David Byrne is planning an immersive new theatre production
'Theater Of The Mind' is coming next August
David Byrne has announced plans for an immersive project entitled Theater of the Mind.
The production is inspired by historical and recent lab research according to the former Talking Heads man.
“It will be in a warehouse, where it’s divided into a bunch of different rooms,” Byrne told Rolling Stone. “A group of 16 audience members will go from room to room and experience these perceptual things. When they leave one room, another group goes in there. That way, you can get 400 people in from 6 pm to 10. You get the same number as if it were a theatre show, but you get more in small groups.”
According to the production company 600 Highwaymen, he previously workshopped a version of Theater of the Mind on Governors Island in New York in late 2017.
But Byrne decided to take it to Denver, Colorado instead. “The Denver Center for the Performing Arts have done immersive things like this before — not quite like this — but they’ve cultivated an audience in Denver,” he said.
Mala Gaonkar, the research analyst who co-wrote the project with Byrne, said in a statement: “For a few years, David and I partnered with several cognitive neuroscience labs to see how some of the most basic human intuitions determine how humans react,”
“What we concluded was the experiments and ideas of the labs we partnered with, several of which we embedded in our narrative, seemed as engaging as any piece of theatre. Theater of the Mind will challenge the ever-changing reality written in our minds and I am thrilled for audiences to think of science and theatre in a new way.”
The production is set to open in Denver in August 2020. No plans to bring it to the UK have been announced yet.
Byrne recently took his American Utopia tour to Broadway. The residency will run until January 20, 2020.


Please follow each step carefully! it is recommended to disconnect from internetwhile creating your wallet and backing up your data
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Currently making my first steps into web design. Learning in progress
Hiring? Click here to get my CV
Let's have a chat! We can talk about coding while we drink some coffee (or tea if you prefer!)
© 2021 Silvia B.


More than 10.000 people are using zUA lOPANGO
We made a powerful relationship with our users, they're happy to use our webiste
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This dashboard serves as the main control hub for all subservers connected to instruments.
Each subserver "calls home" every 10 minutes, as shown by its "Last Updated" time. If a subserver has exceeded more than 10 minutes, chances are it has become disconnected and needs to be reconfigured. Be aware that if you start a machine that is no longer in contact with the server, it will fail silently.
NOTE: Servers should be left in the "Stopped" condition, and only started when ready to use.
Once a server has been started, remote connections can be made using the listed IP address.
| EE Tag # | Machine Name | Description | IP Address | Status | Action | Last Updated |
|---|---|---|---|---|---|---|
| {{ machine.ee_tag }} | {{ machine.name }} | {{ machine.description }} | {{ machine.ip }} |
Running
Stopped
|
|
{{ machine.time_since }} |


Adote um amigo!
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Seja um membroDúvidas
- Qual a idade dos animais?
- Bem variada, temos cachorros de todas as idades, esperando um lar para da r amor e carinho.
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- O processo le em torno de 1 a 3 semanas, nalizaremos todas as opções o mais rapido possivel, se tudo estiver certinho é só assinar e levar seu Pet.
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Contato
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Escolha o porte do seu futuro Pet e veja nossa lista de adoção.
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Hello everyone! My name is Sajal Gupta and if you are reading this you must be wanting to know about me. Well, I am 2nd Year Undergraduate of SGSITS Indore. I am a full-stack Web Developer and have been working on various technologies which you can see in my Skills section down below . Besides development, i also have a good knowledge of Machine Learning and Deep Learning.Other than technical skills , i love to play piano and guitar.
Here i have worked on python project which include the use of technologies like python,Django MySQL and Bootstrap.
Secured 84% in 12th and 10 CGPA in 10th standard
This is a restro website ,which is capable of registering users and accepting their orders. Technologies used in this projects are Node JS ,React JS, Mongodb,Bootstrap.
View ProjectThis is a simple chat application made with socket.io Users just Have to enter their name and same Room no. for chatting
View Project


| MetroCon 2004 - Power Engineering Track |
Abstracts & Biographies
|
See Program Outline and Schedule
Fuel Cells, the Hydrogen
option
Sidney Bolfing, Texas State Technical College
8:30-9:30
Abstract: Based on the results of a two-day DACUM (develop a curriculum) focus group attended by a panel of thirteen noted fuel cell technology experts from across the nation, a curriculum has been developed and presented for approval by the Texas Higher Education Coordinating Board (THECB). The objective of the two-year Fuel Cell Maintenance and Repair Technician program is to provide the graduate with hands-on training and education in fuel system theory, operation, installation, maintenance, troubleshooting and repair. The program includes 72 credit hours of extensive classroom and “hands on” laboratory experience with stationary fuel cells designed for residential, commercial, and industrial applications. Successful graduates will receive an Associate of Applied Science (A.A.S.) degree, and will be prepared to enter the workforce with working background in a wide range of fuel cell types and applications.
Fuel cells range from palm-sized milliwatt devices to large industrial systems producing megawatts of electrical power for manufacturing, to commercial distributed generation applications, and powering single homes that are both grid connected and grid independent. The majority of fuel cells that operate on hydrogen produce very little or no harmful pollutants. Fuel cell systems produce DC and can export AC electrical power if an inverter is used. Most fuel cells also produce highly useful by-products of heat and pure water.
There is little need for fuel cell technicians in Texas presently, due primarily to equipment costs. However, within three to five years, the use of stationary fuel cell systems (as well as demand for qualified fuel cell technicians) is expected to grow at an exponential rate. Predictions indicate demand for fuel cell systems will increase as the costs of equipment is reduced, the cost of fossil fuels increase, and mandates for higher efficiencies and lower emissions.
Biography: Sidney Bolfing, an Electrical/Computerized Control Systems and Robotics senior instructor at TSTC Waco, is the project coordinator for fuel cell curriculum development at Texas State Technical College Waco. As chairman of the Texas Fuel Cell Technology Consortium (TFCTC), he has been instrumental in leading fuel cell curriculum development for two-year colleges dedicated to producing qualified fuel cell technicians for the state of Texas.
Mr. Bolfing has been an instructor at TSTC for 10 years in the Electrical/Computerized Control Systems & Robotics department. As a Senior Instructor at TSTC, he holds a Bachelor of Science degree in Technical Training and Development from the University of Texas, as well as associate’s degrees in Electrical Power Technology and Heating Ventilation Air Conditioning and Refrigeration Technology from Texas State Technical College Waco.
He holds a Texas Master Electrical License and a Texas Air Conditioning
and Refrigeration Contractors License. His professional background includes
positions with Brown and Root Engineering, General Tire Company, Trane Company,
Lux Packaging, Waco Service Inc. and Texas State Technical College Waco. He
also serves as vice president of the Heart of Texas Old Car Club Inc.
Wood Pole Alternatives
Rick Hausmann, PE, TXU Electric Delivery
Wesley Oliphant, Newmark International
Jim Bob Wiles, Shakespeare Composite Structures
9:45-10:45
Abstract: Structures are an integral part of the overhead delivery of electricity from generation to end user. Many factors influence the type of structure that will be designed for a particular application. The program will consist of presentations from representatives of the concrete, fiberglass, and steel pole industries. The presentations will focus on the applications, the advantages, and the limitations of the different types of structures used through out the utility industry.
Biography: Rick Hausmann is a senior
engineer at TXU Electric Delivery Company. He has 22 years of experience with
TXU Electric Delivery Company and is currently responsible for overhead distribution
standards including related material and equipment specifications. Specifically
he is responsible for the distribution standards associated with poles, foundations,
cross-arms, guys, anchors, conductor sags, insulators, pole framing, line hardware,
and joint use spacing and loading. Rick's duties include overseeing and evaluating
new and failed material/equipment to ensure manufacturer compliance with specifications
and designs. Additionally Rick provides technical expertise to internal workgroups
regarding standard design practices, construction methods, and interpretation
of the National Electrical Safety Code. He also is responsible for the completion
of the design, plans, and specifications for complex applications which require
a concrete or steel self-supporting structure.
Rick earned a Bachelor of Science in Civil Engineering from the University of
Missouri and an MBA from Amberton University in Dallas, Texas. He is a licensed
Professional Engineer in the State of Texas as is an active member of several
professional organizations including the American Society of Civil Engineers,
the American Wood Preservers Association, and the Southwest Electric Distribution
Exchange. Rick is married with 3 children and enjoys golf in his spare time.
Wesley J. Oliphant, P.E. - Received his B.S. in Civil Engineering
in 1974 from Texas A&M University, and an MBA from the University of Houston
in 1986. He is a registered Professional Engineer, and has over 28 years experience
in the design and manufacturing of non-wood pole products for Electrical Transmission,
Distribution, Substation, Lighting, and Telecommunication applications. Mr.
Oliphant is currently a Vice President with Valmont-Newmark, a world leader
in the design and manufacturing of spun concrete poles, tubular steel poles,
and fiberglass composite poles for these applications.
Mr. Oliphant also serves on numerous industry committees related to the design and use of non-wood poles, including the ASCE Committee of Electrical Transmission Structures; ASCE Committee for Reliability Based Design of Utility Pole Structures; and, the ASCE Committee for The Design and Use of Spun Concrete Poles.
Lance Kinney, P.E., Texas Board of Professional Engineers
11:00-12:00
Biography: Lance Kinney, P.E., has been with the Texas
Board of Professional Engineers for two years as an engineering specialist working
on projects for the Executive Director. He is in charge of developing the Continuing
Education Program and Rules for the board. Prior to working at the board, Lance
received a Bachelors degree in Physics from the University of Texas in Austin,
and worked for 11 years as a project engineer at Advanced Micro Devices. He
is also currently an adjunct professor at Austin Community College.
Transmission
Grid Management in Texas
Ken Donohoo, Electric Reliability Council
of Texas (ERCOT)
1:30-3:00
Abstract: Transmission congestion in ERCOT and what is being done to resolve it! ERCOT will provide an overview of transmission congestion, its costs, and how ERCOT is resolving it in the operating and planning environments. ERCOT will also present information on infrastructure additions made to the power system.
Biography: Ken joined ERCOT in 1996 and is Manager System Planning, Transmission Services. His team administers transmission planning activities, including collection of power system planning data, within ERCOT. System Planning conducts technical and simple economic assessments and provides strategies, policies, procedures, and methodologies associated with the planning and reliable operation of the grid.
Ken began his tenure with ERCOT as a Senior Transmission Systems Engineer. His responsibilities included regional transmission planning analysis, conducting available transfer capability studies, generation interconnection studies, calculating transmission system losses, studies to allocate transmission costs, and participating in the work of the Technical Advisory Committee Subcommittees and its task forces. Currently, Ken leads, plans and directs the accomplishment of System Planning Transmission Services objectives. He is responsible for providing technical guidance ensuring sound engineering procedures and effective use of facilities to provide system-wide power system planning, interconnect generation, serve load and ensure the reliability and adequacy of the regional network. He facilitates the input, prioritization, and assessment of the overall power system planning effort. He manages technical and simple economic assessments and provides strategies, policies, procedures, and methodologies associated with the planning and reliable operation of the grid. Ken possesses a unique and valuable blend of technical expertise with strong familiarity of power systems that supports long term planning and development.
Ken received a Bachelor of Science Electrical Engineering (BSEE) degree from
the University of Texas at Arlington in 1982. His extensive background includes
engineering budget analysis, transmission planning, transient analysis, insulation
coordination, surge arrester application, switching analysis, wheeling impact,
loss analysis, project management and engineering management. He is a registered
professional engineer in the state of Texas. Ken is also a senior member of
Institute of Electrical and Electronics Engineers (IEEE) and is ERCOT's representative
on the North American Electric Reliability Council Operating Committee Transmission
Subcommittee and the North American Electric Reliability Council Planning Committee
Transmission Issues Subcommittee.
IRAQ Power System Reconstructions
Lt.Col. Robert P. Morris, U.S. Army
Corps of Engineers
3:15-4:45
Abstract: Electric Power Restoration in Iraq immediately following the change in government was a critical issue in creating a new stable and sustainable government for the Iraqi people. This critical infrastructure restoration mission was given to the US Army Corps of Engineers. Lt.Col. Morris will lead the presentation that conveys the complexity of this topic. Restoration of electric service during a war is not an easy task. The US Army Corps of Engineers provided the coordination and leadership needed to facilitate the accomplishment of this vital goal. He will explain how the delivery systems required to support such an important facet of a nations infrastructure are no doubt the very essence of a viable society.
Biography: Lieutenant Colonel Robert P. Morris, Jr.,
P.E., assumed the duties of Deputy District Engineer on June 21, 2002 following
an assignment at the United States Military Academy, West Point, NY, where he
served as the Director of the Center for Environmental and Geographical Sciences
and Assistant Professor in the Department of Geography and Environmental Engineering.
Lieutenant Colonel Morris graduated from the United States Military Academy
with a Bachelor of Science degree with Civil Engineering concentration in 1980
and a Master of Arts degree in Geography in 1990 from the University of North
Carolina at Chapel Hill. His military service schools include the Armed Forces
Staff College, U.S. Army Command and General Staff College, the Combined Arms
Staff Services School, Mapping, Charting & Geodesy Officers Course, Analytical
Photogrammetric Positioning System Course, Junior Officer Maintenance Course,
Engineer Officer Advanced Course, Engineer Officer Basic Course, Atomic Demolition
Munitions Course and Airborne School.
Lieutenant Colonel Morris has held a variety of assignments in the United States,
Middle East and Europe including command of C Company, 78th Engineer Battalion
(Allied Command Europe Mobile Force) in Germany. He has also served as Executive
Officer for the 29th Engineer Battalion (Topographic); Facility Engineer for
Operations and Maintenance for the Defense Intelligence Agency; Facility Engineer
for the Multinational Forces and Observers in Sinai, Egypt; Engineer Plans Officer
for the VII Corps G-3 REFORGER Planning Cell; Construction Officer for 7th Engineer
Brigade; and Assistant Operations Officer, Company Executive Officer, and Platoon
Leader, 20th Engineer Battalion (Combat).
His military awards include the Defense Meritorious Service Medal (two awards),
Meritorious Service Medal (four awards), Army Commendation Medal (two awards),
the Army Achievement Medal (two awards), the Military Outstanding Volunteer
Service Medal. He also has been awarded the Multinational Forces and Observers
Medal and the Parachutist Badge.
Lieutenant Colonel Morris is a registered professional engineer in Florida and
Virginia, a member of the Board of Directors of the National Association of
Environmental Professionals, and a member of the Society of American Military
Engineers and the Association of American Geographers.


C库线程安全函数和不安全函数
http://infocenter.arm.com/help/index.jsp?topic=/com.arm.doc.dui0492c/Chdiedfe.html
线程安全函数
| Functions | Description |
|---|---|
| calloc(),free(),malloc(),realloc() | The heap functions are thread-safe if the mutex* functions are implemented.A single heap is shared between all threads, and mutexes are used to avoid data corruption when there is concurrent access. Each heap implementation is responsible for doing its own locking. If you supply your own allocator, it must also do its own locking. This enables it to do fine-grained locking if required, rather than protecting the entire heap with a single mutex (coarse-grained locking). |
| alloca() | alloca() is thread-safe because it allocates memory on the stack. |
| abort(),raise(),signal(),fenv.h | The ARM signal handling functions and floating-point exception traps are thread-safe.The settings for signal handlers and floating-point traps are global across the entire process and are protected by locks. Data corruption does not occur if multiple threads call signal() or an fenv.h function at the same time. However, be aware that the effects of the call act on all threads and not only on the calling thread. |
| clearerr(), fclose(),feof(),ferror(), fflush(),fgetc(),fgetpos(), fgets(),fopen(),fputc(), fputs(),fread(),freopen(), fseek(),fsetpos(),ftell(), fwrite(),getc(),getchar(), gets(),perror(),putc(), putchar(),puts(),rewind(), setbuf(),setvbuf(),tmpfile(), tmpnam(),ungetc() | The stdio library is thread-safe if the mutex* functions are implemented.Each individual stream is protected by a lock, so two threads can each open their own stdio stream and use it, without interfering with one another.If two threads both want to read or write the same stream, locking at the fgetc() and fputc() level prevents data corruption, but it is possible that the individual characters output by each thread might be interleaved in a confusing way. Note tmpnam() also contains a static buffer but this is only used if the argument is NULL. To ensure that your use of tmpnam() is thread-safe, supply your own buffer space. |
| fprintf(), printf(),vfprintf(), vprintf(), fscanf(),scanf() | When using these functions:the standard C printf() and scanf() functions use stdio so they are thread-safe. the standard C printf() function is susceptible to changes in the locale settings if called in a multithreaded program. |
| clock() | clock() contains static data that is written once at program startup and then only ever read. Therefore, clock() is thread-safe provided no extra threads are already running at the time that the library is initialized. |
| errno | errno is thread-safe.Each thread has its own errno stored in a __user_perthread_libspace block. This means that each thread can call errno-setting functions independently and then check errno afterwards without interference from other threads. |
| atexit() | The list of exit functions maintained by atexit() is process-global and protected by a lock.In the worst case, if more than one thread calls atexit(), the order that exit functions are called cannot be guaranteed. |
| abs(), acos(), asin(),atan(),atan2(), atof(),atol(), atoi(),bsearch(),ceil(), cos(),cosh(),difftime(), div(),exp(),fabs(), floor(),fmod(),frexp(), labs(),ldexp(),ldiv(), log(),log10(),memchr(), memcmp(),memcpy(),memmove(), memset(),mktime(),modf(), pow(),qsort(),sin(), sinh(),sqrt(),strcat(), strchr(),strcmp(),strcpy(), strcspn(),strlcat(),strlcpy(), strlen(),strncat(),strncmp(), strncpy(),strpbrk(),strrchr(), strspn(),strstr(),strxfrm(), tan(), tanh() | These functions are inherently thread-safe. |
| longjmp(), setjmp() | Although setjmp() and longjmp() keep data in __user_libspace, they call the _alloca* functions, that are thread-safe. |
| remove(), rename(), time() | These functions use interrupts that communicate with the ARM debugging environments. Typically, you have to reimplement these for a real-world application. |
| snprintf(), sprintf(),vsnprintf(),vsprintf(), sscanf(),isalnum(),isalpha(), iscntrl(),isdigit(),isgraph(), islower(),isprint(),ispunct(), isspace(),isupper(),isxdigit(), tolower(),toupper(),strcoll(), strtod(),strtol(),strtoul(), strftime() | When using these functions, the string-based functions read the locale settings. Typically, they are thread-safe. However, if you change locale in mid-session, you must ensure that these functions are not affected.The string-based functions, such as sprintf() and sscanf(), do not depend on the stdio library. |
| stdin, stdout, stderr | These functions are thread-safe. |
线程不安全函数
本作品采用知识共享署名-非商业性使用-相同方式共享 4.0 国际许可协议进行许可。


Here is your Clue For Next Task
- You need to write a simple java code.
- giving you simple text to Decrypt
- Message me decrypted Text on WhatsApp
- You will get next clue.for your task
To make it simple , try shifting of alphabet is between 1 to 5(Now its easy)
Code to Decrypt is as Follows
lettc errmzivwevc hiev


Vue.js is a quiet, very popular JavaScript framework with an impressive set of features, a solid community, and MIT license. Don’t tell anybody, but I think I might even like it better than React. With all this, Vue deserves its own set of helpers for R
, just like d3r
and reactR
.
vueR
provides these helpers with its dependency function html_dependency_vue
and ?htmlwidget?.
We’ll start with a recreation of the simple “Hello World” example from the Vue.js documentation. This is the hard way.
library(htmltools) library(vueR) browsable( tagList( html_dependency_vue(), # local and minimized by default tags$div(id="app","{{message}}"), tags$script( " var app = new Vue({ el: '#app', data: { message: 'Hello Vue!' } }); " ) ) )
vueR
gives us an htmlwidget
that can ease the code burden from above.
vueR
is now part of a Github organization, and hopefully will be backed with interest by more than one (me) developer. For most vueR
users, this section will not apply, but I would like to document the build/update step for new versions of Vue
. In getvue.R
, I created some functions for rapid download and deployment of new Vue
versions. Running all of the code in getvue.R
should update local minified and development versions of Vue and also update the version references in vueR
.
I would love for you to participate and help with vueR
, but please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.


This type describes the rotation to rotate a frame 1 into a frame 2 using quaternions (also called Euler parameters) according to the following definition:
Quaternions.Orientation Q; Real n[3]; Real phi(unit="rad"); Q = [ n*sin(phi/2) cos(phi/2) ]
where "n" is the axis of rotation to rotate frame 1 into frame 2 and "phi" is the rotation angle for this rotation. Vector "n" is either resolved in frame 1 or in frame 2 (the result is the same since the coordinates of "n" with respect to frame 1 are identical to its coordinates with respect to frame 2).
The term "quaternions" is preferred over the historically more reasonable "Euler parameters" in order to not get confused with Modelica "parameters".
| Name | Description |
|---|---|
| equalityConstraint | Return the constraint residues to express that two frames have the same quaternion orientation |


Medco E&P to begin production at Temelat gas block in South Sumatra next month
by Norman HarsonoThe government expects the Temelat gas field in South Sumatra to begin production in early December, one month behind schedule.
The Upstream Oil and Gas Regulatory Task Force (SKK Migas) said in a statement on Monday that the project, which began development in 2017, was delayed by problems related to land acquisition and opposition from local residents.
SKK Migas projects head Luky Yusgiantoro said the regulatory body had talked with the field’s developer, Jakarta-based oil and gas company Medco E&P, and "forecast the project will be onstream by December 10, 2019.”
He added that the project’s estimated value was US$11.4 million and gas production was expected to hit 10–12 million cubic feet per day (mmscfd).
Both figures are largely unchanged from the initial estimated value of $11 million and expected production rate of at least 10 million mmscfd.
The block is set to serve industrial gas customers including state-owned gas distributor PGN and fertilizer maker Pupuk Sriwidjaja Palembang (Pusri).


Cell-type-specific transactivation of the parathyroid hormone-related protein gene promoter by the human T-cell leukemia virus type I (HTLV-I) tax and HTLV-II tax proteins.
Abstract
The human T-cell leukemia virus type I (HTLV-I) and HTLV-II Tax proteins are potent transactivators of viral and cellular gene expression. Using deletion mutants, the downstream parathyroid hormone-related protein (PTHrP) promoter is shown to be responsive to both HTLV-I and HTLV-II Tax as well as the AP1/c-jun proto-oncogene. Transactivation of PTHrP by Tax was seen in T cells but not in B-cell lines or fibroblasts. A carboxy terminal Tax deletion mutant was deficient in transactivation of both the PTHrP and IL2R alpha promoters but not the HTLV-I long terminal repeat (LTR). Exogenous provision of NFkB rescued IL2R alpha expression but not the PTHrP promoter. Thus, HTLV-I Tax, HTLV-II Tax, and c-jun transactivate PTHrP and may contribute to the pathogenesis of hypercalcemia in adult T-cell leukemia.


Akshay Radia
Project Portfolio
Akshay Radia is currently a student at UC San Diego enrolled in CSE170: Human Computer Interaction
Projects
- Converted Hadoop NameNode Load Generator to optioneally run as a MapReduce job
- Committer of CLI to Hadoop Yarn Registry
- Wrote a Reduced-C Compiler: Static Semantic Analyzer and Code Generation (to SPARC Assembly)
- MyCity Application: Android App that integrates Google Maps with Google Chat
- ...


{% extends "bootstrap/base.html" %} {% block title %} Tweet Basic Stats Inputs {% endblock title %} {% block content %}
Choose a type of statistic to query the database for. Apply flters before running with the other window. Basic gives you attribute information while descriptive gives you computational data.
Choose filters to limit your results to tweets with data matching the specified fields.
Use a generated ID to reload a previous set of results.


Iterator over the elements of the dense vector-sparse vector multiplication expression. More...
#include <DVecSVecMultExpr.h>
Public Types | |
| using | Element = ValueIndexPair< ElementType > |
| Element type of the sparse vector expression. | |
| using | IteratorType = ConstIterator_< RemoveReference_< RightOperand > > |
| Iterator type of the sparse vector expression. | |
| using | IteratorCategory = std::forward_iterator_tag |
| The iterator category. | |
| using | ValueType = Element |
| Type of the underlying pointers. | |
| using | PointerType = ValueType * |
| Pointer return type. | |
| using | ReferenceType = ValueType & |
| Reference return type. | |
| using | DifferenceType = ptrdiff_t |
| Difference between two iterators. | |
| using | iterator_category = IteratorCategory |
| The iterator category. | |
| using | value_type = ValueType |
| Type of the underlying pointers. | |
| using | pointer = PointerType |
| Pointer return type. | |
| using | reference = ReferenceType |
| Reference return type. | |
| using | difference_type = DifferenceType |
| Difference between two iterators. | |
Public Member Functions | |
| ConstIterator (LeftOperand vec, IteratorType it) | |
| Constructor for the ConstIterator class. More... | |
| ConstIterator & | operator++ () |
| Pre-increment operator. More... | |
| const Element | operator* () const |
| Direct access to the sparse vector element at the current iterator position. More... | |
| const ConstIterator * | operator-> () const |
| Direct access to the sparse vector element at the current iterator position. More... | |
| ReturnType | value () const |
| Access to the current value of the sparse element. More... | |
| size_t | index () const |
| Access to the current index of the sparse element. More... | |
| bool | operator== (const ConstIterator &rhs) const |
| Equality comparison between two ConstIterator objects. More... | |
| bool | operator!= (const ConstIterator &rhs) const |
| Inequality comparison between two ConstIterator objects. More... | |
| DifferenceType | operator- (const ConstIterator &rhs) const |
| Calculating the number of elements between two expression iterators. More... | |
Private Attributes | |
| LeftOperand | vec_ |
| Left-hand side dense vector expression. | |
| IteratorType | it_ |
| Iterator over the elements of the right-hand side sparse vector expression. | |
Iterator over the elements of the dense vector-sparse vector multiplication expression.
|
inline |
Constructor for the ConstIterator class.
| vec | Handle to the left-hand side dense vector expression. |
| it | Iterator to the current position in the right-hand side sparse vector expression. |
|
inline |
Access to the current index of the sparse element.
|
inline |
Inequality comparison between two ConstIterator objects.
| rhs | The right-hand side expression iterator. |
|
inline |
Direct access to the sparse vector element at the current iterator position.
|
inline |
Pre-increment operator.
|
inline |
Calculating the number of elements between two expression iterators.
| rhs | The right-hand side expression iterator. |
|
inline |
Direct access to the sparse vector element at the current iterator position.
|
inline |
Equality comparison between two ConstIterator objects.
| rhs | The right-hand side expression iterator. |
|
inline |
Access to the current value of the sparse element.


If you already have a Palladio project file (.json) you can load one from your computer or a URL.
Upload from your computer
You can load an existing Palladio project by selecting the file from your computer.
Load a remote Palladio file
You can enter the URL of an existing Palladio project file. Please make sure that the server is CORS-enabled.
Create a new Palladio project by uploading your data from a spreadsheet or flat-file, or load data from a SPARQL endpoint. Not sure how Palladio works?
Load .csv or spreadsheet
Copy and paste out of your spreadsheets, drag-and-drop to upload tabular data (e.g. .csv, .tab, .tsv), or enter a URL to a tabular data file to create a new Palladio project. Not sure how to structure your data?
Load data from a SPARQL endpoint (beta)
SPARQL endpoint (beta)
You can load data from a SPARQL endpoint by providing both the endpoint URL and a valid SPARQL query. After you run the SPARQL query you will have the opportunity to validate your data and re-run the query if necessary before loading the data into Palladio.


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java.lang.Object | +--javax.xml.soap.SOAPPart
The container for the SOAP-specific portion of a
SOAPMessage
object. All messages are required to have a
SOAP part, so when a SOAPMessage
object is
created, it will automatically have a SOAPPart
object.
A SOAPPart
object is a MIME part and has the
MIME headers Content-Id, Content-Location, and Content-Type.
Because the value of Content-Type must be "text/xml", a
SOAPPart
object automatically has a MIME header of
Content-Type with its value set to "text/xml". The value must
be "text/xml" because content in the SOAP part of a message
must be in XML format. Content that is not of type "text/xml"
must be in an AttachmentPart
object rather than in
the SOAPPart
object.
When a message is sent, its SOAP part must have the MIME header Content-Type set to "text/xml". Or, from the other perspective, the SOAP part of any message that is received must have the MIME header Content-Type with a value of "text/xml".
A client can access the SOAPPart
object of a
SOAPMessage
object by calling the method
SOAPMessage.getSOAPPart
. The following line of code, in
which message
is a SOAPMessage
object, retrieves the SOAP part of a message.
SOAPPart soapPart = message.getSOAPPart();
A SOAPPart
object contains a
SOAPEnvelope
object, which in turn contains a
SOAPBody
object and a SOAPHeader
object.
The SOAPPart
method getEnvelope
can
be used to retrieve the SOAPEnvelope
object.
| Constructor Summary | |
SOAPPart()
|
| Method Summary | |
abstract void |
addMimeHeader(java.lang.String name,
java.lang.String value)
Creates a MimeHeader object with the specified
name and value and adds it to this SOAPPart
object. |
abstract java.util.Iterator |
getAllMimeHeaders()
Retrieves all the headers for this SOAPPart
object as an iterator over the MimeHeader
objects. |
abstract Source |
getContent()
Returns the content of the SOAPEnvelope as a JAXP
Source object. |
java.lang.String |
getContentId()
Retrieves the value of the MIME header whose name is "Content-Id". |
java.lang.String |
getContentLocation()
Retrieves the value of the MIME header whose name is "Content-Location". |
abstract SOAPEnvelope |
getEnvelope()
Gets the SOAPEnvelope object associated with
this SOAPPart object. |
abstract java.util.Iterator |
getMatchingMimeHeaders(java.lang.String[] names)
Retrieves all MimeHeader objects that match
a name in the given array. |
abstract java.lang.String[] |
getMimeHeader(java.lang.String name)
Gets all the values of the MimeHeader object
in this SOAPPart object that is identified by
the given String . |
abstract java.util.Iterator |
getNonMatchingMimeHeaders(java.lang.String[] names)
Retrieves all MimeHeader objects whose name
does not match a name in the given array. |
abstract void |
removeAllMimeHeaders()
Removes all the MimeHeader objects for this
SOAPEnvelope object. |
abstract void |
removeMimeHeader(java.lang.String header)
Removes all MIME headers that match the given name. |
abstract void |
setContent(Source source)
Sets the content of the SOAPEnvelope object
with the data from the given Source object. |
void |
setContentId(java.lang.String contentId)
Sets the value of the MIME header named "Content-Id" to the given String . |
void |
setContentLocation(java.lang.String contentLocation)
Sets the value of the MIME header "Content-Location" to the given String . |
abstract void |
setMimeHeader(java.lang.String name,
java.lang.String value)
Changes the first header entry that matches the given header name so that its value is the given value, adding a new header with the given name and value if no existing header is a match. |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Constructor Detail |
public SOAPPart()
| Method Detail |
public abstract SOAPEnvelope getEnvelope() throws SOAPException
SOAPEnvelope
object associated with
this SOAPPart
object. Once the SOAP envelope is
obtained, it can be used to get its contents.
SOAPEnvelope
object for this
SOAPPart
object
SOAPException
- if there is a SOAP errorpublic java.lang.String getContentId()
String
giving the value of the MIME
header named "Content-Id"setContentId(java.lang.String)
public java.lang.String getContentLocation()
String
giving the value of the MIME
header whose name is "Content-Location"setContentLocation(java.lang.String)
public void setContentId(java.lang.String contentId)
String
.
contentId
- a String
giving
the value of the MIME header "Content-Id"
java.lang.IllegalArgumentException
- if
there is a problem in setting the content idgetContentId()
public void setContentLocation(java.lang.String contentLocation)
String
.
contentLocation
- a String
giving the value of the MIME header
"Content-Location"
java.lang.IllegalArgumentException
- if
there is a problem in setting the content location.getContentLocation()
public abstract void removeMimeHeader(java.lang.String header)
header
- a String
giving
the name of the MIME header(s) to be removedpublic abstract void removeAllMimeHeaders()
MimeHeader
objects for this
SOAPEnvelope
object.
public abstract java.lang.String[] getMimeHeader(java.lang.String name)
MimeHeader
object
in this SOAPPart
object that is identified by
the given String
.
name
- the name of the header; example:
"Content-Type"
String
array giving all the values for
the specified headersetMimeHeader(java.lang.String, java.lang.String)
public abstract void setMimeHeader(java.lang.String name, java.lang.String value)
Note that RFC822 headers can contain only US-ASCII characters.
name
- a String
giving the
header name for which to searchvalue
- a String
giving the
value to be set. This value will be substituted for the
current value(s) of the first header that is a match if
there is one. If there is no match, this value will be
the value for a new MimeHeader
object.
java.lang.IllegalArgumentException
- if there was a problem with the specified mime header name or valuegetMimeHeader(java.lang.String)
public abstract void addMimeHeader(java.lang.String name, java.lang.String value)
MimeHeader
object with the specified
name and value and adds it to this SOAPPart
object. If a MimeHeader
with the specified
name already exists, this method adds the specified value
to the already existing value(s).
Note that RFC822 headers can contain only US-ASCII characters.
name
- a String
giving the
header namevalue
- a String
giving the
value to be set or added
java.lang.IllegalArgumentException
- if
there was a problem with the specified mime header name
or valuepublic abstract java.util.Iterator getAllMimeHeaders()
SOAPPart
object as an iterator over the MimeHeader
objects.
Iterator
object with all of the Mime
headers for this SOAPPart
objectpublic abstract java.util.Iterator getMatchingMimeHeaders(java.lang.String[] names)
MimeHeader
objects that match
a name in the given array.
names
- a String
array with
the name(s) of the MIME headers to be returned
Iterator
objectpublic abstract java.util.Iterator getNonMatchingMimeHeaders(java.lang.String[] names)
MimeHeader
objects whose name
does not match a name in the given array.
names
- a String
array with
the name(s) of the MIME headers not to be returned
SOAPPart
object except those that match one of the names in the
given array. The nonmatching MIME headers are returned as
an Iterator
object.public abstract void setContent(Source source) throws SOAPException
SOAPEnvelope
object
with the data from the given Source
object.
source
- javax.xml.transform.Source object with the data to
be set
SOAPException
- if there is a problem in
setting the sourcegetContent()
public abstract Source getContent() throws SOAPException
Source
object.
javax.xml.transform.Source
object
SOAPException
- if the implementation cannot
convert the specified Source
objectsetContent(javax.xml.transform.Source)
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Next: /, Previous: +, Up: Numbers Dictionary
-
number ⇒ negation
-
minuend &rest subtrahends^+ ⇒ difference
number, minuend, subtrahend—a number.
negation, difference—a number.
The function - performs arithmetic subtraction and negation.
If only one number is supplied, the negation of that number is returned.
If more than one argument is given, it subtracts all of the subtrahends from the minuend and returns the result.
The function - performs necessary type conversions.
(- 55.55) ⇒ -55.55 (- #c(3 -5)) ⇒ #C(-3 5) (- 0) ⇒ 0 (eql (- 0.0) -0.0) ⇒ true (- #c(100 45) #c(0 45)) ⇒ 100 (- 10 1 2 3 4) ⇒ 0
Might signal type-error if some argument is not a number. Might signal arithmetic-error.
Numeric Operations, Rational Computations, Floating-point Computations, Complex Computations


ConnorBot is a four wheeled robot that my son Connor and I came up with when thinking of projects. All of the hardware except the soldering was put together by him. The software we thought up by Connor and coded by me.


--- layout: page title: Downloads permalink: /downloads/ ---
Here's the GitHub repository for documentation and the download for Tom Rettig's powerful envLib library, which I modernized and maintain for VFP 9.
This version of MsgSvc has all the functionality of the one found in the INTL Toolkit except for the multilingual features. MSGSVC.ZIP (Public Domain).
A class browser add-in that allows you to extract a component and all its parents and children into a single VCX for sharing purposes.
Audits and reports all occurrences of many potential localization problems in your application.
For example, the DEFINE PAD
menu command has PROMPT
, FONT
, KEY
, and MESSAGE
clauses, all of
which tend to be hard-coded. Gotchas will report the exact locations of all occurrences of DEFINE PAD
, and dozens of other commands and functions. Even if you don't use the intl toolkit, this utility will tell you where some of your international coding problems may
lie. GOTCHAS.ZIP Version 1 (10k, April 4 1995).


rev - reverse lines characterwise
rev [option]
The rev utility copies the specified files to standard output, reversing the order of characters in every line. If no files are specified, standard input is read.
-V, --version Display version information and exit.
-h, --help Display help text and exit.
The rev command is part of the util-linux package and is available from
Linux Kernel Archive


This is a simple fictional hospital demo app monitoring patients data.
It is destined for educational purposes.
Learn more


UX/UI - Conducted consumer research, designed mobile prototype, conducted UX testing, submitted grant purposal, created branding materials, and more.
Research, iPad design - Used research from my master's thesis, The Use of Interacitve Media to create Eco-Activism, to create an educational iPad lesson using Adobe Edge Animate.
Research, Test Methods - Sampled two test groups of middle school students to discover the most "sharable" genre and style environmental youtube video about climate change.
UI - The Activist Report Remote is designed for a webTV platform.The "Compass" allows users to navigate through the platform, control the video player, and perform interactive actions.
UX, Video - Conducted over 25 interviews of Elon Univeristy students to gather insight of Nutella consumption in the college setting. I interviewed participants & edited the video.
Interactive Video - The Activist Report is a cross platform political entertainment series. I produced all media content and developed the entire platform. Check out the interactive music video.
Content Strategy - Conducted on-camera client interviews to gather, organize, and coordinate the hierarchy of content to video, design, and development team members.
Visuals - Illistrator, Photoshop, After Effects, Primere, Edge Animate.. I have a close relationship with them all.
Script, Cinematography - Directed production team and operated primary camera for esteem athletics website and social media video. Also, assisted with branding and website layout.


| Interface | Description |
|---|---|
| SArrayNode |
Represents the JSON array data.
|
| SBoolean |
Represents the boolean data.
|
| SClass<T> |
Represents the arbitrary data.
|
| SDouble |
Represents the double data.
|
| SFloat |
Represents the float data.
|
| SInteger |
Represents the integer data.
|
| SJsonNode |
Represents the JSON data.
|
| SKeyOf<V> |
The function object for retrieving keys from values.
|
| SLockable |
Provides lock/unlock functions.
|
| SLong |
Represents the long data.
|
| SNumber<T extends java.lang.Number> | |
| SObjectNode |
Represents the JSON object data.
|
| SScalar<T> |
Represents the scalar data.
|
| SString |
Represents the string data.
|
| SVariable |
Represents the synchronizable variable.
|
| Class | Description |
|---|---|
| SList<V> |
Represents the list data.
|
| SList.Update<V> | |
| SMap<V> |
Represents the map data.
|
| SMap.Update<V> | |
| SMovableList<V> |
Represents the movable list data.
|
| SMovableList.Move<V> | |
| SNavigableMap<V> |
Represents the navigable map data.
|
| SQueue<T> |
Represents a queue and is more efficient for data streams
compared to the
SList . |
| SROQueue<T> |
Represents a read-only queue and is more efficient for data streams
compared to the
SList . |


001 /* $Id: Substitutor.java<PHONE_NUMBER>-09-02 19:09:47Z simonetripodi $ 002 * 003 * Licensed to the Apache Software Foundation (ASF) under one or more 004 * contributor license agreements. See the NOTICE file distributed with 005 * this work for additional information regarding copyright ownership. 006 * The ASF licenses this file to You under the Apache License, Version 2.0 007 * (the "License"); you may not use this file except in compliance with 008 * the License. You may obtain a copy of the License at 009 * 010 * http://www.apache.org/licenses/LICENSE-2.0 011 * 012 * Unless required by applicable law or agreed to in writing, software 013 * distributed under the License is distributed on an "AS IS" BASIS, 014 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 015 * See the License for the specific language governing permissions and 016 * limitations under the License. 017 */ 018 019 package org.apache.commons.digester; 020 021 import org.xml.sax.Attributes; 022 023 /** 024 *
(Logical) Interface for substitution strategies. 025 * (It happens to be implemented as a Java abstract class to allow 026 * future additions to be made without breaking backwards compatibility.) 027 *
 028 *
 029 * Usage: When {@link Digester#setSubstitutor} is set, Digester 030 * calls the methods in this interface to create substitute values which will 031 * be passed into the Rule implementations. 032 * Of course, it is perfectly acceptable for implementations not to make 033 * substitutions and simply return the inputs. 034 *
 035 *
Different strategies are supported for attributes and body text.
 036 * 037 * @since 1.6 038 */ 039 public abstract class Substitutor { 040 041 /** 042 *
Substitutes the attributes (before they are passed to the 043 * Rule implementations's).
 044 * 045 *
Digester will only call this method a second time 046 * once the original Attributes instance can be safely reused. 047 * The implementation is therefore free to reuse the same Attributes instance 048 * for all calls.
 049 * 050 * @param attributes the Attributes passed into Digester by the SAX parser, 051 * not null (but may be empty) 052 * @return Attributes to be passed to the Rule implementations. 053 * This method may pass back the Attributes passed in. 054 * Not null but possibly empty. 055 */ 056 public abstract Attributes substitute(Attributes attributes); 057 058 /** 059 * Substitutes for the body text. 060 * This method may substitute values into the body text of the 061 * elements that Digester parses. 062 * 063 * @param bodyText the body text (as passed to Digester) 064 * @return the body text to be passed to the Rule implementations 065 */ 066 public abstract String substitute(String bodyText); 067 }


Ramesh Dhakal, the owner of Hotel Green Horizon and Nepal Mountain Trekkers, started as a porter. He entered tourism in 1997, following his friends from Dhading to Kathmandu. However, it was the Visit Nepal 1999 that prompted him to be a regular worker in tourism.
Right before the pandemic, he had renovated his hotel, adding a seventy-seat restaurant as a preparation for the Visit Nepal 2020. Now, the investment seems like a lost cause. He has had zero income for more than a year now. Little savings that he had helped bear the costs for a few months. He had to borrow some from his friends as he could not approach any banks or financial institutions due to the lack of collateral. He says that he has no asset or property, everything he had has been invested in the hotel. When asked how the fall in income has hit his business- he pauses and reflects. Perhaps the stories of struggles are complex and layered- than what he wants to or can share in a short interview. He was compelled to lay off 14 of his staff, reducing his workforce from 18 to 4. He now has only one regular staff in trekking, there were 5 earlier. A few guides he knew have left their jobs and have switched to agriculture.
While business has taken a hit and he has had to lay off workers, he has received little to no support from the government. “We pay taxes, provide employment yet there is no help from the government”, he questions.
Ramesh also highlights the latent impacts of COVID. He notes that the escalation in financial troubles and the lockdown due to the pandemic has affected people’s mental health even more than their finances. No one knows what hidden implications these might have. His energy to work more, take tourism to new heights has faded. He used to donate 5% of his income to charity now he doesn’t even feel like working anymore. Rather, he finds it difficult to open up and share.
He represents not just himself but hundreds of other entrepreneurs in Thamel, who have spent decades of their life in the industry. For the longest of times, tourism was their source of bread and butter. The COVID-induced lockdown and travel restrictions have severely impacted their major source of livelihood. “I have spent my years in this sector, and I can’t start from zero again,” he sighs towards the end of the conversation.


{% extends 'base.html' %} {% block page_title %}{{ block.super }}Never miss any water/power outage announcements{% endblock %} {% block page_headline %}Never miss any water or power outage advisories{% endblock %} {% block page_content %}
Get notified about upcoming and ongoing utility interruptions in Davao City. Subscribe to our free service now to stay updated and prepared.
{% include 'basic_signup_form.html' %}| Description | Type | Service | Provider |
|---|---|---|---|
| {{ notice.headline }} | {{ notice.urgency }} | {{ notice.service }} | {{ notice.provider }} |
No upcoming outages to show.
{% endif %}


--- layout: home title: About Me ---
Engineer with a passion for problem solving.
Studied at UCSD and UCLA.
Previously at Meta, eBay & Cisco.


UEFA stadium categories are categories for football stadiums laid out in the UEFA Stadium Infrastructure Regulations.[1] Using these regulations, stadiums are rated as category one, two, three, or four (renamed from elite) in ascending ranking order. These categories replaced the previous method of ranking stadiums on one to five star scale in 2006. A stadium must be category four to host games in the playoffs of the qualifying stage for the UEFA Champions League or any game in the main competition.[2] Category four is also required to host any game in the main competition of the UEFA Europa League[3] or the UEFA European Football Championship.[4]
If a retractable roof is present, its use will be directed by consultation between the UEFA delegate and the main assigned referee.
Although the minimum stadium capacity for category four is 8,000, no stadium with a capacity less than 30,000 has been selected to host a UEFA Europa League Final, and no stadium with a capacity less than 60,000 has been selected to host a UEFA Champions League Final, since these regulations were introduced in 2006.
After the 2007 UEFA Champions League Final, UEFA President Michel Platini stated that he wanted European Cup finals to be held at stadiums with an average capacity of 70,000 to solve security issues.[5] The hosts for the finals between 2009 and 2013 (Stadio Olimpico, Santiago Bernabéu, Wembley Stadium and Allianz Arena) all had capacities of at least 70,000, but the 2014 host (Estádio da Luz) only holds 65,000 spectators.
Finally, stadium capacities for hosting music concerts should never[opinion] be included in the list since such use normally permits the audience to stand on the stadium's playing surface - especially if such concerts are only ever staged during limited periods of the year (such as the summer "closed season" in most football sports) - as both of these usage qualities clearly fall under the definition of "one-off", "temporary" or "secondary" use rather than "regular", "permanent" or "primary" use.[citation needed]
All stadiums with a capacity of 25,000 or more are included. The list includes all such stadiums in any country which is commonly accepted to be within the borders of Europe, including transcontinental countries that are partially in Europe (e.g., Russia and Turkey), or in a non-European country commonly thought to be European for cultural or historic reasons (e.g., Israel, Cyprus, Azerbaijan, Georgia and Armenia).[citation needed]


0 Project complete
Many times what people need is not a brilliant mind that speaks, but a special heart that listens.
0 Project complete
Assist high school students in teaching mathematics - trignometry, linear algebra, geometry, probability and statistics. Providing solutions with each step solution to avoid any conflicts at high level problems.
Assist undergrad students for any course difficulty and spreading awareness among students on Mathematics fundamentals and use of Machine Learning. Aid professor in examinations and academic curriculum.
Development of CRUD applications and web based applications using core Java, J2EE, JDBC, SQL, Object Oriented Programming techniques, with excellent Data Structure and algorithm concepts. Developed and implemented the MVC pattern using STRUTs framework including JSP, Servlets and Action classes. Extensively used core java concepts such as Multi – threading, Exceptions and Collections. Implemented test cases, design documents and coordinated with the design and QA teams. Worked on Data Access Object (DAO) design pattern for designing data access layer.
Analyse use of smelter plant for the running of generator, formation of 3-phase power and transmission towards grid. Prepared 20 reports on different fault analysis from the time of generation to transmission towards commercial households. Implemented signal processing approach towards filtering and performing clustering to detect accuracy of faults using Neural Network approach.
Awarded the most efficient developer during the tenure of development of E-Commerce website for LEVIS.
With an average score of 97% at ASIAN level.
Completed the course in tabla with a SANGEET BISHARAD from Gandharva Mahavidyalaya Mandal, Mumbai National and International artist in the field of Musical Instruments (Tabla). Auditioned live television, radio and doordarshan programmes all over India, with many famous artists. Organized and participated in about 230+ competetions. A scholarship holder at Center for Cultural Resources and Training (CCRT), Delhi.
Handled upon someone's request or personal research.
Worked as a software developer for a year in development of E-commerce site under HYBRIS platform. Possess an extensive skill set on programming knowledge. Has a very keen interest towards vehicle electrification and artificial intelligence. Currently conducting masters under electrical and computer engineering at California State University, Los Angeles and trying to gain more skill set upon Artificial Intelligence and Machine Learning.
5151 State University Drive, Los Angeles, California, USA


You have reached the end of questions
Hopefully you will be a little more ready for your technical interview, good luck! :)
Why not follow me on
twitter
?
Timer
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Key Controls
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to restart timer
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Goals¶
This chapter introduces the basic classes that host the behaviour of the logic system; for the sake of clarity, we proceed in increasing order of complexity, explaining more complex concepts by using simpler ones.
Goal¶
Object subclass: #Goal
instanceVariableNames: ''
classVariableNames: ''
package: 'MicroKanren-Goals'
I and my subclasses represent a small language to construct logical relations. Formally, I adhere to the abstract grammar:
goal ::=failed
|succeed
|binary_goal
|fresh
|eta
|predicate
failed ::= "Ø" succeed ::= "✓" binary_goal ::=goal
(disj
|conj
|unify
| "!" | "≠")goal
disj ::= "|º" conj ::= "&º" unify ::= "=º" fresh ::= "fresh" [var
] + "."goal
eta ::= "eta" "."goal
var ::= "var"Integer
predicate ::=functor
[value
] + "."goal
functor ::=String
"º" value ::=var
|Object
My subclasses have the responsibility to encode combinations of arbitrary goals. In a pure world, they shouldn’t be stateful with respect to a logical computation. In reality, and more important to build visualizations, we will see that some of them keep references to logic objects, variables in particular.
Warning
Although some goals are stateful, their state is related to a computation branch and modified according to the exploration process that looks for substitutions. For any side process that inspects a particular aspect, a copy of the goal has to be made.
To be polymorphic with me, the onState: message has to be implemented, as my subclasses have to; moreover, the reader will understand during the reading of this doc that it is the main message to respond to to drop into a logic computation.
Failed¶
Atomic subclass: #Failed
instanceVariableNames: ''
classVariableNames: ''
package: 'MicroKanren-Goals'
I am a goal that represent logical falsehood, in particular I encode the
goalGrammar:failed
production. The simpler way to create me
is to send the adapting message #asGoal
to false
, as follows
"GoalTest, protocol tests"
testFailed
| g |
g := false asGoal.
self assert: g solutions equals: #( ) modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
Succeed¶
Atomic subclass: #Succeed
instanceVariableNames: ''
classVariableNames: ''
package: 'MicroKanren-Goals'
I am a goal that represent logical truth, in particular I encode the
goalGrammar:succeed
production. The simpler way to create me
is to send the adapting message #asGoal
to true
, as follows
"GoalTest, protocol tests"
testSucceed
| g |
g := true asGoal.
self
assert: g solutions
equals: { Var tautology }
modulo: #asOrderedCollection. " #(#tautology)"
^ self exportComputationTreeOfGoal: g limitedTo: -1
where
"Var class, protocol creating" tautology ^ #tautology
Fresh¶
Suspended subclass: #Fresh
instanceVariableNames: 'variables'
classVariableNames: ''
package: 'MicroKanren-Goals'
I am a goal that introduces logic variables, in particular I encode the
goalGrammar:fresh
production.
"GoalTest, protocol tests"
testFreshFailed
| g |
g := [ :q | false asGoal ] asGoal.
self assert: g solutions equals: #( ) modulo: #asOrderedCollection. " #()"
^ self exportComputationTreeOfGoal: g limitedTo: -1
"GoalTest, protocol tests"
testFreshSucceed
| g |
g := [ :q | true asGoal ] asGoal.
self
assert: g solutions
equals: { 0 asReifiedVar }
modulo: #asOrderedCollection. " an Array(•₀)"
^ self exportComputationTreeOfGoal: g limitedTo: -1
where
"Integer, protocol *MicroKanren-core" asReifiedVar ^ self asReifiedWithVarClass: ReifiedVarand
"Integer, protocol *MicroKanren-core" asReifiedWithVarClass: aClass ^ aClass new id: self; yourself
"GoalTest, protocol tests"
testFreshMultipleVars
| g |
g := [ :q :r | true asGoal ] asGoal.
self
assert: g solutions
equals: (Array with: {
0 asReifiedVar.
1 asReifiedVar })
modulo: #asOrderedCollection. " an Array(an Array(•₀ •₁))"
^ self exportComputationTreeOfGoal: g limitedTo: -1
Moreover, we can also use a block without arguments in order to postpone the computation, for instance to support recursive goals such as
"GoalTest, protocol tests"
testEtaRaw
| g |
g := self eternity: Object new.
self assert: g class equals: Eta
where
"GoalTest, protocol utilities" eternity: x ^ [ self eternity: x ] asGoal
Unify¶
Binary subclass: #Unify
instanceVariableNames: ''
classVariableNames: ''
package: 'MicroKanren-Goals'
I am a goal that represent logical equality, in particular I encode the
goalGrammar:unify
production.
"GoalTest, protocol tests"
testUnifyThreeWithThree
| g |
g := 3 unifyo value: 3.
self
assert: g solutions
equals: { Var tautology }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
where
"Object, protocol *MicroKanren-core" unifyo ^ [ :anObject | self unifyWith: anObject ]and
"Object, protocol *MicroKanren-core" unifyWith: another ^ Unify new left: self; right: another; yourself
"GoalTest, protocol tests"
testUnifySymmetryFourWithVar
| g |
g := [ :q | 4 unifyo value: q ] asGoal.
self assert: g solutions equals: { 4 } modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
"GoalTest, protocol tests"
testUnifySymmetryVarWithFour
| g |
g := [ :q | q unifyo value: 4 ] asGoal.
self assert: g solutions equals: { 4 } modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
"GoalTest, protocol tests"
testUnifyWithTopmostSharing
| g |
g := [ :r |
[ :x :y | r unifyo value: (Array with: x with: y) asCons ]
asGoal ] asGoal.
self
assert: g solutions
equals: {
0 asReifiedVar.
1 asReifiedVar } asCons
modulo: #asOrderedCollection. " (•₀ •₁)"
^ self exportComputationTreeOfGoal: g limitedTo: -1
"GoalTest, protocol tests"
testUnifyWithTopmostWithoutSharing
| g |
g := [ :r |
[ :x :y |
(LinkedList with: x with: r) asCons unifyo value:
(LinkedList with: 1 with: y) asCons ] asGoal ] asGoal.
self
assert: g solutions
equals: { 0 asReifiedVar }
modulo: #asOrderedCollection. " an Array(•₀)"
^ self exportComputationTreeOfGoal: g limitedTo: -1
"GoalTest, protocol tests"
testUnifyWithTopmostSharingWithRepetition
| g |
g := [ :r |
[ :x :y |
(LinkedList
with: x
with: y
with: x
with: y) asCons unifyo value: r ] asGoal ] asGoal.
self
assert: g solutions
equals: {
0 asReifiedVar.
1 asReifiedVar.
0 asReifiedVar.
1 asReifiedVar } asCons
modulo: #asOrderedCollection. " (•₀ •₁ •₀ •₁)"
^ self exportComputationTreeOfGoal: g limitedTo: -1
"GoalTest, protocol tests"
testUnifySharing
| g |
g := [ :r |
[ :x | (r unifyo value: x) , (x unifyo value: true) ] asGoal ]
asGoal.
self
assert: g solutions
equals: { true }
modulo: #asOrderedCollection. " #(true)"
^ self exportComputationTreeOfGoal: g limitedTo: -1
The previous examples show unifications that can be satisfied; on the
contrary, when two objects cannot be equal for any substitution we have
a Failed
goal holding the counterexample, such as
"GoalTest, protocol tests"
testUnifyFourWithThree
| g |
g := 4 unifyo value: 3.
self assert: g solutions equals: #( ) modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
Disj¶
Binary subclass: #Disj
instanceVariableNames: 'combineBlock'
classVariableNames: ''
package: 'MicroKanren-Goals'
I am a goal that represent logical union, in particular I encode the
goalGrammar:disj
production.
On the one hand, false asGoal
is the neutral element for disjunction, so
that both
"GoalTest, protocol tests"
testDisjFalseFalse
| g |
g := false asGoal | false asGoal.
self assert: g solutions equals: #( ) modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
and
"GoalTest, protocol tests"
testDisjFalseTrue
| g |
g := false asGoal | true asGoal.
self
assert: g solutions
equals: { Var tautology }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
behave as usual in logic. On the other hand,
"GoalTest, protocol tests"
testDisjTrueTrue
| g |
g := true asGoal | true asGoal.
self
assert: g solutions
equals: {
Var tautology.
Var tautology }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
surprises with two solutions instead of one because true asGoal |º b
doesn’t bypass
the exploration of the goal b
. For the sake of clarity, two solutions are provided both by
"GoalTest, protocol tests"
testDisjThreeWithVarOrThreeWithVar
| g |
g := [ :a | (3 unifyo value: a) | (3 unifyo value: a) ] asGoal.
self
assert: g solutions
equals: { 3. 3 }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
and
"GoalTest, protocol tests"
testDisjThreeWithThreeOrFourWithVar
| g |
g := [ :a | (3 unifyo value: 3) | (4 unifyo value: a) ] asGoal.
self
assert: g solutions
equals: {
0 asReifiedVar.
4 }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
which leaves the variable unbound in the leftmost path. Disjunction is commutative, so that both
"GoalTest, protocol tests"
testDisjThreeWithVarOrFourWithVar
| g |
g := [ :a | (3 unifyo value: a) | (4 unifyo value: a) ] asGoal.
self
assert: g solutions
equals: { 3. 4 }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
and
"GoalTest, protocol tests"
testDisjFourWithVarOrThreeWithVar
| g |
g := [ :a | (4 unifyo value: a) | (3 unifyo value: a) ] asGoal.
self
assert: g solutions
equals: { 4. 3 }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
are satisfied by the same set of substitutions or, in other words, have the same paths connecting the leaves to the roots. Disjunction is associative, so that both trees
"GoalTest, protocol tests"
testDisjThreeFourThenFive
| g |
g := [ :a |
(3 unifyo value: a) | (4 unifyo value: a) | (5 unifyo value: a) ]
asGoal.
self
assert: g solutions
equals: { 3. 5. 4 }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
and
"GoalTest, protocol tests"
testDisjThreeThenFourFive
| g |
g := [ :a |
(3 unifyo value: a)
| ((4 unifyo value: a) | (5 unifyo value: a)) ] asGoal.
self
assert: g solutions
equals: { 3. 4. 5 }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
have the same set of leaves but different branching structures.
Conj¶
Binary subclass: #Conj
instanceVariableNames: ''
classVariableNames: ''
package: 'MicroKanren-Goals'
I am a goal that represent logical intersection, in particular I encode the
goalGrammar:conj
production.
On the one hand, true asGoal
is the neutral element for disjunction, so
that both
"GoalTest, protocol tests"
testConjTrueTrue
| g |
g := true asGoal , true asGoal.
self
assert: g solutions
equals: { Var tautology }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
and
"GoalTest, protocol tests"
testConjTrueThreeWithThree
| g |
g := [ :q | true asGoal , (3 unifyo value: 3) ] asGoal.
self
assert: g solutions
equals: { 0 asReifiedVar }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
are succeeding goals. On the other hand, false asGoal
makes a conjunction
false asGoal &º b
failing for any goal b
, as in
"GoalTest, protocol tests"
testConjFalseThreeWithVar
| g |
g := [ :q | false asGoal , (3 unifyo value: q) ] asGoal.
self assert: g solutions isEmpty.
^ self exportComputationTreeOfGoal: g limitedTo: -1
Conjunctions essentially propagates unified values by the left hand side subgoal into the right hand side one; for the sake of clarity, the following examples attempts to unify the same variable with two different values yielding no solution (but providing the corresponding counterexample)
"GoalTest, protocol tests"
testConjThreeFour
| g |
g := [ :a | (3 unifyo value: a) , (4 unifyo value: a) ] asGoal.
self assert: g solutions isEmpty.
^ self exportComputationTreeOfGoal: g limitedTo: -1
while the following one succeeds and also shows the commutativity of the operator
"GoalTest, protocol tests"
testConjSymmetry
| g |
g := [ :a | (a unifyo value: 4) , (4 unifyo value: a) ] asGoal.
self assert: g solutions equals: { 4 } modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
In the same spirit, the following examples shows two succeeding conjunctions, the former introduces a variable in a nested goal,
"GoalTest, protocol tests"
testConjThreeFresh
| g |
g := [ :a | (3 unifyo value: a) , [ :b | 4 unifyo value: b ] asGoal ]
asGoal.
self assert: g solutions equals: { 3 } modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
the latter, introduces both variables in the topmost goal
"GoalTest, protocol tests"
testConjThreeFourWithTwoVars
| g |
g := [ :a :b | (3 unifyo value: a) , (4 unifyo value: b) ] asGoal.
self
assert: g solutions
equals: { { 3. 4 } }
modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
Sharing among variables can be shown with both a succeeding example
"GoalTest, protocol tests"
testConjSucceedingSharing
| g |
g := [ :z |
[ :x | (3 unifyo value: x) , (z unifyo value: x) ] asGoal ]
asGoal.
self assert: g solutions equals: #( 3 ) modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
and a failing one
"GoalTest, protocol tests"
testConjFailingSharing
| g |
g := [ :x :y :z |
(3 unifyo value: x) , (z unifyo value: x) , (z unifyo value: 4) ]
asGoal.
self assert: g solutions equals: #( ) modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1
Finally, the combination of a failing conjunction with a succeeding disjunction produces the following computation
"GoalTest, protocol tests"
testConjDisj
| g |
g := [ :a |
(3 unifyo value: a) , (4 unifyo value: a) | (a unifyo value: 0) ]
asGoal.
self assert: g solutions equals: { 0 } modulo: #asOrderedCollection.
^ self exportComputationTreeOfGoal: g limitedTo: -1


Simple calculator
A:
B:
Operation:
Add
Subtract
Divide
Multiply
Result:
Hook test
BeforeFeatures
BeforeFeature
Before
BeforeScenario
BeforeStep
AfterStep
AfterScenario
After
AfterFeature
AfterFeatures
Result:


Usage examples.
In this protocol we show how to analyze genomic variants using the SnpEff pipeline.
Computer hardware: The materials required for this protocol are:# Move to home directory cd # Download and install SnpEff curl -v -L http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip > snpEff_latest_core.zip unzip snpEff_latest_core.zip
cd snpEff java -jar snpEff.jar download -v GRCh37.75A list of pre-built databases for all other species is available by running the following command:
java -jar snpEff.jar databases
We show how to use SnpEff & SnpSitf to annotate, prioritize and filter coding variants.
Dataset: In this genomic annotation example, we use a simulated dataset to show how to find genetic variants of a Mendelian recessive disease, Cystic fibrosis, caused by a high impact coding variant, a nonsense mutation in CFTR gene (G542*). The data files come from the publicly available "CEPH_1463" dataset, sequenced by Complete Genomics, and contains sequencing information for a family consisting of 4 grandparents, 2 parents and 11 siblings.
Although these are healthy individuals, we artificially introduced a known Cystic fibrosis mutation on three siblings (cases) in a manner that was consistent with the underlying haplotype structure.
We now download and un-compress the example data used in this protocol, which, for reasons of space and time, is limited to only chromosome 7 and 17:
# Go to SnpEff's dir cd ~/snpEff # Download sample data curl -v -L http://sourceforge.net/projects/snpeff/files/protocols.zip > protocols.zip unzip protocols.zip
-stats
):
java -Xmx4g -jar snpEff.jar -v -stats ex1.html GRCh37.75 protocols/ex1.vcf > protocols/ex1.ann.vcf
java -Xmx1g -jar SnpSift.jar \ caseControl \ -v \ -tfam protocols/pedigree.tfam \ protocols/ex1.ann.vcf \ > protocols/ex1.ann.cc.vcf
Cases=1,1,3
and Controls=8,6,22
which correspond to the number of homozygous non-reference, heterozygous and total allele counts in cases and controls for each variant.
The program also calculates basic statistics for each variant based on the allele frequencies in the two groups using different models, which can be useful as a starting point for more in-depth statistical analysis.
SnpSift filter
command to reduce the number of candidate loci base on alleles in cases and controls.
SnpSift filter allows users to create powerful filters that select variants using Boolean expressions containing data from the VCF fields.
The expression we use to filter the VCF file "ex1.ann.vcf" is developed as follows.
Cases[0] = 3) & (Controls[0] = 0)
The full command line is:
cat protocols/ex1.ann.cc.vcf | java -jar SnpSift.jar filter \ "(Cases[0] = 3) & (Controls[0] = 0)" \ > protocols/ex1.filtered.hom.vcfThe filtered output file, filtered.hom_cases.vcf, contains over 400 variants satisfying our criteria. This is still too large to analyze by hand, so can we can add another filter to see if any of these variants is expected to have a high impact. To identify variants where any of these impacts is classified as either
HIGH
or MODERATE
we add the condition ANN[*].IMPACT = 'HIGH') | (ANN[*].IMPACT = 'MODERATE')
The new filtering commands become:
cat protocols/ex1.ann.cc.vcf \ | java -jar SnpSift.jar filter \ "(Cases[0] = 3) & (Controls[0] = 0) & ((ANN[*].IMPACT = 'HIGH') | (ANN[*].IMPACT = 'MODERATE'))" \ > protocols/ex1.filtered.vcf
stop_gained
loss of function variant
, whereas the other one is a missense_variant
amino acid change.
The first one is a known Cystic fibrosis variant.
$ cat protocols/ex1.filtered.vcf | ./scripts/vcfInfoOnePerLine.pl 7 117227832 . G T . . AC 14 AN 22 ANN T|stop_gained|HIGH|CFTR|ENSG00000001626|transcript|ENST00000003084|protein_coding|12/27|c.1624G>T|p.Gly542*|1756/6128|1624/4443|542/1480|| ANN T|stop_gained|HIGH|CFTR|ENSG00000001626|transcript|ENST00000454343|protein_coding|11/26|c.1441G>T|p.Gly481*|1573/5949|1441/4260|481/1419|| ANN T|stop_gained|HIGH|CFTR|ENSG00000001626|transcript|ENST00000426809|protein_coding|11/26|c.1534G>T|p.Gly512*|1534/4316|1534/4316|512/1437||WARNING_TRANSCRIPT_INCOMPLETE ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|topological_domain:Cytoplasmic|ENST00000003084|protein_coding||c.1624G>T|||||| ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|domain:ABC_transporter_1|ENST00000003084|protein_coding||c.1624G>T|||||| ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|beta_strand|ENST00000003084|protein_coding|12/27|c.1624G>T|||||| ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|beta_strand|ENST00000454343|protein_coding|11/26|c.1441G>T|||||| ANN T|upstream_gene_variant|MODIFIER|AC000111.5|ENSG00000234001|transcript|ENST00000448200|processed_pseudogene||n.-1C>A|||||1362| ANN T|downstream_gene_variant|MODIFIER|CFTR|ENSG00000001626|transcript|ENST00000472848|processed_transcript||n.*148G>T|||||29| LOF (CFTR|ENSG00000001626|11|0.27) NMD (CFTR|ENSG00000001626|11|0.27) Cases 3 Cases 0 Cases 6 Controls 0 Controls 8 Controls 8 CC_TREND 9.111e-04 CC_GENO NaN CC_ALL 4.025e-02 CC_DOM 6.061e-03 CC_REC 1.000e+00 17 39135205 . ACA GCA,GCG . . AC 16 AC 8 AN 31 ANN GCG|missense_variant|MODERATE|KRT40|ENSG00000204889|transcript|ENST00000377755|protein_coding||c.1045_1047delTGTinsCGC|p.Cys349Arg|1082/1812|1045/1296|349/431|| ANN GCG|missense_variant|MODERATE|KRT40|ENSG00000204889|transcript|ENST00000398486|protein_coding||c.1045_1047delTGTinsCGC|p.Cys349Arg|1208/1772|1045/1296|349/431|| ANN GCA|synonymous_variant|LOW|KRT40|ENSG00000204889|transcript|ENST00000377755|protein_coding|6/7|c.1047T>C|p.Cys349Cys|1082/1812|1047/1296|349/431|| ANN GCA|synonymous_variant|LOW|KRT40|ENSG00000204889|transcript|ENST00000398486|protein_coding|8/9|c.1047T>C|p.Cys349Cys|1208/1772|1047/1296|349/431|| ANN GCA|sequence_feature|LOW|KRT40|ENSG00000204889|region_of_interest:Coil_2|ENST00000398486|protein_coding|6/9|c.1047T>C|||||| ANN GCG|sequence_feature|LOW|KRT40|ENSG00000204889|region_of_interest:Coil_2|ENST00000398486|protein_coding|7/9|c.1045_1047delTGTinsCGC|||||| ANN GCA|sequence_feature|LOW|KRT40|ENSG00000204889|region_of_interest:Rod|ENST00000398486|protein_coding|3/9|c.1047T>C|||||| ANN GCG|sequence_feature|LOW|KRT40|ENSG00000204889|region_of_interest:Rod|ENST00000398486|protein_coding|3/9|c.1045_1047delTGTinsCGC|||||| ANN GCA|3_prime_UTR_variant|MODIFIER|KRT40|ENSG00000204889|transcript|ENST00000461923|nonsense_mediated_decay|8/9|n.*509T>C|||||2348| ANN GCG|3_prime_UTR_variant|MODIFIER|KRT40|ENSG00000204889|transcript|ENST00000461923|nonsense_mediated_decay|8/9|n.*507_*509delTGTinsCGC|||||2346| ANN GCA|downstream_gene_variant|MODIFIER|AC004231.2|ENSG00000234477|transcript|ENST00000418393|antisense||n.*815A>G|||||3027| ANN GCG|downstream_gene_variant|MODIFIER|AC004231.2|ENSG00000234477|transcript|ENST00000418393|antisense||n.*815_*815delACAinsGCG|||||3027| ANN GCA|non_coding_exon_variant|MODIFIER|KRT40|ENSG00000204889|transcript|ENST00000461923|nonsense_mediated_decay|8/9|n.*509T>C|||||| ANN GCG|non_coding_exon_variant|MODIFIER|KRT40|ENSG00000204889|transcript|ENST00000461923|nonsense_mediated_decay|8/9|n.*507_*509delTGTinsCGC|||||| Cases 3 Cases 0 Cases 6 Controls 0 Controls 12 Controls 18 CC_TREND 7.008e-02 CC_GENO NaN CC_ALL 1.700e-01 CC_DOM 1.231e-01 CC_REC 1.000e+00
java -jar SnpSift.jar pedShow \ protocols/pedigree.tfam \ protocols/ex1.filtered.vcf \ protocols/chart
java -Xmx1g -jar SnpSift.jar \ annotate \ -v \ protocols/db/clinvar_00-latest.vcf \ protocols/ex1.ann.cc.vcf \ > protocols/ex1.ann.cc.clinvar.vcf
stop_gained
annotation):
$ cat protocols/ex1.ann.cc.clinvar.vcf \ | java -jar SnpSift.jar filter \ "(exists CLNDBN) & (ANN[*].EFFECT has 'stop_gained') & (ANN[*].GENE = 'CFTR')" \ > protocols/ex1.ann.cc.clinvar.filtered.vcf $ cat protocols/ex1.ann.cc.clinvar.filtered.vcf | ./scripts/vcfInfoOnePerLine.pl 7 117227832 rs113993959 G T . . AC 14 AN 22 ANN T|stop_gained|HIGH|CFTR|ENSG00000001626|transcript|ENST00000003084|protein_coding|12/27|c.1624G>T|p.Gly542*|1756/6128|1624/4443|542/1480|| ANN T|stop_gained|HIGH|CFTR|ENSG00000001626|transcript|ENST00000454343|protein_coding|11/26|c.1441G>T|p.Gly481*|1573/5949|1441/4260|481/1419|| ANN T|stop_gained|HIGH|CFTR|ENSG00000001626|transcript|ENST00000426809|protein_coding|11/26|c.1534G>T|p.Gly512*|1534/4316|1534/4316|512/1437||WARNING_TRANSCRIPT_INCOMPLETE ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|topological_domain:Cytoplasmic|ENST00000003084|protein_coding||c.1624G>T|||||| ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|domain:ABC_transporter_1|ENST00000003084|protein_coding||c.1624G>T|||||| ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|beta_strand|ENST00000003084|protein_coding||c.1624G>T|||||| ANN T|sequence_feature|LOW|CFTR|ENSG00000001626|beta_strand|ENST00000454343|protein_coding||c.1441G>T|||||| ANN T|upstream_gene_variant|MODIFIER|AC000111.5|ENSG00000234001|transcript|ENST00000448200|processed_pseudogene||n.-1C>A|||||1362| ANN T|downstream_gene_variant|MODIFIER|CFTR|ENSG00000001626|transcript|ENST00000472848|processed_transcript||n.*148G>T|||||29| LOF (CFTR|ENSG00000001626|11|0.27) NMD (CFTR|ENSG00000001626|11|0.27) Cases 3 Cases 0 Cases 6 Controls 0 Controls 8 Controls 8 CC_TREND 9.111e-04 CC_GENO NaN CC_ALL 4.025e-02 CC_DOM 6.061e-03 CC_REC 1.000e+00 ASP true CLNACC RCV000007535.6|RCV000058931.3|RCV000119041.1 CLNALLE 1 CLNDBN Cystic_fibrosis|not_provided|Hereditary_pancreatitis CLNDSDB GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT|MedGen|GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT CLNDSDBID NBK1250:C0010674:219700:ORPHA586:190905008|CN221809|NBK84399:C0238339:167800:ORPHA676:68072000 CLNHGVS NC_000007.13:g.117227832G>T CLNORIGIN 1 CLNREVSTAT prof|single|single CLNSIG 5|5|5 CLNSRC CFTR2|HGMD|OMIM_Allelic_Variant|OMIM_Allelic_Variant CLNSRCID G542X|CM900049|602421.0009|602421.0095 GENEINFO CFTR:1080 LSD true NSN true OM true PM true PMC true REF true RS 113993959 RSPOS 117227832 S3D true SAO 1 SSR 0 VC SNV VLD true VP 0x050268000605040002110100 WGT 1 dbSNPBuildID 132
java -Xmx4g -jar snpEff.jar \ -v \ -o gatk \ GRCh37.75 \ protocols/ex1.vcf \ > protocols/ex1.ann.gatk.vcf
java -Xmx4g -jar $HOME/tools/gatk/GenomeAnalysisTK.jar \ -T VariantAnnotator \ -R $HOME/genomes/GRCh37.75.fa \ -A SnpEff \ --variant protocols/ex1.vcf \ --snpEffFile protocols/ex1.ann.gatk.vcf \ -L protocols/ex1.vcf \ -o protocols/ex1.gatk.vcf
We show how to use SnpEff & SnpSitf to annotate, prioritize and filter non-coding variants.
Dataset: This example shows how to perform basic annotation of non-coding variants.
It is based on a short list of 20 non-coding that were identified by sequencing a 700 kb region surrounding the gene T-box transcription factor (TBX5) in 260 patients with congenital heart disease 67.
TBX5 is a transcription factor that plays a well-established dosage-dependent role in heart and limb development.
Coding mutations in TBX5 have been frequently identified in patients with Holt–Oram syndrome, which is associated with abnormal hand, forearm and cardiac development.
Data source: Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease.
java -Xmx4g -jar snpEff.jar \ -v \ -motif \ GRCh37.75 \ protocols/ex2.vcf \ > protocols/ex2.ann.basic.vcf
java -Xmx4g -jar snpEff.jar \ -v \ -motif \ -interval protocols/ex2_regulatory.bed \ GRCh37.75 \ protocols/ex2.vcf \ > protocols/ex2.ann.vcf
java -Xmx1g -jar SnpSift.jar \ phastCons \ -v \ protocols/phastcons \ protocols/ex2.ann.vcf \ > protocols/ex2.ann.cons.vcf
cat protocols/ex2.ann.cons.vcf \ | java -jar SnpSift.jar filter \ "(ANN[*].EFFECT = 'CUSTOM[ex2_regulatory]') & (exists PhastCons) & (PhastCons > 0.9)" \ > protocols/ex2.filtered.vcf
Here we show an example on how to get from Sequencing data to an annotated variants file
# Download the genome, uncompress and rename file wget ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.34_FB2011_02/fasta/dmel-all-chromosome-r5.34.fasta.gz gunzip dmel-all-chromosome-r5.34.fasta.gz mv dmel-all-chromosome-r5.34.fasta dm5.34.fasta # Create a genome index (we assume you installed BWA http://bio-bwa.sourceforge.net/) bwa index -bwtsw dm5.34.fasta # Map sequences to the genome: Create SAI file bwa aln -bwtsw dm5.34.fasta s.fastq > s.sai # Map sequences to the genome: Create SAM file bwa samse dm5.34.fasta s.sai s.fastq > s.sam # Create BAM file (we assume you installed SamTools http://samtools.sourceforge.net/) samtools view -S -b s.sam > s.bam # Sort BAM file (will create s_sort.bam) samtools sort s.bam s_sort # Create VCF file (BcfTools is part of samtools distribution) samtools mpileup -uf dm5.34.fasta s_sort.bam | bcftools view -vcg - > s.vcf # Analyze variants using snpEff java -Xmx4g -jar snpEff.jar dm5.34 s.vcf > s.ann.vcfThis highly simplified sequencing data analysis pipeline, has these basic steps
Here we show an example on how to get from Sequencing data to an annotated variants file
These are slightly more advanced examples. Here we'll try to show how to perform specific tasks. If you want to filter out SNPs from dbSnp, you can do it using SnpSift. You can download SnpSift from the "Downloads" page.
You can download the file for this example here.
Here is how to do it:
SnpSif annotate
and DbSnp# Annotate ID field using dbSnp # Note: SnpSift will automatically download and uncompress dbSnp database if not locally available. java -jar SnpSift.jar annotate -dbsnp file.vcf > file.dbSnp.vcf
java -Xmx4g -jar snpEff.jar eff -v GRCh37.75 file.dbSnp.vcf > file.ann.vcf
java -jar SnpSift.jar filter -f file.ann.vcf "! exists ID" > file.ann.not_in_dbSnp.vcfThe expression using to filter the file is "! exists ID". This means that the ID field does not exists (i.e. the value is empty) which is represented as a dot (".") in a VCF file.
"-"
java -jar SnpSif.jar annotate -dbsnp file.vcf \ | java -Xmx4g -jar snpEff.jar eff -v GRCh37.75 - \ | java -jar SnpSift.jar filter "! exists ID" \ > file.ann.not_in_dbSnp.vcfHere is an example of some entries in the annotated output file. You can see the 'ANN' field was added, predicting STOP_GAINED protein changes:
$ cat demo.1kg.snpeff.vcf | grep stop_gained 1 889455 . G A 100.0 PASS ...;ANN=A|stop_gained|HIGH|... 1 897062 . C T 100.0 PASS ...;ANN=T|stop_gained|HIGH|... 1 900375 . G A 100.0 PASS ...;ANN=A|stop_gained|HIGH|...Note: The real output was edited for readibility reasons.
SnpEff can annotate using user specified (custom) genomic intervals, allowing you to add any kind of annotations you want.
In this example, we are analyzing using a specific version of the Yeast genome (we will assume that the database is not avialable, just to show a more complete example). We also want to add annotaions of genomic regions known as 'ARS', which are defined in a GFF file. This turns out to be quite easy, thanks to SnpEff's "custom intervals" feature. SnpEff allows you to add "custom" annotations from intervals in several formats: TXT, BED, BigBed, VCF, GFF.#--- # Download data #--- $ cd ~/snpEff $ mkdir data/sacCer $ cd data/sacCer $ wget http://downloads.yeastgenome.org/curation/chromosomal_feature/saccharomyces_cerevisiae.gff $ mv saccharomyces_cerevisiae.gff genes.gffNow that we've downloaded the reference genome, we can build the database
#--- # Build #--- $ cd ../.. # Add entry to config file $ echo "sacCer.genome : Yeast" >> snpEff.config # Build database $ java -Xmx1G -jar snpEff.jar build -gff3 sacCer
#--- # Create a features file #--- # GFF files have both genomic records and sequences, we need to know # where the 'records' section ends (it is delimited by a "##FASTA" line) $ grep -n "^#" data/sacCer/genes.gff | tail -n 1 22994:##FASTA # Note that I'm cutting the INFO column (only for readability reasons) $ head -n 22994 data/sacCer/genes.gff \ | grep -v "^#" \ | grep ARS \ | cut -f 1 -d ";" \ > sacCer_ARS_features.gffSo now we have a custom file ready to be used.
#--- # Features annotations example #--- # Create a fake VCF file (one line), this is just an example to show that it works $ echo -e "chrI\t700\t.\tA\tT\t.\t.\t." > my.vcf $ java -jar snpEff.jar -interval sacCer_features.gff sacCer my.vcf > my.ann.vcfIf we take a look at the results, we can see that the "ARS" feature is annotates (see last line)
$ cat my.ann.vcf | grep -v "^#" | cut -f 8 | tr ",;" "\n\n" EFF=missense_variant(LOW|MISSENSE|Cca/Tca|p.Pro55Ser/c.163A>T|84|YAL068W-A|protein_coding|CODING|YAL068W-A_mRNA|1|1|WARNING_REF_DOES_NOT_MATCH_GENOME) upstream_gene_variant(MODIFIER||1780||75|YAL067W-A|protein_coding|CODING|YAL067W-A_mRNA||1) downstream_gene_variant(MODIFIER||1107||120|YAL068C|protein_coding|CODING|YAL068C_mRNA||1) downstream_gene_variant(MODIFIER||51||104|YAL069W|protein_coding|CODING|YAL069W_mRNA||1) custom[sacCer_features](MODIFIER||||||ARS102||||1)


(defmethod add ((c col) (x cons)) (dolist (y x) (add c y)))
If x
is a list, add everything in it.
(defmethod add ((c col) (x cons)) (dolist (y x) (add c y)))
Unless we are skipping stuff, increment n
.
(defmethod add ((c col) x)
(unless (eq #\? x)
(incf (? c n))
(add1 c x)))
(defmethod dist (c x y)
(if (and (eq x #\?) (eq y #\?)) 1 (dist1 x y)))


EVITA A film review by Mark R. Leeper Copyright 1997 Mark R. Leeper
Capsule: The on-again, off-again history of attempts to bring this Webber and Rice musical to the screen finally culminates in a spectacular film starring Madonna, Antonio Banderas and Jonathan Pryce. By now the music is mostly familiar. The politics are superficially explained, but the visuals give the film a great epic feel. It is hard to imagine Madonna will ever have as powerful a role or be as good in another film. Rating: high +2 (-4 to +4) New York Critics: 4 positive, 4 negative, 3 mixed
Eva Peron was dead 26 years before the musical was produced, and it took nearly as long, 19 more years, for that musical to be filmed. It is not clear why the film should be made even now or why the people at Disney thought the American public would be interested in this story of the attractive, blond, and politically-active wife of a controversial reformer President who is popular among the poor but disliked by the rich, the military, and the Right Wing.
Like the play EVITA, the film opens in 1952 with the announcement of the death of Eva Peron. The film then tells in flashback the life story of Eva, supposedly related by Che (Antonio Banderas). Che is every bit as omnipresent here as he was in the musical, but in Alan Parker's film version he is no longer a research chemist developing an insecticide, he is now just sort of a one-man voice of public opinion. (This creates something of a problem with the lyrics of some of the songs. They have images of images of dying insects that now seem to come out of nowhere.) Eva is the illegitimate daughter of a prosperous middle class man. Her life is forged in bitterness by her father's other family refusing to acknowledge her existence or letting her attend her own father's funeral. Her being forcibly ejected from the church is the film's most powerful scene. At age fifteen, still filled with venom, she sleeps with popular singer visiting her village. Seeing this as an opportunity she attaches herself like a lamprey to the singer forcing him to take her to Buenos Aires. In spite of bad treatment, she works her way up a human ladder of men, trading her way up until she allies herself to the powerful and politically ambitious Colonel Juan Peron (Jonathan Pryce). Juan unexpectedly finds himself caught between Eva on one side and the Army and the wealthy of Argentina on the other. It is a moot point which side has a greater loathing of the other. But "Little Eva" brings with her an overwhelming payload of political support from the Descamisados--the poor, "shirtless" workers and Juan rides their support to the Presidency--a very stormy trip.
Madonna Louise Ciccone has not had a very distinguished acting career up to this point but finally seems cast perfectly in a role. Madonna not only resembles Eva Person, both have notoriety for a somewhat salacious background. The biggest drawback to casting Madonna in the role is that she is 38--five years older than Eva Peron was even at her death--and the days are long past when Madonna could reasonably play the fifteen-year-old Eva. Antonio Banderas is transformed from chemist into a sort of narrator and Greek chorus and that causes some problems with his character. It is not clear what his point of view means or if it is even consistent. When Che was envisioned as a real human, he could change his mind about Eva without it being a story problem. But can a narrator or a chorus change his mind in the course of a story? It is not usually done. Ironically the Banderas character has far more lines than does the much more literal character of Pryce. Through much of the film Pryce has only to look good. I was surprised when Pryce speaks toward the middle of the film and I realized that we have not heard his voice in quite a while.
EVITA looks like a very expensive production and Parker has used his budget very cleverly in some cases to make a film that looks extremely extravagant. In some cases it appears he had a whole scene setup with a crowd on the screen only for the length of one line of a song. In fact there are some clever reuses of settings which may or may not be disguised to offset the cost. Part of the spectacle was made possible undoubtedly only because of the comparative low cost of filming in Argentina and Hungary. The two sets of scenes flow together seamlessly. We get to see some impressively-scaled political rallies or major street riots. Camerawork is by Darius Khondji who previously filmed DELICATESSEN, SE7EN, and the amazing CITY OF LOST CHILDREN. His camera is at its most impressive in the long-shots. Too often on the close-ups are plagued by bad synchronization between the singing and the lip movements. Some images go by often too quickly to be completely understood, including what looks like a sort of surrealistic ballroom dance on the occasion of the death of Eva. Webber's and Tim Rice's play gives us only a superficial view of Peronist politics, but then one does not expect an operetta to have the historical content of a GETTYSBURG. We never really see much of Eva Peron's politics beyond her allying herself to the Descamisados and avenging herself against the middle classes. Andrew Lloyd Webber apparently could not resist the opportunity to write one new song eligible for the Academy Award race. That song is "You Must Love Me," and it you want to hear it you must listen carefully. It is such a bland and lackluster piece of music it can slip right by the viewer unnoticed. It sounds more like a bridging piece of music than a song of the caliber of "Don't Cry For Me, Argentina."
As a history film, EVITA is limited by the perfunctory musical script on which it is based, but the look of the film is dazzling. I rate the film a high +2 the -4 to +4 scale.
Mark R. Leeper<EMAIL_ADDRESS>The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
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asap "tests"
Not quite unit tests but this set of examples and comparisons provide some evidence of functionality. Pull up your browsers console to see more verbose logging.
simple comparative examples
- simple.html
- A simple baseline that loads jQuer, jQuery UI and simple.js at the bottom of the page with no prelaoding solution employed.
- simple-asap.html
- The baseline example loading js with asap. Asap is used again in the onload handler to lazy load a jQuery plugin and run it once loaded using the codeReady callback.
- simple-lab.html
- The baseline example loading js with LABjs.
- simple-require.html
- The baseline example loading js with requireJS.
complex page example
- baseline-scripts-at-end-of-document.html
- A baseline complex page with lots of html that laods jQuery, jQuery UI and myCode.js with scripts at the bottom of the page.
- baseline-scripts-in-head.html
- A baseline complex page with lots of html that laods jQuery, jQuery UI and myCode.js with scripts in the head.
- w3Scripts-asap-scripts-at-end-of-document.html
- The complex baseline loading js with asap at the bottom of the page.
- w3Scripts-asap-scripts-in-head.html
- The complex baseline loading js with asap in the head.


The Spectrum ID tab details how peptides were matched to spectra for the various search engines.
The search engine performance table displays how many spectra would be matched at 1% FDR using the search engines separately. The same information is also shown in the corresponding Venn diagram.
This table shows all the spectra per MGF file. Selecting a given row/spectrum will show the spectrum to the right
and the peptides mapped to that spectrum by each search engine, and the PSM retained by PeptideShaker.
The search engine agreement is color coded in the second column of the table. Hold the mouse over a given color
to learn what the colors mean. The same colors are also used in the PSM table in the Overview tab.
The currently selected spectrum is shown here with the annotations corresponding to the currently selected
PSM in the Peptide-Spectrum Matches table at the bottom.
For more details on how to interact with the spectrum see the menu bar below the spectrum.
For each spectrum it is possible to see all peptide assumptions made by the various search engines with the corresponding score and confidence. On top of these the PSM retained by PeptideShaker is displayed. Note that selecting the PSM of choice updates the spectrum annotation.