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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 4a9691a | Lambda Moses | 2019-07-26 | Reran with Ensembl 97 |
| html | 2da533f | Lambda Moses | 2019-07-17 | Build site. |
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| html | 62a20a3 | Lambda Moses | 2019-07-17 | Build site. |
| Rmd | 3cf75fe | Lambda Moses | 2019-07-17 | Added Monocle 2 notebook |
In this vignette, we will process fastq files of the 10x 10k neurons from an E18 mouse, and perform pseudotime analysis with Monocle 2 on the neuronal cell types. Monocle 2 is deprecated, but it can be easily installed from Bioconductor and still has a user base. At present, Monocle 3 is at beta stage of development, and it can be hard to install on Linux servers due to gdal dependency.
If you would like to rerun this notebook, you can git clone this repository or directly download this notebook from GitHub.
This notebook demonstrates the use of command line tools kallisto
and bustools
. Please use kallisto
>= 0.46, whose binary can be downloaded here. The binary of bustools
can be found here.
After you download the binary, you should decompress the file (if it is tar.gz
) with tar -xzvf file.tar.gz
in the bash
terminal, and add the directory containing the binary to PATH
by export PATH=$PATH:/foo/bar
, where /foo/bar
is the directory of interest. Then you can directly invoke the binary on the command line as we will do in this notebook.
We will be using the R packages below. BUSpaRse
is not yet on CRAN or Bioconductor. For Mac users, see the installation note for BUSpaRse
. BUSpaRse
will be used to generate the transcript to gene file for bustools
and to read output of bustools
into R. We will also use Seurat
version 3 which is now on CRAN.
# Install devtools if it's not already installed
if (!require(devtools)) {
install.packages("devtools")
}
# Install from GitHub
devtools::install_github("BUStools/BUSpaRse")
The package SingleR
, which will be used for cell type inference, is only available on GitHub:
devtools::install_github("dviraran/SingleR")
This vignette uses the version of DropletUtils
from Bioconductor version 3.9; the version from Bioconductor 3.8 has a different user interface. If you are using a version of R older than 3.6.0 and want to rerun this vignette, then you can adapt the knee plot code to the older version of DropletUtils
or install DropletUtils
from GitHub. The package monocle
should also be installed from Bioconductor:
if (!require(BiocManager)) {
install.packages("BiocManager")
}
BiocManager::install(c("DropletUtils", "monocle"))
The other R packages below are on CRAN.
library(BUSpaRse)
library(DropletUtils)
library(monocle)
library(SingleR)
library(Matrix)
library(tidyverse)
theme_set(theme_bw())
The dataset we are using is 10x 10k neurons from an E18 mouse (almost 25 GB).
# Download data
if (!file.exists("./data/neuron_10k_v3_fastqs.tar")) {
download.file("http://s3-us-west-2.amazonaws.com/10x.files/samples/cell-exp/3.0.0/neuron_10k_v3/neuron_10k_v3_fastqs.tar", "./data/neuron_10k_v3_fastqs.tar", method = "wget", quiet = TRUE)
}
cd ./data
tar -xvf ./neuron_10k_v3_fastqs.tar
kallisto
indexHere we use kallisto to pseudoalign the reads to the transcriptome and then to create the bus
file to be converted to a sparse matrix. The first step is to build an index of the mouse transcriptome. The transcriptome downloaded here is Ensembl version 97, the most recent version as of writing.
# Mouse transcriptome
if (!file.exists("./data/mm_cdna97.fa.gz")) {
download.file("ftp://ftp.ensembl.org/pub/release-97/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz", "./data/mm_cdna97.fa.gz", method = "wget", quiet = TRUE)
}
kallisto index -i ./output/mm_tr_index97.idx ./data/mm_cdna97.fa.gz
With the index and the fastq files, the kallisto bus
command generates a binary bus
file called output.bus
, which will be sorted and processed to generate a gene count matrix.
cd ./data/neuron_10k_v3_fastqs
kallisto bus -i ../../output/mm_tr_index97.idx -o ../../output/neuron10k -x 10xv3 -t8 \
neuron_10k_v3_S1_L002_R1_001.fastq.gz neuron_10k_v3_S1_L002_R2_001.fastq.gz \
neuron_10k_v3_S1_L001_R1_001.fastq.gz neuron_10k_v3_S1_L001_R2_001.fastq.gz
bustools
For the sparse matrix, most people are interested in how many UMIs per gene per cell, we here we will quantify this from the bus
output, and to do so, we need to find which gene corresponds to each transcript. Remember in the output of kallisto bus
, there’s the file transcripts.txt
. Those are the transcripts in the transcriptome index.
Remember that we downloaded transcriptome FASTA file from Ensembl just now. In FASTA files, each entry is a sequence with a name. In Ensembl FASTA files, the sequence name has genome annotation of the corresponding sequence, so we can extract transcript IDs and corresponding gene IDs and gene names from there.
tr2g <- transcript2gene(fasta_file = "./data/mm_cdna97.fa.gz",
kallisto_out_path = "./output/neuron10k",
verbose = FALSE)
head(tr2g)
#> transcript gene gene_name
#> 1: ENSMUST00000196221.1 ENSMUSG00000096749.2 Trdd1
#> 2: ENSMUST00000179664.1 ENSMUSG00000096749.2 Trdd1
#> 3: ENSMUST00000177564.1 ENSMUSG00000096176.1 Trdd2
#> 4: ENSMUST00000178537.1 ENSMUSG00000095668.1 Trbd1
#> 5: ENSMUST00000178862.1 ENSMUSG00000094569.1 Trbd2
#> 6: ENSMUST00000179520.1 ENSMUSG00000094028.1 Ighd4-1
bustools
requires tr2g
to be written into a tab delimited file of a specific format: No headers, first column is transcript ID, and second column is the corresponding gene ID. Transcript IDs must be in the same order as in the kallisto
index.
# Write tr2g to format required by bustools
save_tr2g_bustools(tr2g, file_save = "./output/tr2g_mm97.tsv")
A whitelist that contains all the barcodes known to be present in the kit is provided by 10x and comes with CellRanger. A CellRanger installation is required, though we will not run CellRanger here.
cp ~/cellranger-3.0.2/cellranger-cs/3.0.2/lib/python/cellranger/barcodes/3M-february-2018.txt.gz \
./data/whitelist_v3.txt.gz
gunzip ./data/whitelist_v3.txt.gz
Then we’re ready to make the gene count matrix. First, bustools
runs barcode error correction on the bus
file. Then, the corrected bus
file is sorted by barcode, UMI, and equivalence classes. Then the UMIs are counted and the counts are collapsed into gene level. Here the |
is pipe in bash, just like the magrittr pipe %>%
in R, that pipes the output of one command to the next.
mkdir ./tmp
bustools correct -w ./data/whitelist_v3.txt -p ./output/neuron10k/output.bus | \
bustools sort -T tmp/ -t4 -p - | \
bustools count -o ./output/neuron10k/genes -g ./output/tr2g_mm97.tsv \
-e ./output/neuron10k/matrix.ec -t ./output/neuron10k/transcripts.txt --genecounts -
rm -r ./tmp
The outputs are explained in the 10xv2 vignette.
Now we can load the matrix into R for analysis.
res_mat <- read_count_output("./output/neuron10k", name = "genes", tcc = FALSE)
dim(res_mat)
#> [1] 36558 1413171
The number of genes seems reasonable. The number of barcodes is way larger than the expected ~10k.
tot_counts <- Matrix::colSums(res_mat)
summary(tot_counts)
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 0.00 1.00 1.00 64.98 2.00 51636.00
The vast majority of “cells” have only no or just a few UMI detected. Those are empty droplets. 10x claims to have cell capture rate of up to 65%, but in practice, depending on how many cells are in fact loaded, the rate can be much lower. A commonly used method to estimate the number of empty droplets is barcode ranking knee and inflection points, as those are often assumed to represent transition between two components of a distribution. While more sophisticated methods exist (e.g. see emptyDrops
in DropletUtils
), for simplicity, we will use the barcode ranking method here. However, whichever way we go, we don’t have the ground truth.
# Compute barcode rank
bc_rank <- barcodeRanks(res_mat, lower = 1000)
Here the knee plot is transposed, because this is more generalizable to multi-modal data, such that those with not only RNA-seq but also abundance of cell surface markers. In that case, we can plot number of UMIs on the x axis, number of cell surface protein tags on the y axis, and barcode rank based on both UMI and protein tag counts on the z axis; it makes more sense to make barcode rank the dependent variable. See this blog post by Lior Pachter for a more detailed explanation.
tibble(total = bc_rank$total, rank = bc_rank$rank) %>%
distinct() %>%
ggplot(aes(total, rank)) +
geom_line() +
geom_vline(xintercept = metadata(bc_rank)$knee, color = "blue", linetype = 2) +
geom_vline(xintercept = metadata(bc_rank)$inflection, color = "green", linetype = 2) +
annotate("text", y = 1000, x = 1.5 * c(metadata(bc_rank)$knee, metadata(bc_rank)$inflection),
label = c("knee", "inflection"), color = c("blue", "green")) +
scale_x_log10() +
scale_y_log10() +
labs(y = "Barcode rank", x = "Total UMI count")
#> Warning: Transformation introduced infinite values in continuous x-axis
| Version | Author | Date |
|---|---|---|
| 62a20a3 | Lambda Moses | 2019-07-17 |
# Remove genes that are not detected and empty droplets
res_mat <- res_mat[Matrix::rowSums(res_mat) > 0, tot_counts > metadata(bc_rank)$inflection]
dim(res_mat)
#> [1] 23516 11037
Now the number of cells is closer to expectation.
Monocle 2 only infers one trajectory for the entire dataset, so non-neuronal cells like endothelial cells and erythrocytes may be mistaken as highly differentiated cells from the neuronal lineage. So we will remove cell types not of the neural or glial lineages. Cell types are also helpful to orient the trajectory; neuronal progenitor cells must come before neurons. Here cell type inference is done programatically with SingleR
, which compares gene expression profiles of individual cells to bulk RNA-seq data of purified known cell types.
data("mouse.rnaseq")
# Convert from gene symbols to Ensembl gene ID
ref_use <- mouse.rnaseq$data
rownames(ref_use) <- tr2g$gene[match(rownames(ref_use), tr2g$gene_name)]
ref_use <- ref_use[!is.na(rownames(ref_use)),]
Then SingleR
will assign each cell a label based on Spearman correlation with known cell types from bulk RNA-seq. These are meanings of the acronyms:
annots <- SingleR("single", res_mat, ref_data = ref_use, types = mouse.rnaseq$types)
inds <- annots$labels %in% c("NPCs", "Neurons", "OPCs", "Oligodendrocytes",
"qNSCs", "aNSCs", "Astrocytes", "Ependymal")
# Only keep these cell types
cells_use <- annots$cell.names[inds]
mat_neu <- res_mat[,cells_use]
df <- data.frame(nGene = Matrix::colSums(mat_neu > 0),
nUMIs = Matrix::colSums(mat_neu))
df %>%
gather(key = "variable") %>%
ggplot(aes(variable, value)) +
geom_violin() +
geom_jitter(size = 0.1, alpha = 0.1, width = 0.3) +
scale_y_log10()
| Version | Author | Date |
|---|---|---|
| 62a20a3 | Lambda Moses | 2019-07-17 |
ggplot(df, aes(nUMIs, nGene)) +
geom_point(size = 0.5, alpha = 0.3) +
scale_x_log10() +
scale_y_log10()
| Version | Author | Date |
|---|---|---|
| 62a20a3 | Lambda Moses | 2019-07-17 |
# Construct CellDataSet object
pd <- data.frame(cell_id = cells_use,
cell_type = annots$labels[inds],
row.names = cells_use)
pd <- new("AnnotatedDataFrame", data = pd)
fd <- data.frame(gene_id = rownames(mat_neu),
gene_short_name = tr2g$gene_name[match(rownames(mat_neu), tr2g$gene)],
row.names = row.names(mat_neu))
fd <- new("AnnotatedDataFrame", data = fd)
cds <- newCellDataSet(mat_neu, phenoData = pd, featureData = fd)
Size factor and dispersion will be used to normalize data and select genes for clustering.
cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds)
#> Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
#> Warning: step size truncated due to divergence
#> Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
#> Warning: step size truncated due to divergence
#> Warning: glm.fit: algorithm did not converge
#> Removing 106 outliers
Genes that aren’t highly expressed enough will not be used for clustering, since they may not give meaningful signal and would only add noise.
disp_table <- dispersionTable(cds)
clustering_genes <- subset(disp_table, mean_expression >= 0.1)
cds <- setOrderingFilter(cds, clustering_genes$gene_id)
cds <- reduceDimension(cds, num_dim = 40, reduction_method = 'tSNE')
cds <- clusterCells(cds, method = "louvain")
plot_cell_clusters(cds, cell_size = 0.5) +
theme(legend.position = "none") +
labs(x = "tSNE1", y = "tSNE2")
| Version | Author | Date |
|---|---|---|
| 62a20a3 | Lambda Moses | 2019-07-17 |
See where the annotated cell types are
plot_cell_clusters(cds, cell_size = 0.5, color_by = "cell_type") +
scale_color_brewer(name = "cell type", type = "qual", palette = "Set2") +
labs(x = "tSNE1", y = "tSNE2") +
theme(legend.position = "right") +
guides(color = guide_legend(override.aes = list(size = 3)))
| Version | Author | Date |
|---|---|---|
| 2da533f | Lambda Moses | 2019-07-17 |
Genes likely to be informative of ordering of cells along the pseudotime trajectory will be selected for pseudotime inference.
diff_genes <- differentialGeneTest(cds, fullModelFormulaStr = "~ Cluster + cell_type",
cores = 10)
# Use top 3000 differentially expressed genes
ordering_genes <- row.names(subset(diff_genes, qval < 1e-3))[order(diff_genes$qval)][1:3000]
cds <- setOrderingFilter(cds, ordering_genes)
Here Monocle 2 will first project the data to 2 dimensions with DDRTree
, and then do trajectory inference (orderCells
).
cds <- reduceDimension(cds, max_components = 2, method = 'DDRTree')
cds <- orderCells(cds)
See what the trajectory looks like. This projection is DDRTree
.
plot_cell_trajectory(cds, color_by = "cell_type", cell_size = 1) +
scale_color_brewer(name = "cell type", type = "qual", palette = "Set2")
| Version | Author | Date |
|---|---|---|
| 62a20a3 | Lambda Moses | 2019-07-17 |
In the kallisto | bustools paper, I used slingshot
for pseudotime analysis (Supplementary Figure 6.5) of this dataset, and found two neuronal end points. The result from Monocle 2 here also shows two main branches. Also, as expected, the stem cells are at the very beginning of the trajectory.
plot_cell_trajectory(cds, color_by = "Pseudotime", cell_size = 1) +
scale_color_viridis_c()
| Version | Author | Date |
|---|---|---|
| 62a20a3 | Lambda Moses | 2019-07-17 |
The pseudotime values are inverted.
cds <- orderCells(cds, reverse = TRUE)
plot_cell_trajectory(cds, color_by = "Pseudotime", cell_size = 1) +
scale_color_viridis_c()
| Version | Author | Date |
|---|---|---|
| 62a20a3 | Lambda Moses | 2019-07-17 |
Monocle 2 can also be used to find genes differentially expressed along the pseudotime trajectory and clusters of such genes.


My name is Isla Holloway .
I live in Apia Samoa.
I am eleven years old.
I am learning how to make a website at CoderDojo.


First of all; you need to install Google Chrome Canary and then Download ZIP.
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Check "Developer mode" option and click "Load unpacked extension..." button and then locate extension folder (directory).
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Open tab you want to broadcast and click icon to start broadcasting your screen.
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Otherwise, right-click; open context-menu and select "Broadcast Screen" option.
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After broadcasting, you can see your room is listed in this page.
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This a Checker calculator that allows users to check the type of triangles depending on the values inputed by the user..


Four main structures
The four main business structures commonly used by small businesses in Australia are:
- Sole trader: an individual trading on their own.
- Partnership: an association of people or entities running a business together, but not as a company.
- Trust: an entity that holds property or income for the benefit of others.
- Company: a legal entity separate from its shareholders.
Choosing a structure
It's important to investigate each option carefully, as choosing your business structure is an important decision.
Your business structure can determine:
- the licenses you require
- how much tax you pay
- whether you're considered an employee, or the owner of the business
- your potential personal liability
- how much control you have over the business
- ongoing costs and volume of paper work for your business.
It is important to note that you can change your business structure throughout the life of your business. As your business grows and expands, you may decide to change your business structure, or to restructure your business.
Obtaining legal or other professional advice can help you understand your own particular circumstances. Speak to your accountant, or use our Advisor Finder tool to find a business adviser, when deciding on your business's structure and type. It is important to determine your business structure and business type before you register a business or company as the steps may differ.
Company
A company is a separate legal entity, unlike a sole trader or a partnership structure. This means the company has the same rights as a natural person and can incur debt, sue and be sued. The company’s owners (the shareholders) can limit their personal liability and are generally not liable for company debts.
A company is a complex business structure, with higher set-up and administrative costs because of additional reporting requirements.
Key aspects of a company:
- Is a separate legal entity.
- Has limited liability compared to other structures.
- Is a more complex business structure to start and run.
- Involves higher set up and running costs than other structures.
- Requires you to understand and comply with all obligations under the Corporations Act 2001.
- Means that business operations are controlled by directors and owned by the shareholders.
- Must be registered for goods and services tax (GST) if the annual GST turnover is $75,000 or more. The registration threshold for non-profit organisations is $150,000.
- Means the money the business earns belongs to the company.
- Requires an annual company tax return to be lodged with the ATO.
Partnership
A partnership is a business structure that involves a number of people who carry on a business together. You may choose a partnership over a sole trader structure for example, if you'll be jointly running the business with another person or a number of people (up to 20).
There are two types of partnerships - general and limited. Partnerships are governed by the Partnership Act 1958.
Key aspects of a partnership:
- It's relatively easy and inexpensive to set up.
- It requires a separate Tax File Number (TFN).
- If you are carrying on an enterprise, you can apply for an Australian Business Number (ABN), but this is not compulsory.
- It's not a separate entity - like a sole trader, you and your business partners are personally liable for the debts of the business.
- You have shared control and management of the business with your partners.
- The partnerships doesn't pay income tax on the income earned. You and each of your partners pay tax on the share of the net partnership income you each receive.
- Requires a partnership tax return to be lodged with the Australian Taxation Office (ATO) each year.
- Each partner is responsible for their own superannuation arrangements - you are not an employee of the partnership.
- You must be registered for GST if the annual income turnover is $75,000 or more.
Trust
A trust is an obligation imposed on a person - a trustee - to hold property or assets (such as business assets) for the benefit of others, known as beneficiaries.
Key aspects of a Trust:
- can be expensive to set-up and operate.
- require a formal trust deed that outlines how the trust operates.
- require the trustee to undertake formal yearly administrative tasks.
- if you operate your business as a trust, the trustee is legally responsible for its operations. A trustee of a trust can be a company, providing some asset protection


scikit-lego¶
We love scikit learn but very often we find ourselves writing custom transformers, metrics and models. The goal of this project is to attempt to consolidate these into a package that offers code quality/testing. This project is a collaboration between multiple companies in the Netherlands. Note that we’re not formally affiliated with the scikit-learn project at all.
Installation¶
Install scikit-lego via pip with
pip install scikit-lego
Alternatively you can fork/clone and run:
pip install --editable .
Usage¶
from sklego.transformers import RandomAdder
from sklearn.preprocessing import StandardScaler
from sklearn.linear_model import LogisticRegression
from sklearn.pipeline import Pipeline
...
mod = Pipeline([
("scale", StandardScaler()),
("random_noise", RandomAdder()),
("model", LogisticRegression(solver='lbfgs'))
])
...


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Asking good questions
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JavaScript vs Ruby
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June 7, 2015
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May 3, 2015
April 26, 2015


--- layout: post status: publish published: true title: Mike Olt and Ryan Kalish Make Cubs Roster author: display_name: Corey Fineran login: Corey email<EMAIL_ADDRESS>url: '' author_login: Corey author_email<EMAIL_ADDRESS>wordpress_id: 9346 wordpress_url: http://ivyenvy.com/?p=9346 date: '2014-03-27 12:31:56 +0000' date_gmt: '2014-03-27 17:31:56 +0000' categories: - Infield - Starting Pitching tags: - Carlos Villanueva - Mike Olt - Chris Rusin - Ryan Kalish comments: - id: 10460 author: Kerry Ward author_email: '' author_url: '' date: '2014-03-27 13:05:41 +0000' date_gmt: '2014-03-27 18:05:41 +0000' content: MIKE OLT! - id: 10461 author: Joshua Waltsak author_email: '' author_url: '' date: '2014-03-27 13:39:50 +0000' date_gmt: '2014-03-27 18:39:50 +0000' content: Good move cubs keeping Olt and kalish - id: 10462 author: Tim Wortman Jr. author_email: '' author_url: '' date: '2014-03-27 14:30:52 +0000' date_gmt: '2014-03-27 19:30:52 +0000' content: I'm very happy with the news. I remember sharing that Olt was working in Arizona early in the off season. Glad all the work payed off - id: 10463 author: Tanner Lawrence author_email: '' author_url: '' date: '2014-03-27 21:45:33 +0000' date_gmt: '2014-03-28 02:45:33 +0000' content: Yes, TD Ameritrade is based out of Omaha and that is where Creighton is at. - id: 10464 author: Tanner Lawrence author_email: '' author_url: '' date: '2014-03-28 07:52:03 +0000' date_gmt: '2014-03-28 12:52:03 +0000' content: What do you think the odds are that Olt wins rookie of the year? - id: 10465 author: Ivy Envy author_email: '' author_url: '' date: '2014-03-28 08:40:53 +0000' date_gmt: '2014-03-28 13:40:53 +0000' content: You know, Tanner Lawrence, I actually hadn't given that much thought. - id: 10466 author: Tanner Lawrence author_email: '' author_url: '' date: '2014-03-28 08:41:51 +0000' date_gmt: '2014-03-28 13:41:51 +0000' content: Me neither until last night. I keep forgetting he will be eligible for it. I think he won't be the favorite but he could be a guy sneaking in the weeds for it! Just a thought! - id: 10467 author: Joshua Waltsak author_email: '' author_url: '' date: '2014-03-28 09:13:16 +0000' date_gmt: '2014-03-28 14:13:16 +0000' content: Tanner Lawrence & Ivy Envy...I think Olt will win Rookie Of The Year because he is an all round complete player ---
When Donnie Murphy was acquired off waivers by the Rangers yesterday, it appeared as though Mike Olt will most likely be the starting 3rd baseman for the Cubs as they start the 2014 season on Monday in Pittsburgh. While I guess we don't technically know if Mike Olt will be starting on Monday, we do know that he is on the Cubs 25-man roster, as is Ryan Kalish.
*EDIT 12:46pm - Carrie Muskat tweeted if Liriano starts for the Pirates on Monday, Olt will start at 3rd base.
Olt's eye issues seem to be behind him and his sore shoulder is feeling well enough for him to start 2014 with the big league team. Olt is batting .275/.321/.608 with 5 HR and 12 RBIs in 56 plate appearances. If Olt can continue to perform at the plate, he offers a nice upgrade over the Valbuena/Murphy tandem we expected. An August infield of Olt, Castro, Baez, Rizzo sounds pretty damn nice.
Ryan Kalish is hitting .275/.370/.300 in Spring Training and worked his way into the outfield picture. I haven't seen a ton of Kalish, but he's got some speed and seems to work counts well.
We also learned today that the Cubs have not yet decided on who will occupy the 5th starter spot:
#Cubs final pitching decisions to be made over weekend. Does not appear they will skip 5th starter's spot in early going of season
— Bruce Miles (@BruceMiles2112) March 27, 2014
I still think Carlos Villanueva should get the spot, but I could see Chris Rusin filling in.
Mike Olt is still a young player and with only 16 games of MLB experience, we can expect some struggles against MLB pitching. But if things go well for Olt, he could be one of the earliest successes (especially at the MLB level) this front office can hang it's hat on.


Iraq Protests
by Associated Press1 / 7Anti-government protesters set fire while security forces close Rasheed Street during clashes in Baghdad, Iraq, Thursday, Nov. 28, 2019. Scores of protesters have been shot dead in the last 24 hours, amid spiraling violence in Baghdad and southern Iraq, officials said. (AP Photo/Khalid Mohammed)
BAGHDAD (AP) — The Latest on anti-government protests in Iraq (all times local):
10 p.m.
Iraqi officials say four protesters were killed amid ongoing violence in Baghdad and southern Iraq, hours after Prime Minister Adel Abdul-Mahdi announced his intention to resign.
Security and hospital officials say one protester was killed and 18 wounded Friday by security forces who fired live rounds and tear gas to repel them on Baghdad’s historic Rasheed Street, near the strategic Ahrar Bridge.
Officials say three protesters were shot dead by security forces in the southern city of Nasiriyah, bringing the total killed there to six on Friday.
Officials say, separately, a Katyusha rocket exploded in an empty lot inside the heavily fortified Green Zone in Baghdad. The officials spoke on condition of anonymity in line with regulations.
At least 400 protesters have been killed since Oct.1, when thousands of Iraqis took to the streets to decry corruption and poor services.
— By Murtada Faraj.
___
4:20 p.m.
Celebrations have erupted in Iraq’s Tahrir Square, where anti-government protesters have been camped out for nearly two months following an announcement by the Iraqi premier that he would be resigning.
The square in central Baghdad has been the epicenter of protests that began Oct. 17 to decry corruption, poor services and lack of jobs.
Shortly after Prime Minister Adel Abdul-Mahdi announced his intention to resign Friday, protesters in Tahrir broke out in song and dance in celebration.
A 25-year-old protester, who identified herself by her first name Amira, said the resignation should have come many weeks ago.
"We will not stop with the Prime Minister, we still have more fighting to do. We will push forward until our demands are met."
___
3:40 p.m.
Iraqi Prime Minister Adel Abdul-Mahdi says he will submit his resignation to Parliament in the wake of anti-government protests, a bit over a year since he took office.
The statement, broadcast on Iraqi TV, comes a day after more than 40 protesters were killed by security forces and shortly after Iraq's top Shiite cleric called on the parliament to withdraw support.
Abdul-Mahdi says he will present to parliament an official memorandum asking for the resignation of the current government.
___
1:30 p.m.
Iraq’s top Shiite cleric is warning of civil war after a deadly day of violence in which security forces shot dead 40 people in the capital and the southern provinces, calling on lawmakers who to “reconsider” their support for the current government.
Grand Ayatollah Ali al-Sistani says the parliament that voted the government of Prime Minister Adil Abdul-Mahdi is “invited to reconsider its choices in that regard,” in his weekly Friday sermon delivered in the holy city of Najaf.
Al-Sistani also said protesters should distinguish between peaceful demonstrators and those with have malign intentions to coopt their movement.
Forty protesters were shot dead by security forces in Baghdad and the southern cities of Najaf and Nasiriya on Thursday, one day after the burning of an Iranian consulate.


addressapp.models package¶
Submodules¶
addressapp.models.address module¶
-
class
addressapp.models.address.
Address
(id, district, municipality, municipality_type, ward)¶ Bases:
django.db.models.base.Model
-
exception
DoesNotExist
¶ Bases:
django.core.exceptions.ObjectDoesNotExist
-
exception
MultipleObjectsReturned
¶ Bases:
django.core.exceptions.MultipleObjectsReturned
-
address
¶
-
district
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
id
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
municipality
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
municipality_type
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
objects
= <django.db.models.manager.Manager object>¶
-
ward
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
exception
-
class
addressapp.models.address.
District
(id, name, status)¶ Bases:
django.db.models.base.Model
-
exception
DoesNotExist
¶ Bases:
django.core.exceptions.ObjectDoesNotExist
-
exception
MultipleObjectsReturned
¶ Bases:
django.core.exceptions.MultipleObjectsReturned
-
id
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
municipality_set
¶ Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
-
name
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
objects
= <django.db.models.manager.Manager object>¶
-
patient_set
¶ Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
-
status
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
exception
-
class
addressapp.models.address.
Municipality
(id, district, name, category, status)¶ Bases:
django.db.models.base.Model
-
exception
DoesNotExist
¶ Bases:
django.core.exceptions.ObjectDoesNotExist
-
exception
MultipleObjectsReturned
¶ Bases:
django.core.exceptions.MultipleObjectsReturned
-
category
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
district
¶ Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Child.parent
is aForwardManyToOneDescriptor
instance.
-
district_id
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
id
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
name
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
objects
= <django.db.models.manager.Manager object>¶
-
patient_set
¶ Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
-
status
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
ward_set
¶ Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
-
exception
-
class
addressapp.models.address.
Ward
(id, municipality, ward, status)¶ Bases:
django.db.models.base.Model
-
exception
DoesNotExist
¶ Bases:
django.core.exceptions.ObjectDoesNotExist
-
exception
MultipleObjectsReturned
¶ Bases:
django.core.exceptions.MultipleObjectsReturned
-
district
¶
-
id
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
location
¶
-
municipality
¶ Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Child.parent
is aForwardManyToOneDescriptor
instance.
-
municipality_id
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
objects
= <django.db.models.manager.Manager object>¶
-
patient_set
¶ Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
-
status
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
ward
¶ A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
-
exception
-
addressapp.models.address.
keygenerator
()¶


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LTUManager Class Reference
| Inherits from | NSObject |
| Declared in | LTUManager.h LTUManager.m |
Tasks
-
+ sharedManager
A shared instance of the LTU Manager
-
+ initializeSharedLTUManagerWithUsername:andPassword:
Create a shared instance of the LTUManager
-
– initWithLTUClient:
Initialize a
LTUManager
with aLTUClient
-
– getProjectsWithSuccess:failure:finished:
Retreive a list of
LTUProject
objects from the LTU API -
– searchInProjects:withImage:success:failure:finished:
Search the LTU API in selected projects with image
-
– cancelAllSearchRequests
Cancel all Search Requests
-
– createVisualInProject:withTitle:withImage:andMetadata:success:failure:finished:
Create a Visual within a project
-
– cancelAllRequests
Cancel all requests
Class Methods
Instance Methods
cancelAllRequests
Cancel all requests
- (void)cancelAllRequests
Discussion
This method will cancel all current requests which include: Searching images, creating visuals, and getting a list of projects.
Declared In
LTUManager.h
cancelAllSearchRequests
Cancel all Search Requests
- (void)cancelAllSearchRequests
Declared In
LTUManager.h
createVisualInProject:withTitle:withImage:andMetadata:success:failure:finished:
Create a Visual within a project
- (void)createVisualInProject:(NSInteger)projectID withTitle:(NSString *)title withImage:(UIImage *)image andMetadata:(NSArray *)metadataArray success:(void ( ^ ) ( LTUVisual *createdVisual ))success failure:(void ( ^ ) ( NSError *error ))failure finished:(void ( ^ ) ( ))finished
Parameters
- projectID
- The project to create the visual in
- title
- Title associated with the Visual
- image
- Image used for the visual
- success
- Block to be executed when a visual was successfully created
- failure
- Block to be executed when creating a visual fails
- finished
- Block that’s always executed AFTER the success/failure blocks
- metadataList
- Array of
LTUMetaData
objects to be added when creating a visual
- Array of
Declared In
LTUManager.h
getProjectsWithSuccess:failure:finished:
Retreive a list of LTUProject
objects from the LTU API
- (void)getProjectsWithSuccess:(void ( ^ ) ( NSArray *projectList ))success failure:(void ( ^ ) ( NSError *error ))failure finished:(void ( ^ ) ( ))finished
Parameters
- success
- Block to be executed when succesfully downloading a list of projects
- failure
- Block to be executed when retrieving the projects failed.
- finished
- Block that’s always executed AFTER the success/failure blocks
Declared In
LTUManager.h
initWithLTUClient:
Initialize a LTUManager
with a LTUClient
- (id)initWithLTUClient:(LTUClient *)client
Declared In
LTUManager.h
searchInProjects:withImage:success:failure:finished:
Search the LTU API in selected projects with image
- (void)searchInProjects:(NSArray *)projectIDs withImage:(UIImage *)image success:(void ( ^ ) ( LTUQuery *queryResult ))success failure:(void ( ^ ) ( NSError *error ))failure finished:(void ( ^ ) ( ))finished
Parameters
- projectIDs
- Array of NSNumbers representing the project IDs to search in.
- image
- An image to search with
- success
- Block to be executed with the
LTUQuery
on succesfully searching the image
- Block to be executed with the
- failure
- Block to be executed when the search image fails.
- finished
- Block that’s always executed AFTER the success/failure blocks
Declared In
LTUManager.h


Element X (not focusable)
Element Y (user or script focusable)
Element Z (script-only focusable)
Set Focus To Element Z
--- layout: example.html title: tabindex shortdesc: tabindex example. docs: > This page's tabindex example. Ref [Is it possible to focus on a div using JavaScript focus() function?](https://stackoverflow.com/questions/3656467/is-it-possible-to-focus-on-a-div-using-javascript-focus-function). tags: "tabindex" ---


Parent and child
This paragraph should include the canvas.
I am a parent and a child.
List of happy things
Make a happy thing


Since 2017 we have run a iBWIM measurement station on the Nakhon Nayak bridge in Thailand.
The bridge is situated in Nakhon Nayak province northeast of Bangkok.
The bridge is instrumented with eight strain gauges under each lane. Six gauges are placed in a line perpendicular to the traffic flow: these carry out the load estimation. Two gauges are placed before and after this line, and measure velocity. Two laser rangefiders supplement these measurements with data detailing the location of the vehicle axles.


General background information¶
In order to get the best of these post, we'll need to explain some basic stuff.
The following services/roles are needed for a Continuous Integration System:- developer PC (duh)
- source control server
- build server
- build server visualizer
- issue/bug tracker
Before you start screaming : this costs a lot to set up, remind that these are roles, it does not mean that each role/service has to be on its own server.
That is advised for best performance, but does not have to be. It depends a lot on how many people are working at the same time, the size of the project, ....
For smaller projects you can easily set all this up on 1 server. Hey, I even set this all up once on my developer laptop ( a machine with 4 gig memory).
Developer PC¶
Get the one you need, specs change so fast these days that providing numbers is not meaningful.
As long as you're comfy with it, it'll do the job :-)
Visual Studio Express and MonoDevelop are great free editors for writing .Net code.
Source Control¶
Source control systems come in a lot of variety, and CCNet supports a lot of them : for a list look at Source Control Blocks.Free and very good ones are svn and git, there are also free providers of these source control systems, so you do not have to maintain these servers/services yourself.
Examples :
- SourceForge (Subversion, Git, Mercurial, Bazaar, CVS)
- GitHub (Git).
There are probably others as well. Or you can setup the source control system of your choice yourself on a system you choose.
Build Server¶
This would be CCNet :-), installed on a server/machine of your choice. Depending on the amount of projects, the size, activity or the kind of actions you do,
one or more build servers can be needed.
Build Server Visualizer¶
This would be CCNet: CCTray and the webDashboard, both can visualize multiple CCNet build servers.
Another nice one is Cradiator This is a WPF-frontend that shows the state of CCNet projects on a big screen, making it ideal to give an overview for a team in the same room.
Issue/bug tracker¶
Even a piece of paper can do this trick, or an excel sheet, but a real issue tracking system is always neat. CCNet has some integration with issue-tracking systems see IssueUrlBuilder
SourceForge also offers issue tracking like Trac and DotProject.
Usages for CCNet¶
CCNet can be used in a variety of setups, I'll list some up that I've setup or heard about, and will provide (detailed) steps to set some up.
Build server¶
This will be the most used setup: get the source from a SourceControl and compile it.
Benefits : you know that the source in your source control is complete (think of 3rd party components)
You can also include testing, source analysis, package creation and so on in CCNet.
And of course you'll have full control on when stuff should be done : on every check in, on set times, nightly builds, ....
Staging Server¶
Once you have a setup package, it is very handy that one can install it on a test server. Depending on the type of software and the needed components to update,this can go from a simple folder to copy (xcopy) to something like :
- create/update a database
- install/update click once apps
- install/update wcf services
- install/update web-sites
- install/update windows services
- install/update SQL-Reports services
- ...
and no, I did not make the last one up, this is what CCNet actually does for me (and it does even more).
For the interested ones, you can read more about that in the posts at RuWi
Also you want this to be automated and repeatable, so no manual actions should be needed, hey with the build in security,
you can even configure it that developers can stage it to a test environment, where testers do some visual tests, and from there on it goes to final QA,
where a product owner can give it's final approval, before it goes to production. Developers can not put a package into the QA environment, this has to be done by a tester.
Scheduler¶
Suppose you do not want to compile source, but do actions at certain times, even here CCNet can help out. There are a lot of triggers built into CCNet.
You can compare this usage with Scheduled Tasks, or the CRON daemon in Linux.
Other cool usages :


#include <JoystickHandler.h>
The update method is called by the input manager, and the input handler increases events by calling the input manager's increaseEventQuantity method.
Definition at line 26 of file JoystickHandler.h.
Public Member Functions | |
| virtual void | initialize () |
| Initializes the input handler. | |
| bool | isEnabled () |
| Returns whether the handler is enabled (processes inputs). | |
| JoystickHandler () | |
| Creates a new joystick handler. | |
| virtual void | resetHelds () |
| Resets all information about held keys, buttons, etc. | |
| void | setEnabled (bool enabled) |
| Sets whether the handler is enabled (processes inputs). | |
| virtual void | shutDown ()=NULL |
| Shuts down the input handler. | |
| virtual void | update ()=NULL |
| Handles all input and updates event quantities. | |
| virtual void | updateExclusive () |
| Updates the handler when the scene's exclusive changes. | |
| virtual | ~JoystickHandler () |
| Destroys the joystick handler. | |
Protected Attributes | |
| bool | enabled |
| Whether the handler is enabled (processes inputs). |
|
|
Creates a new joystick handler.
|
|
|
Destroys the joystick handler.
|
|
|
Initializes the input handler.
|
|
|
Returns whether the handler is enabled (processes inputs). Defaults to true.
|
|
|
Resets all information about held keys, buttons, etc.
|
|
|
Sets whether the handler is enabled (processes inputs). Defaults to true.
|
|
|
Shuts down the input handler.
|
|
|
Handles all input and updates event quantities.
|
|
|
Updates the handler when the scene's exclusive changes.
|
|
|
Whether the handler is enabled (processes inputs). Defaults to true. Definition at line 34 of file JoystickHandler.h. |


The SDKs package RingCentral APIs into easy-to-use libraries for each programming language. Often, you can handle all interaction with the RingCentral API using methods provided in the SDKs without ever needing to learn more about the lower level details of the API communication itself.
Any communication between an external program and RingCentral is performed through one of our APIs. The APIs are agnostic to development platform and language, allowing you much more flexibility.
RingCentral provides documentation for each API we offer. The documentation has details on each API call, including required fields and response details. For a complete list of the RingCentral APIs, visit https://developer.ringcentral.com/api-docs.
Best Practice Tip: Use the RingCentral JavaScript SDKs when you want to build applications intended to run on web browsers and interact with RingCentral.
© 1999 – RingCentral™, Inc. All rights reserved.


Rylla [ad8h], city, in Buffalo Plains [ap70], in Imperia
Last updated Turn #143
Rylla [ad8h], city, in Buffalo Plains [ap70], in Imperia
------------------------------------------------------------------------
12: Elmar [d7q], Pen, with 12 peasants, one worker, 55 pikemen, 23 wagons,
12: arrived from Buffalo Plains [ap70], accompanied by:
12: Celia [i4d], Pen, with one peasant, 30 lt. xbowmen, three wagons,
12: two wild horses, 11 riding horses
12: Tom Sen [p0u], refugee, prisoner
12: Celia [i4d] bought two riding horses [52] from Rylla [ad8h] for
12: 210 gold.
12: Paid a market tax of 52 gold to Rylla [ad8h].
13: Elmar [d7q], Pen, with 12 peasants, one worker, 55 pikemen, 23 wagons,
13: entered Imperial Emporium [b34], accompanied by:
13: Celia [i4d], Pen, with one peasant, 30 lt. xbowmen, three wagons,
13: two wild horses, 13 riding horses
13: Tom Sen [p0u], refugee, prisoner
14: Elmar [d7q], Pen, with 12 peasants, one worker, 55 pikemen, 23 wagons,
14: arrived from Imperial Emporium [b34], accompanied by:
14: Celia [i4d], Pen, with one peasant, 30 lt. xbowmen, three wagons,
14: two wild horses, 13 riding horses
14: Tom Sen [p0u], refugee, prisoner
15: Elmar [d7q], Pen, with 12 peasants, one worker, 55 pikemen, 23 wagons,
15: exited Rylla [ad8h], accompanied by:
15: Celia [i4d], Pen, with one peasant, 30 lt. xbowmen, three wagons,
15: two wild horses, 13 riding horses
15: Tom Sen [p0u], refugee, prisoner
Routes leaving Rylla:
Out, plain, to Buffalo Plains [ap70], 1 day
Garrison [ah4e], garrison, Imperial Empire, with ten peasants
Border closed.
Cities rumored to be nearby:
Imperial City [aa0c], in Imperial Forest [aq70]
Thorbardin [ad7b], in Thorbardin Mountains [ao69]
Eadweard [ad9f], in Buffalo Plains [aq71]
Ilya [ae3l], in Painted Desert [au70]
Market report (tax of 25%):
trade who price qty wt/ea item
----- --- ----- --- ----- ----
buy ad8h 118 7 1 nazgul tail [319]
buy ad8h 9 20 2 orc scalp [331]
buy ad8h 7 9 5 clay pots [95]
buy ad8h 5 14 5 wolf hides [333]
sell ad8h 77 5 1,000 oxen [76]
sell ad8h 105 2 300 riding horses [52]
sell ad8h 825 1 5 Manual of Church of Dol [ed8u]
Inner locations:
Imperial Emporium [b34], Trading Guild, defense 20
It is raining.


-
eglibc 2.19-0ubuntu6.6 -
-
CVE-2015-7547
Multiple stack-based buffer overflows in the (1) send_dg and (2) send_vc functions in the libresolv library in the GNU C Library (aka glibc or libc6) before 2.23 allow remote attackers to cause a denial of service (crash) or possibly execute arbitrary code via a crafted DNS response that triggers a call to the getaddrinfo function with the AF_UNSPEC or AF_INET6 address family, related to performing "dual A/AAAA DNS queries" and the libnss_dns.so.2 NSS module.
Link
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CVE-2015-5277
The get_contents function in nss_files/files-XXX.c in the Name Service Switch (NSS) in GNU C Library (aka glibc or libc6) before 2.20 might allow local users to cause a denial of service (heap corruption) or gain privileges via a long line in the NSS files database.
Link
-
CVE-2015-8778
hcreate((size_t)-1) should fail with ENOMEM
Link
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CVE-2013-2207
pt_chown in GNU C Library (aka glibc or libc6) before 2.18 does not properly check permissions for tty files, which allows local users to change the permission on the files and obtain access to arbitrary pseudo-terminals by leveraging a FUSE file system.
Link
-
CVE-2015-8776
Passing out of range data to strftime() causes a segfault
Link
-
CVE-2015-8779
catopen() Multiple unbounded stack allocations
Link
-
CVE-2015-5180
DNS resolver NULL pointer dereference with crafted record type
Link
-
CVE-2014-9761
nan function unbounded stack allocation
Link
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CVE-2014-8121
DB_LOOKUP in nss_files/files-XXX.c in the Name Service Switch (NSS) in GNU C Library (aka glibc or libc6) 2.21 and earlier does not properly check if a file is open, which allows remote attackers to cause a denial of service (infinite loop) by performing a look-up while the database is iterated over the database, which triggers the file pointer to be reset.
Link
-
CVE-2015-1781
Buffer overflow in the gethostbyname_r and other unspecified NSS functions in the GNU C Library (aka glibc or libc6) before 2.22 allows context-dependent attackers to cause a denial of service (crash) or execute arbitrary code via a crafted DNS response, which triggers a call with a misaligned buffer.
Link
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CVE-2015-8777
The process_envvars function in elf/rtld.c in the GNU C Library (aka glibc or libc6) before 2.23 allows local users to bypass a pointer-guarding protection mechanism via a zero value of the LD_POINTER_GUARD environment variable.
Link
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CVE-2016-1234
glob: buffer overflow with GLOB_ALTDIRFUNC due to incorrect NAME_MAX limit assumption
Link
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CVE-2016-3075
The getnetbyname implementation in nss_dns contains a potentially unbounded alloca call (in the form of a call to strdupa), leading to a stack overflow (stack exhaustion) and a crash if getnetbyname is invoked on a very long name.
Link
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ntp 1:4.2.6.p5+dfsg-3ubuntu<IP_ADDRESS> -
-
CVE-2015-8138
ntp: missing check for zero originate timestamp
Link
-
CVE-2015-7977
reslist NULL pointer dereference
Link
-
CVE-2015-7978
Stack exhaustion in recursive traversal of restriction list
Link
-
CVE-2016-0727
NTP statsdir cleanup cronjob insecure
Link
-
CVE-2015-8139
Origin Leak: ntpq and ntpdc, disclose origin
Link
-
CVE-2015-7976
ntpq saveconfig command allows dangerous characters in filenames
Link
-
CVE-2015-7979
Off-path Denial of Service (DoS) attack on authenticated broadcast mode
Link
-
CVE-2015-8158
Potential Infinite Loop in ntpq
Link
-
CVE-2015-7973
Deja Vu: Replay attack on authenticated broadcast mode
Link
-
CVE-2015-8140
ntpq vulnerable to replay attacks
Link
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CVE-2015-7974
NTP 4.x before 4.2.8p6 and 4.3.x before 4.3.90 do not verify peer associations of symmetric keys when authenticating packets, which might allow remote attackers to conduct impersonation attacks via an arbitrary trusted key, aka a "skeleton key."
Link
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pcre3 1:8.31-2ubuntu2.1 -
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CVE-2016-3191
The compile_branch function in pcre_compile.c in PCRE 8.x before 8.39 and pcre2_compile.c in PCRE2 before 10.22 mishandles patterns containing an (*ACCEPT) substring in conjunction with nested parentheses, which allows remote attackers to execute arbitrary code or cause a denial of service (stack-based buffer overflow) via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror, aka ZDI-CAN-3542.
Link
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CVE-2015-8393
pcregrep in PCRE before 8.38 mishandles the -q option for binary files, which might allow remote attackers to obtain sensitive information via a crafted file, as demonstrated by a CGI script that sends stdout data to a client.
Link
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CVE-2015-8387
PCRE before 8.38 mishandles (?123) subroutine calls and related subroutine calls, which allows remote attackers to cause a denial of service (integer overflow) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
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CVE-2015-8391
The pcre_compile function in pcre_compile.c in PCRE before 8.38 mishandles certain [: nesting, which allows remote attackers to cause a denial of service (CPU consumption) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
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CVE-2015-8390
PCRE before 8.38 mishandles the [: and \\ substrings in character classes, which allows remote attackers to cause a denial of service (uninitialized memory read) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
-
CVE-2015-8394
PCRE before 8.38 mishandles the (?() and (?(R) conditions, which allows remote attackers to cause a denial of service (integer overflow) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
-
CVE-2015-2328
PCRE before 8.36 mishandles the /((?(R)a|(?1)))+/ pattern and related patterns with certain recursion, which allows remote attackers to cause a denial of service (segmentation fault) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
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CVE-2015-8385
PCRE before 8.38 mishandles the /(?|(\k'Pm')|(?'Pm'))/ pattern and related patterns with certain forward references, which allows remote attackers to cause a denial of service (buffer overflow) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
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CVE-2015-8380
The pcre_exec function in pcre_exec.c in PCRE before 8.38 mishandles a // pattern with a \01 string, which allows remote attackers to cause a denial of service (heap-based buffer overflow) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
-
CVE-2015-8386
PCRE before 8.38 mishandles the interaction of lookbehind assertions and mutually recursive subpatterns, which allows remote attackers to cause a denial of service (buffer overflow) or possibly have unspecified other impact via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror.
Link
-
CVE-2015-8382
The match function in pcre_exec.c in PCRE before 8.37 mishandles the /(?:((abcd))|(((?:(?:(?:(?:abc|(?:abcdef))))b)abcdefghi)abc)|((*ACCEPT)))/ pattern and related patterns involving (*ACCEPT), which allows remote attackers to obtain sensitive information from process memory or cause a denial of service (partially initialized memory and application crash) via a crafted regular expression, as demonstrated by a JavaScript RegExp object encountered by Konqueror, aka ZDI-CAN-2547.
Link
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openssl 1.0.1f-1ubuntu2.16 -
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CVE-2016-2842
The doapr_outch function in crypto/bio/b_print.c in OpenSSL 1.0.1 before 1.0.1s and 1.0.2 before 1.0.2g does not verify that a certain memory allocation succeeds, which allows remote attackers to cause a denial of service (out-of-bounds write or memory consumption) or possibly have unspecified other impact via a long string, as demonstrated by a large amount of ASN.1 data, a different vulnerability than CVE-2016-0799.
Link
-
CVE-2016-0797
Multiple integer overflows in OpenSSL 1.0.1 before 1.0.1s and 1.0.2 before 1.0.2g allow remote attackers to cause a denial of service (heap memory corruption or NULL pointer dereference) or possibly have unspecified other impact via a long digit string that is mishandled by the (1) BN_dec2bn or (2) BN_hex2bn function, related to crypto/bn/bn.h and crypto/bn/bn_print.c.
Link
-
CVE-2016-0702
The MOD_EXP_CTIME_COPY_FROM_PREBUF function in crypto/bn/bn_exp.c in OpenSSL 1.0.1 before 1.0.1s and 1.0.2 before 1.0.2g does not properly consider cache-bank access times during modular exponentiation, which makes it easier for local users to discover RSA keys by running a crafted application on the same Intel Sandy Bridge CPU core as a victim and leveraging cache-bank conflicts, aka a "CacheBleed" attack.
Link
-
CVE-2016-0705
Double free vulnerability in the dsa_priv_decode function in crypto/dsa/dsa_ameth.c in OpenSSL 1.0.1 before 1.0.1s and 1.0.2 before 1.0.2g allows remote attackers to cause a denial of service (memory corruption) or possibly have unspecified other impact via a malformed DSA private key.
Link
-
CVE-2016-0798
Memory leak in the SRP_VBASE_get_by_user implementation in OpenSSL 1.0.1 before 1.0.1s and 1.0.2 before 1.0.2g allows remote attackers to cause a denial of service (memory consumption) by providing an invalid username in a connection attempt, related to apps/s_server.c and crypto/srp/srp_vfy.c.
Link
-
CVE-2016-0799
The fmtstr function in crypto/bio/b_print.c in OpenSSL 1.0.1 before 1.0.1s and 1.0.2 before 1.0.2g improperly calculates string lengths, which allows remote attackers to cause a denial of service (overflow and out-of-bounds read) or possibly have unspecified other impact via a long string, as demonstrated by a large amount of ASN.1 data, a different vulnerability than CVE-2016-2842.
Link
-
busybox 1:1.21.0-1ubuntu1 -
-
CVE-2011-5325
path traversal vulnerability in busybox tar
Link
-
CVE-2014-9645
modprobe wrongly accepts paths as module names
Link
-
CVE-2016-2147
OOB heap write due to integer underflow
Link
-
CVE-2016-2148
heap overflow in OPTION_6RD parsing
Link
-
perl 5.18.2-2ubuntu1 -
-
CVE-2016-2381
environment variable confusion
Link
-
CVE-2013-7422
Integer underflow in regcomp.c in Perl before 5.20, as used in Apple OS X before 10.10.5 and other products, allows context-dependent attackers to execute arbitrary code or cause a denial of service (application crash) via a long digit string associated with an invalid backreference within a regular expression.
Link
-
CVE-2014-4330
The Dumper method in Data::Dumper before 2.154, as used in Perl 5.20.1 and earlier, allows context-dependent attackers to cause a denial of service (stack consumption and crash) via an Array-Reference with many nested Array-References, which triggers a large number of recursive calls to the DD_dump function.
Link
-
file 1:5.14-2ubuntu3.3 -
-
CVE-2014-9621
The ELF parser in file 5.16 through 5.21 allows remote attackers to cause a denial of service via a long string.
Link
-
CVE-2014-9620
The ELF parser in file 5.08 through 5.21 allows remote attackers to cause a denial of service via a large number of notes.
Link
-
CVE-2014-9653
readelf.c in file before 5.22, as used in the Fileinfo component in PHP before 5.4.37, 5.5.x before 5.5.21, and 5.6.x before 5.6.5, does not consider that pread calls sometimes read only a subset of the available data, which allows remote attackers to cause a denial of service (uninitialized memory access) or possibly have unspecified other impact via a crafted ELF file.
Link
-
libpng 1.2.50-1ubuntu<IP_ADDRESS> -
-
CVE-2015-8540
underflow read in png_check_keyword in pngwutil.c
Link
-
CVE-2015-8472
Buffer overflow in the png_set_PLTE function in libpng before 1.0.65, 1.1.x and 1.2.x before 1.2.55, 1.3.x, 1.4.x before 1.4.18, 1.5.x before 1.5.25, and 1.6.x before 1.6.20 allows remote attackers to cause a denial of service (application crash) or possibly have unspecified other impact via a small bit-depth value in an IHDR (aka image header) chunk in a PNG image. NOTE: this vulnerability exists because of an incomplete fix for CVE-2015-8126.
Link
-
sudo 1.8.9p5-1ubuntu1.2 -
-
CVE-2015-8239
race condition checking digests/checksums in sudoers
Link
-
CVE-2015-5602
sudoedit in Sudo before 1.8.15 allows local users to gain privileges via a symlink attack on a file whose full path is defined using multiple wildcards in /etc/sudoers, as demonstrated by "/home/*/*/file.txt."
Link
-
pam 1.1.8-1ubuntu2 -
-
CVE-2015-3238
The _unix_run_helper_binary function in the pam_unix module in Linux-PAM (aka pam) before 1.2.1, when unable to directly access passwords, allows local users to enumerate usernames or cause a denial of service (hang) via a large password.
Link
-
CVE-2013-7041
The pam_userdb module for Pam uses a case-insensitive method to compare hashed passwords, which makes it easier for attackers to guess the password via a brute force attack.
Link
-
CVE-2014-2583
Multiple directory traversal vulnerabilities in pam_timestamp.c in the pam_timestamp module for Linux-PAM (aka pam) 1.1.8 allow local users to create aribitrary files or possibly bypass authentication via a .. (dot dot) in the (1) PAM_RUSER value to the get_ruser function or (2) PAM_TTY value to the check_tty funtion, which is used by the format_timestamp_name function.
Link
-
isc-dhcp 4.2.4-7ubuntu12.3 -
-
CVE-2015-8605
ISC DHCP 4.x before 4.1-ESV-R12-P1 and 4.2.x and 4.3.x before 4.3.3-P1 allows remote attackers to cause a denial of service (application crash) via an invalid length field in a UDP IPv4 packet.
Link
-
CVE-2016-2774
ISC DHCP 4.1.x before 4.1-ESV-R13 and 4.2.x and 4.3.x before 4.3.4 does not restrict the number of concurrent TCP sessions, which allows remote attackers to cause a denial of service (INSIST assertion failure or request-processing outage) by establishing many sessions.
Link
-
cpio 2.11+dfsg-1ubuntu1.1 -
-
CVE-2016-2037
The cpio_safer_name_suffix function in util.c in cpio 2.11 allows remote attackers to cause a denial of service (out-of-bounds write) via a crafted cpio file.
Link
-
CVE-2015-1197
cpio 2.11, when using the --no-absolute-filenames option, allows local users to write to arbitrary files via a symlink attack on a file in an archive.
Link
-
gcc-4.8 4.8.4-2ubuntu1~14.04 -
-
CVE-2014-5044
Array memory allocations could cause an integer overflow and thus memory overflow issues at runtime.
Link
-
CVE-2015-5276
The std::random_device class in libstdc++ in the GNU Compiler Collection (aka GCC) before 4.9.4 does not properly handle short reads from blocking sources, which makes it easier for context-dependent attackers to predict the random values via unspecified vectors.
Link
-
util-linux 2.20.1-5.1ubuntu20.7 -
-
CVE-2014-9114
blkid command injection
Link
-
CVE-2013-0157
(a) mount and (b) umount in util-linux 2.14.1, 2.17.2, and probably other versions allow local users to determine the existence of restricted directories by (1) using the --guess-fstype command-line option or (2) attempting to mount a non-existent device, which generates different error messages depending on whether the directory exists.
Link
-
coreutils 8.21-1ubuntu5.3 -
-
libgcrypt11 1.5.3-2ubuntu4.2 -
-
gnutls26 2.12.23-12ubuntu2.3 -
-
CVE-2015-7575
Mozilla Network Security Services (NSS) before 3.20.2, as used in Mozilla Firefox before 43.0.2 and Firefox ESR 38.x before 38.5.2, does not reject MD5 signatures in Server Key Exchange messages in TLS 1.2 Handshake Protocol traffic, which makes it easier for man-in-the-middle attackers to spoof servers by triggering a collision.
Link
-
python3.4 3.4.3-1ubuntu1~14.04.3 -
-
CVE-2014-2667
Race condition in the _get_masked_mode function in Lib/os.py in Python 3.2 through 3.5, when exist_ok is set to true and multiple threads are used, might allow local users to bypass intended file permissions by leveraging a separate application vulnerability before the umask has been set to the expected value.
Link
-
dbus 1.6.18-0ubuntu4.3 -
-
CVE-2015-0245
D-Bus 1.4.x through 1.6.x before 1.6.30, 1.8.x before 1.8.16, and 1.9.x before 1.9.10 does not validate the source of ActivationFailure signals, which allows local users to cause a denial of service (activation failure error returned) by leveraging a race condition involving sending an ActivationFailure signal before systemd responds.


from a literature of logic to a litterature of patterns
what is this talk about? it is about the different styles of writing between programming and fiction.. how they can mutually influence each other, and how different approaches of the problem can open up new avenues.
it is also about the dialectical approaches of top-down and bottom-up, inductive and deductive, formalization and expansion.
first, we talk about style in programming (mccarthy, minsky), between cerebral and embodiment. styles that already existed before (canon), and we can weave in their approaches to fictions (disembodiment, reduction, almightiness)
second, a section on how these stances have influenced writers, showing the interplay between fiction and scientific research. example of eliza: from the formal to the emotional.
third, a part on the new stances. from mccarthy to minsky. from early wittgenstein to late wittgenstein. expand on what this style means cognitively. expand on the patterns
fourth sketch out some consequences; the good, the bad, and the glitch.
sensory data = input data
rokeby - computer as a prosthetic organ for philosophy
does it extend the realm of literature
if it becomes a literature of patterns, what can we say about the unexpected, the glitch (you need it as a counterpoint to a metaphor), the thing that stands out (gmail smart reply i love you). there is also the thread, that it might follow a course of actions, then either fail or succeed and change the further order of execution of events (spectre).
[https://plato.stanford.edu/entries/frege/#FreLif] frege was saying that something should never be taken in isolation, but always within the context of a proposition
move away from aristotelian logic by making all subjects equal, in the sense that they’re always arguments to a predicate
it’s about LOGIK UBER ALLES, and that has somehow moved to the background?
BNR notation, in which there are things, and there are relations. opposite to BNR, which comes later
from mccullough:
but he’s against freud’s dismissal of logic. he seems to like logic, but another “style” of logic
“In his Expertimental Medicine, in French so beautifully clear it set a style of writing, Claude Bernard described the way we push ahead with good experiments and required hypothesese” (A STYLE OF GROUNDING)
p. 25 leibniz, infinitesimal steps, maybe like the process in machine learning of taking small steps in one direction?
he says freud was wrong cause if we could remember everything we would have brains like an elephant—> computers do!
p. 31 “psychology would be a farce unless i really figure out how brains work”
wiener and cybernetics: it’s a big part about statistics and probablities
pitts: the means of input is already modifying it “Instead of the brain computing information digital neuron by digital neuron using the exacting implement of mathematical logic, messy, analog processes in the eye were doing at least part of the interpretive work.”
“This symbolic abstraction made the world transparent but the brain opaque. Once everything had been reduced to information governed by logic, the actual mechanics ceased to matter—the tradeoff for universal computation was ontology” (from the nautilus article)
https://search.proquest.com/openview/260e2fac83cc81510b4ec4d42f1b39bb/1?pq-origsite=gscholar&cbl=18750&diss=y thesis on the relationship between logic and parts of lit (literature of logic) (also borges… writers related to the stream/telecommunications?)
question: to what extent did literary theory/fiction influence ai development?
we have identified sources of scientific thought. what about fiction?
it’s possible that it didn’t happen, which then means that there might not be a mutual influence of these fields (i.e. science -> fiction)
the question then becomes: what is the nature of current developments, and how can we speculate it will change our perception/style/approach?
at the time of mccarthy, they weren’t often departments of CS, just departments of maths
3 approaches to AI:
This is to make it possible for the machine to simulate arbitrary behaviors and try them out.Thesebehaviorsmayberepresentedeitherbynervenets(Minsky1956),byTuringmachines(McCarthy1956),orbycalculatorprograms(Friedberg1958). from https://www.cs.rit.edu/~rlaz/files/mccarthy1959.pdf
Ai: The Tumultuous History Of The Search For Artificial Intelligence
science-fiction.   They constantly monitor inflow from the senses or signals produced by other agents. They perform whatever action they are capable of upon recognition…
We are to thinking what the victorians were to sex
stories that were looked at: children’s stories [https://vivo.brown.edu/docs/e/echarnia_cv.pdf?dt=011415106] phd thesis eugene chiarnak 1972 (supervised by minsky) (+ wittgenstein and his ABC book)
move to frame matching with minsky
roger shank - https://en.wikipedia.org/wiki/Roger_Schank wrote some story-understanding prograns
mccarthy - beckett: the frame theory of knowledge vs. quad
claude shannon: thomas pynchon and thermodynamics link -> not that useful, perhaps periphery example? to read
turing: computing machinery and intelligence
The new problem has the advantage of drawing a fairly sharp line between the physical and the intellectual capacities of a man
The popular view that scientists proceed inexorably from well-established fact to well-established fact, never being influenced by any improved conjecture, is quite mistaken. Provided it is made clear which are proved facts and which are conjectures, no harm can result. Conjectures are of great importance since they suggest useful lines of research.
It seems to me that this criticism depends on a confusion between two kinds of mistake, We may call them “errors of functioning” and “errors of conclusion.” Errors of functioning are due to some mechanical or electrical fault which causes the machine to behave otherwise than it was designed to do. In philosophical discussions one likes to ignore the possibility of such errors; one is therefore discussing “abstract machines.” These abstract machines are mathematical fictions rather than physical objects.
Starting from the assumption that science and literature are isomorphic manifestations of a shared culture (Hayles 1987: 119–20), Hayles contrasts the different “economies of explanation” at work in Shannon and Barthes src


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VIDEO: One injured in north Surrey shooting Sunday
Male victim taken to hospital with non-life threatening injuries
One person has been taken to hospital with non-life threatening injuries, following a shooting in the 13200 block of 104 Avenue in Surrey.
RCMP were called to the scene shortly before noon Sunday, in response to a report of shots fired.
A male victim was located at the scene, suffering from apparent gun shot injuries, and was taken to hospital.
The investigation is in it early stages, however, police say that based on initial information, the incident appears to have been targeted.
The Surrey RCMP General Investigation Unit is in charge of the investigation and the area surrounding the scene is expected to be cordoned off for a significant amount of time.
Officers are interviewing witnesses and canvassing the area for further information and evidence.
Anyone with information who has not already spoken to police is asked to contact the Surrey RCMP at<PHONE_NUMBER> or, to remain anonymous, Crimestoppers, at 1-800-222-8477 or www.solvecrime.ca, quoting file number 2019-174809.


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