses) } function getStatuses(req, res) { // this isn't correct, but gives you a starting point // for the stub this is a fine implementation var username = req.params.users.split(',')[0] // but what if 'users' is not specified as a parameter in the request? // then we use the currently logged in user, i.e., req.user // this returns only one status, but we want to send // an array of all the requested user's statuses res.send({ statuses: [ { username: username, status: 'the status of the user' } ] }) }The API for the endpoints is the same as for the dummy server (i.e., this way we don't need to change any of the frontend code). That api is found here
GET /sample
Just as for the previous assignment, we will employ test driven development as we implement our backend server. Therefore start by writing Jasmine unit tests for each unit of functionality we desire to implement, and then implement that functionality, thereby satisfying the test criteria.
We'll use jasmine-node
for running our unit tests.
To get XML test results, use the following command
./node_modules/.bin/jasmine-node --output testresults --junitreport app_server
I recommend you add the following "scripts" to your package.json file:
{ ... "scripts": { "start": "node index.js", "test": "./node_modules/.bin/jasmine-node app_server", "autotest": "./node_modules/.bin/jasmine-node --color --autotest --output testresults --junitreport app_server" }, ... }where I place all of my server js files in the
app_server
directory. Then I can
type "npm run test
" to run my Jasmine tests and "npm run autotest
" to "watch"
my app_server directory for changes and then run my tests. In this way I can do continuous development and
always can see how my tests respond to changes.
For this assignment, write tests for, and then implement, the following endpoints (see the API page for specification)
GET /status
PUT /status
GET /statuses/:users*?
GET /posts/:id*/
(test both with no :id specified, you should have 3 posts returned, then test with a valid id, and then test with an invalid id)POST /post
(test that adding a post increments the post id, validate the contents of the new post)We do not yet have a database for storing the information the server needs to provide to the client. Therefore we keep all data in memory. For example, we can use a map for status headlines, for example,
var _statues = { } ... function getStatuses(req, res) { // this isn't correct, but gives you a starting point // for the stub this is a fine implementation var username = req.params.users.split(',')[0] // but what if 'users' is not specified as a parameter in the request? // then we use the currently logged in user, i.e., req.user if (!_status[username]) { _status[username] = "Hello World!" } // this returns only one status, but we want to send // an array of all the requested user's statuses res.send({ statuses: [ { username: username, status: _status[username] } ] }) }
Here I prepend underscore to the variable name to help me remember that this is a "global" variable.
Similar to status, we'll have an array for posts. We should start with 3 hardcoded posts in this array. When a new post is added, it should be added to this array. A post has the following schema:
var post = { id: int, author: string, body: string, date: new Date(), comments: [] }A new post will arrive with only the body in the payload. The timestamp is the current time on the server, the author is the currently logged in user, and the id is a unique value determined by the server (the length of the post array would be sufficient for now). The response to
POST /post
is an array of the newly added post, i.e., with it's timetsamp, author, and id values supplied.
The newly added post will automatically be available in the list of all posts
returned by a call to the GET /posts
endpoint.
For now you can supply whatever username you want, just as for the status endpoint above.
Check that your backend works by performming the following commands (either using curl as shown here or Advanced Rest Client or similar)
curl https://ricebookserver.herokuapp.com/posts # you should receieve 3 posts curl -H 'Content-Type: application/json' -d '{ "body": "My first post!"  I assume the value is 12345, let's verify getById works: curl https://ricebookserver.herokuapp.com/posts/12345 # you should get your new post again curl https://ricebookserver.herokuapp.com/posts # you should get 4 posts now
We will use an automated test similiar to these commands to check the functionality of your backend.
When you have completed the implementation of the required pieces of your
backend server you are ready to publish your server to Heroku.
The backend server will be hosted under a different application name than
the frontend web app. If you did not already create a backend Heroku app during
an inclass exercise, then following these steps to
create a git repo and a Heroku application.
Note that we tell git not to add our node_modules
directory to the repo by adding it to the gitignore file (Heroku will automatically install these libraries for us because they are in our package.json file). In the below I have named by server "ricebookserver" you will want
to pick your own name, or omit and Heroku will supply a name for you
git init heroku create ricebookserver echo web: node index.js > Procfile echo node_modules > .gitignore echo npm-debug.log >> .gitignore git add .gitignore Procfile package.json index.js git commit -m 'initial commit' git push heroku master
No need to set a buildpack this time, Heroku should automatically recognize that we have a NodeJS application.
Similar to before, create a file README.json
that has contents similar to what is below (we will read this programmatically so please make sure you follow this style)
{ "netid": "sep1", "frontend": "https://ricebookapp.herokuapp.com", "backend": "https://ricebookserver.herokuapp.com" }
replace "ricebookapp" and "ricebookserver" with the names of your frontend and backend applications, and replace "sep1" with your netID.
We finish the implementation of the frontend of our webapp while continuing to use the dummy server as a backend data store.
Your end-to-end tests will run against your web app running on your local python server. Here are the tasks for your end-to-end test
Include a JUnitXML report of your end-to-end tests: e2e-results/junitresults.xml
Your backend server will be hosted on Heroku, we will use a grading robot to validate your implementation, so be sure you test your deployed server before you submit to turnin.
GET /statuses/:user*?
returns a status message, you do not need to return more than one statusGET /status
returns a status messagePUT /status
updates that statusGET /posts/
returns all posts, 3 hardcoded and any additional that are addedGET /posts/:id
returns the post with the requested id if it exists, none otherwisePOST /post
adds a new post to the list of all posts. Returns the newly added postInlucde a JUnitXML report of your backend unit tests, e.g., testresults/TEST-ValidatePostFunctionality.xml
Your submission directory might look something like this
Note that I have places the status endpoints in profile.js
as a look ahead to
the way in which we will be persisting the data: the status of a user will be stored along
with their other profile information.


Gypsy Folk Tales, by Francis Hindes Groome, [1899], at sacred-texts.com
There were two brothers, one poor and one rich. And the rich one said to him, 'Come with me, brother, to our father.' And the rich one took bread for himself, and the poor one had none.
And the rich one kept eating bread, and the poor one said, 'Give me, too, a bit of bread.'
'If you will give me an eye, I will give you a bit of bread.' 'I will give it you, brother.'
And he took out an eye, and gave him a bit of bread.
And he went further, and he hungered. 'Give me a bit more bread.'
'Give me one more eye.'
'I will give it you, brother.'
Behold, he was blind now, and his brother took him by the hand and led him under the gallows, and left him there; and his brother departed. At nightfall came the devils, and perched on the gallows.
And the biggest devil asked, 'What hast done in the world? where wert walking?'
'I did--I stopped the water.'
'And thou, what hast thou done?'
'The emperor's daughter neither dies nor lives; she is just in torment.'
'And thou, what hast thou done?'
'I did--that a brother dug out a brother's eyes.'
'If he knew, there's a brook here, and if he washed himself, he would see.'
'If the townsfolk knew to go to the mountain and remove the stone, the water would flow again.'
And the third said, 'But if the emperor's daughter knew, under her bed there is a toad, and if she takes it out, and gets ready a bath, and puts the toad in the bath, and if they wash her, she would grow strong.'
Then the cocks crowed, and the devils departed.
So the man dragged himself to the brook, and kept feeling with his hand till he found the water. And he washed his face, and his eyes were restored to him. And he went into the city where they had stopped the water.
So they went to the mountain, and raised the stone; and the water flowed plentifully.
'Well, now, what do you want, man, for releasing the water?'
'Give me a carriage and two horses and a carriageful of money.'
They gave them to him. He went to the emperor's daughter.
And he went and took out the toad, and threw it into the bath; and they washed the emperor's daughter, and she grew stronger and fairer than ever.
'What do you want for making her strong and fair?'
'Give me two horses and a carriageful of money, and give me a driver home.'
So he went home, and sent the servant to his brother, to borrow a bushel. And his brother asked, 'What to do with the bushel?'
'To measure money with.'
His brother gave him the bushel; and went himself and asked his brother, 'Where did you get it, the money, from, and the horses?'
'From there where you left me.'
'Lead me, too, thither to that place. I am sorry, brother.'
'Don't be sorry; you've just got to go. Well, come, brother.'
So they both went to the place where he dug out his eyes.
'Give me, brother, a bit of bread.'
'Give me an eye.'
He gave him an eye, and he gave him a bit of bread.
And they went further. 'Give me, brother, a bit more bread.'
'Give me one more eye.'
'I will, brother.'
So he gave him a bit more bread, and took him by the hand, and led him under the gallows, and left him there, and departed. At nightfall came the devils, and perched on the gallows. And the biggest devil asked, 'What have you done? where have you been to in the world?'
One said, 'Don't tell, for there was lately a blind man under the gallows, and he heard what we said. And he made himself eyes, and made the water run, and raised up the emperor's daughter. Stay, while I look under the gallows.'
And they found the blind man. 'There's a blind man here.' And they rent him all in pieces. Then the devils departed; the man was dead.
This story is told as well as story may be. There is a Gypsy variant, longer but not half so good, from the Hungarian Carpathians, in Miklosich's Beiträge, p. 3:--


Welcome to T-shirt Store
TshirtAccessories: Belt
Cap
HairBand:
Pocket:
Yes
No
Tagline:
Color:
Red
Blue


@import models.users.User
@import helper._
@(addFlightForm: Form[models.FlightSchedule], user: User, env: play.api.Environment)
@admin.adminMain("Add Flight", user){
Add a new Flight
@form(action = routes.AdminController.addFlightSubmit(), 'class -> "form-horizontal", 'role -> "form", 'enctype -> "multipart/form-data"){
@select(
addFlightForm("destination.id"),
options(Destination.options()),
'_label -> "Destination", '_default -> "-- Choose a Destination --",
'_showConstraints -> false, 'class -> "form-control"
)
@inputText(addFlightForm("city"), '_label -> "Destination City", 'class -> "form-control")
@inputText(addFlightForm("origin"), '_label -> "Origin", 'class -> "form-control")
@inputDate(addFlightForm("departure_date"), '_label -> "Departure Date", 'class -> "form-control")
@inputText(addFlightForm("departure_time"), '_label -> "Departure Time", 'class -> "form-control")
@inputText(addFlightForm("arrival_time"), '_label -> "Arrival Time", 'class -> "form-control")
@inputText(addFlightForm("seats"), '_label -> "Total Seats", 'class -> "form-control")
@inputText(addFlightForm("flight_ID"), '_label -> "", 'hidden -> "hidden")
@inputText(addFlightForm("id"), '_label -> "", 'hidden -> "hidden")
@if(env.resource("public/images/flightImages/" + addFlightForm("flight_ID").value() + ".jpg").isDefined) {
} else {
}
}
}


Duke Encounters
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--- title: "What is SDG reporting?" permalink: "/topic/reporting/" layout: "topic" topic-tag: "reporting" show-resources: true ---
SDG reporting refers to the act of publishing and disseminating data and statistics on the SDG indicators for key stakeholders, including UN custodian agencies, government policymakers, businesses, non-governmental organizations (NGOs) and research institutions, and the general public.
According to the 2030 Agenda for Sustainable Development, SDG reporting is to be led by a national government and conducted in compliance with the UN’s Fundamental Principles of Official Statistics. These principles are considered a basic framework that national statistical offices and other statistical organizations must follow in recognizing official statistics as a public good.


THE THIN RED LINE
Reviewed by Harvey Karten, Ph.D. Twentieth Century Fox/ Phoenix Pictures Director: Terrence Malick Writer: Terrence Malick, novel by James Jones Cast: George Clooney, John Cusack, Woody Harrelson, Nick Nolte, Sean Penn, Bill Pullman, John Travolta, Adrien Brody, Ben Chaplin, Jim Caviezel, Elias Koteas
Whatever happened to those seedy old black-and-white war movies that came out during World War 2? As a little kid who was way too young to fight during the early 1940s I used to love going to the neighborhood theater for a double feature of high-action heroics, to cheer on each time an American plane knocked out a "zero" and to laugh at the Japanese--all portrayed as cartoonish characters in their round glasses who had one word vocabularies: "Bonzai! Bonzai!" My friends and I were practically babies when we took in the dauntless deeds of our fighting men, and we were not about to believe that real people were over there getting maimed and killed nor did we have much interest in the geopolitics. There was virtually no character development, but who cared?
For all its wonderful battle scenes, not even Steven Spielberg's masterly "Saving Private Ryan" examined character all that much, though it did explore the rationale behind risking eight lives to free one surviving family member from the dangers on the front. "The Thin Red Line" is another story. When Terrence Malick, who helmed "Badlands" in 1973 (a moody thriller inspired by the Starkweather-Fugate killing spree in the 50s) and "Days of Heaven" in 1978 (yet another mood-piece, visually beautiful, about a love triangle) came back to direct his first movie in twenty years, he must have connected with something. His notice must have been held by the opportunity to address a story with a moody ambiance similar to what he built in his previous films.
"The Thin Red Line" is his version of the sprawling epic of action on one island, Guadalcanal, during World War II. Freely tossing in phrases from James Jones's 1962 novel, he sees the action from the point of view of the narrator, Private Witt (James Caviezel), who went AWOL from his unit several times to share his life with the Melanesian natives in the Solomon Islands chain. We learn early on that the island is of strategic importance to the Japanese because it could provide them with access to Australia and to the sea lanes to America. With Japanese entrenched on a part of the island, on which they have already built an airstrip, the American forces were given the mission of dislodging them and taking control of Guadalcanal.
Cinematogapher John Toll has done an amazing job of capturing the raw natural beauty of the terrain of Queensland, Australia, which was the site of much of the filming--though a part of the photography takes place on location in Guadalcanal. The gorgeous topography is the home of a variety of exquisitely colored birds and mammals of various ilks, including some spooky-looking bats and scary alligators-- who enjoy the perpetually bright, sunny days as much as the local people. Toll captures the peaceful lives of the indigenous clans, whose youngsters play calmly on the beach and never fight the way westerners are wont to do. In only one case do we see the adults squabble, though they appear leery of the Americans at first, neither welcoming them as liberators nor expressing any hostility toward them.
Beauty aside, the real purpose of the film is to capture the meditations of some of the fighting men, principally those of Private Witt and of Private Bell (Ben Chaplin), the latter frequently contemplating the far more pleasant times when he is making love with his fetching wife back home. When the principals are not meditating, they are philosophizing verbally, trading viewpoints and acting out their convictions in the way they command the men. Chief among the views are those of Private Witt, who, examining the peaceful vistas provided by nature, wonders what propels men to war. He is answered by Colonel Tall (Nick Nolte) who sees instead that the vines wrap themselves around one another as though on a mission to choke the life out of the shrubbery. Sgt. Welsh (Sean Penn) comes out with his belief that "there's no world but this one," that we should simply accept our assignments and duties and go on living as best we can with our obligations.
The assaults by the Japanese are enacted realistically, the chief action being an attmept by the Americans to dislodge a machine-gun nest which is taking all too many lives. There are moments of high tension within the U.S. unit, particularly when Captain Staros (Elias Koteas) directly refuses an order by Col. Tall to take a hill even while Tall knows the capture would involve the loss of many men.
Despite the National Geographic-style beauty throughout and some credible if not overly striking battle scenes, "The Thin Red Line" depends too much on its narrative, a series of reflections and philosophic attitudes that would be better absorbed and appreciated on James Jones's pages than on Terrence Malick's staging. Malick has utilized the names of a great many major performers--John Travolta, Woody Harrelson, George Clooney, John Cusack--in cameos that are so brief we can't help thinking he employed these men only for their value on the theater marquees. Their roles could easily have been assumed by extras and, in fact, one of the less-known performers in this movie, James Caviezel, is so convincing (and handsome) that we wonder how some of the more alpha males from Hollywood were able to swallow up such superior thesps. If "The Thin Red Line" did not open in a year that included Steven Spielberg's magnum opus on World War II, it would deserve more serious attention by the Academy. While it remains a powerful work with the signature moodiness or its director, its chief asset is that it may encourage us to reach for the novel.
Rated R. Running Time: 165 minutes. (C) 1998 Harvey Karten
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
Broken URLs inthe reviews are the responsibility of the author.
The formatting of the review is likely to differ from the original due
to ASCII to HTML conversion.
Related links: index of all rec.arts.movies.reviews reviews


{% extends "base.html" %} {% load crispy_forms_tags %} {% block content %}
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CyberJays
Creighton Prep Robotics
CyberJays
About
Our mission is to grow as people and the prevalence of robotics not only at our school but around Omaha through camps and outreach programs. This all while focusing on being exemplary models of kindness and sportsmanship to others. We are the only competing team in Omaha, NE. Also we have made great progress in our rookie year, winning the Rookie Inspire Award at the Kansas City Regionals.
FAQ
Who are you?
We are 6805 CyberJays of Creighton Preparatory School, an all male Jesuit College Preparatory School in Omaha Nebraska.
How much experience do you have?
We were established during the 2018 Competition season. While we have only competed for one year, our team is mostly comprised of members who have past experience with other forms of competitive robotics.
What makes you special?
We are the only competing team in Omaha, NE. Also we have made great progress in our rookie year, winning the Rookie Inspire Award at the Kansas City Regionals. These being a one many other reasons.
How would we reach out to you?
Anyone can come up to us at a tournament and also we can be reached at any time through other methods shown on the Contact Us page, accessible by the link below.
How can I access public copies of your code and other documents?
All public documents and files are made available on the Public Resources Page, which can be found the document below.
Roster
| Name | Role | Year |
|---|---|---|
| Cian Weekly | Acting Captain | Sophmore |
| Cal Tietjen | Acting Driver | Sophmore |
| Abram Wulf | Build/Design Depatment Head | Sophmore |
| Kevin Prososki | Programming Department Head | Sophmore |
| Andrew Hood | Marketing and Public Relations Department Head | Sophmore |
| Tom Knudsen | Electrical Department Head | Sophmore |
| Luke Reinsch | Finance Department Head | Senior |
| Will Randby | Builder | Senior |
| John Royal | Builder, Designer | Sophmore |
| Elwyn Frailey | Mascot, Carpenter | Senior |
| Ben Hall | Graphic Design and Website Developer | Junior |
Pictures


These styling commands are TeX primitives and their use is discouraged. Use the LaTeX equivalents instead.
The usage of TeX primitives will often result in unwanted behaviour, especially when the exact workings are not known.
Overview:
- \rm -> \textrm
- \sf -> \textsf
- \tt -> \texttt
- \it -> \textit
- \sl -> \textsl
- \sc -> \textsc
- \bf -> \textbf


--- layout: post title: "Avoiding destructive criticism by Critiquing in Love" date: 2016-05-18T13:00:11-04:00 categories: - articles tags: - soft skills ---
I wrote a brand new post discussing the value of constructive feedback in the development (and greater work) environment. We like to call it "Critiquing In Love" on the Lessonly team. You can read the post in its entirety at https://www.lessonly.com/blog/avoid-destructive-criticism/.
Special thanks to my wife, Megan Oed, for helping me research, edit and brainstorm the content for this post.


Workplace Experience - Website Designer
Fourth technical year - Software engineering
Technology program - Information technology focus
Python, Python unittest, Selenium for Python, Java
HTML5, CSS3, less, Bootstrap, automatic HTML & CSS validation
Git, Linux, Photoshop, Raspberry Pi, NFC, Twitter-API
SCRUM, Agile development, XP, CI/CD
When I am not programming I like to spend my time either playing a variety of video games or practicing music.
My passion for video games is what got me interested in programming in the first place, with the aspiration of one day
being able to create my own video game.
I am a self-taught piano player, with my interest in practicing music igniting roughly in my second year of high school.
Now I play almost everyday after school as a way to destress and relax.
A small project we did for our school during the Covid-19 pandemic to ensure that the students kept their assigned lunchtime, by scanning their personal NFC tag. The features include checking if the tag belongs to a student at the school, and which class the student scanning the tag belongs to. Then the program checks the schedule of said student to see if it is currently their lunchtime.
A small passion project between me and my friends.
The idea behind the game was to create a multiplayer role-playing game with a timing based combat system. As of now it only consists of a basic version of the combat system.
The game is made using the Godot Game Engine


| Class | ActionMailer::Base |
| In: |
/usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb
|
| Parent: | AbstractController::Base |
Action Mailer allows you to send email from your application using a mailer model and views.
To use Action Mailer, you need to create a mailer model.
$ rails generate mailer Notifier
The generated model inherits from ActionMailer::Base. Emails are defined by creating methods within the model which are then used to set variables to be used in the mail template, to change options on the mail, or to add attachments.
Examples:
class Notifier < ActionMailer::Base default :from =><EMAIL_ADDRESS>:return_path =><EMAIL_ADDRESS>def welcome(recipient) @account = recipient mail(:to => recipient.email_address_with_name, :bcc =><EMAIL_ADDRESS>"Order Watcher<EMAIL_ADDRESS>end end
Within the mailer method, you have access to the following methods:
The hash passed to the mail method allows you to specify any header that a Mail::Message will accept (any valid Email header including optional fields).
The mail method, if not passed a block, will inspect your views and send all the views with the same name as the method, so the above action would send the +welcome.text.plain.erb+ view file as well as the +welcome.text.html.erb+ view file in a +multipart/alternative+ email.
If you want to explicitly render only certain templates, pass a block:
mail(:to => user.emai) do |format| format.text format.html end
The block syntax is useful if also need to specify information specific to a part:
mail(:to => user.emai) do |format| format.text(:content_transfer_encoding => "base64") format.html end
Or even to render a special view:
mail(:to => user.emai) do |format| format.text format.html { render "some_other_template" } end
Like Action Controller, each mailer class has a corresponding view directory in which each method of the class looks for a template with its name.
To define a template to be used with a mailing, create an .erb file with the same name as the method in your mailer model. For example, in the mailer defined above, the template at app/views/notifier/signup_notification.text.plain.erb would be used to generate the email.
Variables defined in the model are accessible as instance variables in the view.
Emails by default are sent in plain text, so a sample view for our model example might look like this:
Hi <%= @account.name %>, Thanks for joining our service! Please check back often.
You can even use Action Pack helpers in these views. For example:
You got a new note! <%=<EMAIL_ADDRESS>25) %>
If you need to access the subject, from or the recipients in the view, you can do that through message object:
You got a new note from <%= message.from %>! <%=<EMAIL_ADDRESS>25) %>
URLs can be generated in mailer views using url_for or named routes. Unlike controllers from Action Pack, the mailer instance doesn‘t have any context about the incoming request, so you‘ll need to provide all of the details needed to generate a URL.
When using url_for you‘ll need to provide the :host, :controller, and :action:
<%= url_for(:host => "example.com", :controller => "welcome", :action => "greeting") %>
When using named routes you only need to supply the :host:
<%= users_url(:host => "example.com") %>
You will want to avoid using the name_of_route_path form of named routes because it doesn‘t make sense to generate relative URLs in email messages.
It is also possible to set a default host that will be used in all mailers by setting the :host option in the ActionMailer::Base.default_url_options hash as follows:
ActionMailer::Base.default_url_options[:host] = "example.com"
This can also be set as a configuration option in config/environment.rb:
config.action_mailer.default_url_options = { :host => "example.com" }
If you do decide to set a default :host for your mailers you will want to use the :only_path => false option when using url_for. This will ensure that absolute URLs are generated because the url_for view helper will, by default, generate relative URLs when a :host option isn‘t explicitly provided.
Once a mailer action and template are defined, you can deliver your message or create it and save it for delivery later:
Notifier.welcome(david).deliver # sends the email mail = Notifier.welcome(david) # => a Mail::Message object mail.deliver # sends the email
You never instantiate your mailer class. Rather, you just call the method you defined on the class itself.
Multipart messages can also be used implicitly because Action Mailer will automatically detect and use multipart templates, where each template is named after the name of the action, followed by the content type. Each such detected template will be added as separate part to the message.
For example, if the following templates existed:
Each would be rendered and added as a separate part to the message, with the corresponding content type. The content type for the entire message is automatically set to multipart/alternative, which indicates that the email contains multiple different representations of the same email body. The same instance variables defined in the action are passed to all email templates.
Implicit template rendering is not performed if any attachments or parts have been added to the email. This means that you‘ll have to manually add each part to the email and set the content type of the email to multipart/alternative.
You can see above how to make a multipart HTML / Text email, to send attachments is just as easy:
class ApplicationMailer < ActionMailer::Base def welcome(recipient) attachments['free_book.pdf'] = File.read('path/to/file.pdf') mail(:to => recipient, :subject => "New account information") end end
Which will (if it had both a welcome.text.plain.erb and welcome.text.html.erb tempalte in the view directory), send a complete multipart/mixed email with two parts, the first part being a multipart/alternative with the text and HTML email parts inside, and the second being a application/pdf with a Base64 encoded copy of the file.pdf book with the filename +free_book.pdf+.
You can also specify that a file should be displayed inline with other HTML. For example a corporate logo or a photo or the like.
To do this is simple, in the Mailer:
class ApplicationMailer < ActionMailer::Base def welcome(recipient) attachments.inline['photo.png'] = File.read('path/to/photo.png') mail(:to => recipient, :subject => "Here is what we look like") end end
And then to reference the image in the view, you create a welcome.html.erb file and make a call to image_tag passing in the attachment you want to display and then call url on the attachment to get the relative content id path for the image source:

Please Don't Cringe
 <%= image_tag attachments['photo.png'].url -%>
As we are using ActionView‘s image_tag method, you can pass in any other options you want:

Please Don't Cringe
 <%= image_tag attachments['photo.png'].url, :alt => 'Our Photo', :class => 'photo' -%>
Action Mailer provides hooks into the Mail observer and interceptor methods. These allow you to register objects that are called during the mail delivery life cycle.
An observer object must implement the :delivered_email(message) method which will be called once for every email sent after the email has been sent.
An interceptor object must implement the :delivering_email(message) method which will be called before the email is sent, allowing you to make modifications to the email before it hits the delivery agents. Your object should make and needed modifications directly to the passed in Mail::Message instance.
Action Mailer provides some intelligent defaults for your emails, these are usually specified in a default method inside the class definition:
class Notifier < ActionMailer::Base default :sender =><EMAIL_ADDRESS>end
You can pass in any header value that a Mail::Message, out of the box, ActionMailer::Base sets the following:
parts_order and charset are not actually valid Mail::Message header fields, but Action Mailer translates them appropriately and sets the correct values.
As you can pass in any header, you need to either quote the header as a string, or pass it in as an underscorised symbol, so the following will work:
class Notifier < ActionMailer::Base default 'Content-Transfer-Encoding' => '7bit', :content_description => 'This is a description' end
Finally, Action Mailer also supports passing Proc objects into the default hash, so you can define methods that evaluate as the message is being generated:
class Notifier < ActionMailer::Base default 'X-Special-Header' => Proc.new { my_method } private def my_method 'some complex call' end end
Note that the proc is evaluated right at the start of the mail message generation, so if you set something in the defaults using a proc, and then set the same thing inside of your mailer method, it will get over written by the mailer method.
These options are specified on the class level, like ActionMailer::Base.template_root = "/my/templates"
| mailer_name | -> | controller_path |
| mailer_name | [W] |
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 373 373: def default(value = nil) 374: self.default_params = default_params.merge(value).freeze if value 375: default_params 376: end
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 367 367: def mailer_name 368: @mailer_name ||= name.underscore 369: end
Instantiate a new mailer object. If method_name is not nil, the mailer will be initialized according to the named method. If not, the mailer will remain uninitialized (useful when you only need to invoke the "receive" method, for instance).
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 441 441: def initialize(method_name=nil, *args) 442: super() 443: @_message = Mail.new 444: process(method_name, *args) if method_name 445: end
Receives a raw email, parses it into an email object, decodes it, instantiates a new mailer, and passes the email object to the mailer object‘s receive method. If you want your mailer to be able to process incoming messages, you‘ll need to implement a receive method that accepts the raw email string as a parameter:
class MyMailer < ActionMailer::Base def receive(mail) ... end end
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 389 389: def receive(raw_mail) 390: ActiveSupport::Notifications.instrument("receive.action_mailer") do |payload| 391: mail = Mail.new(raw_mail) 392: set_payload_for_mail(payload, mail) 393: new.receive(mail) 394: end 395: end
Allows you to add attachments to an email, like so:
mail.attachments['filename.jpg'] = File.read('/path/to/filename.jpg')
If you do this, then Mail will take the file name and work out the mime type set the Content-Type, Content-Disposition, Content-Transfer-Encoding and base64 encode the contents of the attachment all for you.
You can also specify overrides if you want by passing a hash instead of a string:
mail.attachments['filename.jpg'] = {:mime_type => 'application/x-gzip', :content => File.read('/path/to/filename.jpg')}
If you want to use a different encoding than Base64, you can pass an encoding in, but then it is up to you to pass in the content pre-encoded, and don‘t expect Mail to know how to decode this data:
file_content = SpecialEncode(File.read('/path/to/filename.jpg')) mail.attachments['filename.jpg'] = {:mime_type => 'application/x-gzip', :encoding => 'SpecialEncoding', :content => file_content }
You can also search for specific attachments:
# By Filename mail.attachments['filename.jpg'] #=> Mail::Part object or nil # or by index mail.attachments[0] #=> Mail::Part (first attachment)
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 504 504: def attachments 505: @_message.attachments 506: end
Allows you to pass random and unusual headers to the new +Mail::Message+ object which will add them to itself.
headers['X-Special-Domain-Specific-Header'] = "SecretValue"
You can also pass a hash into headers of header field names and values, which will then be set on the Mail::Message object:
headers 'X-Special-Domain-Specific-Header' => "SecretValue", 'In-Reply-To' => incoming.message_id
The resulting Mail::Message will have the following in it‘s header:
X-Special-Domain-Specific-Header: SecretValue
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 466 466: def headers(args=nil) 467: if args 468: @_message.headers(args) 469: else 470: @_message 471: end 472: end
The main method that creates the message and renders the email templates. There are two ways to call this method, with a block, or without a block.
Both methods accept a headers hash. This hash allows you to specify the most used headers in an email message, these are:
You can set default values for any of the above headers (except :date) by using the default class method:
class Notifier < ActionMailer::Base self.default :from =><EMAIL_ADDRESS>:bcc =><EMAIL_ADDRESS>:reply_to =><EMAIL_ADDRESS>end
If you need other headers not listed above, use the headers[‘name’] = value method.
When a :return_path is specified as header, that value will be used as the ‘envelope from’ address for the Mail message. Setting this is useful when you want delivery notifications sent to a different address than the one in :from. Mail will actually use the :return_path in preference to the :sender in preference to the :from field for the ‘envelope from’ value.
If you do not pass a block to the mail method, it will find all templates in the view paths using by default the mailer name and the method name that it is being called from, it will then create parts for each of these templates intelligently, making educated guesses on correct content type and sequence, and return a fully prepared Mail::Message ready to call :deliver on to send.
For example:
class Notifier < ActionMailer::Base default :from =><EMAIL_ADDRESS>def welcome mail(:to =><EMAIL_ADDRESS>end end
Will look for all templates at "app/views/notifier" with name "welcome". However, those can be customized:
mail(:template_path => 'notifications', :template_name => 'another')
And now it will look for all templates at "app/views/notifications" with name "another".
If you do pass a block, you can render specific templates of your choice:
mail(:to =><EMAIL_ADDRESS>do |format| format.text format.html end
You can even render text directly without using a template:
mail(:to =><EMAIL_ADDRESS>do |format| format.text { render :text => "Hello Mikel!" } format.html { render :text => "
Hello Mikel!
" } end
Which will render a multipart/alternative email with text/plain and text/html parts.
The block syntax also allows you to customize the part headers if desired:
mail(:to =><EMAIL_ADDRESS>do |format| format.text(:content_transfer_encoding => "base64") format.html end
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 592 592: def mail(headers={}, &block) 593: # Guard flag to prevent both the old and the new API from firing 594: # Should be removed when old API is removed 595: @mail_was_called = true 596: m = @_message 597: 598: # At the beginning, do not consider class default for parts order neither content_type 599: content_type = headers[:content_type] 600: parts_order = headers[:parts_order] 601: 602: # Call all the procs (if any) 603: default_values = self.class.default.merge(self.class.default) do |k,v| 604: v.respond_to?(:call) ? v.bind(self).call : v 605: end 606: 607: # Handle defaults 608: headers = headers.reverse_merge(default_values) 609: headers[:subject] ||= default_i18n_subject 610: 611: # Apply charset at the beginning so all fields are properly quoted 612: m.charset = charset = headers[:charset] 613: 614: # Set configure delivery behavior 615: wrap_delivery_behavior!(headers.delete(:delivery_method)) 616: 617: # Assign all headers except parts_order, content_type and body 618: assignable = headers.except(:parts_order, :content_type, :body, :template_name, :template_path) 619: assignable.each { |k, v| m[k] = v } 620: 621: # Render the templates and blocks 622: responses, explicit_order = collect_responses_and_parts_order(headers, &block) 623: create_parts_from_responses(m, responses) 624: 625: # Setup content type, reapply charset and handle parts order 626: m.content_type = set_content_type(m, content_type, headers[:content_type]) 627: m.charset = charset 628: 629: if m.multipart? 630: parts_order ||= explicit_order || headers[:parts_order] 631: m.body.set_sort_order(parts_order) 632: m.body.sort_parts! 633: end 634: 635: m 636: end
# File /usr/lib/ruby/gems/1.8/gems/actionmailer-3.0.0.beta4/lib/action_mailer/base.rb, line 640 640: def set_content_type(m, user_content_type, class_default) 641: params = m.content_type_parameters || {} 642: case 643: when user_content_type.present? 644: user_content_type 645: when m.has_attachments? 646: if m.attachments.detect { |a| a.inline? } 647: ["multipart", "related", params] 648: else 649: ["multipart", "mixed", params] 650: end 651: when m.multipart? 652: ["multipart", "alternative", params] 653: else 654: m.content_type || class_default 655: end 656: end


Rebecca He's Portfolio
Loading quote...
Work
Hello! My name is Rebecca and I'm a software engineer at Google in Boston. I've been here for two and a half years and I'm starting to feel confident as a software engineer, but it definitely took me some time. I had imposter syndrome for quite a while (and still have it, to some extent). Here's a blog post I wrote during my junior year internship on imposter syndrome. Warning: there are dorky Harry Potter references.
Anyways, more about what I do - I work on a product called Firebase App Distribution. I mostly do backend, writing code in Java. My team is really collaborative and supportive, and we do a lot of pair programming. We also like to have fun. For Halloween, we dressed up as handmaids from the Handmaid's Tale.
When I'm not coding, I'm leading a Women in Firebase Book Club, mentoring awesome students through this amazing program called SPS, and planning cultural events for the Asian Googler Network.
Hobbies
Outside of work, I have a few different hobbies. First, I like music. I played piano when I was a kid, and I've been trying to keep it up. I also like to sing and am always down for a jam sesh.
I also really like nature. Sometimes I just need to get out of the house and on top of a mountain. It makes me feel zen. I also apparently like taking weird pictures when I go hiking.
I recently got into weight lifting and running. For running, I used to hate it. So much. But ever since the fall of 2018, when I ran my first 5K, I've been more open to it. I'm planning to run my first half marathon in May. Wish me luck!
Personal
My parents immigrated to the United States before I was born. I have a younger brother who is in college. My grandma lives with my family in Maryland (where I'm from).


Dear User 2,
You have been invited to join the project My Project<>"& as the Project Manager.
You will be managing the project on behalf of Lead Organisation 123 who is the lead organisation.
Please sign in to accept this invitation. If you haven't used this service before you must create an account.
Yours sincerely
Innovate UK, part of UK Research and Innovation
Tel: 0300 321 4357
Email: competitions@iuk.ukri.org


| utf8-package {utf8} | R Documentation |
UTF-8 Text Processing
Functions for manipulating and printing UTF-8 encoded text:
as_utf8
attempts to convert character data to UTF-8,
throwing an error if the data is invalid;
utf8_valid
tests whether character data is valid
according to its declared encoding;
utf8_normalize
converts text to Unicode composed
normal form (NFC), optionally applying case-folding and compatibility
maps;
utf8_encode
encodes a character string, escaping all
control characters, so that it can be safely printed to the screen;
utf8_format
formats a character vector by truncating
to a specified character width limit or by left, right, or center
justifying;
utf8_print
prints UTF-8 character data to the screen;
utf8_width
measures the display width of UTF-8 character
strings (many emoji and East Asian characters are twice as wide as other
characters);
output_ansi
and output_utf8
test for
the output connections capabilities.
For a complete list of functions, use library(help = "utf8")
.
Patrick O. Perry


White to play 31
pips White=167 Black=145
(CorrectAnswer= 0/0, ErrorScore= 0)
1. 8/5 6/5 eq: -0.098 51.32% (G: 0.00% B:0.00%) 48.68% (G:12.14% B:0.69%) 2. 24/21 8/7* eq: -0.107 (-0.009) 51.71% (G: 0.00% B:0.00%) 48.29% (G:14.33% B:0.79%) 3. 13/10 8/7* eq: -0.109 (-0.010) 52.19% (G: 0.00% B:0.00%) 47.81% (G:15.15% B:1.32%) 4. 8/7* 7/4 eq: -0.181 (-0.083) 49.55% (G: 0.00% B:0.00%) 50.45% (G:15.90% B:1.33%) 5. 8/7* 6/3 eq: -0.219 (-0.121) 48.71% (G: 0.00% B:0.00%) 51.29% (G:17.61% B:1.68%)


--- layout: post title: District 6 Museum date: 2016-03-08 13:04:58.000000000 -06:00 type: post published: true status: publish categories: - South Africa Reading Tour tags: [] meta: _edit_last: '1' _thumbnail_id: '22491' _wpas_done_all: '1' _mk_post_love: '0' _vc_post_settings: a:2:{s:7:"vc_grid";a:0:{}s:10:"vc_grid_id";a:0:{}} textfalse: '' _layout: right _padding: 'false' _header_toolbar: 'true' _featured_image: 'true' _meta: 'true' _single_featured: '-1' _portfolio_meta_next_prev: '-1' _portfolio_related_project: '-1' _custom_bg: 'false' background_selector_orientation: full boxed_layout_shadow: 'false' body_color: '#fff' body_source: no-image body_cover: 'false' page_color: '#fff' page_source: no-image page_cover: 'false' header_color: '#fff' header_source: no-image header_cover: 'false' banner_color: '#fafafa' banner_source: no-image banner_cover: 'false' footer_color: '#191919' footer_source: no-image footer_cover: 'false' _page_title_intro: none _page_title_padding: '40' _page_title_fullHeight: 'false' _page_title_align: left _page_title_size: '18' _page_title_letter_spacing: '0' _breadcrumb_skin: dark _breadcrumb_custom_color: '#ffffff' _breadcrumb_custom_hover_color: '#000000' _theme_options_build: '' _dynamic_styles: Tjs= author: login: wlftn email<EMAIL_ADDRESS>display_name: lauren first_name: Lauren last_name: '' ---
March 2, 2016, 9:14am SA time | 1:14am IA time
“I will never walk past an empty space & see it as empty.” Bonita, our tour guide at the District 6 Museum, stands in the center of the large sanctuary space of this converted Methodist Church in downtown Cape Town. This building is the only structure, other than the Mosque, still standing from what was once a thriving, diverse and vibrant community of District 6, a neighborhood that apartheid literally tore down.
Bonita is a former resident of District 6 (which is now wasteland in the center of the city) and she talks about the re-remembering that she, and the patrons of this museum are engaged in — “People were actively forgetting back then, because they didn’t want to have information that could be discovered through torture,” she tells us. “They were unable to fully grieve the loss of their homes.” I ask her why this happened; this forced and fast gentrification, this quick cleansing of an area that was beautiful: “Those views were not meant for poor people,” Bonita whispers.
On the floor, protected by plastic, is a large canvas painted with the thick lines and hand-painted labels of the old District 6 map. These are the streets that were demolished. Block after block, painted in bright cobalt blue outlines, these neighborhoods exist only in memory. On the map, names of families have been painted according to where they once lived — families that mingled, mixed, socialized, ate together, watched each other’s kids. There is no longer movement on the map. The paint is still.
Leaning down, I suddenly see the name ‘Fortune’, right below my feet: the surname of my own husband, my own daughter. Our family name. Reading the name strikes me with a deep shock — and a tangible, physical vibration of déjà vu. (Later, a friend will explain to me that 'Fortune' was a common name here among black South Africans, a given name — adopted — and later a slave name in the newly forming States. And I wonder out loud with amazement: could we somehow be connected, genetically — but surely psychically, surely spiritually —, to this diverse and incredible history, across racial and locational boundaries, all the way in an entirely different continent and hemisphere?)
As I look down at the hand-painted name, I catch a glimpse of something in my mind: for a second I can almost see our own family packing up, moving out, leaving our house and home forever, under the watchful eye of a mad government, without explanation.


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Event Log


Gwen Stefani marks 15th anniversary of ‘Love Angel Music Baby’ with special reissue
The hit solo album has been remastered
Gwen Stefani has announced that she’s marking the 15th anniversary of ‘Love Angel Music Baby’ with a special reissue of the album.
The Grammy-nominated first solo effort from the former No Doubt frontwoman was released back in November 2004. It spawned the hit singles ‘What You Waiting For?’, ‘Hollaback Girl’, ‘Rich Girl’ and ‘Cool’.
Taking to Twitter yesterday (November 18), Stefani wrote: “I can’t believe ‘Love Angel Music Baby’ came out 15 years ago this week!” She then confirmed that a “special remastered anniversary edition” of the LP will be arriving this Friday (November 22).

See the post below.
This new edition of the album has been remastered by Chris Gehringer, who has also worked with the likes of Rihanna, Lady Gaga, and Drake.
Next week (November 26), Stefani will continue the celebrations as she performs a medley of ‘Love Angel Music Baby’ cuts during an episode of The Voice.
Reaching Number 4 in the UK Albums Chart, ‘Love Angel Music Baby’ also received high acclaim from critics upon its release. In a four-star review, NME said: “[It’s] one of the most frivolously brilliant slabs of shiny retro-pop anyone’s had the chutzpah to release all year. And that includes The Killers.”
Back in 2017, Gwen Stefani released her ‘You Make It Feel Like Christmas’ festive album. It followed on from 2016’s ‘This Is What The Truth Feels Like’.


class: center, middle, inverse, title-slide # Analysis of RNA-seq data in R and Bioconductor
###
http://rockefelleruniversity.github.io/RU_RNAseq/
--- # RNAseq (part 4) --- ## The data In this session we will use one of our datasets from a splicing factor Knockdown RNAseq experiment found at GEO [here](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101763). I have aligned all FQ to BAM and counted in genes and exons using Rsubread and summariseOverlaps(). --- ## The data All Gene and Exon counts can be found as .RData obects in **data** directory - Counts in disjoint exons can be found at - **data/senescence_ExonCounts.RData** --- ## What we will cover In our first session we will looked at two separate ways we can gain gene expression estimates from raw sequencing data as fastQ files. In our last session we imported our expression estimates to identify differences in the expression of genes between two conditions. In this session we will look at how we can identify differences in the expression of genes between multiple conditions and how we can identify changes in Exon usage to infer changes in transcript usage. --- ## Counts from SummariseOverlaps In our first session we counted our reads in genes using the summarise overlaps function to generate our **RangedSummarizedExperiment** object. I have counted using a **BamFileList** of all T-Reg samples to easily organise my samples and save memory with the **yieldSize** parameter. ```r library(Rsamtools) bamFilesToCount <- c("Sorted_shPTBP1_53_rep1.bam","Sorted_shPTBP1_53_rep2.bam","Sorted_shPTBP1_53_rep3.bam", "Sorted_vec_4OHT_rep1.bam","Sorted_vec_4OHT_rep2.bam","Sorted_vec_4OHT_rep3.bam" ) myBams <- BamFileList(bamFilesToCount,yieldSize = 10000) ``` --- ## Counts from SummariseOverlaps For differential exon usage we must use a non-overlapping, disjoint set of exons to count on. We can produce a non-overlapping set of exons by using the **disjointExons()** function. This is equivalent of us having to create GFF file and using the python script wrapped up in DEXseq package (*dexseq_prepare_annotation.py*). ```r library(GenomicFeatures) library(TxDb.Hsapiens.UCSC.hg19.knownGene) nonOverlappingExons <- disjointExons(TxDb.Hsapiens.UCSC.hg19.knownGene) names(nonOverlappingExons) <- paste(mcols(nonOverlappingExons)$gene_id, mcols(nonOverlappingExons)$exonic_part, sep = "_") nonOverlappingExons[1:2, ] ``` ``` ## GRanges object with 2 ranges and 3 metadata columns: ## seqnames ranges strand | gene_id tx_name ## <Rle> <IRanges> <Rle> | <CharacterList> <CharacterList> ## 1_1 chr19 58858172-58858395 - | 1 uc002qsd.4 ## 1_2 chr19 58858719-58859006 - | 1 uc002qsd.4 ## exonic_part ## <integer> ## 1_1 1 ## 1_2 2 ## ------- ## seqinfo: 93 sequences (1 circular) from hg19 genome ``` --- ## Disjoint Exons ![](imgs/collapsedE1.png) --- ## Disjoint Exons ![](imgs/collapsedE2.png) --- ## Counts from SummariseOverlaps Now we have our disjoint exons to count on we can use the **summarizeOverlaps()**. ```r library(GenomicAlignments) senescence_ExonCounts <- summarizeOverlaps(nonOverlappingExons, myBam, ignore.strand = TRUE, inter.feature = FALSE) senescence_ExonCounts ``` ``` ## class: RangedSummarizedExperiment ## dim: 269121 6 ## metadata(0): ## assays(1): counts ## rownames(269121): 1_1 1_2 ... 9997_3 9997_4 ## rowData names(3): gene_id tx_name exonic_part ## colnames(6): Sorted_shPTBP1_53_rep1.bam Sorted_shPTBP1_53_rep2.bam ... ## Sorted_vec_4OHT_rep2.bam Sorted_vec_4OHT_rep3.bam ## colData names(1): condition ``` --- ## Counts from SummariseOverlaps Our **RangedSummarizedExperiment** contains our counts as a matrix accessible by the **assay()** function. Each row is named by our Exon ID, geneID + exon number. ```r assay(senescence_ExonCounts)[1:2, ] ``` ``` ## Sorted_shPTBP1_53_rep1.bam Sorted_shPTBP1_53_rep2.bam ## 1_1 400 489 ## 1_2 573 970 ## Sorted_shPTBP1_53_rep3.bam Sorted_vec_4OHT_rep1.bam ## 1_1 317 326 ## 1_2 455 452 ## Sorted_vec_4OHT_rep2.bam Sorted_vec_4OHT_rep3.bam ## 1_1 650 508 ## 1_2 801 885 ``` --- ## Counts from SummariseOverlaps We can retrieve the GRanges we counted by the **rowRanges()** accessor function. The GRanges rows contains our disjoint exons used in counting and is in matching order as rows in our count table. ```r rowRanges(senescence_ExonCounts)[1:5, ] ``` ``` ## GRanges object with 5 ranges and 3 metadata columns: ## seqnames ranges strand | gene_id tx_name ## <Rle> <IRanges> <Rle> | <CharacterList> <CharacterList> ## 1_1 chr19 58858172-58858395 - | 1 uc002qsd.4 ## 1_2 chr19 58858719-58859006 - | 1 uc002qsd.4 ## 1_3 chr19 58859832-58860494 - | 1 uc002qsf.2 ## 1_4 chr19 58860934-58861735 - | 1 uc002qsf.2 ## 1_5 chr19 58861736-58862017 - | 1 uc002qsd.4,uc002qsf.2 ## exonic_part ## <integer> ## 1_1 1 ## 1_2 2 ## 1_3 3 ## 1_4 4 ## 1_5 5 ## ------- ## seqinfo: 93 sequences (1 circular) from hg19 genome ``` --- # Differential transcript usage --- ## Differential transcript usage from RNAseq data Previously we have investigated how we may identify changes in the overall abundance on gene. ![](imgs/dge.png) --- ## Differential transcript usage from RNAseq data We may also be interested in identifying any evidence of a changes in transcript usage within a gene. ![](imgs/dtu.png) --- ## Differential transcript usage from RNAseq data Due to the uncertainty in the assignment of reads to overlapping transcripts from the same genes, a common approach to investigate differential transcript usage is to define non-overlapping disjoint exons and identify changes in their usage. ![](imgs/deu2.png) --- # DEXSeq --- ## DEXSeq Options for differential transcript usage are available in R including DEXseq, and Voom/Limma. DEXseq can be a little slow when fitting models but it has options for parallelization. Voom/Limma is significantly faster by comparison, but provides a less informative output. --- ## DEXSeq inputs To use DEXseq package has a similar set up to that seen for DESeq2. We first must define our metadata data.frame of sample groups, with sample rownames matching colnames of our **RangedSummarizedExperiment** object. ```r metaData <- data.frame(condition = c("shPTBP1_53", "shPTBP1_53", "shPTBP1_53", "senescence", "senescence", "senescence"), row.names = colnames(senescence_ExonCounts)) metaData ``` ``` ## condition ## Sorted_shPTBP1_53_rep1.bam shPTBP1_53 ## Sorted_shPTBP1_53_rep2.bam shPTBP1_53 ## Sorted_shPTBP1_53_rep3.bam shPTBP1_53 ## Sorted_vec_4OHT_rep1.bam senescence ## Sorted_vec_4OHT_rep2.bam senescence ## Sorted_vec_4OHT_rep3.bam senescence ``` --- ## DEXseq inputs Previously we have been using **DESeqDataSetFromMatrix()** constructor for DESeq2. In DEXSeq we can use the **DEXSeqDataSet** constructor in a similar manner. As with the **DESeqDataSetFromMatrix()** function, we must provide the counts matrix, our metadata dataframe and our design specifying with metadata columns to test. In addition to this we must provide our exon IDs and gene IDs to the allow for the association of exons to the genes they constitute. ```r countMatrix <- assay(senescence_ExonCounts) countGRanges <- rowRanges(senescence_ExonCounts) geneIDs <- as.vector(unlist(countGRanges$gene_id)) exonIDs <- rownames(countMatrix) ``` --- ## DEXseq inputs We must specify our design to include a sample and exon effect to distinguish change in exon expression from a change in exon usage. Previously we simply added a design formula with our group of interest. ``` ~ GROUPOFINTERERST ``` Now we specify. ``` ~ sample + exon + GROUPOFINTERERST:exon ``` --- ## Running DEXseq Now we can use the **DEXSeqDataSet** constructor as we have **DESeqDataSetFromMatrix()** but in addition we specify the exon ids to the **featureID** argument and the gene ids to the **groupID** argument. ```r library(DEXSeq) ddx <- DEXSeqDataSet(countMatrix, metaData, design = ~sample + exon + condition:exon, featureID = exonIDs, groupID = geneIDs) ddx ``` ``` ## class: DEXSeqDataSet ## dim: 269121 12 ## metadata(1): version ## assays(1): counts ## rownames(269121): 1:1_1 1:1_2 ... 9997:9997_3 9997:9997_4 ## rowData names(4): featureID groupID exonBaseMean exonBaseVar ## colnames: NULL ## colData names(3): sample condition exon ``` --- ## DEXseq from RangedSummarizedExperiment As we have generated a **RangedSummarizedExperiment** for exon counting, we can use the more straightforward **DEXSeqDataSetFromSE** function as we used the **DESeqDataSet** function. We can simply provide our **RangedSummarizedExperiment** and design to the **DEXSeqDataSetFromSE** function. ```r colData(senescence_ExonCounts)$condition <- factor(c("shPTBP1_53", "shPTBP1_53", "shPTBP1_53", "senescence", "senescence", "senescence")) ddx <- DEXSeqDataSetFromSE(senescence_ExonCounts, design = ~sample + exon + condition:exon) ddx ``` ``` ## class: DEXSeqDataSet ## dim: 269121 12 ## metadata(1): version ## assays(1): counts ## rownames(269121): 1:E001 1:E002 ... 9997:E003 9997:E004 ## rowData names(5): featureID groupID exonBaseMean exonBaseVar ## transcripts ## colnames: NULL ## colData names(3): sample condition exon ``` --- ## DEXseq (filtering low exon counts) DEXseq is fairly computationally expensive so we can reduce the time taken by removing exons with little expression up front. Here we can filter any exons which do not have 10 reads in at least two samples (our smallest group size is 3). ```r ToFilter <- apply(assay(senescence_ExonCounts), 1, function(x) sum(x > 10)) > 2 senescence_ExonCounts <- senescence_ExonCounts[ToFilter, ] table(ToFilter) ``` ``` ## ToFilter ## FALSE TRUE ##<PHONE_NUMBER>70 ``` ```r ddx <- DEXSeqDataSetFromSE(senescence_ExonCounts, design = ~sample + exon + condition:exon) ddx ``` ``` ## class: DEXSeqDataSet ## dim: 155870 12 ## metadata(1): version ## assays(1): counts ## rownames(155870): 1:E001 1:E002 ... 9997:E001 9997:E002 ## rowData names(5): featureID groupID exonBaseMean exonBaseVar ## transcripts ## colnames: NULL ## colData names(3): sample condition exon ``` --- ## Running DEXseq in steps. We can normalize, estimate dispersion and test for differential exon usage with the **estimateSizeFactors()**, **estimateDispersions()** and **testForDEU()** functions. Finally we can estimate fold changes for exons using the **estimateExonFoldChanges()** function and specifying metadata column of interest to **fitExpToVar** parameter. ```r ddx <- estimateSizeFactors(ddx) ddx <- estimateDispersions(ddx) ddx <- testForDEU(ddx, reducedModel = ~sample + exon) ddx = estimateExonFoldChanges(ddx, fitExpToVar = "condition") ``` --- ## DEXseq results Once have processed our data through the **DEXseq** function we can use the **DEXSeqResults()** function with our **DEXseq** object. We order table to arrange by pvalue. ```r dxr1 <- DEXSeqResults(ddx) dxr1 <- dxr1[order(dxr1$pvalue), ] ``` --- ## DEXseq function As with DESeq2, the DEXseq has a single workflow function which will normalise to library sizes, estimate dispersion and perform differential exon usage in one go. The returned object is our **DEXSeqResults** results object. ```r dxr1 <- DEXSeq(ddx) dxr1 <- dxr1[order(dxr1$pvalue), ] ``` --- ## DEXseq results The **DEXSeqResults** results object contains significantly more information than the DESeq2 results objects we have seen so far. ```r dxr1[1, ] ``` ``` ## ## LRT p-value: full vs reduced ## ## DataFrame with 1 row and 13 columns ## groupID featureID exonBaseMean dispersion stat pvalue ## <character> <character> <numeric> <numeric> <numeric> <numeric> ## 57142:E008 57142 E008 21482.1 0.00455953 2036.23 0 ## padj senescence shPTBP1_53 log2fold_shPTBP1_53_senescence ## <numeric> <numeric> <numeric> <numeric> ## 57142:E008 0 30.1855 63.8085 4.12122 ## genomicData countData transcripts ## <GRanges> <matrix> <list> ## 57142:E008 chr2:55252222-55254621:- 40618:35656:54755:... uc002ryd.3,uc002rye.3 ``` --- ## DEXseq results The **DEXSeqResults** results object can be converted to a data.frame as with **DESeqResults** objects ```r as.data.frame(dxr1)[1, ] ``` ``` ## groupID featureID exonBaseMean dispersion stat pvalue padj ## 57142:E008 57142 E008 21482.14 0.00455953 2036.225 0 0 ## senescence shPTBP1_53 log2fold_shPTBP1_53_senescence ## 57142:E008 30.18552 63.80855 4.121217 ## genomicData.seqnames genomicData.start genomicData.end ## 57142:E008 chr2 55252222 55254621 ## genomicData.width genomicData.strand ## 57142:E008 2400 - ## countData.Sorted_shPTBP1_53_rep1.bam ## 57142:E008 40618 ## countData.Sorted_shPTBP1_53_rep2.bam ## 57142:E008 35656 ## countData.Sorted_shPTBP1_53_rep3.bam ## 57142:E008 54755 ## countData.Sorted_vec_4OHT_rep1.bam ## 57142:E008 1007 ## countData.Sorted_vec_4OHT_rep2.bam ## 57142:E008 747 ## countData.Sorted_vec_4OHT_rep3.bam transcripts ## 57142:E008 838 uc002ryd.... ``` --- ## Visualizing DEXseq results A very useful feature of the **DEXSeqResults** results objects is the ability to visualise the differential exons along our gene using the **plotDEXSeq()** function and providing our **DEXSeqResults** results object and gene of interest to plot. ```r plotDEXSeq(dxr1, "57142") ``` ![](RU_RNAseq_p4_files/figure-html/da4-1.png)<!-- --> --- ## Visualizing DEXseq results We can specify the parameter **displayTranscripts** to TRUE to see the full gene model. ```r plotDEXSeq(dxr1, "57142", displayTranscripts = TRUE) ``` ![](RU_RNAseq_p4_files/figure-html/da5c-1.png)<!-- --> --- ## Visualizing DEXseq results ![](imgs/RTN4.png) --- ## Visualizing DEXseq results The differential exon usage for Entrez gene 7168 is more complex. ```r plotDEXSeq(dxr1, "7168", displayTranscripts = TRUE) ``` ![](RU_RNAseq_p4_files/figure-html/da5-1.png)<!-- --> --- ## Visualizing DEXseq results ![](imgs/TPM1.png) --- ## Visualizing DEXseq results We can produce an HTML report for selected genes using the **DEXSeqHTML** function. By default this will create a file called *testForDEU.html* within a folder *DEXSeqReport* in the current working directory. ```r DEXSeqHTML(dxr1, "57142") ``` [Link to result here](data/DEXSeqReport/testForDEU.html) --- ## Gene Q values It may be desirable to obtain a pvalue summarising the differential exon usage to a gene level. We can obtain an adjusted p-value per gene with the **perGeneQValue()** with our **DEXSeqResults** results object. The result is a vector of adjusted p-values named by their corresponding gene. ```r geneQ <- perGeneQValue(dxr1) geneQ[1:10] ``` ``` ## 1 100 1000 10000 10001 100033414 100037417 100048912 ## 1 1 1 1 1 1 1 1 ## 100049076 10005 ## 1 1 ``` --- ## Gene Q values We could merge this back to our full results table to provides exon and gene level statistics in one report. ```r gQFrame <- as.data.frame(geneQ, row.names = names(geneQ)) dxDF <- as.data.frame(dxr1) dxDF <- merge(gQFrame, dxDF, by.x = 0, by.y = 1, all = TRUE) dxDF <- dxDF[order(dxDF$geneQ, dxDF$pvalue), ] dxDF[1:2, ] ``` ``` ## Row.names geneQ featureID exonBaseMean dispersion stat ## 97377 57142 0 E008 21482.144 0.004559530 2036.225 ##<PHONE_NUMBER> 0 E009 2805.899 0.004776165 1092.222 ## pvalue padj senescence shPTBP1_53 ## 97377 0.000000e+00 0.000000e+00 30.18552 63.80855 ## 117732 1.619401e-239 1.246016e-234 49.34291 18.36318 ## log2fold_shPTBP1_53_senescence genomicData.seqnames genomicData.start ## 97377 4.121217 chr2 55252222 ## 117732 -4.264727 chr15 63353397 ## genomicData.end genomicData.width genomicData.strand ## 97377 55254621 2400 - ##<PHONE_NUMBER>3472 76 + ## countData.Sorted_shPTBP1_53_rep1.bam ## 97377 40618 ## 117732 619 ## countData.Sorted_shPTBP1_53_rep2.bam ## 97377 35656 ## 117732 668 ## countData.Sorted_shPTBP1_53_rep3.bam countData.Sorted_vec_4OHT_rep1.bam ## 97377 54755 1007 ## 117732 705 4442 ## countData.Sorted_vec_4OHT_rep2.bam countData.Sorted_vec_4OHT_rep3.bam ## 97377 747 838 ##<PHONE_NUMBER> 5206 ## transcripts ## 97377 uc002ryd.... ## 117732 uc002alh.... ``` --- # RNAseq with multiple groups --- --- ## RNAseq with multiple groups So far we have only reviewed a two group comparison of differential expression and differential transcript usage. We can compare multiple groups fairly easily in DESeq2. --- ## The data For this we will be using the Tissue RNAseq datasets from Encode. I have pre-aligned and counted the Tissue RNAseq datasets and provide a **RangedSummarizedExperiment** object **../data/gC_TissueFull.RData** --- ## The data I load our precounted Tissues' reads gene model and the loaded **RangedSummarizedExperiment** contains counts from three groups. ```r load("data/gC_TissueFull.RData") geneCounts_Tissue ``` ``` ## class: RangedSummarizedExperiment ## dim: 24100 6 ## metadata(0): ## assays(1): '' ## rownames(24100):<PHONE_NUMBER>8 ... 100040911 170942 ## rowData names(0): ## colnames(6): Sorted_Heart_1 Sorted_Heart_2 ... Sorted_Liver_1 ## Sorted_Liver_2 ## colData names(0): ``` --- ## DEseq2 input We can update the **colData** slot of our **RangedSummarizedExperiment** object to allow us to make use of metadata in DESeq2 later. ```r colData(geneCounts_Tissue)$Tissue <- c("Heart", "Heart", "Kidney", "Kidney", "Liver", "Liver") ``` --- ## DEseq2 input We can now set up our **DESeq2** object as we have previously and run the **DESeq** workflow function ```r dds <- DESeqDataSet(geneCounts_Tissue, design = ~Tissue) dds <- DESeq(dds) ``` --- ## Running DEseq2 To extract comparisons now we can simply specify the tissues of interest to the results funtion. ```r heartVsLiver <- results(dds, c("Tissue", "Heart", "Liver")) heartVskidney <- results(dds, c("Tissue", "Heart", "Kidney")) heartVskidney ``` ``` ## log2 fold change (MLE): Tissue Heart vs Kidney ## Wald test p-value: Tissue Heart vs Kidney ## DataFrame with 24100 rows and 6 columns ## baseMean log2FoldChange lfcSE stat pvalue ## <numeric> <numeric> <numeric> <numeric> <numeric> ## 497097 1.70942 -0.111433 1.968710 -0.0566022 9.54862e-01 ## 19888 6.07325 1.640170 0.933425 1.7571520 7.88919e-02 ## 20671 64.37483 1.654297 0.413053 4.0050438 6.20060e-05 ## 27395 352.70614 1.049120 0.278011 3.7736704 1.60863e-04 ## 18777 517.65589 -1.997611 0.340689 -5.8634514 4.53344e-09 ## ... ... ... ... ... ... ## 434935 0.0000000 NA NA NA NA ## 100041256 0.0000000 NA NA NA NA ## 100039574 0.0000000 NA NA NA NA ## 100040911 0.0974588 -0.445965 4.996527 -0.089255 0.928879 ## 170942 10.2419060 -1.330817 0.917523 -1.450445 0.146934 ## padj ## <numeric> ## 497097 9.79719e-01 ## 19888 1.66810e-01 ## 20671 2.81050e-04 ## 27395 6.81433e-04 ## 18777 3.52364e-08 ## ... ... ## 434935 NA ## 100041256 NA ## 100039574 NA ## 100040911 NA ## 170942 0.27357 ``` --- ## Comparing multiple results To identify genes specifically upregulated in Heart versus other tissues. We can then overlap the upregulated genes from the Heart vs Liver and Heart vs Kidney comparisons. First we convert **DESeqResults** objects into a data.frame, remove NAs and extract most interesting columns to us. ```r heartVsLiverDF <- as.data.frame(heartVsLiver) heartVskidneyDF <- as.data.frame(heartVskidney) heartVsLiverDF <- heartVsLiverDF[!is.na(heartVsLiverDF$padj), ] heartVskidneyDF <- heartVskidneyDF[!is.na(heartVskidneyDF$padj), ] heartVsLiverDF <- heartVsLiverDF[, c("log2FoldChange", "padj")] heartVskidneyDF <- heartVskidneyDF[, c("log2FoldChange", "padj")] ``` --- ## Comparing multiple results We can then update the column names and merge our data.frame to have a single table of most useful information. ```r colnames(heartVskidneyDF) <- paste0("HeartVsKidney", "_", colnames(heartVskidneyDF)) colnames(heartVsLiverDF) <- paste0("HeartVsLiver", "_", colnames(heartVsLiverDF)) fullTable <- merge(heartVsLiverDF, heartVskidneyDF, by = 0) fullTable[1:2, ] ``` ``` ## Row.names HeartVsLiver_log2FoldChange HeartVsLiver_padj ## 1 100017 -0.5992115 0.2119439 ## 2 100019 -0.6497866 0.1418297 ## HeartVsKidney_log2FoldChange HeartVsKidney_padj ## 1 0.1578806 0.8036222 ## 2 -0.1634218 0.7819743 ``` --- ## Comparing multiple results Now we can extract our genes upregulated in Heart in both conditions. ```r upInHeart <- fullTable$HeartVsLiver_log2FoldChange > 0 & fullTable$HeartVsKidney_log2FoldChange > 0 & fullTable$HeartVsLiver_padj < 0.05 & fullTable$HeartVsKidney_padj < 0.05 upInHeartTable <- fullTable[upInHeart, ] upInHeartTable[1:2, ] ``` ``` ## Row.names HeartVsLiver_log2FoldChange HeartVsLiver_padj ## 15 100038347 4.950045 1.057785e-49 ## 37 100038575 2.454005 2.159250e-02 ## HeartVsKidney_log2FoldChange HeartVsKidney_padj ## 15 4.342545 2.003141e-50 ## 37 3.161305 1.040576e-03 ``` --- ## Do genes overlap? We can also make a logical data.frame of whether a gene was upregulated in Heart for both Liver and Kidney comparisons. ```r forVenn <- data.frame(UpvsLiver = fullTable$HeartVsLiver_log2FoldChange > 0 & fullTable$HeartVsLiver_padj < 0.05, UpvsKidney = fullTable$HeartVsKidney_log2FoldChange > 0 & fullTable$HeartVsKidney_padj < 0.05) forVenn[1:3, ] ``` ``` ## UpvsLiver UpvsKidney ## 1 FALSE FALSE ## 2 FALSE FALSE ## 3 FALSE TRUE ``` --- ## Do genes overlap? We can use **limmas'** **vennDiagram()** to produce a venn diagram of overlap in upregulation in heart vs Liver or Kidney. ```r library(limma) vennDiagram(forVenn) ``` ![](RU_RNAseq_p4_files/figure-html/tissue10-1.png)<!-- --> --- ## RNAseq with multiple groups When dealing with multiple groups it may be of interest to identify genes are highly variable between groups but with low variability within groups, akin to an Anova test. In DESeq2, we can identify genes significantly changing across groups by comparing our models with and without our groups of interest using the **results** function. - Tissue model ``` ~ Tissue ``` - No groups model ``` ~ 1 ``` --- ## Likelihood-ratio test To compare out two models we must set the parameter of **reduced** to our alternative model of no groups. We also set the **test** parameter to **LRT** to allow us to compare the models. ```r dds2 <- DESeq(dds, test = "LRT", reduced = ~1) acrossGroups <- results(dds2) acrossGroups <- acrossGroups[order(acrossGroups$pvalue), ] acrossGroups[1:3, ] ``` ``` ## log2 fold change (MLE): Tissue Liver vs Heart ## LRT p-value: '~ Tissue' vs '~ 1' ## DataFrame with 3 rows and 6 columns ## baseMean log2FoldChange lfcSE stat pvalue padj ## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> ## 16483 125680.4 -2.29486 1.583024 1642.43 0.00000e+00 0.00000e+00 ## 17888 43583.9 -14.87459 0.652461 1566.29 0.00000e+00 0.00000e+00 ## 21956 16505.0 -15.05883 1.057810 1431.06 1.77388e-311 1.01844e-307 ``` --- ## Likelihood-ratio test We can use the **plotCounts()** to get review expression profile of a gene, one at a time. We define the gene of interest to **gene** parameter and **intgroup** to specify metadata column to group counts by. ```r plotCounts(dds2, gene = "17888", intgroup = "Tissue") ``` ![](RU_RNAseq_p4_files/figure-html/tissue12-1.png)<!-- --> --- ## RNAseq with multiple groups We can combine our result with our previous table of pair-wise contrasts to provide information on where differences between groups exist. ```r acrossGroups <- as.data.frame(acrossGroups[, c("pvalue", "padj")]) colnames(acrossGroups) <- paste0("AllGroups", "_", colnames(acrossGroups)) allGroups <- merge(fullTable, acrossGroups, by.x = 1, by.y = 0, all = TRUE) allGroups <- allGroups[order(allGroups$AllGroups_pvalue), ] allGroups[1:2, ] ``` ``` ## Row.names HeartVsLiver_log2FoldChange HeartVsLiver_padj ## 5257 16483 2.294861 2.469712e-01 ## 6057 17888 14.874592 1.625126e-111 ## HeartVsKidney_log2FoldChange HeartVsKidney_padj AllGroups_pvalue ## 5257 -16.69262 2.090655e-140 0 ## 6057 14.84458 2.099275e-218 0 ## AllGroups_padj ## 5257 0 ## 6057 0 ``` --- # Time for an exercise. [Link_to_exercises](../../exercises/exercises/RNAseq_part4_exercise.html) [Link_to_answers](../../exercises/answers/RNAseq_part4_answers.html)


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Preparation time
30 mins to 1 hour
Cooking time
30 mins to 1 hour
Serves
Serves 4
For the salsa, place the garlic, chilli, onion and coriander into a large pestle and mortar and crush to a paste.
Add the tomato and crush together, before adding the beer and canned tomatoes. Mix to combine.
Season to taste with salt and freshly ground black pepper.
Transfer this mixture to a pan (or a traditional Mexican lava stone pestle), place over a high heat and bring to the boil - take care if you're using a stone pestle as it will get very hot.
Reduce the heat and simmer for 20 minutes. Add more salt and freshly ground black pepper, to taste, and keep warm.
For the molcajete base, heat a griddle pan until hot. Toss the chicken strips with olive oil and salt and freshly ground black pepper in a small bowl. Place the chicken onto the griddle pan to start cooking while you season the steak.
Season the steak with salt and freshly ground black pepper, to taste, and add the steak and chorizo to the griddle pan.
Cook the meat for 2-3 minutes, then turn over and cook for a further another 2-3 minutes, or until cooked all the way through. Remove the meat from the griddle and set aside in a warm place to rest.
Add the whole spring onions to the griddle pan and griddle for 1-2 minutes. Remove and set aside in a warm place.
For the refried beans, heat a saucepan until hot and add the sunflower oil and onions and fry until golden-brown.
Add the beans, along with the water from one of the cans. Stir, add the chicken stock and bring to the boil.
Reduce the heat and simmer for 5-8 minutes.
Remove the beans from the heat and allow to cool slightly. Purée with a hand-held blender and season with salt and freshly ground black pepper. Reheat the beans if necessary.
To serve, toast the tortillas under the grill.
The salsa should either be served hot in the lava stone pestle, or, if using a saucepan, pour into a normal kitchen pestle and mortar and serve from there.
Slice the steak and place into the salsa in the pestle, along with the chorizo and chicken. Garnish the top with the grilled spring onions, avocado and chopped coriander. Serve the refried beans and toasted tortillas alongside.


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Senior, CS Major, likes long walks on the beach
First year online CS graduate student, a research scientist in Medical Science.
Senior, B.S. Computer Science, hobbies include intramural sports and beer brewing.
Senior, Computer Science Major, love cats and Japanese Anime


Across: 1. see 3dn. 9. It's said to come from empty vessels pounding me my grain (9) 10. see 3dn. 11. Used 3dn to be groovy (6) 12. Bandage small 17 down pop star (8) 14.  Pure instinct has control of 17 (4) 18. Sell one out of the film (4) 19. Agent from European nation grabbing his easiest opening (10) 21. Legal institution profits from those whose price is right (8) 22. Isaac, moving trilogies (the first one way back) (6) 25. Famous Edwardian retreat? (5) 26. Knight of the grail has smile following little look at layer (9) 27,1dn. Two sound transporting ships pause for fifth month with men & boys suffering skeletal weakness (6 3 6 3 5 2 5) Down: 1. see 27ac. 2. Games put out telepathic reception spectrum (5) 3,1ac,10ac. What foils foil? (3 3 2 8 4 3 5) 4. Wrong to proceed from death to birth perhaps (4) 5. Get thin gin preparation as applied to poor belts (10) 6. Like posted confirmation (6) 7. Overly tough exterior diminished and impotent (9) 8. Challengers serve nuanced network (9 6) 13. Insect repellant oil lent car eccentricity (10) 15. A TV pair to sabotage a player of 26 (9) 17. An old one may be 7, but two old ones appear here (8) 20. Stain surrounding oddly dour old god (6) 23. Fool satellite with hacker's final intervention (5) 24. Drop from building (4)


Before Change
if self.to_train == 1:
batch = self.sample()
clock.set_batch_size(len(batch))
pdparams, v_preds = self.calc_pdparam_v(batch)
advs, v_targets = self.calc_advs_v_targets(batch, v_preds)
policy_loss = self.calc_policy_loss(batch, pdparams, advs) // from actor
After Change
// forward passes for losses
states = batch["states"]
actions = batch["actions"]
v_preds = self.calc_v(states, net=self.critic_net)
q1_preds = self.calc_q(states, actions, self.q1_net)
q2_preds = self.calc_q(states, actions, self.q2_net)
pdparams = self.calc_pdparam(states)
action_pd = policy_util.init_action_pd(self.body.ActionPD, pdparams)


{% extends "transformation-base.html" %} {% block content %} {% load modelview_tags %} {% include "transformation/snippets/title_snippet.html" with format='RDB' %} {% for hidden in form.hidden_fields %} {{ hidden }} {% endfor %}
In this step, you can specify the RDF subject(s). For each table it can be constructed from a base URI, the table name and a combination of the content of one or multiple column names.
If you change the default values, please assure that for different subjects the subject URIs are distinct.
What is waiting for you:
You will be confronted with instructing the converter how to generate meaningful unique subject URIs for the individual lines of your data. In order to do so, you will
How it typically works:
The URIs of the subjects of the generated RDF statements are typically composed of
Simple setting:
If the typical procedure is too cumbersome to you, you may want to get the subject URIs automatically set to blank nodes without meaningful names, by checking the box 'use blank nodes'. Please note that the advantage of having expressive subject URIs is lost in this case.
Base URI:
Use Blank Nodes only
Provide a subject
Base URI:
To build your subject URI, click the column name fields below into the subject URI field.{% endif %}
| {% else %} |
{% endif %}
{% if column.isPrimaryKey == 'PRI' %}
{{ column.name }} (Primary Key) {% else %} {{ column.name }} {% endif %} {% if not column.hasNullValues %} NOT NULL {% else %} {% endif %} {% if ":" in column.foreign_key_string %} {% for fkey in fkeys %} {% if fkey.0 == table.name and fkey.3 in column.foreign_key_string and fkey.4 in column.foreign_key_string %} {{ column.foreign_key_string }} {% endif %} {% endfor %} {% endif %} |
{% endfor %}
| {{ value }} | {% else %}{% endif %} {% endfor %} |


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Use this tool to generate/customize/build flags to run QEMU with.
{{ cmdWarning }}
To initialize a disk file, use fallocate or dd. Cache types.
{{ diskWarning }}
This method requires some more in-depth configuration. For help setting things up on Debian, please consider reading this page on network configuration with Proxmox.
{{ ipWarning }}
{{ vncWarning }}
{{ flags }}


Trekking is a form of walking, undertaken with the specific purpose of exploring and enjoying the scenery. It usually takes place on trails in areas of relatively unspoiled wilderness."
The great mountain ranges are some of the most beautiful and interesting areas of the world to visit. As they are often not served by roads, they can also be the most remote and difficult places to get to and the only real way to see them is on foot. For some people the trekking may be an end in itself, for others it is a means to enjoy the magnificent panoramas and often the peoples of the mountains with their culture, traditions and religions provide an equal interest to the scenery.
Cultural Treks & Expedition is a pioneer adventure trekking company, the leading organizer of tours, trekking holidays & mountaineering, with the widest choice of the destination, style and duration in Nepal, Tibet, Bhutan and Sikkim/Darjeeling (India).
A tours, trekking, mountaineering, rafting and jungle safari and other related holidays should not be exactly that a holiday, not an arduous ordeal – unless, of course, that what you want. In order to help you choose the itinerary that is right for you, we give each of our holidays grade, and supply information on the number of days walking maximum and average altitudes etc, in the trip description. In addition we answer you below holidays with cost and about our services. We hope that you will find this helpful in matching your ability and aspirations to a particular holiday.


JINGLE ALL THE WAY A film review by Michael John Legeros Copyright 1996 Michael John Legeros
(Fox) Directed by Brian Levant Written by Harry Elfont, Deborah Kaplan, and Randy Kornfield Cast Arnold Schwarzenegger, Sinbad, Phil Hartman, Robert Conrad, Rita Wilson, Jake Lloyd, James Belushi MPAA Rating "PG" Running Time 96 minutes Reviewed at General Cinemas at Pleasant Valley, Raleigh, NC (22NOV96)
==
This big-budget Christmas comedy has a coarse and very obvious wit, which would be perfect for kids if this were a kid's movie. I'm not sure it is, even though the humor is as broad as the shoulders of its star, Arnold Schwarzenegger. The Terminator plays a daddy desperate to find the most coveted toy in Minneapolis-- a Turbo Man doll-- on the day before Christmas. Sure, the wee ones will love seeing Arnie chased through a living room by a reindeer, pummeled by purses in the Mall of America, and all the roughhouse rowdiness between him and Sinbad, who plays his postal-carrying rival. But what will they make of the darker elements, like Phil Hartman's lecherous next-door neighbor? Or Schwarz- enegger slugging a Conga line of Clauses in a bootleg toy factory? Or, my favorite, the smoldering head of a wise man that gets drop-kicked into a crowd of carolers? (Heh. Who *hasn't* wanted to cause unrest among ye merry gentlemen?) Tolerating the rest of the movie, with its lazy plotting, frantic pacing, and a message that violence is a solution to everything, is a greater challenge. As is accepting the fantasy ending, which, while extremely upbeat, veers uncomfortably into LAST ACTION HERO territory. Stay through the credits for the final gag. Great soundtrack, too, with several swingin' tunes from the Brian Setzer Orchestra.
Grade: C+
--
Mike Legeros - Raleigh, NC, USA, Earth<EMAIL_ADDRESS>(h) -<EMAIL_ADDRESS>(w) I'm also on the Web! http://www.pagesz.net/~legeros/
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