Docker Desktop for Mac をはじめよう
読む時間の目安: 16 分Docker Desktop へようこそ！
Docker Desktop for Mac に関するこのページでは、Docker Desktop Community 安定版リリースについて説明します。 Edge 版リリースにおいて利用可能な機能に関しては Edge リリースノート を参照してください。 また Docker Desktop Enterprise (DDE) リリースについては Docker Desktop Enterprise を参照してください。
Docker には、コンテナー化アプリケーションをビルド、実行し、共有するための開発プラットフォームがすべて含まれています。 Mac 上において Docker をはじめるには Docker Desktop が最適です。
Docker Desktop のインストール を参照して、ダウンロード情報、システム前提条件、インストール手順を確認してください。
バージョンの確認
利用している docker
、docker-compose
のバージョンが最新であること、そして Docker.app
との互換性があることを確認します。
以下に示すバージョン出力は、利用しているものにより異なるかもしれません。
$ docker --version
Docker version 19.03, build c97c6d6
Explore the application
-
コマンドラインターミナルを開いて、単純な Docker イメージ hello-world が動作するかどうかを確認します。
$ docker run hello-world Unable to find image 'hello-world:latest' locally latest: Pulling from library/hello-world ca4f61b1923c: Pull complete Digest: sha256:ca0eeb6fb05351dfc8759c20733c91def84cb8007aa89a5bf606bc8b315b9fc7 Status: Downloaded newer image for hello-world:latest Hello from Docker! This message shows that your installation appears to be working correctly. ...
-
Docker 化されたウェブサーバーを起動します。 上の
hello-world
イメージの場合と同じように、ローカルにそのイメージが見つからないときは Docker Hub からプルされます。$ docker run --detach --publish=80:80 --name=webserver nginx
-
ウェブブラウザーから
http://localhost/
にアクセスして nginx ホームページを開きます。 デフォルトの HTTP ポートを指定しているので、URL の最後に:80
をつける必要はありません。Early beta releases used
docker
as the hostname to build the URL. Now, ports are exposed on the private IP addresses of the VM and forwarded tolocalhost
with no other host name set. -
View the details on the container while your web server is running (with
docker container ls
ordocker ps
):$ docker container ls CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 56f433965490 nginx "nginx -g 'daemon off" About a minute ago Up About a minute <IP_ADDRESS>:80->80/tcp, 443/tcp webserver
-
Stop and remove containers and images with the following commands. Use the “all” flag (
--all
or-a
) to view stopped containers.$ docker container ls $ docker container stop webserver $ docker container ls -a $ docker container rm webserver $ docker image ls $ docker image rm nginx
Preferences
Choose the Docker menu > Preferences from the menu bar and configure the runtime options described below.
一般 (General) タブ
「一般」(General) タブにおいて Docker の起動や更新をいつ行うのか定めます。
-
Start Docker Desktop when you log in: Automatically starts Docker Desktop when you open your session.
-
Automatically check for updates: デフォルトでは、Docker Desktop の更新チェックは自動的に行われ、利用可能な更新がある場合は通知されます。 Docker のメインメニューにある Check for Updates を実行すれば、いつでも手動による更新ができます。
-
Include VM in Time Machine backups: Select this option to back up the Docker Desktop virtual machine. This option is disabled by default.
-
Securely store Docker logins in macOS keychain: Docker Desktop stores your Docker login credentials in macOS keychain by default.
-
Send usage statistics: Docker Desktop sends diagnostics, crash reports, and usage data. This information helps Docker improve and troubleshoot the application. Clear the check box to opt out.
Click Switch to the Edge version to learn more about Docker Desktop Edge releases.
リソース (Resources) タブ
「リソース」(Resources) タブは、CPU、メモリ、ディスク、プロキシー、ネットワークといったリソースを設定します。
Advanced
On the Advanced tab, you can limit resources available to Docker.
Advanced settings are:
CPUs: By default, Docker Desktop is set to use half the number of processors available on the host machine. To increase processing power, set this to a higher number; to decrease, lower the number.
Memory: By default, Docker Desktop is set to use 2
GB runtime memory,
allocated from the total available memory on your Mac. To increase the RAM, set this to a higher number. To decrease it, lower the number.
Swap: Configure swap file size as needed. The default is 1 GB.
Disk image size: Specify the size of the disk image.
Disk image location: Specify the location of the Linux volume where containers and images are stored.
You can also move the disk image to a different location. If you attempt to move a disk image to a location that already has one, you get a prompt asking if you want to use the existing image or replace it.
File sharing
Use File sharing to allow local directories on the Mac to be shared with Linux containers.
This is especially useful for
editing source code in an IDE on the host while running and testing the code in a container.
By default the /Users
, /Volume
, /private
, /tmp
and /var/folders
directory are shared. If your project is outside this directory then it must be added
to the list. Otherwise you may get Mounts denied
or cannot start service
errors at runtime.
File share settings are:
-
Add a Directory: Click
+
and navigate to the directory you want to add. -
Apply & Restart makes the directory available to containers using Docker’s bind mount (
-v
) feature.There are some limitations on the directories that can be shared:
- The directory must not exist inside of Docker.
For more information, see:
- Namespaces in the topic on osxfs file system sharing.
- Volume mounting requires file sharing for any project directories outside of
/Users
.)
Proxies
Docker Desktop detects HTTP/HTTPS Proxy Settings from macOS and automatically
propagates these to Docker. For example, if you set your
proxy settings to http://proxy.example.com
, Docker uses this proxy when
pulling containers.
Your proxy settings, however, will not be propagated into the containers you start. If you wish to set the proxy settings for your containers, you need to define environment variables for them, just like you would do on Linux, for example:
$ docker run -e HTTP_PROXY=http://proxy.example.com:3128 alpine env
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
HOSTNAME=b7edf988b2b5
TERM=xterm
HOME=/root
HTTP_PROXY=http://proxy.example.com:3128
For more information on setting environment variables for running containers, see Set environment variables.
Network
You can configure Docker Desktop networking to work on a virtual private network (VPN). Specify a network address translation (NAT) prefix and subnet mask to enable Internet connectivity.
Docker Engine
The Docker Engine page allows you to configure the Docker daemon to determine how your containers run.
Type a JSON configuration file in the box to configure the daemon settings. For a full list of options, see the Docker Engine dockerd commandline reference.
Click Apply & Restart to save your settings and restart Docker Desktop.
Command Line
On the Command Line page, you can specify whether or not to enable experimental features.
試験的な機能は、将来の製品に搭載される機能をいち早く試すことができるものです。 ただし現段階でのこの機能は、テストとフィードバックのためだけを意図しています。 したがってリリース時には予告なく変更される場合があり、将来のリリースでは完全に削除されることもあります。 試験的な機能は本番環境では利用しないでください。 Docker ではこの試験的機能に対するサポートは行っていません。
Docker CLI において試験的機能を有効にするには、
config.json
ファイルを編集してexperimental
を有効に設定してください。Docker Desktop メニューから試験的機能を有効にするには、Settings (macOS の場合は Preferences) > Command Line をクリックし、Enable experimental features チェックを有効にします。 そして Apply & Restart をクリックしてください。
Docker CLI における現時点での試験的機能については Docker CLI 試験的機能 の一覧を参照してください。
On both Docker Desktop Edge and Stable releases, you can toggle the experimental features on and off. If you toggle the experimental features off, Docker Desktop uses the current generally available release of Docker Engine.
You can see whether you are running experimental mode at the command line. If
Experimental
is true
, then Docker is running in experimental mode, as shown
here. (If false
, Experimental mode is off.)
> docker version
Client: Docker Engine - Community
Version: 19.03.1
API version: 1.40
Go version: go1.12.5
Git commit: 74b1e89
Built: Thu Jul 25 21:18:17 2019
OS/Arch: darwin/amd64
Experimental: true
Server: Docker Engine - Community
Engine:
Version: 19.03.1
API version: 1.40 (minimum version 1.12)
Go version: go1.12.5
Git commit: 74b1e89
Built: Thu Jul 25 21:17:52 2019
OS/Arch: linux/amd64
Experimental: true
containerd:
Version: v1.2.6
GitCommit: 894b81a4b802e4eb2a91d1ce216b8817763c29fb
runc:
Version: 1.0.0-rc8
GitCommit: 425e105d5a03fabd737a126ad93d62a9eeede87f
docker-init:
Version: 0.18.0
GitCommit: fec3683
Kubernetes
Docker Desktop includes a standalone Kubernetes server that runs on your Mac, so that you can test deploying your Docker workloads on Kubernetes.
The Kubernetes client command, kubectl
, is included and configured to connect
to the local Kubernetes server. If you have kubectl
already installed and
pointing to some other environment, such as minikube
or a GKE cluster, be sure
to change context so that kubectl
is pointing to docker-desktop
:
$ kubectl config get-contexts
$ kubectl config use-context docker-desktop
If you installed kubectl
with Homebrew, or by some other method, and
experience conflicts, remove /usr/local/bin/kubectl
.
-
To enable Kubernetes support and install a standalone instance of Kubernetes running as a Docker container, select Enable Kubernetes. To set Kubernetes as the default orchestrator, select Deploy Docker Stacks to Kubernetes by default.
Click Apply & Restart to save the settings. This instantiates images required to run the Kubernetes server as containers, and installs the
/usr/local/bin/kubectl
command on your Mac.When Kubernetes is enabled and running, an additional status bar item displays at the bottom right of the Docker Desktop Settings dialog.
The status of Kubernetes shows in the Docker menu and the context points to
docker-desktop
. -
By default, Kubernetes containers are hidden from commands like
docker service ls
, because managing them manually is not supported. To make them visible, select Show system containers (advanced) and click Apply and Restart. Most users do not need this option. -
To disable Kubernetes support at any time, clear the Enable Kubernetes check box. The Kubernetes containers are stopped and removed, and the
/usr/local/bin/kubectl
command is removed.For more about using the Kubernetes integration with Docker Desktop, see Deploy on Kubernetes.
Reset
Reset and Restart options
On Docker Desktop Mac, the Restart Docker Desktop, Reset to factory defaults, and other reset options are available from the Troubleshoot menu.
For information about the reset options, see Logs and Troubleshooting.
Dashboard
The Docker Desktop Dashboard enables you to interact with containers and applications and manage the lifecycle of your applications directly from your machine. The Dashboard UI shows all running, stopped, and started containers with their state. It provides an intuitive interface to perform common actions to inspect and manage containers and existing Docker Compose applications. For more information, see Docker Desktop Dashboard.
Add TLS certificates
You can add trusted Certificate Authorities (CAs) (used to verify registry server certificates) and client certificates (used to authenticate to registries) to your Docker daemon.
Add custom CA certificates (server side)
All trusted CAs (root or intermediate) are supported. Docker Desktop creates a certificate bundle of all user-trusted CAs based on the Mac Keychain, and appends it to Moby trusted certificates. So if an enterprise SSL certificate is trusted by the user on the host, it is trusted by Docker Desktop.
To manually add a custom, self-signed certificate, start by adding the certificate to the macOS keychain, which is picked up by Docker Desktop. Here is an example:
$ sudo security add-trusted-cert -d -r trustRoot -k /Library/Keychains/System.keychain ca.crt
Or, if you prefer to add the certificate to your own local keychain only (rather than for all users), run this command instead:
$ security add-trusted-cert -d -r trustRoot -k ~/Library/Keychains/login.keychain ca.crt
See also, Directory structures for certificates.
Note: You need to restart Docker Desktop after making any changes to the keychain or to the
~/.docker/certs.d
directory in order for the changes to take effect.
For a complete explanation of how to do this, see the blog post Adding Self-signed Registry Certs to Docker & Docker Desktop for Mac.
Add client certificates
You can put your client certificates in
~/.docker/certs.d/<MyRegistry>:<Port>/client.cert
and
~/.docker/certs.d/<MyRegistry>:<Port>/client.key
.
When the Docker Desktop application starts, it copies the ~/.docker/certs.d
folder on your Mac to the /etc/docker/certs.d
directory on Moby (the Docker
Desktop xhyve
virtual machine).
You need to restart Docker Desktop after making any changes to the keychain or to the
~/.docker/certs.d
directory in order for the changes to take effect.The registry cannot be listed as an insecure registry (see Docker Engine. Docker Desktop ignores certificates listed under insecure registries, and does not send client certificates. Commands like
docker run
that attempt to pull from the registry produce error messages on the command line, as well as on the registry.
Directory structures for certificates
If you have this directory structure, you do not need to manually add the CA certificate to your Mac OS system login:
/Users/<user>/.docker/certs.d/
└── <MyRegistry>:<Port>
├── ca.crt
├── client.cert
└── client.key
The following further illustrates and explains a configuration with custom certificates:
/etc/docker/certs.d/ <-- Certificate directory
└── localhost:5000 <-- Hostname:port
├── client.cert <-- Client certificate
├── client.key <-- Client key
└── ca.crt <-- Certificate authority that signed
the registry certificate
You can also have this directory structure, as long as the CA certificate is also in your keychain.
/Users/<user>/.docker/certs.d/
└── <MyRegistry>:<Port>
├── client.cert
└── client.key
To learn more about how to install a CA root certificate for the registry and how to set the client TLS certificate for verification, see Verify repository client with certificates in the Docker Engine topics.
Install shell completion
Docker Desktop comes with scripts to enable completion for the docker
and docker-compose
commands. The completion scripts may be
found inside Docker.app
, in the Contents/Resources/etc/
directory and can be
installed both in Bash and Zsh.
Bash
Bash has built-in support for
completion To activate completion for Docker commands, these files need to be
copied or symlinked to your bash_completion.d/
directory. For example, if you
installed bash via Homebrew:
etc=/Applications/Docker.app/Contents/Resources/etc
ln -s $etc/docker.bash-completion $(brew --prefix)/etc/bash_completion.d/docker
ln -s $etc/docker-compose.bash-completion $(brew --prefix)/etc/bash_completion.d/docker-compose
Add the following to your ~/.bash_profile
:
[ -f /usr/local/etc/bash_completion ] && . /usr/local/etc/bash_completion
OR
if [ -f $(brew --prefix)/etc/bash_completion ]; then
. $(brew --prefix)/etc/bash_completion
fi
Zsh
In Zsh, the completion
system takes care of things. To activate completion for Docker commands,
these files need to be copied or symlinked to your Zsh site-functions/
directory. For example, if you installed Zsh via Homebrew:
etc=/Applications/Docker.app/Contents/Resources/etc
ln -s $etc/docker.zsh-completion /usr/local/share/zsh/site-functions/_docker
ln -s $etc/docker-compose.zsh-completion /usr/local/share/zsh/site-functions/_docker-compose
Fish-Shell
Fish-shell also supports tab completion completion
system. To activate completion for Docker commands,
these files need to be copied or symlinked to your Fish-shell completions/
directory.
Create the completions
directory:
mkdir -p ~/.config/fish/completions
Now add fish completions from docker.
ln -shi /Applications/Docker.app/Contents/Resources/etc/docker.fish-completion ~/.config/fish/completions/docker.fish
ln -shi /Applications/Docker.app/Contents/Resources/etc/docker-compose.fish-completion ~/.config/fish/completions/docker-compose.fish
Give feedback and get help
To get help from the community, review current user topics, join or start a discussion, log on to our Docker Desktop for Mac forum.
To report bugs or problems, log on to Docker Desktop for Mac issues on GitHub, where you can review community reported issues, and file new ones. See Logs and Troubleshooting for more details.
For information about providing feedback on the documentation or update it yourself, see Contribute to documentation.
Docker Hub
Select Sign in /Create Docker ID from the Docker Desktop menu to access your Docker Hub account. Once logged in, you can access your Docker Hub repositories and organizations directly from the Docker Desktop menu.
For more information, refer to the following Docker Hub topics:
Two-factor authentication
Docker Desktop enables you to sign into Docker Hub using two-factor authentication. Two-factor authentication provides an extra layer of security when accessing your Docker Hub account.
You must enable two-factor authentication in Docker Hub before signing into your Docker Hub account through Docker Desktop. For instructions, see Enable two-factor authentication for Docker Hub.
After you have enabled two-factor authentication:
-
Go to the Docker Desktop menu and then select Sign in / Create Docker ID.
-
Enter your Docker ID and password and click Sign in.
-
After you have successfully signed in, Docker Desktop prompts you to enter the authentication code. Enter the six-digit code from your phone and then click Verify.
After you have successfully authenticated, you can access your organizations and repositories directly from the Docker Desktop menu.
Where to go next
-
Try out the walkthrough at Get Started.
-
Dig in deeper with Docker Labs example walkthroughs and source code.
-
For a summary of Docker command line interface (CLI) commands, see Docker CLI Reference Guide.
-
Check out the blog post, What’s New in Docker 17.06 Community Edition (CE).


Academic and Work Experience¶
- PhD Candidate | Jul 2019 - Jul 2022 | University of Queensland, Brisbane
Bioinformatics PhD developing integration methods for biological data, see current research and recently developed software below for more information. Supervisors: Associate Professor Mikael Boden, Professor Stefan Thor and Associate Professor Jessica Mar
- Research Assistant | Aug 2018 - Aug 2019 | University of Queensland - SCMB, Brisbane
Worked with collaborators on an ancestral sequence reconstruction tool (pipeline development and data processing). System administration tasks such as server management.
- Software Engineer | Jan - Aug 2018 | intelliHR, Brisbane
Produced proof of concept machine learning model to predict attrition. Worked with designers to improve the user experience.
- Research Scholar | Winter 2017 & Summer 2018 | University of Queensland - SCMB, Brisbane
Developed two JavaScript visualisation tools: 1) to facilitate the analysis of epigenetic data, and 2) to investigate partial order graphs of sequence content.
- Research Technician | Aug 2016 - Dec 2017 | University of Melbourne - Stemformatics, Melbourne
Developed client side charts, completed industry based Honors developing a metabolic pathway visualisation tool (Omicxview) in collaboration with Metabolomics Australia.
- Research Attachment | Jan - May 2016 | GUSTO, Singapore
Produced open source MRI noise reduction software to quantify brown and white adipose tissue.
- Forensics Intern | Summer 2016 | KPMG, Brisbane
Used data analytics to identify fraudulent transactions.
- Electrical Engineering Intern | Winter 2016 | ImpediMed, San Diego
Benchmarked a new bioimpedence device in preparation for FDA approval.
Current Research¶
Analysing regulatory programs in FH-deficient cells¶
This project is a collaboration with Christina Schmidt from the Frezza lab. We are analysing the regulatory programs of FH-deficient kidney cells that Christina developed during her PhD. FH is a component of the TCA cycle, with mutations in FH leading to a specific hereditary form of kidney cancer. Given FH is integral to the metabolic process, cells that lack FH under-go a metabolic transformation. The Frezza lab have found that epigenetic changes such as pre- and post-translational modifications play an important role in the cellular transformation initiated by FH loss. In order to analyse on what level genes are regulated (and by which modifications), Christina produced a number of biological assays on the FH-deficient cell-line. Given the complexity of disentangling the regulatory programs we developed R and python based software to analyse on which level each gene is regulated. We do this in a semi-supervised manner, coupling biological knowledge of regulatory programs with the unbiased integrative power of variational-autoencoders. This work has been presented at Vizbi 2021 and we will be releasing a paper soon. We are working on extending the model to publicly available data in TCGA and CPTAC. Given our method is amenable to small datasets we are investigating the capacity of our model to determine regulatory patterns in underrepresented populations in TCGA.
Analysing the spatial and temporal regulation of PRC2 in developing mouse brains¶
This project is a collaboration with Stefan Thor, and my main lab, with Mikael Boden. Stefan and his lab developed a comprehensive transcriptome dataset that spans across the anterior-posterior (A-P) developmental axis in mice.  Human’s, mice, and flies all belong to this category (bilateria), however, the amount of cells and complexity of the brain regions increases with the complexity of the animal. How does the brain expand? How are specific cell types generated at just the right time during development? And what distinguishes different brain regions, such as the forebrain, midbrain and hindbrain? It is known that epigenetics (dynamic changes that can determine which genes will be expressed) plays an integral role in controlling this system. One particular protein, PRC2, which applies an epigenetic mark (H3K27me3) that acts to repress (“turn off”) genes is of particular interest as it selectively applies H3K27me3 during development. We seek to increase the understanding of PRC2’s tissue specific control during embryonic development by 1) developing a comprehensive transcriptome dataset of a wild-type, and also knock-out of PRC2 (by knocking out a key gene Eed). Given we are testing so many different conditions there were too many pairwise comparisons for correlation based analyses. To overcome this, we used a variational-autoencoder to build a generative model of the PRC2 landscape for each gene. This landscape was used to understand how genes express, and are regulated across mouse brain development. We will be releasing our paper on this soon.
Supervised projects¶
Single Cell ATAC-seq peak reproducibility¶
I am co-supervising a masters student, Wengu Pan, at the University of Queensland (completed remotely from SuZhou city, JiangSu province, China). Wenyu’s project seeks to analyse the effect of removing, or retaining low quality peaks in single cell ATAC seq data. Given scATAC methods only capture a small proportion of peaks, is it better to retain all information, or does this leave downstream analysis methods more susceptible to noise? Wenyu is using the rank product test to evaluate the reproducibility of peaks across cells on a dataset of in vitro cardiac differentiation from human pluripotent stem cells from our collaborators, Nathan Palpant and Sophie Shen.
DNA Methylation patterns across TCGA¶
Over the summer (2020/2021) I co-supervised Anastassia Demeshko, a masters student in public health, on her project to analyse method bias when assigning DNA methylation changes to genes. Generally, it is reported that DNA-methylation, when found in the promoter of a gene, causes the nearby gene to be repressed. However, does the data actually fit this hypothesis? When does this stand true, and when does this break down? Given there is no gold-standard method for assigning DNA-methylation changes to genes we use the standard approach of assigning CpG methylation values to genes if they fell within a distance from the TSS of a gene. Anastasia found that how we assign DNA methylation changes to genes drastically affects the results of a study and the assumed regulatory programs governed by DNA methylation. Anastassia’s work also examined summary statistics and found that using the median value of DNA-methylation was less susceptible to bias that using the maximum change in DNA methylation.
During this period I also co-supervised Alice Schulz, an undergraduate statistics/genetics student, on her project which aimed to define and identify a methylation tendency score. Here we asked, are there specific regions of the genome which are more likely to be affected in tumours as compared with normal tissue. We also sought to investigate which regions had the biggest effect on the expresion of near-by genes. Alice first found distinct patterns of DNA-methlylation unique to each tumour type, and then found that by taking into account the proportions of changes in different regions of methylation (CpG islands vs UTR’s) a more robust methylation tendency score as produced.
Recently developed software¶
sci-vae¶
Sci-VAE is an implementation of a variational autoencoder (VAE) in Keras that I developed to use VAEs to integrate biological data. The implementation allows for customisations to the VAE to be passed in via CLI (and a JSON file) or in python and R scripts (see examples).
The VAE implementation expects a data matrix with features as columns (no headers) and rows as training data (no row IDs). The first thing the VAE will do is transform your data between 0 and 1 so you don’t need to do this prior to running the VAE.
I show several examples, using MNIST, IRIS dataset and then also a publicly available histone modification and RNAseq dataset from encode (for those bioinformaticians out there). There are also some useful visualisations that I was having to repeat often when inspecting the latent space so check out the Vis functions if you’re interested (these are also in the examples).
Lastly, there is a optimisation library that allows you to optimise the VAE architecture based on building a separable latent space based on classification. If you choose to use this you’ll also need to pass in labels into the VAE. Check out some tests for how to run this - it uses an evolutionary algorithm. Code will be released soon (with the papers above).
sci-diffMethGenes¶
Sci-dmg aims to assign a change in DNA methylation (as calculated by an external tool) to genes in a consistent and unbiased manner. The user provides a DMR file, a file with the percentage of DNA Methylation, and also the DMCs. Using these, sci-DMG consolidates the DMR’s and DMC’s that are consistent. DMR regions (significant q <= 0.1) with at least 60% of DMCs (q < 0.1) agreeing with the DMR change in methylation direction were kept. Genes with multiple DMRs were removed if the DMRs were not in agreement (meth. Diff. direction). If the DMRs were in agreement, the CpG with the highest DNA methylation difference in the direction of change is assigned as the methylation value (change and padj) for that gene i.e. as the driver CpG behind the gene’s change in DNA methylation. Note the cutoff values are all adjustable. Future works includes assigning not only based on promoter but also on methylation assigned in UTR, on exons, etc.
Any tool can be used to produce the DMC’s and DMR’s, two such tools are MethylKit and MethylSig many others exist.
sci-epi2gene¶
Sci-epi2gene maps events annotated to a genome location to nearby genes - i.e. peaks from histone modification data ChIP-seq experiemnts stored as bed data, or DNA methylation data in csv format (e.g. output from DMRseq or methylKit).
The user provides a SORTED gene annotation file with start, end, and direction for each gene (we recommend using sci-biomart.
The user then selects how to annotate, i.e. whether it is in the promoter region, or overlaps the gene body. Finally, the parameters for overlap on each side are chosen. This algorithm only runs through the file once, so should have computational complexity of O(N).
It is available under the GNU General Public License (Version 3).
This package is a wrapper that allows various epigenetic data types to be annotated to genes. I also wanted to have different upper flanking and lower flanking distances that took into account the directionality of the strand and also an easy output csv file that can be filtered and used in downstream analyses. This is why I keep all features that fall within the annotation region of a gene (example below):
- The overlapping methods are as follows:
Overlaps: this means does ANY part of the peak/feature overlap the gene body + some buffer before the TSS and some buffer on the non-TSS side
Promoter: does ANY part of the peak/feature overlap with the TSS of the gene taking into account buffers on either side of the TSS.
As you can see from the above screenshot using IGV, the input peaks are in purple, and the output peaks as annotated to genes are in green. The function convert_to_bed converts the output csv to bed files for viewing. This example shows that a peak/feature can be annotated to multiple genes. Peaks/features outside of the regions of genes (e.g. the first peak) are dropped from the output.
We show this example in the notebook, where we use IGV to view the tracks (see image below).
Lastly, there are sometimes differences between annotations (i.e. the TSS on your annotation in IGV may differ to the annotation you input to sciepi2gene), naturally, how your genes/features are annotated depends on the input file so if you see differences check this first!
Please post questions and issues related to sci-epi2gene on the Issues section of the GitHub repository.
sci-downloadAnnotateTCGA¶
Sci-Download-Annotate-TCGA is a wrapper around the functions provided by TCGA and the GDC data portal. Long story short, I was needing to merge many of the data (RNAseq and DNA methylation) together from TCGA and I wanted to keep track of the demographics of the patients to ensure I had a balanced dataset. I also wanted to easily find genes in groups of patients with mutations. I found no easy ways to do these things, so I made this wrapper to be able to:
Create a dataframe of many RNAseq datasets from TCGA (and automatically download these)
Merge RNAseq and DNA methylation datasets so for each gene I could see a cross mode profile
Annotate each experiment with demographic information
Anotate each gene with mutation information and search for genes with specific mutations through the API.
This package provides the above in python notebooks, R markdown, and a CLI.
It is available under the GNU General Public License (Version 3).
Please post questions and issues related to sci-dat on the Issues section of the GitHub repository.
sci-motf¶
sci-moTF is a simple package to help with finding motifs that are enriched in different clusters, that are also expressed in your dataset and make it easier to draw inferences on which TFs may be driving the observed changes.
The input to sci-motf is: 1) the output of FIMO , fimo.tsv, 2) a CSV file with gene identifier (e.g. name), cluster, log2FC, and p-value.
sci-biomart¶
Sci-biomart is a simple wrapper around the API from BioMart, but I found existing packages were not quite sufficent for what I was wanting to do. The handy thing about this is that most queries can be performed in a single line, and you can also use it for running in a pipeline (since it supports CLI).
Here you can simply get the list of all genes and perform other biomart functions such as mapping between human and mouse.
It is available under the GNU General Public License (Version 3).
Please post questions and issues related to sci-loc2gene on the Issues section of the GitHub repository.
sci-RNAprocessing¶
Scirnap (sci-RNAprocessing) is a wrapper for some commonly used programs for processing RNAseq data. I created this wrapper to make pipelines more reproducible while keeping things completely modular and allowing for any other program to be added. The main thing I like is that there are consistent log files output and the direct path to a program can be passed (I’ve found this useful on shared servers.) It has made it super easy for me to reproduce pipelines while not adding overhead. Code will be released soon mid 2021.
Previous projects¶
Graphical Representation of Ancestral Sequence Prediction¶
GRASP enables users to perform ancestral sequence prediction and visualisation via a web-interface. My role consisted largely of developing the web, and backend architecture to support the web tool and the implementation of the optimal path finding algorithm through the POAG.
“We developed Graphical Representation of Ancestral Sequence Predictions (GRASP) to infer and explore ancestral variants of protein families with more than 10,000 members. GRASP uses partial order graphs to represent homology in very large datasets, which are intractable with current inference tools and may, for example, be used to engineer proteins by identifying ancient variants of enzymes. We demonstrate that (1) across three distinct enzyme families, GRASP predicts ancestor sequences, all of which demonstrate enzymatic activity, (2) within-family insertions and deletions can be used as building blocks to support the engineering of biologically active ancestors via a new source of ancestral variation, and (3) generous inclusion of sequence data encompassing great diversity leads to less variance in ancestor sequence.” from the documentation
Authors: Gabriel Foley, Ariane Mora, Connie M Ross, Scott Bottoms, Leander Sutzl, Marnie L Lamprecht, Julian Zaugg, Alexandra Essebier, Brad Balderson, Rhys Newell, Raine ES Thomson, Bostjan Kobe, Ross T Barnard, Luke Guddat, Gerhard Schenk, Joerg Carsten, Yosephine Gumulya, Burkhard Rost, Dietmar Haltrich, Volker Sieber, Elizabeth MJ Gillam, Mikael Boden
GRASP preprint
OmixView¶
Abstract: Omicxview is an interactive visualisation portal that enables researchers to display large metabolic datasets on well-defined Escher pathways. It addresses the gap between very simple static views, such as the common approach of colouring KEGG pathways, and the comprehensive networks such as Reactome, which can be so complex that the signal of interest is dwarfed by background information. Omicxview overlays experimental data onto metabolic pathways, providing users with intuitive ways to explore large multi-omic datasets. Authors: Ariane Mora, Rowland Mosbergen, Steve Englart, Othmar Korn, Mikael Boden and Christine A Wells.
Oral Presentation at E-Research Australasia, (Oct 2017)
Oral Presentation at Joining the Dots Symposium (Aug 2017)
Footnote¶
Figures contain images generated using BioRender.


2018-11-12 Malaysia starts issuing Bachelor Degree cert via NEM? Wish I could have my certificates on the blockchain as well cn


1 Week 1
Week 1 covers calculating sampling distributions. Below is the activity.
Complete all Exercises, and submit answers to Questions on the Coursera platform.
1.1 Getting Started
1.1.1 Load packages
In this lab we will explore the data using the dplyr
package and visualize it using the ggplot2
package for data visualization. The data can be found in the companion package for this course, statsr
.
Let’s load the packages.
library(statsr)
library(dplyr)
library(shiny)
library(ggplot2)
1.1.2 The data
We consider real estate data from the city of Ames, Iowa. The details of every real estate transaction in Ames is recorded by the City Assessor’s office. Our particular focus for this lab will be all residential home sales in Ames between 2006 and 2010. This collection represents our population of interest. In this lab we would like to learn about these home sales by taking smaller samples from the full population. Let’s load the data.
data(ames)
We see that there are quite a few variables in the data set, enough to do a very in-depth analysis. For this lab, we’ll restrict our attention to just two of the variables: the above ground living area of the house in square feet (area
) and the sale price (price
).
We can explore the distribution of areas of homes in the population of home sales visually and with summary statistics. Let’s first create a visualization, a histogram:
ggplot(data = ames, aes(x = area)) +
geom_histogram(binwidth = 250)
Let’s also obtain some summary statistics. Note that we can do this using the summarise
function. We can calculate as many statistics as we want using this function, and just string along the results. Some of the functions below should be self explanatory (like mean
, median
, sd
, IQR
, min
, and max
). A new function here is the quantile
function which we can use to calculate values corresponding to specific percentile cutoffs in the distribution. For example quantile(x, 0.25)
will yield the cutoff value for the 25th percentile (Q1) in the distribution of x. Finding these values are useful for describing the distribution, as we can use them for descriptions like “the middle 50% of the homes have areas between such and such square feet”.
ames %>%
summarise(mu = mean(area), pop_med = median(area),
sigma = sd(area), pop_iqr = IQR(area),
pop_min = min(area), pop_max = max(area),
pop_q1 = quantile(area, 0.25), # first quartile, 25th percentile
pop_q3 = quantile(area, 0.75)) # third quartile, 75th percentile
## # A tibble: 1 x 8
## mu pop_med sigma pop_iqr pop_min pop_max pop_q1 pop_q3
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1500. 1442 506.<PHONE_NUMBER> 1126 1743.
- Which of the following is false?
- The distribution of areas of houses in Ames is unimodal and right-skewed.
- 50% of houses in Ames are smaller than 1,499.69 square feet.
- The middle 50% of the houses range between approximately 1,126 square feet and 1,742.7 square feet.
- The IQR is approximately 616.7 square feet.
- The smallest house is 334 square feet and the largest is 5,642 square feet.
1.2 The unknown sampling distribution
In this lab we have access to the entire population, but this is rarely the case in real life. Gathering information on an entire population is often extremely costly or impossible. Because of this, we often take a sample of the population and use that to understand the properties of the population.
If we were interested in estimating the mean living area in Ames based on a sample, we can use the following command to survey the population.
samp1 <- ames %>%
sample_n(size = 50)
This command collects a simple random sample of size
50 from the ames
dataset, which is assigned to samp1
. This is like going into the City Assessor’s database and pulling up the files on 50 random home sales. Working with these 50 files would be considerably simpler than working with all 2930 home sales.
Exercise: Describe the distribution of this sample? How does it compare to the distribution of the population? Hint: sample_n
function takes a random sample of observations (i.e. rows) from the dataset, you can still refer to the variables in the dataset with the same names. Code you used in the previous exercise will also be helpful for visualizing and summarizing the sample, however be careful to not label values mu
and sigma
anymore since these are sample statistics, not population parameters. You can customize the labels of any of the statistics to indicate that these come from the sample.
# type your code for the Exercise here, and Run Document
ggplot(samp1, aes(x = area)) + geom_histogram(binwidth = 200)
# The distribution is symmetric unlike the population distribution
If we’re interested in estimating the average living area in homes in Ames using the sample, our best single guess is the sample mean.
samp1 %>%
summarise(x_bar = mean(area))
## # A tibble: 1 x 1
## x_bar
## <dbl>
## 1 1271.
Depending on which 50 homes you selected, your estimate could be a bit above or a bit below the true population mean of 1,499.69 square feet. In general, though, the sample mean turns out to be a pretty good estimate of the average living area, and we were able to get it by sampling less than 3% of the population.
- Suppose we took two more samples, one of size 100 and one of size 1000. Which would you think would provide a more accurate estimate of the population mean?
- Sample size of 50.
- Sample size of 100.
- Sample size of 1000.
Let’s take one more sample of size 50, and view the mean area in this sample:
ames %>%
sample_n(size = 1000) %>%
summarise(x_bar = mean(area))
## # A tibble: 1 x 1
## x_bar
## <dbl>
## 1 1506.
Not surprisingly, every time we take another random sample, we get a different sample mean. It’s useful to get a sense of just how much variability we should expect when estimating the population mean this way. The distribution of sample means, called the sampling distribution, can help us understand this variability. In this lab, because we have access to the population, we can build up the sampling distribution for the sample mean by repeating the above steps many times. Here we will generate 15,000 samples and compute the sample mean of each. Note that we are sampling with replacement, replace = TRUE
since sampling distributions are constructed with sampling with replacement.
sample_means50 <- ames %>%
rep_sample_n(size = 50, reps = 15000, replace = TRUE) %>%
summarise(x_bar = mean(area))
ggplot(data = sample_means50, aes(x = x_bar)) +
geom_histogram(binwidth = 20)
Here we use R to take 15,000 samples of size 50 from the population, calculate the mean of each sample, and store each result in a vector called sample_means50
. Next, we review how this set of code works.
Exercise: How many elements are there in sample_means50
? Describe the sampling distribution, and be sure to specifically note its center. Make sure to include a plot of the distribution in your answer.
# type your code for the Exercise here, and Run Document
#No. of elements in sample_means50
dim(sample_means50)
## [1] 15000 2
# Center of sampling distribution
sample_means50 %>%
summarise(means = mean(x_bar))
## # A tibble: 1 x 1
## means
## <dbl>
## 1 1500.
#Given that 15000 samples are considered, the distribution resembles a normal distribution and it looks symmetric. Sample means vary around the population mean equally.
1.3 Interlude: Sampling distributions
The idea behind the rep_sample_n
function is repetition. Earlier we took a single sample of size n
(50) from the population of all houses in Ames. With this new function we are able to repeat this sampling procedure rep
times in order to build a distribution of a series of sample statistics, which is called the sampling distribution.
Note that in practice one rarely gets to build sampling distributions, because we rarely have access to data from the entire population.
Without the rep_sample_n
function, this would be painful. We would have to manually run the following code 15,000 times
ames %>%
sample_n(size = 50) %>%
summarise(x_bar = mean(area))
as well as store the resulting sample means each time in a separate vector.
Note that for each of the 15,000 times we computed a mean, we did so from a different sample!
Exercise: To make sure you understand how sampling distributions are built, and exactly what the sample_n
and do
function do, try modifying the code to create a sampling distribution of 25 sample means from samples of size 10, and put them in a data frame named sample_means_small
. Print the output. How many observations are there in this object called sample_means_small
? What does each observation represent?
# type your code for the Exercise here, and Run Document
sample_means_small <- ames %>%
rep_sample_n(size = 10, reps = 25, replace = TRUE) %>%
summarise(x_bar_practice = mean(area))
- How many elements are there in this object called
sample_means_small
?- 0
- 3
- 25
- 100
- 5,000
# type your code for Question 3 here, and Run Document
dim(sample_means_small)
## [1] 25 2
sample_means_small
## # A tibble: 25 x 2
## replicate x_bar_practice
## <int> <dbl>
## 1 1 1641.
## 2 2 1465.
## 3 3 1680
## 4 4 1395.
## 5 5 1488.
## 6 6 1591.
## 7 7 1461.
## 8 8 1406.
## 9 9 1366
## 10 10 1257.
## # ... with 15 more rows
- Which of the following is true about the elements in the sampling distributions you created?
- Each element represents a mean square footage from a simple random sample of 10 houses.
- Each element represents the square footage of a house.
- Each element represents the true population mean of square footage of houses.
1.4 Sample size and the sampling distribution
Mechanics aside, let’s return to the reason we used the rep_sample_n
function: to compute a sampling distribution, specifically, this one.
ggplot(data = sample_means50, aes(x = x_bar)) +
geom_histogram(binwidth = 20)
The sampling distribution that we computed tells us much about estimating the average living area in homes in Ames. Because the sample mean is an unbiased estimator, the sampling distribution is centered at the true average living area of the population, and the spread of the distribution indicates how much variability is induced by sampling only 50 home sales.
In the remainder of this section we will work on getting a sense of the effect that sample size has on our sampling distribution.
Exercise: Use the app below to create sampling distributions of means of area
s from samples of size 10, 50, and 100. Use 5,000 simulations. What does each observation in the sampling distribution represent? How does the mean, standard error, and shape of the sampling distribution change as the sample size increases? How (if at all) do these values change if you increase the number of simulations?
- It makes intuitive sense that as the sample size increases, the center of the sampling distribution becomes a more reliable estimate for the true population mean. Also as the sample size increases, the variability of the sampling distribution ________.
- decreases
- increases
- stays the same
Exercise: Take a random sample of size 50 from price
. Using this sample, what is your best point estimate of the population mean?
# type your code for this Exercise here, and Run Document
samp1 %>%
summarise(mu_price = mean(price))
## # A tibble: 1 x 1
## mu_price
## <dbl>
## 1 161474.
Exercise: Since you have access to the population, simulate the sampling distribution for \(\bar{x}_{price}\) by taking 5000 samples from the population of size 50 and computing 5000 sample means. Store these means in a vector called sample_means50
. Plot the data, then describe the shape of this sampling distribution. Based on this sampling distribution, what would you guess the mean home price of the population to be?
# type your code for this Exercise here, and Run Document
sample_means50 <- ames %>%
rep_sample_n(size = 50, reps = 5000, replace = TRUE) %>%
summarise(x_bar_price = mean(price))
ggplot(sample_means50,aes(x = x_bar_price)) + geom_histogram(binwidth = 1000)
Exercise: Change your sample size from 50 to 150, then compute the sampling distribution using the same method as above, and store these means in a new vector called sample_means150
. Describe the shape of this sampling distribution, and compare it to the sampling distribution for a sample size of 50. Based on this sampling distribution, what would you guess to be the mean sale price of homes in Ames?
# type your code for this Exercise here, and Run Document
sample_means150 <- ames %>%
rep_sample_n(size = 150, reps = 5000, replace = TRUE) %>%
summarise(x_bar_price = mean(price))
ggplot(sample_means150,aes(x = x_bar_price)) + geom_histogram(binwidth = 1000)
So far, we have only focused on estimating the mean living area in homes in Ames. Now you’ll try to estimate the mean home price.
Note that while you might be able to answer some of these questions using the app you are expected to write the required code and produce the necessary plots and summary statistics. You are welcomed to use the app for exploration.
Exercise: Take a sample of size 15 from the population and calculate the mean price
of the homes in this sample. Using this sample, what is your best point estimate of the population mean of prices of homes?
# type your code for this Exercise here, and Run Document
samp1price <- ames %>%
sample_n(size = 15)
samp1price %>%
summarise(mean(price))
## # A tibble: 1 x 1
## `mean(price)`
## <dbl>
## 1 196388.
Exercise: Since you have access to the population, simulate the sampling distribution for \(\bar{x}_{price}\) by taking 2000 samples from the population of size 15 and computing 2000 sample means. Store these means in a vector called sample_means15
. Plot the data, then describe the shape of this sampling distribution. Based on this sampling distribution, what would you guess the mean home price of the population to be? Finally, calculate and report the population mean.
# type your code for this Exercise here, and Run Document
sample_means15 <- ames %>%
rep_sample_n(size = 15, reps = 2000, replace = TRUE) %>%
summarise(x_bar_price15 = mean(price))
ggplot(sample_means15,aes(x = x_bar_price15)) + geom_histogram(binwidth = 1000)
ames %>%
summarise(mu_price = mean(price))
## # A tibble: 1 x 1
## mu_price
## <dbl>
## 1 180796.
Exercise: Change your sample size from 15 to 150, then compute the sampling distribution using the same method as above, and store these means in a new vector called sample_means150
. Describe the shape of this sampling distribution, and compare it to the sampling distribution for a sample size of 15. Based on this sampling distribution, what would you guess to be the mean sale price of homes in Ames?
# type your code for this Exercise here, and Run Document
sample_means150 <- ames %>%
rep_sample_n(size = 150, reps = 2000, replace = TRUE) %>%
summarise(x_bar_price150 = mean(price))
ggplot(sample_means150,aes(x = x_bar_price150)) + geom_histogram(binwidth = 1000)
- Which of the following is false?
-
The variability of the sampling distribution with the smaller sample size (
sample_means50
) is smaller than the variability of the sampling distribution with the larger sample size (sample_means150
). - The means for the two sampling distribtuions are roughly similar.
- Both sampling distributions are symmetric.
-
The variability of the sampling distribution with the smaller sample size (
# type your code for Question 6 here, and Run Document
# Comparing variability between two sampling distributions (n=50), (n =150)
sample_means50 %>%
summarise( max(x_bar_price)-min(x_bar_price))
## # A tibble: 1 x 1
## `max(x_bar_price) - min(x_bar_price)`
## <dbl>
## 1 77994.
sample_means150 %>%
summarise(max(x_bar_price150) - min(x_bar_price150))
## # A tibble: 1 x 1
## `max(x_bar_price150) - min(x_bar_price150)`
## <dbl>
## 1 46172.
This is a derivative of an OpenIntro lab, and is released under a Attribution-NonCommercial-ShareAlike 3.0 United States license.


vmsplice - splice user pages to/from a pipe
#define _GNU_SOURCE /* See feature_test_macros(7) */
#include <fcntl.h>
#include <sys/uio.h>
ssize_t vmsplice(int fd, const struct iovec *iov,
unsigned long nr_segs, unsigned int flags);
If fd is opened for writing, the vmsplice() system call maps
nr_segs ranges of user memory described by iov into a pipe. If
fd is opened for reading, the vmsplice() system call fills
nr_segs ranges of user memory described by iov from a pipe. The
file descriptor fd must refer to a pipe.
The pointer iov points to an array of iovec
structures as defined in <sys/uio.h>:
struct iovec {
void *iov_base; /* Starting address */
size_t iov_len; /* Number of bytes */
};
The flags argument is a bit mask that is composed by ORing
together zero or more of the following values:
- SPLICE_F_MOVE
- Unused for vmsplice(); see splice(2).
- SPLICE_F_NONBLOCK
- Do not block on I/O; see splice(2) for further details.
- SPLICE_F_MORE
- Currently has no effect for vmsplice(), but may be implemented in
the future; see splice(2).
- SPLICE_F_GIFT
- The user pages are a gift to the kernel. The application may not modify
this memory ever, otherwise the page cache and on-disk data may differ.
Gifting pages to the kernel means that a subsequent splice(2)
SPLICE_F_MOVE can successfully move the pages; if this flag is not
specified, then a subsequent splice(2) SPLICE_F_MOVE must
copy the pages. Data must also be properly page aligned, both in memory
and length.
Upon successful completion, vmsplice() returns the number of bytes
transferred to the pipe. On error, vmsplice() returns -1 and
errno is set to indicate the error.
- EAGAIN
- SPLICE_F_NONBLOCK was specified in flags, and the operation
would block.
- EBADF
- fd either not valid, or doesn't refer to a pipe.
- EINVAL
- nr_segs is greater than IOV_MAX; or memory not aligned if
SPLICE_F_GIFT set.
- ENOMEM
- Out of memory.
The vmsplice() system call first appeared in Linux 2.6.17; library
support was added to glibc in version 2.5.
This system call is Linux-specific.
vmsplice() follows the other vectorized read/write type functions when it
comes to limitations on the number of segments being passed in. This limit is
IOV_MAX as defined in <limits.h>. Currently, this limit is
1024.
vmsplice() really supports true splicing only from user
memory to a pipe. In the opposite direction, it actually just copies the
data to userspace. But this makes the interface nice and symmetric and
enables people to build on vmsplice() with room for future
improvement in performance.
splice(2), tee(2), pipe(7)
This page is part of release 5.05 of the Linux man-pages project. A
description of the project, information about reporting bugs, and the latest
version of this page, can be found at https://www.kernel.org/doc/man-pages/.


--- redirect_from: /ru/DependencyWalker.html title: "DependencyWalker" ---
Dependency Walker builds hierarchical tree of the dynamic libraries used by process.
It may work either ‘offline’ without actual executable run or ‘online’ monitoring all modules, debug messages, threads initializations and many other low-level information.


SessionAnalyzer¶
-
class
Data_Reduction.SLATool.
SessionAnalyzer
(project=None, dss=None, year=None, DOY=None)¶ Bases:
object
Tool for reducing multiple data reduction sessions
- Attributes::
datapath DOY DSS examiners logger project projectdatapath projworkpath year
- Example::
In [1]: from Data_Reduction.SLATool import SessionAnalyzer In [2]: sa = SessionAnalyzer(project=’67P’, year=2015, DOY=204) In [3]: x, sum_y, sum_Tsys, sum_intgr = sa.get_average()
Methods Summary
Tsys_scaling
([weather_data, examiner_keys, Tatm])factors to rescale the system powers or temperatures to K based on FE noise
fit_Tsys_to_airmass
([weather_data, …])Fit tipping curve data implicit in sessions elev and Tsys data
get_average
([source])Computes average spectrum for a source in the session
get_good_weather_data
([examiner_keys])Get data from specific datasets for analyzing environmental conditions.
Gets a list of sources from all the datasets in the session
creates the directory path to the data from the session
open_datafiles
(datafiles)Opens the files for the session in /usr/local/RA_data/FITS
rescale_Tsys
(gain, siggain, Kpam, sigKpam)rescale system temperatures from tipping curve fits
Methods Documentation
-
Tsys_scaling
(weather_data=None, examiner_keys=None, Tatm=250)¶ factors to rescale the system powers or temperatures to K based on FE noise
:param weather_data : consolidated environmental data :type weather_data : dict
:param examiner_keys : keys of files from this date to be included :type examiner_keys : list of int
:param Tatm : air temperature along line of sight :type Tatm : float
-
fit_Tsys_to_airmass
(weather_data=None, examiner_keys=None, Tatm=250, linear=True)¶ Fit tipping curve data implicit in sessions elev and Tsys data
Returns numpy arrays with indices for sig/ref state, subchannel, beam, IF. The first returned value is the zero airmass intercept and the second its standard deviation. The second returned value is K/airmass
:param weather_data : consolidated environmental data :type weather_data : dict
:param examiner_keys : keys of files from this date to be included :type examiner_keys : list of int
:param Tatm : air temperature along line of sight :type Tatm : float
:param linear : use the linear (low tau) approximation :type linear : True
-
get_average
(source='67P_CG_201')¶ Computes average spectrum for a source in the session
Prints r.m.s. noise for each dataset and all datasets together
:param source : source for which averaging is done
-
get_good_weather_data
(examiner_keys=None)¶ Get data from specific datasets for analyzing environmental conditions.
Returns a dict with keys ‘TAMBIENT’, ‘WINDDIRE’, ‘UNIXtime’, ‘TSYS’, ‘HUMIDITY’, ‘PRESSURE’, ‘ELEVATIO’, ‘WINDSPEE’. The data asociated with each key is a dict with numpy array for (SIG state) True and for False. The ‘TSYS’ array has four axes representing:
time index - 0-based sequence in order of matplotlib datenum subchannel - CYCLE value beam - 1-based number sequence IF - 1-based number sequence, usually representing pol
The other keys have only a time axis.
-
get_sources
()¶ Gets a list of sources from all the datasets in the session
-
make_session_names
()¶ creates the directory path to the data from the session
It is crafted from the name of the first FITS file
-
open_datafiles
(datafiles)¶ Opens the files for the session in /usr/local/RA_data/FITS
-
rescale_Tsys
(gain, siggain, Kpam, sigKpam)¶ rescale system temperatures from tipping curve fits


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Kbeznak Parmatonic
Kbeznak Parmatonic
What is kbeznak parmatonic?
Kbeznak Parmatonic is a meaningless word created by Dr. James Caverlee of CSE Dept at Texas A&M.
But now you may ask why using a meaningless word?
Actually it is intended to be created as meaningless and no use so that students in the course CSCE 670 can customize the search results of it in Google and compete with their website ranking, this is also referred to as SEO (Search Engine Optimization) contest.
Stats:
As of when the homework is first posted, there is 0 result in searching the key word Kbeznak Parmatonic in Google or Bing, but now one day before the homework deadline, we created about 100 pages and over 50 of them have been indexed by Google
We also refer users to here and Guanlun’s blog for more info.
You can use the editor on GitHub to maintain and preview the content for your website in Markdown files.

Key Factors that influences website ranking
- On-page factors
- Keywords
Include any keywords you aim for ranking on your website, positions to put keywords so that they are well recognized by Google includes but not limited to: title tags, H1 tags and meta descriptions
Also be noticed it’s not always good to include keywords again and again anywhere throughout the web page, this might negatively influence that final ranking results as their weights might be cut significantly due to the repeative occurences.
Another useful point is that the placement and relevancy are much more important than the keyword frequency, keywords should better appear in the thesis statement of your page, i.e., the first sentence or the first 100 words.
Footers and sidebars are the least to consider by search engines usually.
Keywords in your domain url can improve the SEO results also.
- Content
- Quality content
Content should be natural, i.e., contents should be formatted and aimed for human reading, not meaningless combinations like machine-generated, modern search engines are encoupled with advanced learning techniques to understand the semantics of website contents and will give preferences to websites with high-quality and natural contents.
Also make sure you have a clear architecture and organization for your contents overall, keep sentences and paras short by breaking frequently and organizing using headers and subtitles.
While keeping single paras and sentences shorter, a longer content in total on a page may be a strong indicator of high content quality.
- Content freshness
Content freshness might also influence Google ranking! We refer readers to the article here for how to keep fresh contents to get better ranking on search engines.
Several external factors that influence freshness ranking are 1) number of external sites links to your website 2) links from fresh websites to your content 3) the publish date, last modified time can also influence the freshness ranking results.
- Trust, authority and expertise
- Content quality, amount and web info all contribute to the authority factor of you website
- A good site architecture or sitemap can help establishing an authority at a high level
- A blog together with your website may help establish authority, the timeliness of your blog can also at the meantime guarantee freshness
- Customer reviews might also influence the quality and authority ranking.
- Site internal links and site level info
- site level signals
The security level of your website, for example, using HTTPS is regarded as an lightweight signal that proves the authority and quality of a business website.
Mobile friendliness: if your website supports mobile devices or is tailored for mobile viewing, it will be recognized as a high-quality site with higher possibility.
Site speed: a website that is slow to access usually indicates that it’s hosted by personals or small businesses that usually provides low-authority contents.
The overall site arch, sitemap, is also considered by Google for ranking, a clear website sitemap can greatly improve the ranking results.
- internal links
Internal links are usually recognized as an internal vote for different pages in your website overall.
- In/Out links
- Outbound links
out links are a trust signal, a work that links to proper references for backing up itself usually is recognized as a good one.

- Backlinks
Number of backlinks to your website is apparently a signal that your website has high quality of contents as well as authority, especially backlinks from relevant sites.
Links from a diverse range of websites is also a plus.
Links from high authority or high quality websites are one of the most significant factors for your ranking.
- Domain name and URL
- A good domain name is an indication that your websites will be well reputed, both the domain name age, expiration date and keywords in domain name count in the ranking.
- static URL organization caters to crawlers much better.
- Make your URLs in a shallower directory level and closer-to-root position to increase weight in ranking.
Markdown
Markdown is a lightweight and easy-to-use syntax for styling your writing. It includes conventions for
Another kbeznak parmatonic can be found here
Syntax highlighted code block
# Header 1
## Header 2
### Header 3
Kbeznak Parmatonic for csce 670 homework by dr. James Caverlee
**Bold** and _Italic_ and `Code` text
[Link](url) and ![Image](src)
Trends (Top Search Key Words):
- Warriors
- Galaxy S9
- NBA Young Boy
- Walking Dead
- Rick Nash
For more details see GitHub Flavored Markdown.
Jekyll Themes
Your Pages site will use the layout and styles from the Jekyll theme you have selected in your repository settings. The name of this theme is saved in the Jekyll _config.yml
configuration file.
Having trouble with Pages? Check out our documentation or contact support and we’ll help you sort it out.


"CHESTNUT TREE "(Hebrews ’armon; i.e., “naked”), mentioned in connection with Jacob’s artifice regarding the cattle (Genesis 30:37). It is one of the trees of which, because of its strength and beauty, the Assyrian empire is likened (Ezekiel 31:8; R.V., “plane trees”). It is probably the Oriental plane tree (Platanus orientalis) that is intended. It is a characteristic of this tree that it annually sheds its outer bark, becomes“naked.” The chestnut tree proper is not a native of Palestine.
"CHESTNUT TREE "(Hebrews ’armon; i.e., “naked”), mentioned in connection with Jacob’s artifice regarding the cattle (Genesis 30:37). It is one of the trees of which, because of its strength and beauty, the Assyrian empire is likened (Ezekiel 31:8; R.V., “plane trees”). It is probably the Oriental plane tree (Platanus orientalis) that is intended. It is a characteristic of this tree that it annually sheds its outer bark, becomes“naked.” The chestnut tree proper is not a native of Palestine.


Fix for Vi's broken arrow key support in iTerm
I originally posted this at isaacschlueter.com on Tuesday, April 17th, 2007. I’ve incorporated the info from the comments into the main post. Special thanks to: radius, benstiglitz, and Higgaion for helping to provide more information.
So, I got turned on to iTerm, a prettier and more user-friendly alternative to Apple’s native Terminal.app.
However, for some reason, I got the following error message whenever I tried to use arrow keys in Vi:
Usage: [[
The problem is that Vi is faithfully responding to the TERM variable that iTerm is sending. (I’m not sure why Terminal.app and PuTTY don’t suffer from this issue, but c'est la vie.) So, I thought, you should keep the terminal setting in iTerm to xterm-color, since this is great for most things, but then add this setting to your .exrc file to tame Vi:
set term=linux
I wasn’t sure why that fixed it, but it did. set term=cons25
was another fix that I found, but it seemed to break when I had line numbers turned on, because all tab characters are turned into backticks (`
).
Of course, that’ll break if you use a different terminal setting on another program, so Higgaion suggested putting this into your .vimrc or .exrc instead:
if $TERM_PROGRAM == 'iTerm.app'
set term=linux
endif
However, the same problem occurs when using the more
and less
commands—the arrow keys are broken, but the hjkl keys worked just like they do in Vi. Since there’s no .morerc
or .lessrc
to set the term variable, I was dismayed.
According to benstiglitz:
The default termcap on Mac OS X specifies that applications should enter application-specific cursor mode when capturing the display. iTerm is faithfully sending the application-mode sequences, but most terminal emulators just ignore the app-mode escape sequences and send normal key sequences instead.
So, this is being determined by iTerm’s behavior, so should be fixable in iTerm’s settings. I poked around in iTerm’s menus. Under Bookmarks > Manage Profiles > Terminal Profiles > Default, you can set the default terminal type to linux
. Then you can enjoy proper arrow key support in every situation under iTerm, without futzing with config files in your home directory. Incidentally, it seems that linux
has the same color support as xterm-color
, so nothing is lost.


“We shall pick up an existence by its frogs,” wrote [Charles] Fort in a memorable phrase; but he also told of falls of alkali, asbestos, ashes, axes;
of beef, birds, bitumen, blood, brick, and butter;
of carbonate of soda, charcoal, cinders, coal, coffee beans, and coke;
of fibres, fish, flesh, and flints;
of gelatin, grain, and greenstone;
of hay;
of ice, insects, and iron;
of larvae, leaves, and lizards;
of manna;
of nostoc;
of sands, seeds, silk, snakes, soot, spiderwebs, stones, and sulphur;
of turpentine, and turtles;
of water, and worms.
Damon Knight, Charles Fort : Prophet Of The Unexplained (Gollancz 1971)


There are many fun activities you can partake in during your stay at the resort:
Meditation
Self-led cooking classes
Solo island exploration tour (includes a Geiger counter!)
Journaling
Dancing (by yourself)
Pool (to be reopened soon)
Home


‘He has something different’: David Luiz raves about Arsenal youngster
David Luiz has his say on the talent shown by Gabriel Martinelli at Arsenal this season.
by The Sport Review staffDavid Luiz is backing Gabriel Martinelli to be a big success at Arsenal in the years to come.
The teenage Brazilian forward has been getting used to life at Arsenal after having signed for the Gunners from Ituano in July of this year.
The 18-year-old has scored three goals and made one assist in three Europa League games for Arsenal so far this season, and he has also made four appearances from the bench in the Premier League for Unai Emery’s men.
Martinelli will be hoping to hold down more of a regular spot in the starting line-up at Arsenal in the coming weeks and months as he looks to try and help the Gunners climb the Premier League table.
Fellow Brazilian David Luiz has been impressed by what he has seen from his compatriot and he is expecting big things from him in the coming seasons.
Speaking in an interview with Arsenal’s website, David Luiz said: “I began admiring him for his work, mentality, his football, and his desire to learn every day.
“I’ve had the chance to meet many players, many young talents from several different countries, and Gabi has something different.
“If he keeps it up, he will experience great things in football. I think that is what has surprised me so far.
“I met his parents, it’s not a coincidence that he has been successful. His upbringing had education, purpose, and it’s a great pleasure to be here with Gabriel.
“He welcomed me here, he was here before me. We try to have the best possible relationship, we help each other out.”
Arsenal will return to Premier League action on Saturday afternoon when they host Southampton in the top flight.
They are aiming to return to winning ways in the top flight after the disappointment of their 2-0 loss to Leicester City last time out.


Veto
Crystal's House Party
Add To Que
Search
Submit
Lyrics
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
This is Song Name This is Song Name This is Song Name
by Drake
This is Song Name This is Song Name This is Song Name
by Drake
TEST


val totalAmount: Int
The total price of this line item. Note: This is the total price after multiplying by the quantity, not the price of an individual item.


Volunteer
Introduction
On 9-10 November 2019, I volunteered at the
in Guangzhou. It was held by one of the most influential game media in China - . Many famous game companies participated in the show such as Xbox, Ubisoft, Tencent Games, NetEase Games. Many indie game developers also came to promote their new games. Moreover, the organizer invited American actor Roger Clark, who provided the voice and motion capture for Arthur Morgan in Red Dead Redemption 2, and Japanese game producer, the father of the Castlevania Koji Igarashi to give a talk.My Job
I volunteered at Tencent A.C.E Program. This program aims to help small game studios and indie game developers to release their game on the mobile platform. I was responsible for promoting the mobile version of the Slay The Spire. My job was Introducing the game, facilitating smooth running of the game show and helping the players in need of assistance. Although volunteering was tiring, it was very meaningful. Not only did I make friends with other volunteers, but also I had a deeper connection with the game industry.
Notable Experience —— A Meaningful Talk With Mr. Ryan Clark
This experience provided me with a very good opportunity to get in contact with players, game companies, game media, and indie game developers. I was thrilled to speak face-to-face with founder and CEO of Brace Yourself Games Mr. Ryan Clark, designer of Crypt of the NecroDancer and Cadence of Hyrule, who was showcasing his new game Phantom Brigade. He gave me a lot of very useful suggestions for entering the games industry, emphasizing how games companies have very high standards nowadays in terms of skills and design, He also told me that the best way to learn is to keep making games and build experience on bigger projects, and when I asked him what the secret of his games was, he replied that, without question, it was the unique and interesting gameplay. This valuable conversation has benefited me a lot and made me reflect on what I still lack to accomplish my dream.


Therefore let us strive, with every labor, every effort, and all our desires, that we might deserve, God willing, to come to such a great and excellent gift. For it is useful, beneficial, glorious, and eternal for us, because no death, no inconstancy, no forgetfulness can take it away, but it will make us rejoice in everlasting exultation with the Lord in the sweet homeland.
But if for any of the brothers, as Vergil said, "Cold blood bars the way to the heart," so that he can't be perfectly educated by either mortal or divine letters, yet with a moderate amount of knowledge he would surely chose what follows: "May the country and bountiful rivers in the valleys please me." For neither is it strange for monks to tend gardens, cultivate fields, or rejoice in the fruitfulness of fruit trees: for it is read in the hundred and twenty seventh psalm: "You will eat the labors of your fruit: you are blessed, and it will be well for you."
But if they're looking for authorities for this pursuit, Gargilius Martialis wrote beautifully about gardens. He carefully set forth both the nourishment of vegetables and their virtues, so that from the perusal of that treatise, the Lord providing, each man might be both satisfied and healed; I have left you this treatise, along with other books.
In the same way Columella and Aemilianus stood out from the others as commendable authors on tending fields, bees, doves, and not least on feeding fish. Now Columella, eloquent and fluent, glides through diverse kinds of agriculture in sixteen books. He is suitable more for the skilled than the inexperienced, so that through his works the studious may be satisfied not only with ordinary fruit but even with the most pleasing dishes. Aemilianus, on the other hand, a most eloquent author, has discussed gardens and cattle and other things with a very plain clarity in twelve books. I have left these for you, among others, for reading over and over, the Lord providing.
Nevertheless these are the things to be prepared for pilgrims and the sick, things that become heavenly, although they seem to be terrestrial. For how excellent it is, when you are ill, to be nourished by sweet fruits or young doves, or to eat fish, or delight in the sweetness of honey!
For indeed, as he taught us to offer cold water to a poor man in the name of our Lord, how much more pleasing it will be to give very agreeable food to diverse needy people, from whom we could accept the fruits of a greater recompense in that day of judgment! We ought not to ignore any means by which mankind can be commendably aided.
Accordingly, the location of the Vivarium monastery encourages you to prepare many things for pilgrims and the needy, since you have irrigated gardens and the nearby Pellena river, flowing and teeming with fish. It can't be held to be dangerous, either for the height of its waves or their contemptible shallowness. It flows to you skillfully controlled, wherever that is judged necessary, and sufficient for your gardens and mills. For it is at hand when it is wanted, and when it has fulfilled its promises it withdraws to a distance; being thus dedicated to a certain service, it doesn't turn rudely rough, nor can it be away when it is sought.
The seas likewise are near you, and they are accessible for various types of fishing, and a fish that is caught can be, if you wish, shut up in a fish pond. For we built there, with the Lord's help, pleasant ponds, where a multitude of fish may wander behind a reliable dam; so like the caves of the mountains that it might have no idea that it is a captive, but thinks that it has freedom, and food to get, and normal hollows to shelter in.
We also ordered baths to be constructed, suitably prepared for sick bodies, where the transparent water of the springs flows gracefully, which is known to be most pleasingly both for drinking and bathing.
And so may it happen that your monastery is sought by others more than you yourselves can rightly desire foreign places. In truth, as you know, these pleasures are matters of the present, not the future hope of the faithful: this is transitory, while that is going to remain without end. But, placed there, may we be conveyed to those better desires, which might make us reign with Christ.
For if in the Vivarium monastery, as it is worthwhile to believe, having been favored with divine grace, you are properly instructed by the experience of the cloisters, and if any elevated person happens to desire purified souls, you have Mt Castellum for a sweet retreat, where as anchorites, if it please the Lord, you can happily live. For there are places that are remote and resemble the wilderness, since they prove to be enclosed in ancient encircling walls. And so it will be fit for you, now trained and well tested, to choose that dwelling place, if the ascent has been previously prepared in your heart. For in choosing you know one of two things, either what you can desire or what you can endure.
It is such that, when the uprightness of monastic life is kept, whoever cannot teach others with words, may at least instruct them by the sanctitiy of his behavior.
But I confess that, whatever things can be accomplished among you by physical labor, nevertheless it is perhaps not without cause that studying ancient scholars (if they write truthfully) pleases me more; both because they beneficially instruct my mind when I re-read the divine scriptures, and because, by writing, they disseminate the precepts of the Lord far and wide. Their blessed intention, their praise-worthy assiduity, is is to preach by means of the handwriting of men, to recount speeches with their fingers, to give a silent greeting to mortal men, and to fight against the illicit deceptions of the devil with pen and ink. For Satan receives a wound for every word that a scribe of the Lord writes. And so the dissemination of one's work goes out from a single site through different provinces. His work is read in holy places; the people hear it and turn away from evil desire and serve the Lord with a pure mind. He does work while away from his work.
But to keep copyists from mixing up words with altered letters or an uninformed editor from not knowing how to correct errors, they should read about ancient orthography, that is, Velius Longus, Curtius Valerianus, Papirianus, Adamantius Martyrius on V and B, the same on the first, middle and last syllables, the same on the letter B placed in a noun in three ways, and Eutychen on aspiration, and also Foca on the difference in genders. With a keen inquisitiveness, I acquired as many of these as I could.
And to keep anyone from being disturbed by the forsaken obscurity of memorable books (for in mixing ancient declensions for they were the most part confused), I applied myself to a great zeal of effort to compile for you a book, titled "On Orthography", with select rules, so that, with your doubt lifted away, your spirit might more freely advance down the path of amendment. We have found that Diomedes and likewise Theoctistus had written about such an art to some extent; if they are found, you yourselves should likewise obtain selections of them. Perhaps you can even find others, through whom your knowledge can be better instructed.
Still, the ones that you have are memorable. If they are reread with a constant devotion, the fog of ignorance is ripped away from you, so that has been hitherto unknown is now held for the most part to be very well known.
Along with these we added the learned masters in book covers, so that the external form will clothe the beauty of the sacred letters beyond their dignities, perhaps copying some part of that example of the parable of the master, who draped wedding gowns on those whom were deemed worthy of an inviation to a dinner in the glory of a heavenly banquet. In these ways the varied styles of bindings should be depicted in a single book, if I am not mistaken, with good taste, so that the student can choose a book-cover of whatever appearance he himself prefers.
We also prepared mechanical oil lamps for the night watch. These keepers of illuminating flames, nuturing by themselves the fire, even without human attention, amply guard the most fertile abundant brightness of light when an abundance of oil is not lacking, however much they are continually scorched by burning flames.
But neither have we suffered you to be at all ignorant of clocks, which are known to be of great advantage to human kind. Therefore you know that one clock, a sundial, has prepared what the brightness of the sun indicates; indeed that another, a water clock, continually shows the passage of the hours, day and night, for the brightness of the sun is often known to be absent for days on end.
Therefore, these things were attended to so that the soldiers of Christ, admonished by the most certain signs, are summoned to practice the divine labor as if by resounding trumpets.
But I also tell you, you distinguished brothers who treat the health of the human body with painstaking care, and who devote the kindness of blessed tenderness to those who take refuge at holy places, who sorrow for those at risk, grieve for those burdened with pain, and are always distressed in your own grief in other calamities, so that you will serve the tired with sincere devotion, as the knowledge of your art teaches you, to receive from it the reward which will recompense them for all time. And therefore learn at least the nature of herbs and manage compounding with a concerned mind, but don't put your hope in herbs, nor safety in human actions. For although the art of medicine was ordained by the Lord, it is nonetheless He who causes men to be healthy, who indubitably grants life; for it was written, "Everything that you do in word or in deed, do in the name of the Lord Jesus, giving thanks to God and to the father through him."
But if you were not well versed in Greek books, you have especially the herb-book of Dioscorides, who discusses and describes the herbs of the field in marvelous accuracy. After these, read Hippocrates and Galen translated into Latin, that is, the Therapeutica of Galen, dedicated to the philosopher Glauco, and a certain anonymous work that is compiled from various authors. Next, Caelius Aurelius' On Medicine and Hippocrates' On Herbs and Treatments and various other compositions on the art of healing, which, with God's aid, I have left for you, shelved in our library.


Interpol seeks eight fugitives for crimes against women
by EUobserverInterpol appealed on Monday for help to find eight men accused of crimes against women, including murder and sexual assault, Reuters writes. The suspects include two wanted by Russia and one each from Denmark, Norway, Ukraine, Brazil, Cyprus, and the United States. "The appeal (…) is a stark reminder of how women and girls universally experience violence and abuse across the world," Interpol said in a statement.


--- layout: default title: Jacob Fosso Tande, Computational Scientist ---
I am computational Scientist with roots in chemistry. I hail from the West region of the Republic of Cameroon. I speak three languages, Ngemba, French and English, and I hold a bachelor of science in chemistry from the University of Buea in the South West Region of Cameroon. I am very happy that East Tennessee State University, with the precious help of Prof. Huang, gave me the opportunity to study in the US.


This website template is released under a Creative Commons Attribution 2.5 License
We request you retain the full copyright notice below including the link to www.metamorphozis.com.
This not only gives respect to the large amount of time given freely by the developers
but also helps build interest, traffic and use of our free and paid designs. If you cannot (for good
reason) retain the full copyright we request you at least leave in place the
Website Templates line, with Website Templates linked to www.metamorphozis.com. If you refuse
to include even this then support may be affected.
You are allowed to use this design only if you agree to the following conditions:
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For support visit http://www.metamorphozis.com/contact/contact.php
The Metamorphosis Design : 2010


Theme:
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Global drawer (default)
Local drawer
A context for an drawer...
Local drawer
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Contrasts
In this tab, you can define contrasts to compute at the first-level after the design-matrix is fit to the fMRI activation time-course.
As there are often no experimental conditions in naturalistic studies, it often makes the most sense to simply propagate the individual estimates for each predictor of interest (e.g. non-confounds).
We can achieve this using "dummy contrasts", in which each Predictor is given a dummy-coded contrast of the same name.
To do this for all non-confounds, simply click Generate Dummy Contrasts
.

Defining a custom contrast
To define a contrast, click Add Contrast
. First, you must give the contrast a name.
Next, select the predictors to include in this contrast. All predictors not selected will be given a weight of 0.
Finally, enter the weights for the selected predictors.
In this example, we are contrasting building
and daylight
using t
contrast.
As in the transformations tab, you can re-order, trash, and edit existing contrasts.


| Methods Summary | ||
|---|---|---|
public static
|
#
calculateReference( int $orderId )
Calculate reference number with 7-3-1 method.
See ENG: http://www.pangaliit.ee/en/settlements-and-standards/reference-number-of-the-invoice
EST: http://www.pangaliit.ee/et/arveldused/7-3-1meetod
|
|
public static
|
||
public static
|
#
generateEcuno( )
Generates transaction number for ECommerce protocol
Format: YYYYMM + rand between 100 000 - 999 999
|
|
public static
|


How to tell when to visit the hospital for labor
by AfricaParentDuring the last trimester, your body starts to prepare for birth. This can be a confusing time and up-and-down hormones don’t help. Knowing when you’re in labour and when to go to hospital in labour could help you feel more confident in the final few weeks.
We Explain below, how to know that labour has begun. This is so that you know when to go to hospital.
Signs That Say When To Go To Hospital In Labour
1. Having a bloody show
The ‘show’ may be the first sign that you’re ready for labour. During pregnancy, a mucous plug builds up in your cervix. As your cervix prepares for birth, it opens up and the plug comes away. The show is usually a stringy, jelly-like discharge and can be blood-tinged or have old brownish blood in it. When you have a show, you’ll probably wonder am I in labour? Things may be imminent or you might have a bit of a wait – labour could begin in a few hours or a few weeks yet.
2. Waters breaking
Your waters breaking can feel like a light trickle or a sudden gush. This is the surest sign that baby is on the way and you should contact your midwife.
If you’re unsure yours has broken, wear a panty liner (don’t use a tampon). If it’s still wet in an hour’s time, it’s time to call the midwife. Your water is usually the colour of straw and could be mistaken for wee. If you notice fresh period-like blood, get to the hospital as soon as possible.
3. Real contractions versus a trial run
Contractions can come throughout your pregnancy, or just in your labour first stage, and it’s important to know the difference between a real contraction and Braxton Hicks contractions. – there’s nothing worse than bundling yourself off to the hospital just to be sent home after a false alarm.
A contraction is when the womb tightens and relaxes to push your baby down and open your cervix. The best way to describe ‘true’ labour pains is like intense period cramps. Braxton Hicks is usually a painless tightening of the abdomen. If you’re unsure, call your midwife for advice.
4. Timing your contractions
You won’t want to rush to hospital as soon as your contractions start – although you’re excited to meet baby, they could keep you waiting a while yet. Until active labour starts, you’ll be a lot more comfortable at home. Time your contractions carefully (if you’re in pain, get your partner to help).
Contact the hospital and prepare to go in once they’re lasting 30 to 40 seconds and come every five minutes. Another way to spot when you should make the call is when your contractions become too painful to speak through.
Make yourself comfortable
Labour is a long and tiring process. Here are a few ways you can keep comfortable while waiting to go to hospital:
- keep fluid levels up
- move around slowly to relieve the pain
- try breathing exercises
- get your birth partner to rub your back
Research suggests that women will have a more positive labour if they stay at home during the early stages. Remember labour can go on for a while. So make sure you’re comfortable, try to move about, keep hydrated and load up on snacks. Giving birth can be harder than running a marathon!
When you notice the signs of labour, remind yourself you can do this. Childbirth is natural and your birth partner and midwife are here for you every step of the way. Remember, it’s not long now until that precious moment when you meet your new arrival.
When to go to hospital in labour with your second baby
That’s right, there can be a difference in labour with your first and second baby, and it’s not just your state of mind. In general your second labour will progress faster and won’t require quite as much pushing (great news!). It is also common for women having their second baby to go into labour sooner, often before their due date, so be prepared.
This article was first published on AfricaParent.com
Copyright 2019 TheCable. All rights reserved. This material, and other digital content on this website, may not be reproduced, published, broadcast, rewritten or redistributed in whole or in part without prior express written permission from TheCable.
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Welcome to Kids Corner
The Heart’s Kids Club provides lots of fun activities with an educational twist. Kids can join for free and will receive a goody bag and a membership card on induction. Each workshop will be interactive, educational, and will introduce children to important concepts that they will really enjoy. Children must be accompanied by a responsible adult at all times and workshop places are available on a first come, first served basis.
If you are parent looking for a place where your child will grow the best, look further, talk to us now. Our offerings
Our offerings
-
School Pickups
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Extensive Library
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Outdoor Trips
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Healthy Food
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First Aid Services
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Games and Аctivities
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Upcoming CAMPS
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Soccer Camp
15h February 2019
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Soccer Camp
15h February 2019
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Soccer Camp
15h February 2019
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A Visit from St. Nicholas (Twas the Night Before Christmas)
by Clement Clarke Moore
Additional Information
- Year Published: 1823
- Language: English
- Country of Origin: United States of America
- Source: Troy: Troy Sentinel, 1823
-
Readability:
- Flesch–Kincaid Level: 1.7
- Word Count: 548
- Genre: Poetry
- Keywords: christmas, holidays, santa, traditions
- ✎ Cite This
Downloads
‘Twas the night before Christmas, when all through the house
Not a creature was stirring, not even a mouse;
The stockings were hung by the chimney with care,
In hopes that St. Nicholas soon would be there;
The children were nestled all snug in their beds,
While visions of sugar-plums danced in their heads;
And mamma in her ‘kerchief, and I in my cap,
Had just settled down for a long winter’s nap,
When out on the lawn there arose such a clatter,
I sprang from the bed to see what was the matter.
Away to the window I flew like a flash,
Tore open the shutters and threw up the sash.
The moon on the breast of the new-fallen snow
Gave the lustre of mid-day to objects below,
When, what to my wondering eyes should appear,
But a miniature sleigh, and eight tiny reindeer,
With a little old driver, so lively and quick,
I knew in a moment it must be St. Nick.
More rapid than eagles his coursers they came,
And he whistled, and shouted, and called them by name;
“Now, Dasher! now, Dancer! now, Prancer and Vixen!
On, Comet! on Cupid! on, Donder and Blitzen!
To the top of the porch! to the top of the wall!
Now dash away! dash away! dash away all!”
As dry leaves that before the wild hurricane fly,
When they meet with an obstacle, mount to the sky,
So up to the house-top the coursers they flew,
With the sleigh full of toys, and St. Nicholas too.
And then, in a twinkling, I heard on the roof
The prancing and pawing of each little hoof.
As I drew in my hand, and was turning around,
Down the chimney St. Nicholas came with a bound.

His eyes—how they twinkled! his dimples how merry!

He was chubby and plump, a right jolly old elf,
And I laughed when I saw him, in spite of myself;
A wink of his eye and a twist of his head,
Soon gave me to know I had nothing to dread;
He spoke not a word, but went straight to his work,
And filled all the stockings; then turned with a jerk,
And laying his finger aside of his nose,
And giving a nod, up the chimney he rose;
He sprang to his sleigh, to his team gave a whistle,
And away they all flew like the down of a thistle.


Contains common functionality shared between Issues and MergeRequests
Namespace
Methods
Instance Public methods
is_assigned?()
Link
Source: show
# File app/roles/issue_commonality.rb, line 51 def is_assigned? !!assignee_id end
is_being_closed?()
Link
Source: show
# File app/roles/issue_commonality.rb, line 59 def is_being_closed? closed_changed? && closed end
is_being_reassigned?()
Link
Source: show
# File app/roles/issue_commonality.rb, line 55 def is_being_reassigned? assignee_id_changed? end
is_being_reopened?()
Link
Source: show
# File app/roles/issue_commonality.rb, line 63 def is_being_reopened? closed_changed? && !closed end


Email Images Alt Tags
Microsoft Outlook
Untitled Image From The Library of Congress Digital Archive Collection. First, insert the image into your email, in this case, Outlook. After the image is inserted into the document, right-click on the image itself, and a dialog box will open. Enter the alt text in that dialog box.
Gmail
As of February 2019, there is not an easy or convenient way to add an alt text to an image in gmail. (There "are" complicated" ways to do it). To that end, ensure a description of the image is associated with the image when you send via gmail.
Resources
-
Resources on Alternative Text for Images
As accessed 15 February 2019
-
An Alt Decision Tree
As accessed 15 February 2019


Rick, Tom and Annabel are waiting to play "Pin the Tail on the Piglet". Mum pins the piglet up and cuts off its tail. The piglet cries. Mum blindfolds Rick, spins him and hands him the tail and a big pin. Rick pins the tail on the piglet's back. The piglet is cross. It stamps its feet. Annabel tries. She pins the piglet's tail on its leg. The piglet grunts. It is offended. Tom pins the piglet's tail on its bum. The piglet spins its tail and grins. Mum, Rick and Annabel clap.
in-context


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