--- layout: default nav: tutorial ---
This tutorial will show you how to implement infinite scroll with only a few lines of IntercoolerJS.
Here are the steps for implementing infinite scroll
tbody
so
we can target it for appending.
span
to the last element in the table that uses the
ic-append-from
,
ic-target
, and
ic-trigger-on
attributes to trigger appending to the table body.
Here is a diff between the will-paginate code and Intercooler code:
https://github.com/LeadDyno/intercooler-tutorial-app/commit/13daf988bc86c5da1e62fea8def155e3e8ea5307


captainwhippet.com
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instafeedjs.com
for the javascript to get the thumbnails!


Our Mission is to provide and expand the knowledge of people who are interested in reading Manga's.
Naruto has sold over 220 million copies worldwide as of 2015, making it the 4th highest grossing manga series of all time. It was nominated for the 19th Tezuka Osamu Cultural Prize in 2014, and in the same year Masashi Kishimoto was awarded Rookie of the Year in the media fine arts category by Japan's Agency for Cultural Affairs. Numerous databooks, artbooks, novels, and fanbooks on the series have been released. Eight summary volumes featuring unaltered color pages, larger dimensions, and exclusive interviews, covering the first part of the series were released between November 7, 2008 and April 10, 2009.Click here for more Info.
In 2005, Bleach won the 50th Shogakukan Manga Award in the shounen category. The series has been published in English by VIZ Media under the Shonen Jump imprint since July 6, 2004 and in 3-in-1 omnibus edition since June 7, 2011; a hardcover collector's edition for volume one was released by VIZ Media on August 5, 2008. It has also been published in Portuguese (Brazil) by Panini Comics and Planet Manga since July 2007.Click here for more Info.
One Piece is the highest selling manga series of all time, with over 380 million copies in circulation as of 2015. Volume 67 of the series currently holds the record for highest first print run of any manga (including books) of all time in Japan, with 4.05 million in 2012. The series was a finalist for the Tezuka Osamu Cultural Prize three times in a row from 2000 to 2002. In 2012, it won the 41st Japan Cartoonists Association Award Grand Prize, alongside Kimuchi Yokoyama's Neko Darake. VIZ Media has published One Piece in English under the Shonen Jump imprint since January 2, 2003 and in 3-in-1 omnibus editions since December 1, 2009. VIZ Media released two boxed sets for the manga, one includes the first 23 volumes of the manga and was released on November 5, 2013 while the other set includes volumes 24-46 and was released on November 4, 2014.Click here for more Info.
Death Note has inspired three live-action films, a TV drama series as well as a stage musical. The series has also inspired numerous copycat crimes outside of Japan. The manga was published in English by VIZ Media under the Shonen Jump Advanced imprint from October 10, 2005 and July 3, 2007 and again in 2-in-1 omnibuses (subtitled Black edition) from December 28, 2010 to November 1, 2011. A special hardcover edition of the first volume was released on September 16, 2008 and a complete box set was released on October 7, 2008, which included a guidebook titled Death Note 13: How to Read. It was also published in Brazil by Jbc from June 2007 to August 2008, and again in 2-in-1 edition (Black edition) from June 2013 to December 2013. It was published in Italy by Planet Manga from November 2006 to September 2008.Click here for more Info.
Shingeki no Kyojin won the Kodansha Manga Award in the shounen category in 2011 and was nominated for both the 16th and 18th annual Tezuka Osamu Cultural Prize as well as the 4th Manga Taishou Award. The series was the second highest selling manga series of 2013, with 15,933,801 copies sold. It has received several spin-off series—both manga and novel; two guidebooks titled Inside and Outside were released on April 9 and September 9, 2013, featuring concept art, character profiles and interviews, which were combined into one and published by Kodansha USA on September 16, 2014; a drama CD created with the anime's staff was included in the January 2014 issue of the magazine; and a two-part live-action film directed by Shinji Higuchi was released in Japanese theaters on August 1 and September 15, 2015 respectively.Click here for more Info.
In 2009, Fairy Tail won the 33rd Kodansha Manga Award in shounen manga category, the Japan Expo Awards for the same category, and the Society for the Promotion of Japanese Animation's Industry Award for best comedy manga. The series was initially published in English by Del Rey Comics, releasing volume 1 on March 25, 2008 up until volume 12 on September 28, 2010. Kodansha Comics USA picked up the license and released volume 13 on May 10, 2011, a large size 5-in-1 omnibus edition subtitled as Master's Edition have also been published since November 10, 2015. It has also been published in Spanish by Norma Editorial since October 30, 2008; in Italian by Star Comics since January 3, 2008; in Brazil by JBC since October 2010; and in Polish by Studio JG since April 2016.Click here for more Info.
Tokyo Ghoul ranked 12th in the 2015 Kono Manga ga Sugoi! magazine in the male readers category. The manga was the 27th best-selling manga series in Japan in 2013 with 1,666,348 estimated sales; 4th in 2014 with 6,946,203 copies sold; and 13th in 2015 with an estimated sales of 3,576,177 copies sold. An artbook titled Tokyo Ghoul [zakki] was released on October 17, 2014. The series has been published in English by VIZ Media under the VIZ Signature imprint since June 16, 2015. The final volumes is set to release on August 15, 2017. It has also been published in Spanish by Norma Editorial from March 20, 2015 to June 23, 2016 and by Ivrea Argentina starting December 12, 2016; in German by KAZÉ Manga since May 2, 2014; in Polish by Waneko since April 15, 2015; and in Brazilian Portuguese by Panini Comics and Planet Manga since July 2015.Click here for more Info.


69_duydn95.py
class Solution:
def getMinDistSum(self, positions: List[List[int]]) -> float:
directions = {(-1, 0), (1, 0), (0, -1), (0, 1)}
lower_limit = 10**-5
def dist_sum(p):
s = 0
for i in range(len(positions)):
distx = abs(positions[i][0] - p[0])
disty = abs(positions[i][1] - p[1])
s += ((distx * distx) + (disty * disty)) ** 0.5
return s
current_point = [0, 0]
for i in range(len(positions)):
current_point[0] += positions[i][0]
current_point[1] += positions[i][1]
current_point[0] /= len(positions)
current_point[1] /= len(positions)
minDist = dist_sum(current_point)
k = 0
while (k < len(positions)):
for i in range(len(positions)):
if i == k:
continue
p = [positions[i][0], positions[i][1]]
newd = dist_sum(p)
if newd < minDist:
minDist = newd
current_point[0] = p[0]
current_point[1] = p[1]
k += 1
test_distance = 100
flag = 0
while (test_distance > lower_limit):
flag = 0
for dr in directions:
p = [current_point[0] + test_distance * dr[0], current_point[1] + test_distance * dr[1]]
newd = dist_sum(p)
if newd < minDist:
minDist = newd
current_point[0] = p[0]
current_point[1] = p[1]
flag = 1
break
if flag == 0:
test_distance /= 2
# print(test_distance)
return minDist


UK PM Johnson's Conservatives on 41%, Labour 30% in Survation poll
LONDON (Reuters) - Support for British Prime Minister Boris Johnson’s Conservative Party narrowed by three points in a Survation poll reported by a journalist on Sunday, with 41% of respondents saying they would vote Conservative compared with 30% for Labour.
The poll, which was due for release on Monday but was published on Twitter by the Independent newspaper’s chief political commentator John Rentoul, said support for the Conservatives was down 1 point compared with last week, while Labour rose by 2 points.
The pro-EU Liberal Democrats were on 15%, up 1 point, while the Brexit Party was unchanged on 5%.


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Ovm
The Ovm project aims to develop a customizable framework for research in virtual machines and object-oriented programming language runtime systems.
Ovm has been used to implement a Real-time Java virtual machine.
The Ovm framework is released under an open source licence.


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General Principles of Conduct
- Act in a professional and ethical manner at all times
- Act for the benefit of clients
- Act with independence and objectivity
- Act with skill, competence, and diligence
- Communicate with clients in a timely and accurate manner
- Uphold the applicable rules governing capital markets
Asset Manager Code of Professional Conduct
- Loyalty to Clients
- Investment Process and Actions
- Trading
- Risk Management, Compliance, and Support
- Performance and Valuation
- Disclosures
A. Loyalty to Clients
Managers must:
- Place client interest before their own
- Preserve the confidentiality of information communicated by clients within the scope of the Manager-client relationship
- Refuse to participate in any business relationship or accept any gift that could reasonably be expected to affect their independence, objectivity, or loyalty to clients
B. Investment Process and Actions
Managers must:
- Use reasonable care and prudent judgment when managing client assets
- Not engage in practices designed to distort prices or artificially inflate trading volume with the intent to mislead market participants
- Deal fairly and objectively with all clients when providing investment information, making investment recommendations, or taking investment action
- Have a reasonable and adequate basis for investment decisions
B. Investment Process and Actions (cont'd)
Managers must:
- When managing a portfolio or pooled fund according to a specific mandate, strategy, or style:
- Take only investment actions consistent with the stated objectives and constraints of that portfolio or fund
- Provide adequate disclosures and information so investors can consider any proposed changes in the investment style or strategy
B. Investment Process and Actions (cont'd)
- When managing separate accounts adn before providing investment advice or taking investment action on behalf of the client:
- Evaluate and understand the client's investment objectives, risk tolerance, liquidity needs, financial constraints, unique circumstances and any other relevant information that would affect investment policy
- Determine that an investment is suitable to a client's financial situation
C. Trading
Managers must:
- Not act or cause others to act on MNPI that could affect the value of a publicly traded investment
- Give priority to investments made on behalf of the client over those that benefit the Manager's own interests
- Use commissions generated from client trades to pay for only investment-related products or services that directly assist the Manager in its investment decision making process, and not in the management of the firm
- Maximize client portfolio value by seeking best execution for all client transactions
- Establish policies to ensure fair and equitable trade allocation among client accounts
D. Risk Management, Compliance, and Support
Managers must:
- Develop and maintain policies and procedures to ensure that their activities comply with the provisions of the Code and all applicable legal and regulatory requirements
- Appoint a compliance officer responsible for administering the policies and procedures and for investigating complaints regarding the conduct of the Manager or its personnel
- Enssure that portfolio information provided to clients is accurate and complete and arrange for independent third-party confirmation or review of such information
D. Risk Management, Compliance, and Support (cont'd)
Managers must:
- Maintain records for an appropriate period of time in an easily accessible format
- Employ qualified staff and sufficient human and technological resources to thoroughly investigate, analyze, implement, and monitor investment decisions and actions
- Establish a business-continuity plan to address disaster recovery or periodic disruptions of the financial markets
- Establish a firmwide risk management process that identifies, measures, and manages the risk position of the Manager and its investments, including the sources, nature, and degree of risk exposure
E. Performance and Valuation
Managers must:
- Present performance information that is fair, accurate, relevant, timely, and complete. Managers must not misrepresent the performance of individual portfolios or of the firm
- Use fair-market prices to value client holdings and apply, in good faith, methods to determine the fair value of any securities for which no independent, third-paty market quotation is readily available
F. Disclosures
Managers must:
- Communicate with clients on an ongoing and timely basis
- Ensure that disclosures are truthful, accurate, complete, and understandable and are presented in a format that communicates the information effectively
- Include any material facts when making disclosures or providing information to clients regarding themselves, their personnel, investments, or the investment process
F. Disclosures (cont'd)
Managers must:
- Disclose the following:
- Conflicts of interest generated by any relationship with brokers or other entities, other client accounts, fee structures, or other matters
- Regulatory or disciplinary action taken against the Manager or its personnel related to professional conduct
- The investment process, including information regarding lock-up periods, strategies, risk factors, and use of derivatives and leveragte
- Management fees and other investment costs charged to investors, including what costs are included in the fees and the methodologies for determining fees and costs
F. Disclosures (cont'd)
Managers must:
- Disclose the following
- The amount of any soft or bundled commissions, the goods and/or services received in return, and how those goods and/or services benefit the client
- The performance of clients' investments on a regular and timely basis
- Valuation methods used to make investment decisions and value client holdings
- Shareholder voting policies
- Trade allocation policies
- Results of the review or audit of the fund or account
- Significant personnel or organizational changes
- Risk management processes


Steelta348.github.io
Please select your Carbolite Gero product, model and controller from the operating manual database to find the complete operating manual. If you are looking for the manual of a discontinued model, please contact.
Used Machinery GPC12/200 Furnace - Carbolite, Tool room and Bench Top Furnaces - Surface Treatment, Finishing Plant Equipment, ALDRIDGE, WALSALL, - United Kingdom - Machines by dealer RILEY INDUSTRIES LTD OW1638. Carbolite GPC12/200 Furnace - Riley Surface World. Used Carbolite for sale. Top quality machinery listings. Operating manual / instructions download - Carbolite. Manuali di istruzione Please select your Carbolite Gero product, model and controller from the operating manual database to find the complete operating manual If you are looking for the manual of a discontinued model, please contact.
Carbolite GPC 12/200 Handbücher. Carbolite GPC General Purpose Chamber Furnaces - Spectra. Search for used carbolite. Find Carbolite for sale on Machinio.
Carbolite - GPC12/200 Furnace Tool room and Bench. GPC 12/65 - gzlaijie-resolver.com. Installation, Operation Maintenance Instructions 1200°C - 1300°C Chamber Furnaces GPC models This manual is for the guidance of operators of the above Carbolite products. Carbolite GPC General Purpose Chamber Furnaces - This furnace reaches a temperature of 1200 degrees Celsius, holds up to 36 liters, and has a 9000W power supply.
Carbolite GPC 12/200 The Carbolite GPC 12/200 general purpose chamber furnace is a free standing furnace with a 1200°C, temperature range and an internal 200 litre capacity. Applications in general industry include:. GPC 12/65 We can sell the products of CARBOLITE at a Advantage price. Guang Zhou Lai Jie Electric Co.,LTD. Please contact with “Tommy” for the price. Manuali di istruzione Carbolite. Carbolite GPC 12/200 The Carbolite GPC 12/200 general purpose chamber furnace is a free standing furnace with a 1200°C, temperature range and an internal 200 litre capacity. Installation, Operation Maintenance Instructions.


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Cowboys LB Vander Esch Missing 2nd Game With Neck Injury
Dallas Cowboys linebacker Leighton Vander Esch will sit out a second game because of lingering issues from a neck injury sustained last month against Philadelphia.
The second-year player was ruled out of Sunday's game at New England. Vander Esch was experiencing discomfort, and doctors determined after an MRI on Thursday that he would sit against the Patriots and possibly miss more games.
Coach Jason Garrett said Friday the club wasn't ready to rule out Vander Esch against Buffalo on Thanksgiving. The linebacker missed a game for the first time in his career against the New York Giants after an open week following the injury against the Eagles on Oct. 20.
Vander Esch played against Minnesota and Detroit the past two weeks and is second to Jaylon Smith in tackles with 87, according to the team stats.
A first-round pick out of Boise State in 2018, Vander Esch led the Cowboys with a club rookie record of 176 tackles and made the Pro Bowl as an injury replacement for Carolina's Luke Kuechly.


You did it, your Jujube example is up and running
Things to do
Checksum calculating sample resource
here


Class 1 Lab
Would you like to play a game?
What is your favorite color?
What is your favorite thing to Netflix and chill to?
If you could eat anything right now, what would it be and why?


All components
Documentation
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Hello, my name is Abdelrahman Ayman Shaker, a Front-End developer, and I'd like to share my very first try with you and to know your feedback about my work!
To notify me your visiting, you should sign up!
yes, am interested


Keep track of your Amiibos. Easiest way to find your favorite Amiibo !
Just click on the Amiibo you have !


- Author
- André Flores
Basic functions for use of the RTC
◆ RTC_ADDR_REG
| #define RTC_ADDR_REG 0x70 /** @brief RTC address register */ |
◆ RTC_DATA_REG
| #define RTC_DATA_REG 0x71 /** @brief RTC data register */ |
◆ RTC_HOUR_ADDR
| #define RTC_HOUR_ADDR 4 /** @brief RTC hours' address */ |
◆ RTC_MIN_ADDR
| #define RTC_MIN_ADDR 2 /** @brief RTC minutes' address */ |
◆ RTC_SEC_ADDR
| #define RTC_SEC_ADDR 0 /** @brief RTC seconds' address */ |
◆ rtc_get_time()
| void rtc_get_time |
( |
uint8_t * |
sec, |
|
|
uint8_t * |
min, |
|
|
uint8_t * |
hour |
|
) |
| |
Gets time from rtc saves values in the parameters' addresses in binary.
- Parameters
-
| sec | Pointer to the seconds' address |
| min | Pointer to the minutes' address |
| hour | Pointer to the hours' address |
◆ rtc_update_time()
Number of calls to the RTC.
Updates the time saved in static variables. Should be called once every second.


Leicester, Chelsea leapfrog City; Arsenal, Spurs fall behind
by AGENCE FRANCE PRESSELONDON, United Kingdom, Nov 9 – Leicester moved up to second in the Premier League as a 2-0 victory over Arsenal on Saturday further dented the Gunners’ hopes of a top-four finish.
Chelsea were also 2-0 victors against Crystal Palace as they too jumped above Manchester City into third.
But it was another woeful afternoon for north London’s big two as Tottenham were held 1-1 at home by Sheffield United to slip to 12th.
League leaders Liverpool host City in a highly-anticipated clash between the champions of Europe and champions of England at Anfield on Sunday.
Leicester and Chelsea took advantage of kicking off a day earlier to move a point ahead of City and close to within five of Liverpool.
The Foxes’ superior goal difference takes them into second as second-half strikes from Jamie Vardy and James Maddison piled more pressure on beleaguered Arsenal boss Unai Emery.
“I’m playing probably the best that I ever have,” said Vardy, one of the heroes of Leicester’s remarkable 2015/16 Premier League title win.
“There’s a lot of momentum round the club and everyone’s enjoying themselves. That enjoyment comes with winning.”
Arsenal are now eight points adrift of the top four and will fall even further behind should City avoid defeat at Anfield.
“We are very ambitious in our target, but we know we need time and patience,” said Emery, who faces an anxious wait to see if his wish will be granted by the Arsenal board with a two-week international break coming up.
Chelsea were equally as impressive with a patient performance to break down a defensively dogged Crystal Palace at Stamford Bridge.
Tammy Abraham opened the scoring as the England striker pounced on a deft flick through by Willian seven minutes into the second half.
Christian Pulisic then secured all three points when the American headed home his fifth goal in his last three Premier League games.
– Tottenham down to 12th –
Tottenham were lucky to even escape with a point as Sheffield United impressed once more to move up to fifth.
“The reality is that for different reasons we are not showing the performances that we expect,” said Spurs boss Mauricio Pochettino.
“We are not in a good position in the table.”
A rare defensive error from the Blades set up Son Heung-min to open the scoring with his eighth goal of the season just before the hour mark.
David McGoldrick thought he had levelled almost immediately, but after a three-minute delay the goal was ruled out for John Lundstram being millimetres offside in the build-up.
To their credit, Chris Wilder’s men were not downhearted and survived another VAR review when George Baldock’s cross from the right evaded everyone and found the bottom corner.
West Ham’s woes continued as Manuel Pellegrini’s men were beaten 3-0 at Burnley to stretch their winless streak to seven games.
Ashley Barnes opened the scoring after 11 minutes as Burnley never looked back.
Chris Wood doubled the hosts’ advantage after earlier having a goal ruled out by VAR for offside and a miserable day for the visitors at Turf Moor was summed up when goalkeeper Roberto punched a corner into his own net.
Everton moved six points clear of the relegation zone thanks to a 2-1 win at Southampton to ease the pressure on Marco Silva.
Tom Davies gave the Toffees the perfect start at St Mary’s before Danny Ings equalised early in the second half.
But Richarlison struck the winner 15 minutes from time to secure Everton’s first away league win since March.
Newcastle are now seven points clear of the drop zone as they came from behind to beat Bournemouth 2-1 at St James’ Park thanks to goals from DeAndre Yedlin and Ciaran Clark.
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phasemap documentation
The phasemap function returns or sets a cyclic colormap with a constant lightness profile appropriate for plotting phase.
Contents
Syntax
phasemap M = phasemap(N) phasemap(...,'rad') phasemap(...,'deg')
Description
phasemap sets the current colormap to a 256-level phase map.
M = phasemap(N) returns an Nx3 matrix of RGB values for a phase colormap.
phasemap(...,'rad') sets axis limits of current colormap to caxis([-pi pi]).
phasemap(...,'deg') sets axis limits of current colormap to caxis([-180 180]).
Example 1: Radians:
Imagine some phase map ph in radians, which we'll wrap with phasewrap:
ph = phasewrap(2*peaks(900)); imagesc(ph) colorbar phasemap
Example 2: N-levels of degrees:
Imagine some phase map ph in degrees, which we'll wrap with phasewrap. Be sure to specify 'degrees' when calling phasewrap:
ph = phasewrap(100*peaks(900),'degrees'); imagesc(ph) colorbar phasemap(12) phasebar('location','se')
Author Info
This function was written by Chad A. Greene of the University of Texas at Austin's Institute for Geophysics (UTIG), May 2016. RGB values for this colormap were developed by Kristen Thyng. An aesthetically-pleasing and well-written summary of her cmocean colormaps can can be found here and her GitHub repository containing several nice colormaps is here.


Fibonacci
HelloWorld
Syntax
BuiltInTypes
Collections
Configuration
Share Code
Run
Clear Output
Evaluate
Print JSON Representation
Print AST
Run and Print Mem


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Twitter introduced public posting and follow concept from the beginning and have been copied by Google+ and more recently by Facebook with the subscribe button.
But profile follow is a one way selectors. It partially cover the issue because it ignore that a single person produce infos on differentes domains.
As a normal human, I am curious about several subjects and I produce infos about several subjects.
 These are completely unrelated subjects followed by completely different people I don’t want to bother with non accurate infos. To prevent that, I have to use multiple profiles and split my identity across them. It can become a nightmare or drive me Schizophrenic.
So following an identity is not enough. To be efficient we should follow somebody about subjects.
for example I can follow @DHHon Ruby or programming but not on skate boarding.
One social profile/identity should propose several subjects (including a global one). I should post to a subject the same way today I post to a google circle, but as the opposite of google circles, this is not me choosing people receiving infos, this is people choosing to follow my public subjects.
This way we get the double filter of choosing the most interesting people only on subject we care about.
The main drawback of this method is to reduce Serendipity which is the life of the internet. As a first response, I should say that every infos producer will have the responsibility of posting unrelated infos on subjects at a frequency acceptable to his followers.


vignettes/06ColonyManagerTutorial.Rmd
06ColonyManagerTutorial.Rmd
This tutorial demonstrates the major functions used within GeneKeepR provided by the nprcgenekeepr package. This is a brief tutorial that illustrates a typical workflow and does not explore all possible workflows.
Please provide any comments, questions, or bug reports through the GitHub issue tracker at https://github.com/rmsharp/nprcgenekeepr/issues.
Go to https://cran.r-project.org/mirrors.html and click on one of the links within the US (ex. https://ftp.osuosl.org/pub/cran/). Then proceed to download the latest version of R for your desired operating system. Note: IT may have to install if you do not have administrative permissions on the computer.
To get the most recent version you can install GeneKeepR from GitHub with the following code.
install.packages("devtools") devtools::install_github("rmsharp/nprcgenekeepr")
All missing packages should be automatically installed.
You can start GeneKeepR from the R console with
library(nprcgenekeepr) runGeneKeepR()
This will result in the opening screen where you tell the application how to find the pedigree you will be using.
Most of the screen is filled with information about formatting a text or Excel worksheet pedigree file.
Scrolling down to the middle of the opening screen exposes a table that describes a pedigree file and further instructions.
*********
Scrolling down to the bottom of the opening screen exposes more pedigree file instructions, a table that describes a genotype file and instructions regarding use of a genotype file.
The following is an example of the pedigree file format.
Without genotypes:
With genotypes:
In this introductory tutorial, we will use an Excel file containing a hypothetical pedigree of macaques. We will work with the gray box on the left at the top of the screen.
A Microsoft Excel workbook with a single worksheet is the default file type; though comma (.csv), semi-colon (.txt), and tab (.txt) separated value files are all acceptable formats.
The Example_Pedigree.xlsx file we are using is from a CSV file created as shown below and then saved in an Excel format. Alternatively, you may download this example pedigree from the nprc consortium web page.
Select the Browse button and select the pedigree file from your file system.
It is important to make sure the minimum parent age is low enough for the animals in your pedigree. For our example pedigree, we are changing it from 4 years to 2 years of age since these macaques may reproduce as early as two years of age.
Selected Read and Check Pedigree will read in the file and test to see if the pedigree file has all of the columns needed and the pedigree is internally consistent.
Several error types, shown below, are detected the application.
| Error | Definition |
|---|---|
| failedDatabaseConnection | Database connection failed: configuration or permissions are invalid |
| missingColumns | Columns that must be within the pedigree file are missing. |
| invalidDateRows | Values, which are supposed to be dates, cannot be interpreted as a date. |
| suspiciousParents | Parents were too young on the date of birth of to have been the parent. |
| femaleSires | Individuals listed as female or hermaphroditic and as a sire. |
| maleDams | Individuals are listed as male and as a dam. |
| sireAndDam | Individuals who are listed as both a sire and a dam. |
| duplicateIds | IDs listed more than once. |
| fatalError | System Crash. These are unanticipated errors that should be reported to the package maintainer |
| changedCols | Columns that have been changed to conform to the program (ex: id -> Ego ID). |
The Pedigree Browser tab defaults to displaying 10 rows of the pedigree at a time, but you can choose to display 10, 25, 50, or 100 rows. You can choose to display UNKNOWN IDs in the rows displayed. UNKNOWN IDs (UIDs) are used to label unknown parents of animals with one known parent. The program calculates additional columns based on the input pedigree.
I have place red lines under the UNKNOWN IDs in the partial pedigree list below for clarity. These IDs have no meaning other than they all begin with the letter U and are following with a left alphanumeric string of five places.
In this example pedigree, when you deselect the Display Unknown IDs checkbox. The number of rows reduces from 3,694 to 2,322, because there were 1,372 UNKNOWN animals generated when constructing the pedigree to provide sire and dam placeholders for all animals.
The Pedigree Browser tab displays the full pedigree by default but allows you to select a subset of the pedigree by entering a list of animals of interest (focal animals).
You can enter in the animal IDs by typing them into the text box directly as shown below (FJS7RQ, H6T2FF, HEVL3L, I04JZV, S63QDN). Deselect the Display Unknown IDs checkbox and select the Trim pedigree based on focal animals checkbox. (See top right of image below).
Trimming the pedigree based on focal animals will keep only animals in the pedigree that are related to the focal animals selected.
Select the Update Focal Animals button to tell the application to read your list of animals, trim the pedigree based on that list, and display the trimmed pedigree below. You will end up with 54 animals in your pedigree.
Also, you can import a list of focal animals by selecting the Browse button under Choose CSV file with focal animals. This file can be constructed by creating a simple text file with commas between animal IDs or by placing individual animal IDs on separate lines.
Focal animals are the list of animals that will be used in the following analysis. In most cases, we recommend using all alive animals in the breeding population. By selecting focal animals, the number of pedigree entrees does not change, but the population membership flag will be set to “true” for the focal animals, and “false” for all other animals.
After entering your list of focal animals, you can select to trim the pedigree so that it will only include relatives of the focal animals you have selected. This will reduce the number of members within the pedigree to all animals required to connect all of the focal animals in the pedigree.
A pedigree trimmed based on focal animals will have only the relatives of those animals remaining. In this instance there are only a total of 85 focal animals and their relatives. Note: focal animals and their relatives will only be included in the same pedigree when the original pedigree file uploaded indicates a common ancestor for them. Otherwise, focal animals and their relatives will be sorted into separate pedigrees in the output, with each separate pedigree indicated by its own number.
You can remove the animals from the list of focal animals by selecting the Clear Focal Animals checkbox and selecting the Update Focal Animals button. This will read in an empty ID list, clear the box of IDs, and bring back all of the trimmed away IDs.
Deselect the Clear Focal Animals checkbox and reselect the Update Focal Animals button before continuing with the tutorial so that we will be working with the trimmed pedigree.
The Pedigree Age Plot tab displays a standard pyramid plot for the pedigree as selected in the Pedigree Browser tab. This is showing 332 living animals from the entire example pedigree.
Select the Genetic Value Analysis tab and enter the number of simulations and genome uniqueness threshold desired. See the Genetic Value Analysis and Breeding Group Description tab for a breakdown of the calculation.
We recommend trying multiple numbers of simulations to arrive at an ideal number that produces consistent results (i.e., 1,000). Genome uniqueness values are calculated using a gene-drop simulation according to MacCluer et al. (1986) and Ballou & Lacy (1995), by assigning unique alleles to all pedigree founders, and simulating their segregation throughout the pedigree according to Mendelian rules. Genome uniqueness is a measure of the probability that an animal possesses founder alleles that are present in at most x other animals (usually 0-3), and thus are rare and at risk of being lost from the population. A range of 2 to 100,000 simulations may be selected. A minimum of 1,000 simulations is recommended. A genome uniqueness threshold value between 0-3 should also be selected, as desired.
Select the Begin Analysis button to start the gene dropping process, which you can monitor with the progress meter in the lower right corner of the display.
As soon as the calculations are completed, a table showing the results of the analysis is displayed in 10 rows. The calculations for 1000 iterations of the gene dropping algorithm took 1 minute 38 seconds with the example pedigree of 3,691 animals using a MacBook Pro (Mid 2014), 2.8 GHz Intel Core i7 with 16 GB of 1600 MHz DDR3 memory.
Again you can select how many rows to display at once by changing the values in the Show entries selection tool, or you may view results for a specific set of animals by entering their IDs in the box above. The default is to display the analysis for the list of focal animals.
Searching down the table of results in the Value Designation column you can see starting at row 268 the values change from High Value to Low Value. Though not shown here, the value of Undetermined in the Value Designation column means the animal did not have parentage information. Infants or very young animals without assigned parents are given an “Undetermined” designation. Founders also do not have parentage information but are high value by definition.
The Summary Statistics and Plots tab used results from the Genetic Value Analysis tab. Definitions of genome uniqueness and kinship are located in the Genetic Value Analysis and Breeding Group Description tab. Additionally, definitions of founder equivalents and founder genome equivalents are located at the bottom of the Summary Statistics and Plots tab.
The Export Kinship Matrix button creates a CSV file that has a row and column for each individual in the genetic analysis plus a first row and first column each containing the IDs.
The first few rows of such a file are shown below.
The First-Order Relationships button creates a CSV file that has the following columns defined: an unnamed column for row number, id, parents, offspring, siblings, and total. Counts are based off known relationships. The first few rows of such a file are shown below.
The Export Female Founders and Export Male Founders buttons creates a CSV file that has the following columns defined: an unnamed column for row number, id, sires, dam, sex, gen, birth, exit, age, recordStatus, population, and pedNum. The first few rows of such a file are shown below.
The six plots provide histograms and boxplots for the kinship coefficients, the Z-scores of the kinship coefficients, and the genome uniqueness scores. These plots may also be downloaded as desired.
Selecting the Breeding Group Formation tab brings forward the screen shown below. In this screen you can form breeding groups using one of three workflows based on your source of animals selected under Choose one group formation workflow:.
Further you must specify how you want to construct the breeding groups with regard to the groups’ sex ratios. The third of the three options (User specified sex ratio of breeders) causes the appearance of the field where you can fill in the sex ratio (F/M) that you want to have in the formed breeding groups. The sex ratio algorithm will form a group as nearly to the selected ratio as possible given the size of the group. Limits in the availability of either sex will restrict the size of the groups formed.
The Make Groups button appears once you select the source of animals you are going to use. However, you probably will be making additional selections using other controls on the screen.
The most common source of animals will be the high-value animals found by the genetic analysis.
You can either type in the number of groups that you want to form or select the number of groups using the arrows on the right edge of the Number of Groups Desired field, which is outlined in blue in the image below.
There are often behavioral constraints, such as preexisting social groups, that dictate the need to have some animals maintained together. This need is readily accommodated by pre-seeding groups with those social groups. You may select the Optional: Seed Groups with Specific Animals field if you decide to place some animals together within the groups because you know them to be compatible with each other.
This has been done in the example below using six groups with differing numbers of seed animals. Note the selection of having animals below the minimum parent age of two being grouped with their mother.
Each group has all of the seed animals that were assigned to it plus additional animals that could be added while satisfying the requirements imposed by the selected settings. I have indicated the seed animals for the first group with red rectangles.
Display of kinship values requires that the Include kinship in display of groups checkbox be selected prior to group formation.
A group of ten animals was formed in the next run after choosing to include kinship and selecting the Make Groups button.
The option to select a desired sex ratio allows you to select any ratio desired. However, the ratio obtained is limited by the availability of animals that meet all criteria you have set.
Selecting a sex ratio of 2.5 with 6 groups as is illustrated resulted in 5 groups of 20 with a ratio of 14:6 (2.3) and 1 group of 23 with a ratio of 16:7 (2.3).
Groups can be individually exported into file names and locations of your choosing. The corresponding kinship matrix for each group can also be exported.


Loco for burritos and tacos? Seek therapy at Singapore’s newest Mexican joint
by Coconuts SingaporeLove Mexican food but don’t want to compromise your diet? There’s a new fast food joint in town that fits the bill.
Mad Mex, located in the swanky Marina Bay Financial Center Tower 3, offers customers a choice of burritos, naked burritos, tacos, nachos, quesadillas, ensaladas and something called the Grande Melt, which is basically a wrap with a fajita inside.
The restaurant follows a “no pork, no lard” rule. But there’s still a variety of protein options including chicken, Veracruz tofu, chorizo chicken and beef barbacoa (extra S$0.50).
Prices range from S$8.90 for small burritos to S$12.50 for regular nachos or the Grande Melt.
Why is there a S$0.50 charge for beef barbacoa? That’s because it takes extra time and effort to prepare.
According to Mad Mex, the beef barbacoa is slow-cooked over a low fire for eight hours until all the flesh is broken down, resulting in smooth and luscious mouthfuls of meat.
Vegetarians need fret not, as the flavorful Veracruz Tofu is made with tasty olives and parsley (making it actually more Mediterranean than Mexican).
Spice up meals at Mad Mex further with sauces tuned to tolerance levels – from mild Roasted Tomato Salsa and Salsa Verde to the sizzling Spicy Picante Habanero. Each sauce is made with chilies imported from Mexico.
Mad Mex’s Singapore opening comes a year after Singapore fast-food chain 4fingers bought a 50% stake in the Australian chain. It is also setting its eyes on more outlets in Singapore as well as across the border in Malaysia.
It is already a household name in Australia and New Zealand, where it has 70 outlets.
FIND IT
Mad Mex
Opens Mon-Fri and PH Eve:
8am-8pm
Marina Bay Financial Centre Tower 3
12 Marina Boulevard #02-05
More F&B news from the Little Red Dot at Coconuts.co/Singapore/lifestyle.


This is a guided setup wizard designed to simplify the creation of a battery profile configuration file for the particular batteries being used. Fill out the on-page instructions as accurately as possible to generate a profile.
Once completed the generated profile will automatically be loaded into the utility for review and upload.
| < Toolbar | Battery Profile > |


/* Created By: Mohd Sanaullah Ghayasi. Dated On: 19-02-2018 */ Recover Password Update your password To reset the password to the account of<EMAIL_ADDRESS>type the new password below. new password repeat password UPDATE PASSWORD
To reset the password to the account of<EMAIL_ADDRESS>type the new password below.


Minimal Demo
Features
- Supports touch
- Custom colors
- Custom background colors
- Custom stroke size
- Add images
- Save drawn as (svg | png | jpeg | base64) images
- Experimental (undo-redo)
License
ng-whiteboard is under MIT license. That basically means you can use it as you want to.
Contributing
The project is open for contributors.
You can Create pull requests, submit bugs, suggest new features.
If you like it give it a star on GitHub.


Input & output¶
Input¶
The PCGR workflow accepts two types of input files:
- An unannotated, single-sample VCF file (>= v4.2) with called somatic variants (SNVs/InDels)
- A copy number segment file
IMPORTANT NOTE: GRCh37 is the reference genome build currently supported by PCGR
PCGR can be run with either or both of the two input files present.
VCF¶
- We strongly recommend that the input VCF is compressed and indexed using bgzip and tabix
- If the input VCF contains multi-allelic sites, these will be subject to decomposition
- Variants used for reporting should be designated as ‘PASS’ in the VCF FILTER column
IMPORTANT NOTE 1: Considering the VCF output for the numerous somatic SNV/InDel callers that have been developed, we have a experienced a general lack of uniformity and robustness for the representation of somatic variant genotype data (e.g. variant allelic depths (tumor/normal), genotype quality etc.). Variant genotype data found as INFO tags in the input VCF can be specified as optional arguments to the PCGR workflow, which in turn can be used for interactive filtering in the tumor report.
IMPORTANT NOTE 2: PCGR generates a number of VCF INFO annotation tags that is appended to the query VCF. We will therefore encourage the users to submit query VCF files that have not been subject to annotations by other means, but rather a VCF file that comes directly from variant calling. If not, there are likely to be INFO tags in the query VCF file that coincide with those produced by PCGR.
Copy number segments¶
The tab-separated values file with copy number aberrations MUST contain the following four columns:
- Chromosome
- Start
- End
- Segment_Mean
Here, Chromosome, Start, and End denote the chromosomal segment (GRCh37), and Segment_Mean denotes the log(2) ratio for a particular segment, which is a common output of somatic copy number alteration callers. Below shows the initial part of a copy number segment file that is formatted correctly according to PCGR’s requirements:
Chromosome Start End Segment_Mean
1 3218329 3550598 0.0024
1 3552451 4593614 0.1995
1 4593663 6433129 -1.0277
Output - Interactive HTML report¶
An interactive and tier-structured HTML report that shows the most relevant findings in the query cancer genome is provided with the following naming convention:
sample_id.pcgr.html
The sample_id is provided as input by the user, and reflects a unique identifier of the tumor-normal sample pair to be analyzed.
The report is structured in six main sections, described in more detail below:
Annotation sources
- Lists underlying tools and annotation sources (versions)
Somatic SNVs/InDels
Summary statistics - indicate number of SNVs/InDels as well as number of coding/non-coding variants
- Note that coding refers to protein-altering and variants at canonical splice-sites (donor, acceptor)
Mutational burden (TMB) - given a coding target region size specified by the user, an estimate of the mutational burden is provided
Tier statistics - indicate number of variant found in each tier (see below)
Global distribution - allelic support - distribution (histogram) of variant allelic support for somatic variants (will only be present in the report if specific fields in input VCF is defined and specified by the user)
Global variant browser - permits filtering of the whole SNV/Indel dataset by various criteria (call confidence, variant sequencing depth, variant consequence etc.)
Variants are organized into five tiers (interactive datatables) according to clinical utility
- Tier 1 - constitutes variants linked to predictive, prognostic, diagnostic, and predisposision biomarkers in the CIViC database and the Cancer Biomarkers Database
- Tier 2 - includes other coding variants that are found in known cancer mutation hotspots, predicted as cancer driver mutations, or curated as disease-causing
- Tier 3 - includes other coding variants found in oncogenes or tumor suppressor genes
- Tier 4 - includes other coding variants
- Tier 5 - includes non-coding variants
- will only present if specified by the user (‘–list_noncoding’)
- NOTE: The tier structure is inspired by recommended variant prioritization by Dienstmann et al., 2014. The table below shows the correspondence between the terminology for reportable variants used by Dienstmann et al. and the tiers in PCGR:
Dienstmann et al., 2014 (Figure 2) PCGR Actionable Tier 1 Other relevant variants Tier 2 & Tier 3 Unknown* Tier 4 (Tier 5) *While Dienstmann et al. suggest that the Unknown category should be categorized according to pathways, the PCGR employs an arrangement of variant results according to genes, using a literature-derived score of oncogenic potential (KEGG pathway information is also linked).
Somatic CNA analysis
- Segments - amplifications and homozygous deletions
- Based on user-defined/default log-ratio thresholds of gains/losses, the whole CNA dataset can be navigated further through filters:
- cytoband
- type of CNA event - focal (less than 25% of chromosome arm affected) or broad
- log ratio
- Proto-oncogenes subject to copy number amplifications
- Datatable listing known proto-oncogenes covered by user-defined/default amplifications and potential targeted therapies
- Tumor suppressor genes subject to homozygous deletions
- Datatable listing known tumor suppressor genes covered by user-defined/default losses and potential targeted therapies
- Copy number aberrations as biomarkers for prognosis, diagnosis,
predisposition, and drug response
- Interactive data table where the user can navigate aberrations acting as biomarkers across therapeutic contexts, tumor types, evidence level etc.
- Segments - amplifications and homozygous deletions
MSI status
- Indicates predicted microsatellite stability from the somatic mutation profile and supporting evidence (details of the underlying MSI statistical classifier can be found here)
- Note that the MSI classifier was trained on exome samples.
- Will only be present in the report if specified by the user in the configuration file (‘msi = true’)
Mutational signatures
- Estimation of relative contribution of 30 known mutational signatures in tumor sample (using deconstructSigs as the underlying framework)
- Datatable with signatures and proposed underlying etiologies
- Will only be present in the report if specified by the user in the configuration file (‘mutsignatures = true’)
- Trimer (i.e. DNA 3-mer) normalization can be configured according to sequencing approach used (WES, WXS etc.) using the ‘mutsignatures_normalization’ option, as can the minimum number of mutations required for analysis (option ‘mutsignatures_mutation_limit’) and the maximum number of mutational signatures in the search space (option ‘mutsignatures_signature_limit’)
References
- Supporting scientific literature (key report elements)
- View an example report for a breast tumor sample (TCGA)
- View an example report for a colon adenocarcinoma sample (TCGA)
The HTML reports have been tested using the following browsers:
- Safari (10.0.3)
- Mozilla Firefox (52.0.2)
- Google Chrome (57.0.2987.110)
Output - Somatic SNVs/InDels¶
Variant call format - VCF¶
A VCF file containing annotated, somatic calls (single nucleotide variants and insertion/deletions) is generated with the following naming convention:
sample_id.pcgr.vcf.gz
Here, the sample_id is provided as input by the user, and reflects a unique identifier of the tumor-normal sample pair to be analyzed. Following common standards, the annotated VCF file is compressed with bgzip and indexed with tabix. Below follows a description of all annotations/tags present in the VCF INFO column after processing with the PCGR annotation pipeline:
VEP consequence annotations¶
- CSQ - Complete consequence annotations from VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE| EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position| Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND| FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|APPRIS|CCDS| ENSP|SWISSPROT|TREMBL|UNIPARC|RefSeq|DOMAINS|HGVS_OFFSET|HGVSg|AF| AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomAD_AF|gnomAD_AFR_AF| gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF| gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|MOTIF_NAME| MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE
- Consequence - Impact modifier for the consequence type (picked by VEP’s –flag_pick_allele option)
- Gene - Ensembl stable ID of affected gene (picked by VEP’s –flag_pick_allele option)
- Feature_type - Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature (picked by VEP’s –flag_pick_allele option)
- Feature - Ensembl stable ID of feature (picked by VEP’s –flag_pick_allele option)
- cDNA_position - Relative position of base pair in cDNA sequence (picked by VEP’s –flag_pick_allele option)
- CDS_position - Relative position of base pair in coding sequence (picked by VEP’s –flag_pick_allele option)
- CDS_CHANGE - Coding, transcript-specific sequence annotation (picked by VEP’s –flag_pick_allele option)
- Amino_acid_start - Protein position indicating absolute start of amino acid altered (fetched from Protein_position)
- Amino_acid_end - Protein position indicating absolute end of amino acid altered (fetched from Protein_position)
- Protein_position - Relative position of amino acid in protein (picked by VEP’s –flag_pick_allele option)
- Amino_acids - Only given if the variant affects the protein-coding sequence (picked by VEP’s –flag_pick_allele option)
- Codons - The alternative codons with the variant base in upper case (picked by VEP’s –flag_pick_allele option)
- IMPACT - Impact modifier for the consequence type (picked by VEP’s –flag_pick_allele option)
- VARIANT_CLASS - Sequence Ontology variant class (picked by VEP’s –flag_pick_allele option)
- SYMBOL - Gene symbol (picked by VEP’s –flag_pick_allele option)
- SYMBOL_SOURCE - The source of the gene symbol (picked by VEP’s –flag_pick_allele option)
- STRAND - The DNA strand (1 or -1) on which the transcript/feature lies (picked by VEP’s –flag_pick_allele option)
- ENSP - The Ensembl protein identifier of the affected transcript (picked by VEP’s –flag_pick_allele option)
- FLAGS - Transcript quality flags: cds_start_NF: CDS 5’, incomplete cds_end_NF: CDS 3’ incomplete (picked by VEP’s –flag_pick_allele option)
- SWISSPROT - Best match UniProtKB/Swiss-Prot accession of protein product (picked by VEP’s –flag_pick_allele option)
- TREMBL - Best match UniProtKB/TrEMBL accession of protein product (picked by VEP’s –flag_pick_allele option)
- UNIPARC - Best match UniParc accession of protein product (picked by VEP’s –flag_pick_allele option)
- HGVSc - The HGVS coding sequence name (picked by VEP’s –flag_pick_allele option)
- HGVSp - The HGVS protein sequence name (picked by VEP’s –flag_pick_allele option)
- HGVSp_short - The HGVS protein sequence name, short version (picked by VEP’s –flag_pick_allele option)
- HGVS_OFFSET - Indicates by how many bases the HGVS notations for this variant have been shifted (picked by VEP’s –flag_pick_allele option)
- MOTIF_NAME - The source and identifier of a transcription factor binding profile aligned at this position (picked by VEP’s –flag_pick_allele option)
- MOTIF_POS - The relative position of the variation in the aligned TFBP (picked by VEP’s –flag_pick_allele option)
- HIGH_INF_POS - A flag indicating if the variant falls in a high information position of a transcription factor binding profile (TFBP) (picked by VEP’s –flag_pick_allele option)
- MOTIF_SCORE_CHANGE - The difference in motif score of the reference and variant sequences for the TFBP (picked by VEP’s –flag_pick_allele option)
- CELL_TYPE - List of cell types and classifications for regulatory feature (picked by VEP’s –flag_pick_allele option)
- CANONICAL - A flag indicating if the transcript is denoted as the canonical transcript for this gene (picked by VEP’s –flag_pick_allele option)
- CCDS - The CCDS identifier for this transcript, where applicable (picked by VEP’s –flag_pick_allele option)
- INTRON - The intron number (out of total number) (picked by VEP’s –flag_pick_allele option)
- EXON - The exon number (out of total number) (picked by VEP’s –flag_pick_allele option)
- DOMAINS - The source and identifier of any overlapping protein domains (picked by VEP’s –flag_pick_allele option)
- DISTANCE - Shortest distance from variant to transcript (picked by VEP’s –flag_pick_allele option)
- BIOTYPE - Biotype of transcript or regulatory feature (picked by VEP’s –flag_pick_allele option)
- TSL - Transcript support level (picked by VEP’s –flag_pick_allele option)>
- PUBMED - PubMed ID(s) of publications that cite existing variant - VEP
- PHENO - Indicates if existing variant is associated with a phenotype, disease or trait - VEP
- GENE_PHENO - Indicates if overlapped gene is associated with a phenotype, disease or trait - VEP
- ALLELE_NUM - Allele number from input; 0 is reference, 1 is first alternate etc - VEP
- REFSEQ_MATCH - The RefSeq transcript match status; contains a number of flags indicating whether this RefSeq transcript matches the underlying reference sequence and/or an Ensembl transcript (picked by VEP’s –flag_pick_allele option)
- PICK - Indicates if this block of consequence data was picked by VEP’s –flag_pick_allele option
- VEP_ALL_CONSEQUENCE - All transcript consequences (Consequence:SYMBOL:Feature_type:Feature:BIOTYPE) - VEP
Gene information¶
- ENTREZ_ID - Entrez gene identifier
- APPRIS - Principal isoform flags according to the APPRIS principal isoform database
- UNIPROT_ID - UniProt identifier
- DISGENET_CUI - Tumor types associated with gene, as found in DisGeNET. Tumor types are listed as MedGen concept IDs
- TUMOR_SUPPRESSOR - Gene is predicted as tumor suppressor candidate according to (TSGene v2.0)
- ONCOGENE - Gene is curated as an oncogene according to (TSGene v2.0)
- ONCOSCORE - Literature-derived score for cancer gene relevance Bioconductor/OncoScore, range from 0 (low oncogenic potential) to 1 (high oncogenic potential)
- INTOGEN_DRIVER - Gene is predicted as a cancer driver in the IntoGen Cancer Drivers Database - 2014.12
Variant effect and protein-coding information¶
- CANCER_MUTATION_HOTSPOT - mutation hotspot codon in cancerhotspots.org. Format: gene_symbol | codon | q-value
- UNIPROT_FEATURE - Overlapping protein annotations from UniProt KB
- INTOGEN_DRIVER_MUT - Indicates if existing variant is predicted as driver mutation from IntoGen Catalog of Driver Mutations
- EFFECT_PREDICTIONS - Predictions of effect of variant on protein
function and pre-mRNA splicing from database of non-synonymous
functional predictions - dbNSFP
v3.4. Predicted
effects are provided by different sources/algorithms (separated by
‘&’):
- SIFT (Jan 2015)
- LRT (2009)
- MutationTaster (data release Nov 2015)
- MutationAssessor (release 3)
- FATHMM (v2.3)
- PROVEAN (v1.1 Jan 2015)
- FATHMM_MKL
- DBNSFP_CONSENSUS_SVM (Ensembl/consensus prediction, based on support vector machines)
- DBNSFP_CONSENSUS_LR (Ensembl/consensus prediction, logistic regression based)
- SPLICE_SITE_EFFECT_ADA (Ensembl/consensus prediction of splice-altering SNVs, based on adaptive boosting)
- SPLICE_SITE_EFFECT_RF (Ensembl/consensus prediction of splice-altering SNVs, based on random forest)
- M-CAP
- MutPred
- GERP
Variant frequencies/annotations in germline/somatic databases¶
- AFR_AF_GNOMAD - African/American germline allele frequency (Genome Aggregation Database release 1)
- AMR_AF_GNOMAD - American germline allele frequency (Genome Aggregation Database release 1)
- GLOBAL_AF_GNOMAD - Adjusted global germline allele frequency (Genome Aggregation Database release 1)
- SAS_AF_GNOMAD - South Asian germline allele frequency (Genome Aggregation Database release 1)
- EAS_AF_GNOMAD - East Asian germline allele frequency (Genome Aggregation Database release 11)
- FIN_AF_GNOMAD - Finnish germline allele frequency (Genome Aggregation Database release 1)
- NFE_AF_GNOMAD - Non-Finnish European germline allele frequency (Genome Aggregation Database release 1)
- OTH_AF_GNOMAD - Other germline allele frequency (Genome Aggregation Database release 1)
- AFR_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from AFR (African)
- AMR_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from AMR (Ad Mixed American)
- EAS_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from EAS (East Asian)
- EUR_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from EUR (European)
- SAS_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from SAS (South Asian)
- GLOBAL_AF_1KG - 1000G Project - phase 3 germline allele frequency for all 1000G project samples (global)
- DBSNPRSID - dbSNP reference ID
- DBSNPBUILDID - Initial dbSNP build ID for rsID
- DBSNP_MAPPINGSTATUS - Status with respect to the genomic mappability of the flanking sequence of the rsID
- DBSNP_VALIDATION - Categories of evidence that support the variant in dbSNP
- DBSNP_SUBMISSIONS - Number of individual submissions to rsID
- GWAS_CATALOG_PMID - Variant is linked to phenotype through the GWAS Catalog, literature in PMID list
- GWAS_CATALOG_TRAIT_URI - List of trait URIs for GWAS-associated variant
- COSMIC_MUTATION_ID - Mutation identifier in Catalog of somatic mutations in cancer database, as provided by VEP
- COSMIC_CODON_FRAC_GW - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_CODON_COUNT_GW - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_SITE_HISTOLOGY - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_CANCER_TYPE_GW - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_CANCER_TYPE_ALL - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_SITE_HISTOLOGY - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_CANCER_TYPE_GW - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_SAMPLE_SOURCE - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_DRUG_RESISTANCE - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_FATHMM_PRED - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_VARTYPE - Deprecated in 0.5.0 due to COSMIC licensing restrictions
- COSMIC_CONSEQUENCE - Deprecated in 0.5.0 due to COSMIC licensing restrictions
Clinical associations¶
- CLINVAR_MSID - ClinVar Measure Set/Variant ID
- CLINVAR_PMIDS - Associated Pubmed IDs for variant in ClinVar
- CLINVAR_SIG - Clinical significance for variant in ClinVar
- CLINVAR_VARIANT_ORIGIN - Origin of variant (somatic, germline, de novo etc.) for variant in ClinVar
- DOCM_DISEASE - Associated disease types for variant in Database of Curated Mutations
- DOCM_PMID - Associated Pubmed IDs for variant in Database of Curated Mutations
Other¶
- CHEMBL_COMPOUND_ID - antineoplastic drugs targeting the encoded protein (from Drug-Gene Interaction Database, drugs are listed as ChEMBL compound identifiers)
- CIVIC_ID, CIVIC_ID_2 - Variant identifiers in the CIViC database, CIVIC_ID refers to markers mapped at variant level, CIVIC_ID_2 refers to region markers (codon, exon etc.)
- CBMDB_ID - Variant identifier in the Cancer Biomarkers database
Tab-separated values (TSV)¶
Annotated List of all SNVs/InDels¶
We provide a tab-separated values file with most important annotations for SNVs/InDels. The file has the following naming convention:
sample_id.pcgr.snvs_indels.tiers.tsv
The SNVs/InDels are organized into different tiers (as defined above for the HTML report)
The following variables are included in the tiered TSV file:
1. GENOMIC_CHANGE - Identifier for variant at the genome (VCF) level, e.g. 1:g.152382569A>G
Format: (<chrom>:g.<position><ref_allele>><alt_allele>)
2. GENOME_VERSION - Assembly version, e.g. GRCh37
3. VCF_SAMPLE_ID - Sample identifier
4. VARIANT_CLASS - Variant type, e.g. SNV/insertion/deletion
5. SYMBOL - Gene symbol
6. GENE_NAME - Gene description
7. CCDS - CCDS identifier
8. ENTREZ_ID - Entrez gene identifier
9. UNIPROT_ID - UniProt protein identifier
10. ONCOSCORE - Literature-derived score for cancer gene relevance
11. ONCOGENE - Gene is curated as an oncogene according to TSGene
12. TUMOR_SUPPRESSOR - Gene is predicted as tumor suppressor
candidate according to TSGene
13. DISGENET_CUI - Associated tumor types from DisGeNET (MedGen concept IDs)
14. DISGENET_TERMS - Associated tumor types from DisGeNET (MedGen concept terms)
15. CONSEQUENCE - Variant consequence (as defined above for VCF output:
Consequence)
16. PROTEIN_CHANGE - Protein change (HGVSp without reference accession)
17. PROTEIN_DOMAIN - Protein domain
18. CDS_CHANGE - composite VEP-based variable for coding change, format:
Consequence:Feature:cDNA_position:EXON:HGVSp_short
19. HGVSp
20. HGVSc
21. EFFECT_PREDICTIONS - as defined above for VCF
22. CANCER_MUTATION_HOTSPOT - mutation hotspot codon in
cancerhotspots.org. Format: gene_symbol | codon | q-value
23. INTOGEN_DRIVER_MUT - Indicates if existing variant is predicted as
driver mutation from IntoGen Catalog of Driver Mutations
24. VEP_ALL_CONSEQUENCE - all VEP consequences
25. DBSNP - dbSNP reference cluster ID
26. DBSNPBUILDID - initial dbSNP build ID for rsID
27. COSMIC_MUTATION_ID - COSMIC mutation ID
28. TCGA_PANCANCER_COUNT - Global count of variant across TCGA cohorts
29. CHEMBL_COMPOUND_ID - Compounds (as ChEMBL IDs) that target the encoded protein (from DGIdb)
30. CHEMBL_COMPOUND_TERMS - Compounds (as drug names) that target the encoded protein (from DGIdb)
31. CLINVAR - variant origin and associated traits associated with variant
32. CLINVAR_SIG - clinical significance of CLINVAR variant
33. GLOBAL_AF_GNOMAD - global germline allele frequency in gnomAD
34. GLOBAL_AF_1KG - 1000G Project - phase 3, germline allele frequency
for all 1000G project samples (global)
35. CALL_CONFIDENCE - confidence indicator for somatic variant
36. DP_TUMOR - sequencing depth at variant site (tumor)
37. AF_TUMOR - allelic fraction of alternate allele (tumor)
38. DP_NORMAL - sequencing depth at variant site (normal)
39. AF_NORMAL - allelic fraction of alternate allele (normal)
40. TIER
41. TIER_DESCRIPTION
Biomarkers among SNVs/InDEls¶
For tumor samples that have variant hits in Tier 1 we provide an additional file with all associated clinical evidence items. The file has the following naming convention:
sample_id.pcgr.snvs_indels.biomarkers.tsv
The format of the biomarker TSV file is as follows:
1. GENOMIC_CHANGE - Identifier for variant at the genome (VCF) level, e.g. 1:g.152382569A>G
Format: (<chrom>:g.<position><ref_allele>><alt_allele>)
2. GENOME_VERSION - Assembly version, e.g. GRCh37
3. VCF_SAMPLE_ID - Sample identifier
4. SYMBOL - Gene symbol
5. CONSEQUENCE - Variant consequence
6. BM_CLINICAL_SIGNIFICANCE - The association with diagnostic/prognostic end point or treatment
7. BM_EVIDENCE_LEVEL - The type of experiment from which the evidence is curated (validated, clinical, pre-clinical, case study, and inferential)
8. BM_EVIDENCE_TYPE - Category of clinical action/relevance implicated by event (Predictive, Prognostic, Predisposing and Diagnostic)
9. BM_EVIDENCE_DIRECTION - An indicator of whether the evidence statement supports or refutes the clinical significance of an event
10. BM_CANCER_TYPE - Specific disease or disease subtype that is associated with this event and its clinical implication
11. BM_THERAPEUTIC_CONTEXT - For predictive evidence, indicates the therapy for which sensitivity or resistance is indicated
12. BM_RATING - A rating on a 5-star scale, portraying the curators trust in the experiments from which the evidence is curated
13. BM_CITATION - Publication(s) where the event was described/explored/guidelines/trials
14. TIER
15. TIER_DESCRIPTION
Mutational signatures¶
For each tumor sample, we apply the deconstructSigs package to delineate the known mutational signatures. The inferred, weighted contributions by each signature and their underlying, proposed etiologies are given in a TSV file with the following naming convention:
sample_id.pcgr.mutational_signatures.tsv
The format of the mutational signatures TSV file is as follows:
1. Signature_ID - ID of signature from COSMIC's 30 reference signatures
2. Weight - inferred weight of signature in the tumor sample
3. Cancer_types - cancer types in which the signature has been observed
4. Proposed_aetiology - proposed underlying etiology
5. Trimer_normalization_method - method used for trimer count normalization (deconstructSigs)
6. SampleID - Sample identifier
Output - Somatic copy number aberrations¶
1. Tab-separated values (TSV)¶
Copy number segments are intersected with the genomic coordinates of all transcripts from (ENSEMBL/GENCODE’s basic gene annotation). In addition, we attach cancer-relevant annotations for the affected transcripts. The naming convention of the compressed TSV file is as follows:
sample_id.pcgr.cna_segments.tsv.gz
The format of the compressed TSV file is the following:
1. chrom - chromosome
2. segment_start - start of copy number segment
3. segment_end - end of copy number segment
4. segment_length_Mb - length of segment in Mb
5. event_type - focal or broad (covering more than 25% of chromosome arm)
6. cytoband
7. LogR - Copy log-ratio
8. ensembl_gene_id
9. symbol - gene symbol
10. ensembl_transcript_id
11. transcript_start
12. transcript_end
13. transcript_overlap_percent - percent of transcript length covered by CN segment
14. name - gene name description
15. biotype - type of gene
16. disgenet_cui - tumor types associated with gene (from DisGeNET, tumor types
are listed as MedGen concept IDs (CUI)
17. tsgene - tumor suppressor gene status (TSgene database)
18. tsgene_oncogene - oncogene status (TSgene database)
19. intogen_drivers - predicted driver gene status (IntoGen Cancer Drivers Database)
20. chembl_compound_id - antineoplastic drugs targeting the encoded protein
(from DGIdb, drugs are listed as ChEMBL compound identifiers)
21. gencode_gene_biotype
22. gencode_tag
23. gencode_release


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Dolores Clara Fernandez was born on April 10, 1930 in Dawson, a small mining town in the mountains of northern New Mexico. Her father Juan Ferånández, a farm worker and miner by trade, was a union activist who ran for political office and won a seat in the New Mexico legislature in 1938. Dolores spent most of her childhood and early adult life in Stockton, California where she and her two brothers moved with their mother, following her parents’ divorce.
According to Dolores, her mother’s independence and entrepreneurial spirit was one of the primary reasons she became a feminist. Dolores’ mother Alicia was known for her kindness and compassion towards others. She offered rooms at affordable rates in her 70 room hotel, which she acquired after years of hard work. Alicia welcomed low-wage workers in the hotel, and often, waived the fee for them altogether. She was an active participant in community affairs, involved in numerous civic organizations and the church. Alicia encouraged the cultural diversity that was a natural part of Dolores’ upbringing in Stockton. The agricultural community where they lived was made up of Mexican, Filipino, African-American, Japanese and Chinese working families.
Alicia’s community activism was reflected in Dolores’ involvement as a student at Stockton High School. She was active in numerous school clubs, was a majorette, and a dedicated member of the Girl Scouts until the age of 18. Upon graduating Dolores continued her education at the University of Pacific’s Delta College in Stockton earning a provisional teaching credential. During this time she married Ralph Head and had two daughters, Celeste and Lori. While teaching she could no longer bear to see her students come to school with empty stomachs and bare feet, and thus began her lifelong journey of working to correct economic injustice.
Grand Rapids will pay a $190,000 settlement to a Latino American war veteran who was wrongfully detained by federal immigration officials. The City Commission unanimously approved the payment to Jilmar Ramos-Gomez on Tuesday to resolve a Michigan Department of Civil Rights complaint. Ramos-Gomez was detained last December by U.S. Immigration and Customs Enforcement (ICE) officials for deportation after he was arrested on trespassing charges, said immigration attorneys. ICE and county officials had confused Ramos-Gomez, 27, with being an immigrant even though he had his U.S. passport and other ID on him at the time of his arrest.
The detention outraged his family and civil rights attorneys who say it's an example of how immigration and county officials have become overzealous in immigration enforcement. They also say it's an example of racial profiling of Latinos by immigration officials, and police.
"I don't feel good about what they did to my son," Maria Gomez-Velaquez, his mother, told the Detroit Free Press during a phone interview. "They were not listening to my son even though he had ID on him. It's not right. My son is from here, he's born here, a United States citizen. He served in the Marines, the military, but they don't care what my son did for his country."
This week, U.S. Immigration and Customs Enforcement raided seven Mississippi food processing plants and arrested 680 workers for immigration violations. The moral cost of these raids to our shared humanity is apparent in stories like that of a tearful 13-year-old boy waving goodbye to his mother or an 11-year old girl pleading for her father’s release. But some people might feel differently, believing such scenes are just the cost of enforcing our immigration laws. If that’s you, I urge you to weigh another cost instead: the sheer financial expense of such cruelty.
First, there’s lost income. ICE was created in 2003 to “protect national security and public safety after /11,” but this week’s raids were not about security or safety or terrorism. They targeted immigrants while they worked to support their families and our economy. Many of the arrested individuals now leave behind jobs that won’t be filled and children and spouses who now live without a family member and their associated income. Their communities and local businesses will suffer down the line. And state and local governments will lose the associated tax revenues; undocumented workers pay an estimated $12 billion a year in taxes.
Then there are the costs of enforcement and detention. ICE Acting Director Matt Albence admitted that the raids required a yearlong investigation and 600 agents to execute. The 680 arrested individuals now languish in detention facilities. According to ICE, the average daily cost of detaining one person is $134. Some estimates place the cost at closer to $200 per day. Given this administration’s immigration policies, from family separation to zero tolerance to mass raids, the number of immigrants in detention is rapidly expanding, not retracting. For every person who leaves detention, another replaces them, if not two. Even using ICE’s conservative figure of $134, the cost of keeping one immigrant in detention is almost $50,000 per year. The detention expense alone for the group detained on Wednesday is approximately $100,000 a day, $3 million per month, and $36 million a year. Given that more raids are coming, these costs are only going to go up.
settling into a sense of safety is hard when your life’s catalog of memories teaches you the opposite lesson. Imagine: You fled from a government militia intent on murdering you; swam across a river with the uncertain hope of sanctuary on the far bank; had the dawning realization that you could never return to your village, because it had been torched; and heard pervasive rumors of former neighbors being raped and enslaved. Imagine that, following all this, you then found yourself in New York City, with travel documents that were unreliable at best.
This is the shared narrative of thousands of emigrants from the West African nation of Mauritania. The country is ruled by Arabs, but these refugees were members of a black subpopulation that speaks its own languages. In 1989, in a fit of nationalism, the Mauritanian government came to consider these differences capital offenses. It arrested, tortured, and violently expelled many black citizens. The country forcibly displaced more than 70,000 of them and rescinded their citizenship. Those who remained behind fared no better. Approximately 43,000 black Mauritanians are now enslaved—by percentage, one of the largest enslaved populations in the world.
After years of rootless wandering—through makeshift camps, through the villages and cities of Senegal—some of the Mauritanian emigrants slowly began arriving in the United States in the late 1990s. They were not yet adept in English, and were unworldly in almost every respect. But serendipity—and the prospect of jobs—soon transplanted their community of roughly 3,000 to Columbus, Ohio, where they clustered mostly in neighborhoods near a long boulevard that bore a fateful name: Refugee Road. It commemorated a moment at the start of the 19th century, when Ohio had extended its arms to accept another influx of strangers, providing tracts of land to Canadians who had expressed sympathy for the American Revolution.


Lambdas¶
- Gordon has two aims:
- Easily deploy and manage lambdas.
- Easily connect those lambdas to other AWS services (kinesis, dynamo, s3, etc...)
Lambdas are simple functions written in any of the supported AWS languages (python, javascript and java). If you want to know more, you can read AWS documentation in the topic:
Working with lambdas is quite easy to start with, but once you want to develop some complex integrations, it becomes a bit of a burden to deal with all the required steps to put some changes live. Gordon tries to make the entire process as smooth as possible.
In gordon, Lambdas are resources that you’ll group and define within apps. The idea is to keep Lambdas with the same business domain close to each other in the same app.
Before we continue, there is a bit of terminology we need to make clear:
| Term | Description |
|---|---|
lambda |
Is a static working piece of code ready to be run on AWS. |
lambda version |
Static point-in-time representation of a working lambda. |
lambda alias |
Pointer to a lambda. |
code bucket |
S3 bucket where your lambda code is uploaded. |
code |
S3 Object which contains your lambda code and all required libraries/packages (zip) |
code version |
S3 Object Version of one of your lambda code. |
runtime |
Language in which the lambda code is written (python, javascript or java) |
What gordon will do for you?¶
- Download any external requirement you lambdas might have.
- Create a zip file with your lambda, packages and libraries.
- Upload this file to S3.
- Create a lambda with your code and settings (memory, timeout...)
- Publish a new version of the lambda.
- Create an alias named
current
pointing to this new version. - Create a new IAM Role for this lambda and attach it.
As result, your lambda will be ready to run on AWS!
As you can imagine, this is quite a lot of things to do every time you want to simply deploy a new change! That’s where gordon tries to help.
With simply two commands, build
and apply
you’ll be able to deploy your changes again and again with no effort.
Why the current alias is important?¶
The current
alias gordon creates pointing to your most recent lambda is really important.
When gordon creates a new event sources (like S3, Dynamo or Kinesis), it’ll make those call the lambda aliased as current
instead of the $LATEST
.
This is really important to know, because it enables you to (in case of neccesary) change your current
alias to point to any previous version of the same lambda without
needing to re-configure all related event sources.
Any subsequent deploy to the same stage will point the current
alias to your latest function.
For more information you can read AWS Lambda Function Versioning and Aliases.
Anatomy of a Lambda¶
The following is the anatomy of a lambda in gordon.
lambdas:
{ LAMBDA_NAME }:
code: { PATH }
handler: { STRING }
memory: { NUMBER }
timeout: { NUMBER }
runtime: { RUNTIME_NAME }
description: { STRING }
build: { STRING }
role: { MAP }
vpc: { STRING }
context: { CONTEXT_NAME }
context-destination: { PATH }
auto-vpc-policy: { BOOLEAN }
auto-run-policy: { BOOLEAN }
cli-output: { BOOLEAN }
policies:
{ POLICY_NAME }:
{ MAP }
...
The best way to organize you lambdas is to register them inside the settings.yml
file of your apps within your Project.
Lambda Properties¶
Lambda Name¶
| Name | Key of the lambdas map. |
| Required | Yes |
| Valid types | string |
| Max length | 30 |
| Description | Name for your lambda. Try to keep it as short and descriptive as possible. |
code¶
| Name | code |
| Required | Yes |
| Valid types | string |
| Max length | 30 |
| Description | Path where the code of your lambda is |
When creating lambdas you can:
- Put all the code of your lambda in the same file and make
code
point to it: code: code.py
code: example.js
- Put all the code of your lambda in the same file and make
- Put your code in several files within a folder and make
code
point to this directory: code: myfolder
- Remember: When you point
code
to a directory you need to remember to specify theruntime
property of your lambda as gordon can’t infer it from the filename.
- Put your code in several files within a folder and make
Simple python lambda:
lambdas:
hello_world:
code: functions.py
Folder javascript lambda:
lambdas:
hello_world:
code: myfolder
handler: file.handler
runtime: nodejs4.3
Java lambda:
lambdas:
hello_world:
code: myfolder
handler: example.Hello::handler
runtime: java8
handler¶
| Name | handler |
| Required | No |
| Default | handler |
| Valid types | string , reference |
| Max length | 30 |
| Description | Name of the function within code which will be the entry point of you lambda. |
lambdas:
hello_world:
code: functions.py
handler: my_handler
For lambdas using the java runtime, this handler will need to have the following format (package.class::method
):
lambdas:
hello_world:
code: helloworld
runtime: java8
handler: helloworld.Hello::handler
Note
For more information about Java handlers Java Programming Model Handler Types
memory¶
| Name | memory |
| Required | No |
| Default | 128 |
| Valid types | integer , reference |
| Max | 1536 |
| Min | 128 |
| Description | Amount of memory your lambda will get provisioned with |
lambdas:
hello_world:
code: functions.py
memory: 1536
timeout¶
| Name | timeout |
| Required | No |
| Default | 3 |
| Valid types | integer , reference |
| Max | 300 |
| Min | 1 |
| Description | The function execution time (in seconds) after which Lambda terminates the function |
Because the execution time affects cost, set this value based on the function’s expected execution time.
lambdas:
hello_world:
code: functions.py
timeout: 300
runtime¶
| Name | runtime |
| Required | Depends |
| Valid types | runtime |
| Description | Runtime of your lambda |
Valid runtimes:
| Runtime | AWS Runtime |
|---|---|
node , nodejs , node0.10 and nodejs0.10 |
nodejs |
node4.3 and nodejs4.3 |
nodejs4.3 |
python and python2.7 |
python2.7 |
java and java8 |
java8 |
If you don’t specify any runtime, Gordon tries to auto detect it based on the extensions of the code
file.
| Extension | AWS Runtime |
|---|---|
.js |
nodejs4.3 |
.py |
python2.7 |
For folder based lambdas the code
property is a directory and not a file, so the runtime can’t be inferred.
For these situations, you can manually specify the runtime using this setting:
lambdas:
hello_world:
code: hellojava
runtime: java8
description¶
| Name | description |
| Required | No |
| Default | Empty |
| Valid types | string , reference |
| Description | Human-readable description for your lambda. |
lambdas:
hello_world:
code: functions.py
description: This is a really simple function which says hello
build¶
| Name | build |
| Required | No |
| Valid types | string , list |
| Description | Build process for collecting resources of your lambda |
This property defines which are the commands gordon needs to run in order to collect all the resources from your lambda and copying them to an empty target directory. Once the collection command finishes, gordon will create a zip file with the content of that folder.
This property has one default implementation per available runtime (Java, Javascript, Python), which covers most of the simple use cases, but there are certain use situations where you might need further fine control.
These are the default implementations gordon will use if you leave this property blank:
Python
build:
- cp -Rf * {target}
- echo "[install]\nprefix=" > {target}/setup.cfg
- {pip_path} install -r requirements.txt -q -t {target} {pip_install_extra}
- cd {target} && find . -name "*.pyc" -delete
Node
build:
- cp -Rf * {target}
- cd {target} && {npm_path} install {npm_install_extra}
Java
build: {gradle_path} build -Ptarget={target} {gradle_build_extra}
As you can see, the value of build
can be either a string or a list of strings. Gordon will process them sequentially within your lambda directory.
There are certain variables you can use to customize this build
property.
| Variable | Description |
|---|---|
target |
Destination folder where you need to put the code of your lambda |
pip_path |
pip path. You can customize this using the pip-path setting in your settings |
npm_path |
npm path. You can customize this using the npm-path setting in your settings |
gradle_path |
gradle path. You can customize this using the gradle-path setting in your settings |
pip_install_extra |
Extra arguments you can define using pip-install-extra in your settings |
npm_install_extra |
Extra arguments you can define using npm-install-extra in your settings |
gradle_build_extra |
Extra arguments you can define as part of gradle-build-extra in your settings |
project_path |
Root directory of your project |
project_name |
Name of your project |
lambda_name |
Name of your lambda |
This is the minimal version of what a build command that copies your lambda directory would look like:
lambdas:
hello_world:
code: mycode
runtime: python
handler: code.handler
build: cp -Rf * {target}
You can use this build
property in conjunction with some more powerful build tools such as Makefile
, npm
, gulp
, grunt
or simple bash
files.
In this example, we make babel
process our javascript files, and leave them in TARGET
.
lambdas:
hello_world:
code: mycode
runtime: node
handler: code.handler
build: TARGET={target} npm run build
{
"babel": {
"presets": [
"es2015"
]
},
"devDependencies": {
"babel-cli": "^6.8.0",
"babel-preset-es2015": "^6.6.0"
},
"scripts": {
"build": "babel *.js --out-dir $TARGET"
}
}
role¶
| Name | role |
| Required | No |
| default | Gordon will create a minimal role for this function |
| Valid types | arn |
| Description | ARN of the lambda role this function will use. |
If not provided, gordon will create one role for this function and include all necessary policies
(This is the default and most likely behaviour you want).
lambdas:
hello_world:
code: functions.py
role: arn:aws:iam::account-id:role/role-name
vpc¶
| Name | vpc |
| Required | No |
| Valid types | vpc-name |
| Description | Name of the vpc where this lambda should be deployed. |
If the Lambda function requires access to resources in a VPC, specify a VPC configuration that Lambda uses to set up an elastic network interface (ENI). The ENI enables your function to connect to other resources in your VPC, but it doesn’t provide public Internet access.
If your function requires Internet access (for example, to access AWS services that don’t have VPC endpoints), configure a Network Address Translation (NAT) instance inside your VPC or use an Amazon Virtual Private Cloud (Amazon VPC) NAT gateway. For more information, see NAT Gateways in the Amazon VPC User Guide.
lambdas:
hello_world:
code: functions.py
vpc: my-vpc
You need to define some properties about your vpc (in this example my-vpc
) in the project settings.
---
project: vpcexample
...
vpcs:
my-vpc:
security-groups:
- sg-00000000
subnet-ids:
- subnet-1234567a
- subnet-1234567b
- subnet-1234567c
If auto-vpc-policy
is True
, gordon will attach to your lambda role the required policy which would allow it to access the vpc. If it is False
, you’ll need
to do this by yourself.
context¶
| Name | context |
| Required | No |
| default | default |
| Valid types | context-name |
| Description | Name of the context you want to inject into this lambda. |
For more information about contexts you can read about them in Contexts.
lambdas:
hello_world:
code: functions.py
context: context_name
context-destination¶
| Name | context-destination |
| Required | No |
| default | .context |
| Valid types | string |
| Description | Path where gordon should put the context json file. |
For more information about contexts you can read about them in Contexts.
lambdas:
hello_world:
code: functions.py
context-destination: my-customize-context-file.json
cli-output¶
| Name | cli-output |
| Required | No |
| Default | True |
| Valid types | boolean |
| Description | Output the lambda ARN as part of the apply output |
policies¶
| Name | policies |
| Required | No |
| Valid types | map |
| Description | Map of AWS policies to attach to the role of this lambda. |
This is the way you’ll give permissions to you lambda to connect to other AWS services such as dynamodb, kinesis, s3, etc... For more inforamtion AWS IAM Policy Reference
In the following example we attach one policy called example_bucket_policy
to our lambda hello_world
in order to make it possible to read and write a
S3 bucket called EXAMPLE-BUCKET-NAME
.
lambdas:
hello_world:
code: functions.py
policies:
example_bucket_policy:
Version: "2012-10-17"
Statement:
-
Action:
- "s3:ListBucket"
- "s3:GetBucketLocation"
Resource: "arn:aws:s3:::EXAMPLE-BUCKET-NAME"
Effect: "Allow"
-
Action:
- "s3:PutObject"
- "s3:GetObject"
- "s3:DeleteObject"
- "dynamodb:GetRecords"
Resource: "arn:aws:s3:::EXAMPLE-BUCKET-NAME/*"
Effect: "Allow"
auto-vpc-policy¶
| Name | auto-vpc-policy |
| Required | No |
| Default | True |
| Valid types | boolean |
| Description | Automatically attach to your lambda enough permissions to get a vpc configured. |
If auto-vpc-policy
is True
, and you lambda has one vpc
configured, gordon will attach to your lambda role the required policy which would allow it to
access the vpc. If it is False
, you’ll need to do this by yourself.
{
"Version": "2012-10-17",
"Statement": [
{
"Effect": "Allow",
"Action": [
"ec2:CreateNetworkInterface"
],
"Resource": [
"*"
]
}
]
}
auto-run-policy¶
| Name | auto-run-policy |
| Required | No |
| Default | True |
| Valid types | boolean |
| Description | Automatically attach to your lambda enough permissions to let it run and push logs to CloudWatch Logs. |
If auto-run-policy
is True
, gordon will attach to your lambda role the required policy which would allow it to run and push logs.
{
"Version": "2012-10-17",
"Statement": [
{
"Effect": "Allow",
"Action": [
"lambda:InvokeFunction"
],
"Resource": [
"*"
]
},
{
"Effect": "Allow",
"Action": [
"logs:CreateLogGroup",
"logs:CreateLogStream",
"logs:PutLogEvents"
],
"Resource": "arn:aws:logs:*:*:*",
}
]
}


Malaysia inflation: Benign demand pressures - ANZ
by Dhwani MehtaAnalysts at Australia and New Zealand Banking Group (ANZ) offers their quick reaction to the Malaysian inflation data released earlier this Wednesday.
Key Quotes:
“Malaysia’s inflation remained unchanged at 1.1% y/y in October. On balance, demand side inflationary pressures have been benign and our forecast for higher inflation next year primarily reflects policy changes.
Considering the evolving trajectory for growth and inflation, our base case is still for a 25bp cut in the policy rate next year.
It is, however, conceivable that Bank Negara Malaysia (BNM) may choose to preserve its policy space after the recent cut in the statutory reserve requirement (SRR).”


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2014 Chevrolet Silverado 1500 Work Truck
2014 Chevrolet Silverado 1500 Work Truck
- 13 In Stock
- 230 Views
- Inquiries
- 13 In Stock
- Video
-
MSRP: $51,625
-
Internet Price: 146,092
-
Rebate: -$750
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Final Price: $45,342
-
You Save: $6,283
-
Special low 0% APR
Show Incentive Details3 Day Exchange Policiy
We want you to be satisfied.Complimentary Car Wash
Car washes at time of service.Estimate Your Monthly Payment
Exterior
Deep Ruby Metallic
Interior
Dark Ash with Jet Black Interior Accents
*This 2015 Chevrolet Silverado... Features include: 4.3L Engine, Tow Package, Traction Control and Side Airbags. May include Lease or Finance Incentives. Price includes: $1,500 - General Motors Consumer Cash Program. Exp. 03/31, $1,000 - Chevrolet National Purchase Bonus Cash. Exp. 03/31
- December 15, 2013
- price2724
- Olyphant, PA
I had an amazing experience dealing with Motorworld Toyota. The process was seamless from start to finish. From talking with Laura via email and phone to talking with Jay Thomas on the phone the night before, he assured me that he would get me into the car that I wanted, and he did just that. As soon as I arrived at the dealership, I was greeted by Adrian, who was very friendly and took me to Jay to discuss the cars I would be interested in. I can't say enough good things about Adrian, I will recommend everyone who is looking to buy a Toyota to her. She made my car buying process feel very laid back and not rushed at all. She didn't pressure me to make a decision immediately and was not put off if I wanted to test drive more than one car to be sure. I never had such a laid back car buying experience. Both Jay and Adrian made the whole process fun, and seamless.
Read full review on DealerRater
- All Wheel Drive
- Power Steering
- 4-Wheel Disc Brakes
- Aluminum Wheels
- Tires - Front Performance
- Tires - Rear Performance
- Temporary Spare Tire
- Sun/Moonroof
- Sun/Moon Roof
- Automatic Headlights
- Heated Mirrors
- Power Mirror(s)
- Integrated Turn Signal Mirrors
- Mirror Memory
- Intermittent Wipers
- Variable Speed Intermittent Wipers
- Audio system with AM/FM radio, CD player (reads MP3 format), satellite radio
- Steering wheel mounted & rear audio controls
- Ten speakers
- Adaptive cruise control
- Trip computer: includes average speed, average fuel economy and range for remaining fuel
- Luxury trim: leather on shifter, wood/woodgrain on doors and wood/woodgrain on dashboard
- Remote power locks, includes power windows
- Remote glass sunroof
- Leather upholstery
- Heated ventilated bucket driver seat with five 10-way power; details: memorized height, power lumbar and memorized tilt, heated ventilated bucket front passenger seat: with four 8-way power; details: power height and power tilt
Rothbard Chevrolet
- 3372 W. Highland Rd.
- Highland, MI 48357
- Get Directions
- Sales:<PHONE_NUMBER>
- Service:<PHONE_NUMBER>
Estimate Your Monthly Payment
2016 Chevrolet Silverado 2500HD Work Truck
33,195 miles; Crossover, White
-
MSRP: $27,520
-
Dealer Discount: -$1,967
-
Pre-Paid Visa or Bonus: - $1,250
-
Sale Price: $24,303
2016 Chevrolet Silverado 2500HD Work Truck
33,195 miles; Crossover, White
-
MSRP: $27,520
-
Dealer Discount: -$1,967
-
Pre-Paid Visa or Bonus: - $1,250
-
Sale Price: $24,303
2016 Chevrolet Silverado 2500HD Work Truck
33,195 miles; Crossover, White
-
MSRP: $27,520
-
Dealer Discount: -$1,967
-
Pre-Paid Visa or Bonus: - $1,250
-
Sale Price: $24,303
2016 Chevrolet Silverado 2500HD Work Truck
33,195 miles; Crossover, White
-
MSRP: $27,520
-
Dealer Discount: -$1,967
-
Pre-Paid Visa or Bonus: - $1,250
-
Sale Price: $24,303
2016 Chevrolet Silverado 2500HD Work Truck
33,195 miles; Crossover, White
-
MSRP: $27,520
-
Dealer Discount: -$1,967
-
Pre-Paid Visa or Bonus: - $1,250
-
Sale Price: $24,303
2016 Chevrolet Silverado 2500HD Work Truck
33,195 miles; Crossover, White
-
MSRP: $27,520
-
Dealer Discount: -$1,967
-
Pre-Paid Visa or Bonus: - $1,250
-
Sale Price: $24,303
While we make every effort to ensure the data listed here is correct, there may be instances where some of the factory rebates, incentives, options or vehicle features may be listed incorrectly as we get data from multiple data sources. PLEASE MAKE SURE to confirm the details of this vehicle (such as what factory rebates you may or may not qualify for) with the dealer to ensure its accuracy. Dealer can not be held liable for data that is listed incorrectly.


C++ Bitsets
C++ Bitsets give the programmer a set of bits as a data structure.
Bitsets can be manipulated by various binary operators such as
logical AND, OR, and so on.
Display all entries for C++ Bitsets on one
page, or view entries individually:
| Bitset Constructors |
create new bitsets |
| Bitset Operators |
compare and assign bitsets |
| any |
true if any bits are set |
| count |
returns the number of set bits |
| flip |
reverses the bitset |
| none |
true if no bits are set |
| reset |
sets bits to zero |
| set |
sets bits |
| size |
number of bits that the bitset can
hold |
| test |
returns the value of a given
bit |
| to_string |
string representation of the
bitset |
| to_ulong |
returns an integer representation
of the bitset |


Match Play. Double Match Point. How should Red play 55?
pips Red=142 White=105
(CorrectAnswer= 0/0, ErrorScore= 0)
For once I am going to let one of my regular commenters, Leo, provide the answer as his explanation is both concise and accurate:
It seems counter intuitive to run 23/13(2), being down in the race and taking the pressure off White's two blots on his 12 and 9pt. However, if you're stopping at 23/18(2) where are the other two 5s? 9/4(2) is all well and good, but those checkers are already doing a good job of constraining White's back checker and now the 10-pt is no longer part of the prime. Any other two 5s just worsen Red’s position. 23/13(2) it is then.
Thank you, Leo. In fact, any play other than 23/13(2) is an outright blunder.
It seems counter intuitive to run 23/13(2), being down in the race and taking the pressure off White's two blots on his 12 and 9pt. However, if you're stopping at 23/18(2) where are the other two 5s? 9/4(2) is all well and good, but those checkers are already doing a good job of constraining White's back checker and now the 10-pt is no longer part of the prime. Any other two 5s just worsen Red’s position. 23/13(2) it is then.
Thank you, Leo. In fact, any play other than 23/13(2) is an outright blunder.
1. Cubeful 2-ply 23/13(2) Eq.: +0.216 0.608 0.067 0.003 - 0.392 0.069 0.001 2. Cubeful 2-ply 23/18(2) 9/4(2) Eq.: +0.135 (-0.081) 0.568 0.103 0.005 - 0.432 0.089 0.002 3. Cubeful 2-ply 23/18(2) 11/1 Eq.: +0.100 (-0.116) 0.550 0.098 0.005 - 0.450 0.088 0.002 4. Cubeful 0-ply 23/18(2) 7/2(2) Eq.: +0.029 (-0.188) 0.514 0.087 0.004 - 0.486 0.080 0.000 5. Cubeful 0-ply 23/18(2) 11/6 10/5 Eq.: +0.003 (-0.213) 0.502 0.073 0.004 - 0.498 0.073 0.000